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Holm RH, Rempala GA, Choi B, Brick JM, Amraotkar AR, Keith RJ, Rouchka EC, Chariker JH, Palmer KE, Smith T, Bhatnagar A. Dynamic SARS-CoV-2 surveillance model combining seroprevalence and wastewater concentrations for post-vaccine disease burden estimates. Commun Med (Lond) 2024; 4:70. [PMID: 38594350 PMCID: PMC11004132 DOI: 10.1038/s43856-024-00494-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/28/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Despite wide scale assessments, it remains unclear how large-scale severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination affected the wastewater concentration of the virus or the overall disease burden as measured by hospitalization rates. METHODS We used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and linked vaccination and hospitalization data, from April 2021-August 2021 in Jefferson County, Kentucky (USA). Our susceptible ( S ), vaccinated ( V ), variant-specific infected (I 1 andI 2 ), recovered ( R ), and seropositive ( T ) model ( S V I 2 R T ) tracked prevalence longitudinally. This was related to wastewater concentration. RESULTS Here we show the 64% county vaccination rate translate into about a 61% decrease in SARS-CoV-2 incidence. The estimated effect of SARS-CoV-2 Delta variant emergence is a 24-fold increase of infection counts, which correspond to an over 9-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration have the strongest correlation (r = 0.95) at 1 week lag. CONCLUSIONS Our study underscores the importance of continuing environmental surveillance post-vaccine and provides a proof-of-concept for environmental epidemiology monitoring of infectious disease for future pandemic preparedness.
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Grants
- P20 GM103436 NIGMS NIH HHS
- This study was supported by Centers for Disease Control and Prevention (75D30121C10273), Louisville Metro Government, James Graham Brown Foundation, Owsley Brown II Family Foundation, Welch Family, Jewish Heritage Fund for Excellence, the National Institutes of Health, (P20GM103436), the Rockefeller Foundation, the National Sciences Foundation (DMS-2027001), and the Basic Science Research Program National Research Foundation of Korea (NRF) (RS-2023-00245056).
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Affiliation(s)
- Rochelle H Holm
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Grzegorz A Rempala
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
| | - Boseung Choi
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
- Division of Big Data Science, Korea University, Sejong, South Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon, South Korea
| | | | - Alok R Amraotkar
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Rachel J Keith
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
| | - Julia H Chariker
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
| | - Kenneth E Palmer
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, 40202, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Ted Smith
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Aruni Bhatnagar
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, Louisville, KY, 40202, USA.
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Gripshover TC, Wahlang B, Head KZ, Luo J, Bolatimi OE, Smith ML, Rouchka EC, Chariker JH, Xu J, Cai L, Cummins TD, Merchant ML, Zheng H, Kong M, Cave MC. Multiomics Analysis of PCB126's Effect on a Mouse Chronic-Binge Alcohol Feeding Model. Environ Health Perspect 2024; 132:47007. [PMID: 38619879 PMCID: PMC11018247 DOI: 10.1289/ehp14132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Environmental pollutants, including polychlorinated biphenyls (PCBs) have been implicated in the pathogenesis of liver disease. Our group recently demonstrated that PCB126 promoted steatosis, hepatomegaly, and modulated intermediary metabolism in a rodent model of alcohol-associated liver disease (ALD). OBJECTIVE To better understand how PCB126 promoted ALD in our previous model, the current study adopts multiple omics approaches to elucidate potential mechanistic hypotheses. METHODS Briefly, male C57BL/6J mice were exposed to 0.2 mg / kg polychlorinated biphenyl (PCB) 126 or corn oil vehicle prior to ethanol (EtOH) or control diet feeding in the chronic-binge alcohol feeding model. Liver tissues were collected and prepared for mRNA sequencing, phosphoproteomics, and inductively coupled plasma mass spectrometry for metals quantification. RESULTS Principal component analysis showed that PCB126 uniquely modified the transcriptome in EtOH-fed mice. EtOH feeding alone resulted in > 4,000 differentially expressed genes (DEGs), and PCB126 exposure resulted in more DEGs in the EtOH-fed group (907 DEGs) in comparison with the pair-fed group (503 DEGs). Top 20 significant gene ontology (GO) biological processes included "peptidyl tyrosine modifications," whereas top 25 significantly decreasing GO molecular functions included "metal/ion/zinc binding." Quantitative, label-free phosphoproteomics and western blot analysis revealed no major significant PCB126 effects on total phosphorylated tyrosine residues in EtOH-fed mice. Quantified hepatic essential metal levels were primarily significantly lower in EtOH-fed mice. PCB126-exposed mice had significantly lower magnesium, cobalt, and zinc levels in EtOH-fed mice. DISCUSSION Previous work has demonstrated that PCB126 is a modifying factor in metabolic dysfunction-associated steatotic liver disease (MASLD), and our current work suggests that pollutants also modify ALD. PCB126 may, in part, be contributing to the malnutrition aspect of ALD, where metal deficiency is known to contribute and worsen prognosis. https://doi.org/10.1289/EHP14132.
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Affiliation(s)
- Tyler C. Gripshover
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, Kentucky, USA
- University of Louisville Superfund Research Program, University of Louisville, Louisville, Kentucky, USA
| | - Banrida Wahlang
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, Kentucky, USA
- University of Louisville Superfund Research Program, University of Louisville, Louisville, Kentucky, USA
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky, USA
| | - Kimberly Z. Head
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, Kentucky, USA
- Hepatobiology & Toxicology COBRE, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Jianzhu Luo
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Oluwanifemi E. Bolatimi
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Melissa L. Smith
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Eric C. Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA
- Kentucky IDeA Network of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, Kentucky, USA
| | - Julia H. Chariker
- Kentucky IDeA Network of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, Kentucky, USA
- Department of Neuroscience Training, University of Louisville, Louisville, Kentucky, USA
| | - Jason Xu
- Department of Pediatrics, Pediatric Research Institute, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Lu Cai
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky, USA
- Department of Pediatrics, Pediatric Research Institute, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Timothy D. Cummins
- Division of Nephrology and Hypertension, Department of Medicine and Clinical Proteomics Center, University of Louisville, Louisville, Kentucky, USA
| | - Michael L. Merchant
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky, USA
- Division of Nephrology and Hypertension, Department of Medicine and Clinical Proteomics Center, University of Louisville, Louisville, Kentucky, USA
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, Kentucky, USA
| | - Hao Zheng
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky, USA
| | - Maiying Kong
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky, USA
- Department of Bioinformatics and Biostatistics School of Public Health and Information Sciences, University of Louisville, Louisville, Kentucky, USA
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, Kentucky, USA
- Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
| | - Matthew C. Cave
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, Kentucky, USA
- University of Louisville Superfund Research Program, University of Louisville, Louisville, Kentucky, USA
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky, USA
- Hepatobiology & Toxicology COBRE, University of Louisville School of Medicine, Louisville, Kentucky, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, Kentucky, USA
- The Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky, USA
- The Liver Transplant Program at UofL Health – Jewish Hospital Trager Transplant Center, Louisville, Kentucky, USA
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Walter MN, Montoya-Durango D, Rodriguez W, Wang Y, Zhang J, Chariker JH, Rouchka EC, Maldonado C, Bennett A, McClain CJ, Barve S, Gobejishvili L. Hepatocyte-specific mitogen-activated protein kinase phosphatase 1 in sexual dimorphism and susceptibility to alcohol induced liver injury. Front Immunol 2024; 15:1316228. [PMID: 38370409 PMCID: PMC10871047 DOI: 10.3389/fimmu.2024.1316228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/03/2024] [Indexed: 02/20/2024] Open
Abstract
Background It is well established that females are more susceptible to the toxic effects of alcohol, although the exact mechanisms are still poorly understood. Previous studies noted that alcohol reduces the expression of mitogen-activated protein kinase phosphatase 1 (MKP1), a negative regulator of mitogen-activated protein kinases (MAPK) in the liver. However, the role of hepatocyte- specific MKP1 in the pathogenesis of alcohol-associated liver disease (ALD) remains uncharacterized. This study aimed to evaluate the role of hepatocyte-specific MKP1 in the susceptibility and sexual dimorphism in alcohol-induced liver injury. Methods C57Bl/6 mice were used in an intragastric ethanol feeding model of alcohol-associated steatohepatitis (ASH). Hepatocyte-specific Mkp1-/- knockout and (Mkp1+/+ "f/f" male and female mice were subjected to the NIAAA chronic plus binge model. Primary mouse hepatocytes were used for in vitro studies. Liver RNA sequencing was performed on an Illumina NextSeq 500. Liver injury was evaluated by plasma alanine transaminase (ALT), hepatic ER stress and inflammation markers. Statistical analysis was carried out using ANOVA and the unpaired Student's t-test. Results ASH was associated with the severe injury accompanied by increased endoplasmic reticulum (ER) stress and significant downregulation of Dusp1 mRNA expression. In vitro, ethanol treatment resulted in a time-dependent decrease in Dusp1 mRNA and protein expression in primary hepatocytes in both males and females; however, this effect was significantly more pronounced in hepatocytes from females. In vivo, female mice developed more liver injury in a chronic plus binge model which was accompanied by a significant decrease in liver Dusp1 mRNA expression. In comparison, liver Dusp1 was not changed in male mice, while they developed milder injury to alcohol. Mkp1 deletion in hepatocytes led to increased alcohol induced liver injury, ER stress and inflammation in both sexes. Conclusion Hepatocyte Mkp1 plays a significant role in alcohol induced liver injury. Alcohol downregulates Mkp1 expression in hepatocytes in a sex dependent manner and could play a role in sexual dimorphism in increased female susceptibility to alcohol.
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Affiliation(s)
- Mary Nancy Walter
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Diego Montoya-Durango
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Walter Rodriguez
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Yali Wang
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY, United States
| | - JingWen Zhang
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Julia H. Chariker
- Department of Neuroscience Training, University of Louisville, Louisville, KY, United States
- Kentucky IDeA Networks of Biomedical Research Excellence, (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, United States
| | - Eric C. Rouchka
- Kentucky IDeA Networks of Biomedical Research Excellence, (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, United States
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, United States
| | - Claudio Maldonado
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Anton Bennett
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | - Craig James McClain
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, United States
- Robley Rex Veterans Affairs (VA) Medical Center, Louisville, KY, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, United States
- Alcohol Research Center, University of Louisville, Louisville, KY, United States
- Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY, United States
| | - Shirish Barve
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, United States
- Alcohol Research Center, University of Louisville, Louisville, KY, United States
- Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY, United States
| | - Leila Gobejishvili
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY, United States
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, United States
- Alcohol Research Center, University of Louisville, Louisville, KY, United States
- Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY, United States
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4
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Cook D, Flannigan MD, Chariker JH, Hare JM. DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978. Front Cell Infect Microbiol 2024; 13:1324091. [PMID: 38274737 PMCID: PMC10808703 DOI: 10.3389/fcimb.2023.1324091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Acinetobacter baumannii strain 17978 is an opportunistic pathogen possessing a DNA damage response (DDR) in which multiple error-prone polymerase genes are co-repressed by a UmuD homolog, UmuDAb, and the small Acinetobacter-specific protein DdrR. Additionally, these regulators coactivate nine other genes. We identified the DNA damage-inducible transcriptome for wildtype, umuDAb, and recA strains, and later established the ddrR DDR transcriptome. However, the ATCC 17978 reference genome had several assembly errors and lacked the 44 kb virulence locus, AbaAL44, that is present in the strain 17978 UN. Methods For this project, we combined our earlier single-end read RNAseq data with the ddrR paired-end reads and aligned these data to the improved 17978 UN genome assembly that resembled our laboratory strain, 17978 JH. Results New DESeq2 analyses verified previous differentially expressed genes (DEGs) but also found 339 genes in 17978 JH that were not annotated or physically present in the older genome assembly. Sixty-three were differentially expressed after DNA damage, and 182 had differential basal expression when comparing umuDAb, ddrR, or recA strains to wildtype, with 94 genes' expression unchanged. This work identified and characterized the 55 gene DNA damage-repressible transcriptome, 98% of which required either umuDAb or ddrR for repression. Two-thirds of these DEGs required both regulators. We also identified 110 genes repressed only in the ddrR strain, ~50% of which were due to increased basal expression levels. Basal gene expression in the ddrR mutant was further dysregulated independent of the DDR. Over 800 genes were upregulated, and over 1200 genes were downregulated compared to wildtype expression. Half of A. baumannii's essential genes were upregulated in the ddrR strain, including cell division genes, and two-thirds of these were downregulated in the umuDAb strain. Discussion The ddrR mutant upregulated genes enriched in translation, RNA metabolism, protein metabolism, AA/FA/cell-structure synthesis, and transport, while downregulating genes enriched in quorum sensing, biofilm production, secretion systems, pilus production, cell adhesion, and aromatics and chlorine degradation. Our data underscore the need for accurate and appropriately matched genome assemblies and indicate that ddrR affects approximately 60% of the genome, rendering it a potential target for Acinetobacter baumannii infection treatment.
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Affiliation(s)
- Deborah Cook
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States
| | - Mollee D. Flannigan
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States
| | - Julia H. Chariker
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, United States
| | - Janelle M. Hare
- Department of Biology and Chemistry, Morehead State University, Morehead, KY, United States
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5
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Forston MD, Wei GZ, Chariker JH, Stephenson T, Andres K, Glover C, Rouchka EC, Whittemore SR, Hetman M. Enhanced oxidative phosphorylation, re-organized intracellular signaling, and epigenetic de-silencing as revealed by oligodendrocyte translatome analysis after contusive spinal cord injury. Sci Rep 2023; 13:21254. [PMID: 38040794 PMCID: PMC10692148 DOI: 10.1038/s41598-023-48425-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Reducing the loss of oligodendrocytes (OLs) is a major goal for neuroprotection after spinal cord injury (SCI). Therefore, the OL translatome was determined in Ribotag:Plp1-CreERT2 mice at 2, 10, and 42 days after moderate contusive T9 SCI. At 2 and 42 days, mitochondrial respiration- or actin cytoskeleton/cell junction/cell adhesion mRNAs were upregulated or downregulated, respectively. The latter effect suggests myelin sheath loss/morphological simplification which is consistent with downregulation of cholesterol biosynthesis transcripts on days 10 and 42. Various regulators of pro-survival-, cell death-, and/or oxidative stress response pathways showed peak expression acutely, on day 2. Many acutely upregulated OL genes are part of the repressive SUZ12/PRC2 operon suggesting that epigenetic de-silencing contributes to SCI effects on OL gene expression. Acute OL upregulation of the iron oxidoreductase Steap3 was confirmed at the protein level and replicated in cultured OLs treated with the mitochondrial uncoupler FCCP. Hence, STEAP3 upregulation may mark mitochondrial dysfunction. Taken together, in SCI-challenged OLs, acute and subchronic enhancement of mitochondrial respiration may be driven by axonal loss and subsequent myelin sheath degeneration. Acutely, the OL switch to oxidative phosphorylation may lead to oxidative stress that is further amplified by upregulation of such enzymes as STEAP3.
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Affiliation(s)
- Michael D Forston
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - George Z Wei
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Julia H Chariker
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
- Neuroscience Training, University Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Tyler Stephenson
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Kariena Andres
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Charles Glover
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Eric C Rouchka
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Scott R Whittemore
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Michal Hetman
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
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Holm RH, Rempala G, Choi B, Brick JM, Amraotkar A, Keith R, Rouchka EC, Chariker JH, Palmer K, Smith TR, Bhatnagar A. Wastewater and seroprevalence for pandemic preparedness: variant analysis, vaccination effect, and hospitalization forecasting for SARS-CoV-2, in Jefferson County, Kentucky. medRxiv 2023:2023.01.06.23284260. [PMID: 36656780 PMCID: PMC9844017 DOI: 10.1101/2023.01.06.23284260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Despite wide scale assessments, it remains unclear how large-scale SARS-CoV-2 vaccination affected the wastewater concentration of the virus or the overall disease burden as measured by hospitalization rates. We used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and linked vaccination and hospitalization data, from April 2021-August 2021 in Jefferson County, Kentucky (USA). Our susceptible (S), vaccinated (V), variant-specific infected (I_1 and I_2), recovered (R), and seropositive (T) model (SVI_2 RT) tracked prevalence longitudinally. This was related to wastewater concentration. The 64% county vaccination rate translated into about 61% decrease in SARS-CoV-2 incidence. The estimated effect of SARS-CoV-2 Delta variant emergence was a 24-fold increase of infection counts, which corresponded to an over 9-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration had the strongest correlation (r = 0.95) at 1 week lag. Our study underscores the importance of continued environmental surveillance post-vaccine and provides a proof-of-concept for environmental epidemiology monitoring of infectious disease for future pandemic preparedness.
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7
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Neupane A, Chariker JH, Rouchka EC. Analysis of Nucleotide Variations in Human G-Quadruplex Forming Regions Associated with Disease States. Genes (Basel) 2023; 14:2125. [PMID: 38136947 PMCID: PMC10742762 DOI: 10.3390/genes14122125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
While the role of G quadruplex (G4) structures has been identified in cancers and metabolic disorders, single nucleotide variations (SNVs) and their effect on G4s in disease contexts have not been extensively studied. The COSMIC and CLINVAR databases were used to detect SNVs present in G4s to identify sequence level changes and their effect on the alteration of the G4 secondary structure. A total of 37,515 G4 SNVs in the COSMIC database and 2378 in CLINVAR were identified. Of those, 7236 COSMIC (19.3%) and 457 (19%) of the CLINVAR variants result in G4 loss, while 2728 (COSMIC) and 129 (CLINVAR) SNVs gain a G4 structure. The remaining variants potentially affect the folding energy without affecting the presence of a G4. Analysis of mutational patterns in the G4 structure shows a higher selective pressure (3-fold) in the coding region on the template strand compared to the reverse strand. At the same time, an equal proportion of SNVs were observed among intronic, promoter, and enhancer regions across strands.
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Affiliation(s)
- Aryan Neupane
- School of Graduate and Interdisciplinary Studies, University of Louisville, Louisville, KY 40292, USA;
| | - Julia H. Chariker
- Department of Neuroscience Training, University of Louisville, Louisville, KY 40292, USA;
- Kentucky IDeA Network of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
| | - Eric C. Rouchka
- Kentucky IDeA Network of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA
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8
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Rouchka EC, de Almeida C, House RB, Daneshmand JC, Chariker JH, Saraswat-Ohri S, Gomes C, Sharp M, Shum-Siu A, Cesarz GM, Petruska JC, Magnuson DSK. Construction of a Searchable Database for Gene Expression Changes in Spinal Cord Injury Experiments. J Neurotrauma 2023. [PMID: 37917105 DOI: 10.1089/neu.2023.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Spinal cord injury (SCI) is a debilitating condition with an estimated 18,000 new cases annually in the United States. The field has accepted and adopted standardized databases such as the Open Data Commons for Spinal Cord Injury (ODC-SCI) to aid in broader analyses, but these currently lack high-throughput data despite the availability of nearly 6000 samples from over 90 studies available in the Sequence Read Archive. This limits the potential for large datasets to enhance our understanding of SCI-related mechanisms at the molecular and cellular level. Therefore, we have developed a protocol for processing RNA-Seq samples from high-throughput sequencing experiments related to SCI resulting in both raw and normalized data that can be efficiently mined for comparisons across studies, as well as homologous discovery across species. We have processed 1196 publicly available RNA-Seq samples from 50 bulk RNA-Seq studies across nine different species, resulting in an SQLite database that can be used by the SCI research community for further discovery. We provide both the database as well as a web-based front-end that can be used to query the database for genes of interest, differential gene expression, genes with high variance, and gene set enrichments.
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Affiliation(s)
- Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, USA
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, Kentucky, USA
- Bioinformatics Program, University of Louisville, Louisville, Kentucky, USA
| | - Carlos de Almeida
- Translational Neuroscience Program, University of Louisville, Louisville, Kentucky, USA
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA
| | - Randi B House
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA
- Department of Bioengineering, University of Louisville, Louisville, Kentucky, USA
| | - Jonah C Daneshmand
- Bioinformatics Program, University of Louisville, Louisville, Kentucky, USA
| | - Julia H Chariker
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, Kentucky, USA
- Department of Neuroscience Training, University of Louisville, Louisville, Kentucky, USA
| | - Sujata Saraswat-Ohri
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA
- Department of Neurological Surgery, University of Louisville, Louisville, Kentucky, USA
| | - Cynthia Gomes
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky, USA
| | - Morgan Sharp
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA
- Department of Neurological Surgery, University of Louisville, Louisville, Kentucky, USA
| | - Alice Shum-Siu
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA
- Department of Neurological Surgery, University of Louisville, Louisville, Kentucky, USA
| | - Greta M Cesarz
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA
| | - Jeffrey C Petruska
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA
- Department of Neurological Surgery, University of Louisville, Louisville, Kentucky, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky, USA
| | - David S K Magnuson
- Translational Neuroscience Program, University of Louisville, Louisville, Kentucky, USA
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, Kentucky, USA
- Department of Neurological Surgery, University of Louisville, Louisville, Kentucky, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky, USA
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9
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Montoya-Durango D, Walter MN, Rodriguez W, Wang Y, Chariker JH, Rouchka EC, Maldonado C, Barve S, McClain CJ, Gobejishvili L. Dysregulated Cyclic Nucleotide Metabolism in Alcohol-Associated Steatohepatitis: Implications for Novel Targeted Therapies. Biology (Basel) 2023; 12:1321. [PMID: 37887031 PMCID: PMC10604143 DOI: 10.3390/biology12101321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/29/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND Cyclic nucleotides are second messengers, which play significant roles in numerous biological processes. Previous work has shown that cAMP and cGMP signaling regulates various pathways in liver cells, including Kupffer cells, hepatocytes, hepatic stellate cells, and cellular components of hepatic sinusoids. Importantly, it has been shown that cAMP levels and enzymes involved in cAMP homeostasis are affected by alcohol. Although the role of cyclic nucleotide signaling is strongly implicated in several pathological pathways in liver diseases, studies describing the changes in genes regulating cyclic nucleotide metabolism in ALD are lacking. METHODS Male C57B/6 mice were used in an intragastric model of alcohol-associated steatohepatitis (ASH). Liver injury, inflammation, and fibrogenesis were evaluated by measuring plasma levels of injury markers, liver tissue cytokines, and gene expression analyses. Liver transcriptome analysis was performed to examine the effects of alcohol on regulators of cyclic AMP and GMP levels and signaling. cAMP and cGMP levels were measured in mouse livers as well as in livers from healthy human donors and patients with alcohol-associated hepatitis (AH). RESULTS Our results show significant changes in several phosphodiesterases (PDEs) with specificity to degrade cAMP (Pde4a, Pde4d, and Pde8a) and cGMP (Pde5a, Pde6d, and Pde9a), as well as dual-specificity PDEs (Pde1a and Pde10a) in ASH mouse livers. Adenylyl cyclases (ACs) 7 and 9, which are responsible for cAMP generation, were also affected by alcohol. Importantly, adenosine receptor 1, which has been implicated in the pathogenesis of liver diseases, was significantly increased by alcohol. Adrenoceptors 1 and 3 (Adrb), which couple with stimulatory G protein to regulate cAMP and cGMP signaling, were significantly decreased. Additionally, beta arrestin 2, which interacts with cAMP-specific PDE4D to desensitize G-protein-coupled receptor to generate cAMP, was significantly increased by alcohol. Notably, we observed that cAMP levels are much higher than cGMP levels in the livers of humans and mice; however, alcohol affected them differently. Specifically, cGMP levels were higher in patients with AH and ASH mice livers compared with controls. As expected, these changes in liver cyclic nucleotide signaling were associated with increased inflammation, steatosis, apoptosis, and fibrogenesis. CONCLUSIONS These data strongly implicate dysregulated cAMP and cGMP signaling in the pathogenesis of ASH. Future studies to identify changes in these regulators in a cell-specific manner could lead to the development of novel targeted therapies for ASH.
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Affiliation(s)
- Diego Montoya-Durango
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40290, USA; (D.M.-D.); (M.N.W.); (W.R.); (Y.W.); (C.M.)
| | - Mary Nancy Walter
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40290, USA; (D.M.-D.); (M.N.W.); (W.R.); (Y.W.); (C.M.)
| | - Walter Rodriguez
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40290, USA; (D.M.-D.); (M.N.W.); (W.R.); (Y.W.); (C.M.)
| | - Yali Wang
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40290, USA; (D.M.-D.); (M.N.W.); (W.R.); (Y.W.); (C.M.)
| | - Julia H. Chariker
- Department of Neuroscience Training, University of Louisville, Louisville, KY 40290, USA;
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40290, USA;
| | - Eric C. Rouchka
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40290, USA;
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA
| | - Claudio Maldonado
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40290, USA; (D.M.-D.); (M.N.W.); (W.R.); (Y.W.); (C.M.)
| | - Shirish Barve
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY 40290, USA; (S.B.); (C.J.M.)
- Alcohol Research Center, University of Louisville, Louisville, KY 40290, USA
| | - Craig J. McClain
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY 40290, USA; (S.B.); (C.J.M.)
- Alcohol Research Center, University of Louisville, Louisville, KY 40290, USA
- Robley Rex VA Medical Center, Louisville, KY 40206, USA
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY 40290, USA
| | - Leila Gobejishvili
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40290, USA; (D.M.-D.); (M.N.W.); (W.R.); (Y.W.); (C.M.)
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY 40290, USA; (S.B.); (C.J.M.)
- Alcohol Research Center, University of Louisville, Louisville, KY 40290, USA
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10
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Forston MD, Wei G, Chariker JH, Stephenson T, Andres K, Glover C, Rouchka EC, Whittemore SR, Hetman M. Enhanced oxidative phosphorylation, re-organized intracellular signaling, and epigenetic de-silencing as revealed by oligodendrocyte translatome analysis after contusive spinal cord injury. Res Sq 2023:rs.3.rs-3164618. [PMID: 37546871 PMCID: PMC10402259 DOI: 10.21203/rs.3.rs-3164618/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Reducing the loss of oligodendrocytes (OLs) is a major goal for neuroprotection after spinal cord injury (SCI). Therefore, the OL translatome was determined in Ribotag:Plp1-CreERT2 mice at 2, 10, and 42 days after moderate contusive T9 SCI. At 2 and 42 days, mitochondrial respiration- or actin cytoskeleton/cell junction/cell adhesion mRNAs were upregulated or downregulated, respectively. The latter effect suggests myelin sheath loss/morphological simplification which is consistent with downregulation of cholesterol biosynthesis transcripts on days 10 and 42. Various regulators of pro-survival-, cell death-, and/or oxidative stress response pathways showed peak expression acutely, on day 2. Many acutely upregulated OL genes are part of the repressive SUZ12/PRC2 operon suggesting that epigenetic de-silencing contributes to SCI effects on OL gene expression. Acute OL upregulation of the iron oxidoreductase Steap3 was confirmed at the protein level and replicated in cultured OLs treated with the mitochondrial uncoupler FCCP. Hence, STEAP3 upregulation may mark mitochondrial dysfunction. Taken together, in SCI-challenged OLs, acute and subchronic enhancement of mitochondrial respiration may be driven by axonal loss and subsequent myelin sheath degeneration. Acutely, the OL switch to oxidative phosphorylation may lead to oxidative stress that is further amplified by upregulation of such enzymes as STEAP3.
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Affiliation(s)
| | - George Wei
- University of Louisville School of Medicine
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11
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Gao Y, Wei GZ, Forston MD, Rood B, Hodges ER, Burke D, Andres K, Morehouse J, Armstrong C, Glover C, Slomnicki LP, Ding J, Chariker JH, Rouchka EC, Saraswat Ohri S, Whittemore SR, Hetman M. Opposite modulation of functional recovery following contusive spinal cord injury in mice with oligodendrocyte-selective deletions of Atf4 and Chop/Ddit3. Sci Rep 2023; 13:9193. [PMID: 37280306 DOI: 10.1038/s41598-023-36258-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/31/2023] [Indexed: 06/08/2023] Open
Abstract
The integrated stress response (ISR)-activated transcription factors ATF4 and CHOP/DDIT3 may regulate oligodendrocyte (OL) survival, tissue damage and functional impairment/recovery in white matter pathologies, including traumatic spinal cord injury (SCI). Accordingly, in OLs of OL-specific RiboTag mice, Atf4, Chop/Ddit3 and their downstream target gene transcripts were acutely upregulated at 2, but not 10, days post-contusive T9 SCI coinciding with maximal loss of spinal cord tissue. Unexpectedly, another, OL-specific upregulation of Atf4/Chop followed at 42 days post-injury. However, wild type versus OL-specific Atf4-/- or Chop-/- mice showed similar white matter sparing and OL loss at the injury epicenter, as well as unaffected hindlimb function recovery as determined by the Basso mouse scale. In contrast, the horizontal ladder test revealed persistent worsening or improvement of fine locomotor control in OL-Atf4-/- or OL-Chop-/- mice, respectively. Moreover, chronically, OL-Atf-/- mice showed decreased walking speed during plantar stepping despite greater compensatory forelimb usage. Therefore, ATF4 supports, while CHOP antagonizes, fine locomotor control during post-SCI recovery. No correlation between those effects and white matter sparing together with chronic activation of the OL ISR suggest that in OLs, ATF4 and CHOP regulate function of spinal cord circuitries that mediate fine locomotor control during post-SCI recovery.
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Affiliation(s)
- Yonglin Gao
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - George Z Wei
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, 40292, USA
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Michael D Forston
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Benjamin Rood
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Emily R Hodges
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Darlene Burke
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Kariena Andres
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Johnny Morehouse
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Christine Armstrong
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Charles Glover
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
| | - Lukasz P Slomnicki
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Jixiang Ding
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, 40292, USA
| | - Julia H Chariker
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, KY, 40292, USA
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, KY, 40292, USA
| | - Sujata Saraswat Ohri
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Scott R Whittemore
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40292, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40292, USA
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, 40292, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40292, USA
| | - Michal Hetman
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, 511 S. Floyd St., MDR616, Louisville, KY, 40202, USA.
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40292, USA.
- Department of Anatomical Sciences and Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40292, USA.
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, 40292, USA.
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40292, USA.
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12
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Wang Y, Qin H, Cai Y, Chen X, Li H, Montoya-Durango DE, Ding C, Hu X, Chariker JH, Sarojini H, Chien S, Rouchka EC, Zhang HG, Zheng J, Qiu F, Yan J. Natural γδT17 cell development and functional acquisition is governed by the mTORC2- c-Maf-controlled mitochondrial fission pathway. iScience 2023; 26:106630. [PMID: 37192973 PMCID: PMC10182300 DOI: 10.1016/j.isci.2023.106630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 05/18/2023] Open
Abstract
Natural IL-17-producing γδ T cells (γδT17 cells) are unconventional innate-like T cells that undergo functional programming in the fetal thymus. However, the intrinsic metabolic mechanisms of γδT17 cell development remain undefined. Here, we demonstrate that mTORC2, not mTORC1, selectively controls the functional fate commitment of γδT17 cells through regulating transcription factor c-Maf expression. scRNA-seq data suggest that fetal and adult γδT17 cells predominately utilize mitochondrial metabolism. mTORC2 deficiency results in impaired Drp1-mediated mitochondrial fission and mitochondrial dysfunction characterized by mitochondrial membrane potential (ΔΨm) loss, reduced oxidative phosphorylation (OXPHOS), and subsequent ATP depletion. Treatment with the Drp1 inhibitor Mdivi-1 alleviates imiquimod-induced skin inflammation. Reconstitution of intracellular ATP levels by ATP-encapsulated liposome completely rescues γδT17 defect caused by mTORC2 deficiency, revealing the fundamental role of metabolite ATP in γδT17 development. These results provide an in-depth insight into the intrinsic link between the mitochondrial OXPHOS pathway and γδT17 thymic programming and functional acquisition.
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Affiliation(s)
- Yunke Wang
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hui Qin
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Department of Dermatology, Shanghai Jiaotong University Ruijin Hospital, Shanghai, China
| | - Yihua Cai
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Xu Chen
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Department of Clinical Immunology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Li
- Functional Immunomics Core, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Diego Elias Montoya-Durango
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Chuanlin Ding
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Xiaoling Hu
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Julia H. Chariker
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, USA
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core University of Louisville, Louisville, KY, USA
| | - Harshini Sarojini
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Sufan Chien
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Eric C. Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core University of Louisville, Louisville, KY, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Huang-Ge Zhang
- Department of Microbiology and Immunology, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Jie Zheng
- Department of Dermatology, Shanghai Jiaotong University Ruijin Hospital, Shanghai, China
| | - Fuming Qiu
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Yan
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
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13
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Piell KM, Petri BJ, Head KZ, Wahlang B, Xu R, Zhang X, Pan J, Rai SN, de Silva K, Chariker JH, Rouchka EC, Tan M, Li Y, Cave MC, Klinge CM. Disruption of the Mouse Liver Epitranscriptome by Long-term Aroclor 1260 Exposure. Environ Toxicol Pharmacol 2023; 100:104138. [PMID: 37137421 DOI: 10.1016/j.etap.2023.104138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/05/2023]
Abstract
Chronic environmental exposure to polychlorinated biphenyls (PCBs) is associated with non-alcoholic fatty liver disease (NAFLD) and exacerbated by a high fat diet (HFD). Here, chronic (34 wks.) exposure of low fat diet (LFD)-fed male mice to Aroclor 1260 (Ar1260), a non-dioxin-like (NDL) mixture of PCBs, resulted in steatohepatitis and NAFLD. Twelve hepatic RNA modifications were altered with Ar1260 exposure including reduced abundance of 2'-O-methyladenosine (Am) and N(6)-methyladenosine (m6A), in contrast to increased Am in the livers of HFD-fed, Ar1260-exposed mice reported previously. Differences in 13 RNA modifications between LFD- and HFD- fed mice, suggest that diet regulates the liver epitranscriptome. Integrated network analysis of epitranscriptomic modifications identified a NRF2 (Nfe2l2) pathway in the chronic, LFD, Ar1260-exposed livers and an NFATC4 (Nfatc4) pathway for LFD- vs. HFD-fed mice. Changes in protein abundance were validated. The results demonstrate that diet and Ar1260 exposure alter the liver epitranscriptome in pathways associated with NAFLD.
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Affiliation(s)
- Kellianne M Piell
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292
| | - Belinda J Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292
| | - Kimberly Z Head
- University of Louisville Hepatobiology and Toxicology Center
| | - Banrida Wahlang
- University of Louisville Hepatobiology and Toxicology Center
| | - Raobo Xu
- University of Louisville Hepatobiology and Toxicology Center; Department of Chemistry, University of Louisville College of Arts and Sciences
| | - Xiang Zhang
- University of Louisville Hepatobiology and Toxicology Center; Department of Chemistry, University of Louisville College of Arts and Sciences; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS)
| | - Jianmin Pan
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267; Cancer Data Science Center, Biostatistics and Informatics Shared Resource, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267
| | - Shesh N Rai
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267; Cancer Data Science Center, Biostatistics and Informatics Shared Resource, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267
| | - Kalpani de Silva
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292; Department of Neuroscience Training, University of Louisville, Louisville, KY 40292
| | - Julia H Chariker
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292; Department of Neuroscience Training, University of Louisville, Louisville, KY 40292
| | - Eric C Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292; KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292
| | - Min Tan
- Division of Surgical Oncology, Department of Surgery, University of Louisville School of Medicine; Louisville, KY 40292
| | - Yan Li
- Division of Surgical Oncology, Department of Surgery, University of Louisville School of Medicine; Louisville, KY 40292
| | - Matthew C Cave
- University of Louisville Hepatobiology and Toxicology Center; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS); Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine; Louisville, KY 40292; The University of Louisville Superfund Research Center
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS).
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14
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Ambadapoodi RS, Arnold FW, Chariker JH, Glynn A, Lauer W, Marimuthu S, Rouchka EC, Smith ML, Wolf LA. Persistent SARS-CoV-2 Infection in a Multiple Sclerosis Patient on Ocrelizumab: A Case Report. Res Sq 2023:rs.3.rs-2768759. [PMID: 37066424 PMCID: PMC10104259 DOI: 10.21203/rs.3.rs-2768759/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
A 44-year-old female patient with multiple sclerosis (MS) treated with ocrelizumab was hospitalized with SARS-CoV-2 pneumonia three times over the course of five months, eventually expiring. Viral sequencing of samples from her first and last admissions suggests a single persistent SARS-CoV-2 infection. We hypothesize that her immunocompromised state, due to MS treatment with an immunosuppressive monoclonal antibody, prevented her from achieving viral clearance.
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Affiliation(s)
| | - Forest W. Arnold
- Division of Infectious Diseases, School of Medicine, University of Louisville, Louisville, KY
| | - Julia H. Chariker
- Neuroscience Training Department, University of Louisville, Louisville, KY
| | - Alex Glynn
- Division of Infectious Diseases, School of Medicine, University of Louisville, Louisville, KY
| | - William Lauer
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY
| | - Subathra Marimuthu
- Division of Infectious Diseases, School of Medicine, University of Louisville, Louisville, KY
| | - Eric C. Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY
| | - Melissa L. Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY
| | - Leslie A. Wolf
- Division of Infectious Diseases, School of Medicine, University of Louisville, Louisville, KY
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15
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Neupane A, Chariker JH, Rouchka EC. Structural and Functional Classification of G-Quadruplex Families within the Human Genome. Genes (Basel) 2023; 14:genes14030645. [PMID: 36980918 PMCID: PMC10048163 DOI: 10.3390/genes14030645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
G-quadruplexes (G4s) are short secondary DNA structures located throughout genomic DNA and transcribed RNA. Although G4 structures have been shown to form in vivo, no current search tools that examine these structures based on previously identified G-quadruplexes and filter them based on similar sequence, structure, and thermodynamic properties are known to exist. We present a framework for clustering G-quadruplex sequences into families using the CD-HIT, MeShClust, and DNACLUST methods along with a combination of Starcode and BLAST. Utilizing this framework to filter and annotate clusters, 95 families of G-quadruplex sequences were identified within the human genome. Profiles for each family were created using hidden Markov models to allow for the identification of additional family members and generate homology probability scores. The thermodynamic folding energy properties, functional annotation of genes associated with the sequences, scores from different prediction algorithms, and transcription factor binding motifs within a family were used to annotate and compare the diversity within and across clusters. The resulting set of G-quadruplex families can be used to further understand how different regions of the genome are regulated by factors targeting specific structures common to members of a specific cluster.
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Affiliation(s)
- Aryan Neupane
- School of Graduate and Interdisciplinary Studies, University of Louisville, Louisville, KY 40292, USA
| | - Julia H. Chariker
- Department of Neuroscience Training, University of Louisville, Louisville, KY 40292, USA
- Kentucky IDeA Network of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
| | - Eric C. Rouchka
- Kentucky IDeA Network of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40292, USA
- Correspondence: ; Tel.: +1-(502)-852-3060
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Rouchka EC, de Almeida C, House RB, Daneshmand JC, Chariker JH, Saraswat-Ohri S, Gomes C, Sharp M, Shum-Siu A, Cesarz GM, Petruska JC, Magnuson DS. Construction of a searchable database for gene expression changes in spinal cord injury experiments. bioRxiv 2023:2023.02.01.526630. [PMID: 36778366 PMCID: PMC9915599 DOI: 10.1101/2023.02.01.526630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spinal cord injury (SCI) is a debilitating disease resulting in an estimated 18,000 new cases in the United States on an annual basis. Significant behavioral research on animal models has led to a large amount of data, some of which has been catalogued in the Open Data Commons for Spinal Cord Injury (ODC-SCI). More recently, high throughput sequencing experiments have been utilized to understand molecular mechanisms associated with SCI, with nearly 6,000 samples from over 90 studies available in the Sequence Read Archive. However, to date, no resource is available for efficiently mining high throughput sequencing data from SCI experiments. Therefore, we have developed a protocol for processing RNA-Seq samples from high-throughput sequencing experiments related to SCI resulting in both raw and normalized data that can be efficiently mined for comparisons across studies as well as homologous discovery across species. We have processed 1,196 publicly available RNA-seq samples from 50 bulk RNA-Seq studies across nine different species, resulting in an SQLite database that can be used by the SCI research community for further discovery. We provide both the database as well as a web-based front-end that can be used to query the database for genes of interest, differential gene expression, genes with high variance, and gene set enrichments.
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Affiliation(s)
- Eric C. Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, University of Louisville, Louisville, KY USA
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville School of Medicine, 522 East Gray Street, Louisville, KY USA 40202
- Bioinformatics Program, School of Interdisciplinary and Graduate Studies, University of Louisville, Louisville, KY
| | - Carlos de Almeida
- Translational Neuroscience Program, School of Interdisciplinary and Graduate Studies, University of Louisville, Louisville, KY
- Kentucky Spinal Cord Injury Research Center, School of Medicine, University of Louisville, Louisville, KY
| | - Randi B. House
- Kentucky Spinal Cord Injury Research Center, School of Medicine, University of Louisville, Louisville, KY
- Department of Bioengineering, Speed School of Engineering, University of Louisville, Louisville, KY
| | - Jonah C. Daneshmand
- Bioinformatics Program, School of Interdisciplinary and Graduate Studies, University of Louisville, Louisville, KY
| | - Julia H. Chariker
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville School of Medicine, 522 East Gray Street, Louisville, KY USA 40202
- Department of Neuroscience Training, School of Medicine, University of Louisville, Louisville, KY
| | - Sujata Saraswat-Ohri
- Kentucky Spinal Cord Injury Research Center, School of Medicine, University of Louisville, Louisville, KY
- Department of Neurological Surgery, School of Medicine, University of Louisville, Louisville, KY USA
| | - Cynthia Gomes
- Kentucky Spinal Cord Injury Research Center, School of Medicine, University of Louisville, Louisville, KY
- Department of Anatomical Sciences and Neurobiology, School of Medicine, University of Louisville, Louisville, KY
| | - Morgan Sharp
- Kentucky Spinal Cord Injury Research Center, School of Medicine, University of Louisville, Louisville, KY
- Department of Neurological Surgery, School of Medicine, University of Louisville, Louisville, KY USA
| | - Alice Shum-Siu
- Kentucky Spinal Cord Injury Research Center, School of Medicine, University of Louisville, Louisville, KY
- Department of Neurological Surgery, School of Medicine, University of Louisville, Louisville, KY USA
| | - Greta M. Cesarz
- Kentucky Spinal Cord Injury Research Center, School of Medicine, University of Louisville, Louisville, KY
| | - Jeffrey C. Petruska
- Kentucky Spinal Cord Injury Research Center, School of Medicine, University of Louisville, Louisville, KY
- Department of Neurological Surgery, School of Medicine, University of Louisville, Louisville, KY USA
- Department of Anatomical Sciences and Neurobiology, School of Medicine, University of Louisville, Louisville, KY
| | - David S.K. Magnuson
- Translational Neuroscience Program, School of Interdisciplinary and Graduate Studies, University of Louisville, Louisville, KY
- Kentucky Spinal Cord Injury Research Center, School of Medicine, University of Louisville, Louisville, KY
- Department of Neurological Surgery, School of Medicine, University of Louisville, Louisville, KY USA
- Department of Anatomical Sciences and Neurobiology, School of Medicine, University of Louisville, Louisville, KY
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Neupane A, Chariker JH, Rouchka EC. Analysis of nucleotide variations in human g-quadruplex forming regions associated with disease states. bioRxiv 2023:2023.01.30.526341. [PMID: 36778288 PMCID: PMC9915501 DOI: 10.1101/2023.01.30.526341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
While the role of G4 G quadruplex structures has been identified in cancers and metabolic disorders, single nucleotide variations (SNVs) and their effect on G4s in disease contexts have not been extensively studied. The COSMIC and CLINVAR databases were used to detect SNVs present in G4s to identify sequence level changes and their effect on alteration of G4 secondary structure. 37,515 G4 SNVs in the COSMIC database and 2,115 in CLINVAR were identified. Of those, 7,236 COSMIC (19.3%) and 416 (18%) of the CLINVAR variants result in G4 loss, while 2,728 (COSMIC) and 112 (CLINVAR) SNVs gain a G4 structure. The gene ontology term "GnRH (Gonadotropin-releasing hormone) secretion" is enriched in 21 genes in this pathway that have a G4 destabilizing SNV. Analysis of mutational patterns in the G4 structure show a higher selective pressure (3-fold) in the coding region on the template strand compared to the non-template strand. At the same time, an equal proportion of SNVs were observed among intronic, promoter and enhancer regions across strands. Using GO and pathway enrichment, genes with SNVs for G4 forming propensity in the coding region are enriched for Regulation of Ras protein signal transduction and Src homology 3 (SH3) domain binding.
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Affiliation(s)
- Aryan Neupane
- School of Graduate and Interdisciplinary Studies, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Julia H. Chariker
- Department of Neuroscience Training, University of Louisville, Louisville, Kentucky, 40292, United States of America
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, Kentucky, 40292, United States of America
| | - Eric C. Rouchka
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, Kentucky, 40292, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky 40292, United States of America
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Ding C, Shrestha R, Zhu X, Geller AE, Wu S, Woeste MR, Li W, Wang H, Yuan F, Xu R, Chariker JH, Hu X, Li H, Tieri D, Zhang HG, Rouchka EC, Mitchell R, Siskind LJ, Zhang X, Xu XG, McMasters KM, Yu Y, Yan J. Inducing trained immunity in pro-metastatic macrophages to control tumor metastasis. Nat Immunol 2023; 24:239-254. [PMID: 36604547 PMCID: PMC10636755 DOI: 10.1038/s41590-022-01388-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 11/10/2022] [Indexed: 01/07/2023]
Abstract
Metastasis is the leading cause of cancer-related deaths and myeloid cells are critical in the metastatic microenvironment. Here, we explore the implications of reprogramming pre-metastatic niche myeloid cells by inducing trained immunity with whole beta-glucan particle (WGP). WGP-trained macrophages had increased responsiveness not only to lipopolysaccharide but also to tumor-derived factors. WGP in vivo treatment led to a trained immunity phenotype in lung interstitial macrophages, resulting in inhibition of tumor metastasis and survival prolongation in multiple mouse models of metastasis. WGP-induced trained immunity is mediated by the metabolite sphingosine-1-phosphate. Adoptive transfer of WGP-trained bone marrow-derived macrophages reduced tumor lung metastasis. Blockade of sphingosine-1-phosphate synthesis and mitochondrial fission abrogated WGP-induced trained immunity and its inhibition of lung metastases. WGP also induced trained immunity in human monocytes, resulting in antitumor activity. Our study identifies the metabolic sphingolipid-mitochondrial fission pathway for WGP-induced trained immunity and control over metastasis.
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Affiliation(s)
- Chuanlin Ding
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
| | - Rejeena Shrestha
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Xiaojuan Zhu
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
| | - Anne E Geller
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Shouzhen Wu
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
| | - Matthew R Woeste
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Wenqian Li
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Haomin Wang
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Fang Yuan
- Department of Chemistry, University of Louisville, Louisville, KY, USA
| | - Raobo Xu
- Department of Chemistry, University of Louisville, Louisville, KY, USA
| | - Julia H Chariker
- Department of Neuroscience, KBRIN Bioinformatics Core, University of Louisville, Louisville, KY, USA
| | - Xiaoling Hu
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
| | - Hong Li
- Functional Immunomics Core, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - David Tieri
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Huang-Ge Zhang
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY, USA
| | - Robert Mitchell
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
| | - Leah J Siskind
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, KY, USA
| | - Xiaoji G Xu
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Kelly M McMasters
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA
| | - Yan Yu
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Jun Yan
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA.
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY, USA.
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Mroczkowska JE, Chariker JH, Zhang M, Waigel S, Rouchka EC, Raj AB, Tse WT. Coupled Single-Cell Transcriptome and Epitope Analysis Identifies Cell Surface Markers of TCF7 Expression in CAR-T Cells. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00307-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Woolley CR, Chariker JH, Rouchka EC, Ford EE, Hudson EA, Waigel SJ, Smith ML, Mitchell TC. Reference long-read isoform-aware transcriptomes of 4 human peripheral blood lymphocyte subsets. G3 (Bethesda) 2022; 12:jkac253. [PMID: 36161486 PMCID: PMC9635627 DOI: 10.1093/g3journal/jkac253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Long-read sequencing technologies such as isoform sequencing can generate highly accurate sequences of full-length mRNA transcript isoforms. Such long-read transcriptomics may be especially useful in investigations of lymphocyte functional plasticity as it relates to human health and disease. However, no long-read isoform-aware reference transcriptomes of human circulating lymphocytes are readily available despite being valuable as benchmarks in a variety of transcriptomic studies. To begin to fill this gap, we purified 4 lymphocyte populations (CD4+ T, CD8+ T, NK, and Pan B cells) from the peripheral blood of a healthy male donor and obtained high-quality RNA (RIN > 8) for isoform sequencing and parallel RNA-Seq analyses. Many novel polyadenylated transcript isoforms, supported by both isoform sequencing and RNA-Seq data, were identified within each sample. The datasets met several metrics of high quality and have been deposited to the Gene Expression Omnibus database (GSE202327, GSE202328, GSE202329) as both raw and processed files to serve as long-read reference transcriptomes for future studies of human circulating lymphocytes.
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Affiliation(s)
- Cassandra R Woolley
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Julia H Chariker
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA
- Department of Neuroscience Training, University of Louisville, Louisville, KY 40202, USA
| | - Eric C Rouchka
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Easton E Ford
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Elizabeth A Hudson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Sabine J Waigel
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Thomas C Mitchell
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Brown Cancer Center, University of Louisville Health, Louisville, KY 40202, USA
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21
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Scheurlen KM, Chariker JH, Kanaan Z, Littlefield AB, George JB, Seraphine C, Rochet A, Rouchka EC, Galandiuk S. The NOTCH4-GATA4-IRG1 axis as a novel target in early-onset colorectal cancer. Cytokine Growth Factor Rev 2022; 67:25-34. [DOI: 10.1016/j.cytogfr.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022]
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22
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Geller AE, Shrestha R, Woeste MR, Guo H, Hu X, Ding C, Andreeva K, Chariker JH, Zhou M, Tieri D, Watson CT, Mitchell RA, Zhang HG, Li Y, Martin Ii RCG, Rouchka EC, Yan J. The induction of peripheral trained immunity in the pancreas incites anti-tumor activity to control pancreatic cancer progression. Nat Commun 2022; 13:759. [PMID: 35140221 PMCID: PMC8828725 DOI: 10.1038/s41467-022-28407-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Despite the remarkable success of immunotherapy in many types of cancer, pancreatic ductal adenocarcinoma has yet to benefit. Innate immune cells are critical to anti-tumor immunosurveillance and recent studies have revealed that these populations possess a form of memory, termed trained innate immunity, which occurs through transcriptomic, epigenetic, and metabolic reprograming. Here we demonstrate that yeast-derived particulate β-glucan, an inducer of trained immunity, traffics to the pancreas, which causes a CCR2-dependent influx of monocytes/macrophages to the pancreas that display features of trained immunity. These cells can be activated upon exposure to tumor cells and tumor-derived factors, and show enhanced cytotoxicity against pancreatic tumor cells. In orthotopic models of pancreatic ductal adenocarcinoma, β-glucan treated mice show significantly reduced tumor burden and prolonged survival, which is further enhanced when combined with immunotherapy. These findings characterize the dynamic mechanisms and localization of peripheral trained immunity and identify an application of trained immunity to cancer.
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Affiliation(s)
- Anne E Geller
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Rejeena Shrestha
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Matthew R Woeste
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Division of Surgical Oncology, The Hiram C. Polk, Jr., MD Department of Surgery, University of Louisville, Louisville, KY, USA
| | - Haixun Guo
- Department of Radiology, University of Louisville, Louisville, KY, USA
| | - Xiaoling Hu
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Chuanlin Ding
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Kalina Andreeva
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, USA
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, Kentucky, USA
| | - Julia H Chariker
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, USA
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, Kentucky, USA
| | - Mingqian Zhou
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - David Tieri
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Robert A Mitchell
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Huang-Ge Zhang
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA
| | - Yan Li
- Division of Surgical Oncology, The Hiram C. Polk, Jr., MD Department of Surgery, University of Louisville, Louisville, KY, USA
| | - Robert C G Martin Ii
- Division of Surgical Oncology, The Hiram C. Polk, Jr., MD Department of Surgery, University of Louisville, Louisville, KY, USA
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, Kentucky, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Jun Yan
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA.
- Division of Immunotherapy, The Hiram C. Polk, Jr., MD Department of Surgery, Immuno-Oncology Program, Brown Cancer Center, University of Louisville, Louisville, KY, USA.
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Rouchka EC, Chariker JH, Saurabh K, Waigel S, Zacharias W, Zhang M, Talley D, Santisteban I, Puccio M, Moyer S, Holm RH, Yeager RA, Sokoloski KJ, Fuqua J, Bhatnagar A, Smith T. The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale. Pathogens 2021; 10:1271. [PMID: 34684220 PMCID: PMC8541652 DOI: 10.3390/pathogens10101271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/03/2021] [Accepted: 09/28/2021] [Indexed: 01/08/2023] Open
Abstract
Throughout the course of the ongoing SARS-CoV-2 pandemic there has been a need for approaches that enable rapid monitoring of public health using an unbiased and minimally invasive means. A major way this has been accomplished is through the regular assessment of wastewater samples by qRT-PCR to detect the prevalence of viral nucleic acid with respect to time and location. Further expansion of SARS-CoV-2 wastewater monitoring efforts to include the detection of variants of interest/concern through next-generation sequencing has enhanced the understanding of the SARS-CoV-2 outbreak. In this report, we detail the results of a collaborative effort between public health and metropolitan wastewater management authorities and the University of Louisville to monitor the SARS-CoV-2 pandemic through the monitoring of aggregate wastewater samples over a period of 28 weeks. Through the use of next-generation sequencing approaches the polymorphism signatures of Variants of Concern/Interest were evaluated to determine the likelihood of their prevalence within the community on the basis of their relative dominance within sequence datasets. Our data indicate that wastewater monitoring of water quality treatment centers and smaller neighborhood-scale catchment areas is a viable means by which the prevalence and genetic variation of SARS-CoV-2 within a metropolitan community of approximately one million individuals may be monitored, as our efforts detected the introduction and emergence of variants of concern in the city of Louisville. Importantly, these efforts confirm that regional emergence and spread of variants of interest/concern may be detected as readily in aggregate wastewater samples as compared to the individual wastewater sheds. Furthermore, the information gained from these efforts enabled targeted public health efforts including increased outreach to at-risk communities and the deployment of mobile or community-focused vaccination campaigns.
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Affiliation(s)
- Eric C. Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville, 323 E. Chestnut St., Louisville, KY 40202, USA;
- KY INBRE Bioinformatics Core, University of Louisville, 522 E. Gray St., Louisville, KY 40202, USA;
| | - Julia H. Chariker
- KY INBRE Bioinformatics Core, University of Louisville, 522 E. Gray St., Louisville, KY 40202, USA;
| | - Kumar Saurabh
- Brown Cancer Center, University of Louisville, 530 S. Jackson St., Louisville, KY 40202, USA;
| | - Sabine Waigel
- Department of Medicine, University of Louisville, 530 S. Jackson St., Louisville, KY 40402, USA; (S.W.); (W.Z.)
| | - Wolfgang Zacharias
- Department of Medicine, University of Louisville, 530 S. Jackson St., Louisville, KY 40402, USA; (S.W.); (W.Z.)
| | - Mei Zhang
- Department of Neuroscience, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA;
| | - Daymond Talley
- Louisville/Jefferson County Metropolitan Sewer District, Morris Forman Water Quality Treatment Center, 4522 Algonquin Parkway, Louisville, KY 40211, USA;
| | - Ian Santisteban
- Department of Pharmacology and Toxicology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA;
- Center for Predictive Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Madeline Puccio
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA; (M.P.); (R.H.H.); (R.A.Y.); (A.B.); (T.S.)
| | - Sarah Moyer
- Department of Health Management and System Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray St., Louisville, KY 40202, USA;
- Department of Public Health and Wellness, Louisville Metro Government, 400 E. Gray St., Louisville, KY 40202, USA
| | - Rochelle H. Holm
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA; (M.P.); (R.H.H.); (R.A.Y.); (A.B.); (T.S.)
| | - Ray A. Yeager
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA; (M.P.); (R.H.H.); (R.A.Y.); (A.B.); (T.S.)
- Department of Environmental and Occupational Health Sciences, School of Public Health and Information Sciences, University of Louisville, 485 E. Gray St., Louisville, KY 40202, USA
| | - Kevin J. Sokoloski
- Center for Predictive Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
- Department of Microbiology and Immunology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Joshua Fuqua
- Department of Pharmacology and Toxicology, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA;
- Center for Predictive Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Aruni Bhatnagar
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA; (M.P.); (R.H.H.); (R.A.Y.); (A.B.); (T.S.)
| | - Ted Smith
- Christina Lee Brown Envirome Institute, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY 40202, USA; (M.P.); (R.H.H.); (R.A.Y.); (A.B.); (T.S.)
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Rouchka EC, Chariker JH, Alejandro B, Adcock RS, Singhal R, Ramirez J, Palmer KE, Lasnik AB, Carrico R, Arnold FW, Furmanek S, Zhang M, Wolf LA, Waigel S, Zacharias W, Bordon J, Chung D. Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients. Sci Rep 2021; 11:15715. [PMID: 34344959 PMCID: PMC8333042 DOI: 10.1038/s41598-021-95197-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022] Open
Abstract
Key elements for viral pathogenesis include viral strains, viral load, co-infection, and host responses. Several studies analyzing these factors in the function of disease severity of have been published; however, no studies have shown how all of these factors interplay within a defined cohort. To address this important question, we sought to understand how these four key components interplay in a cohort of COVID-19 patients. We determined the viral loads and gene expression using high throughput sequencing and various virological methods. We found that viral loads in the upper respiratory tract in COVID-19 patients at an early phase of infection vary widely. While the majority of nasopharyngeal (NP) samples have a viral load lower than the limit of detection of infectious viruses, there are samples with an extraordinary amount of SARS-CoV-2 RNA and a high viral titer. No specific viral factors were identified that are associated with high viral loads. Host gene expression analysis showed that viral loads were strongly correlated with cellular antiviral responses. Interestingly, however, COVID-19 patients who experience mild symptoms have a higher viral load than those with severe complications, indicating that naso-pharyngeal viral load may not be a key factor of the clinical outcomes of COVID-19. The metagenomics analysis revealed that the microflora in the upper respiratory tract of COVID-19 patients with high viral loads were dominated by SARS-CoV-2, with a high degree of dysbiosis. Finally, we found a strong inverse correlation between upregulation of interferon responses and disease severity. Overall our study suggests that a high viral load in the upper respiratory tract may not be a critical factor for severe symptoms; rather, dampened antiviral responses may be a critical factor for a severe outcome from the infection.
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Affiliation(s)
- Eric C Rouchka
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY, USA
- Kentucky IDeA Network of Biomedical Research Excellence (KY-INBRE) Bioinformatics Core, Louisville, KY, USA
| | - Julia H Chariker
- Kentucky IDeA Network of Biomedical Research Excellence (KY-INBRE) Bioinformatics Core, Louisville, KY, USA
- Department of Neuroscience Training, University of Louisville, Louisville, KY, USA
| | - Brian Alejandro
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Robert S Adcock
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Richa Singhal
- Kentucky IDeA Network of Biomedical Research Excellence (KY-INBRE) Bioinformatics Core, Louisville, KY, USA
- Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Julio Ramirez
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Division of Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Kenneth E Palmer
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Amanda B Lasnik
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Ruth Carrico
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Division of Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Forest W Arnold
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Division of Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Stephen Furmanek
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Division of Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Mei Zhang
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- Genomics Core Facility, University of Louisville, Louisville, KY, USA
| | - Leslie A Wolf
- Division of Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Sabine Waigel
- Department of Medicine, University of Louisville, Louisville, KY, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Genomics Core Facility, University of Louisville, Louisville, KY, USA
| | - Wolfgang Zacharias
- Department of Medicine, University of Louisville, Louisville, KY, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Genomics Core Facility, University of Louisville, Louisville, KY, USA
| | - Jose Bordon
- Washington Health Institute, George Washington University School of Medicine, Washington, D.C, USA
- Department of Medicine, George Washington University School of Medicine, Washington, D.C, USA
| | - Donghoon Chung
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY, USA.
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY, USA.
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Abstract
The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) viral genome is an RNA virus consisting of approximately 30,000 bases. As part of testing efforts, whole genome sequencing of human isolates has resulted in over 1,600 complete genomes publicly available from GenBank. We have performed a comparative analysis of the sequences, in order to detect common mutations within the population. Analysis of variants occurring within the assembled genomes yields 417 variants occurring in at least 1% of the completed genomes, including 229 within the 5' untranslated region (UTR), 152 within the 3'UTR, 2 within intergenic regions and 34 within coding sequences.
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Affiliation(s)
- Eric C. Rouchka
- Department of Computer Science and Engineering, University of Louisville, Louisville, Kentucky, United States of America
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, Kentucky, United States of America
| | - Julia H. Chariker
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, Kentucky, United States of America
- Neuroscience Training Program, University of Louisville, Louisville, Kentucky, United States of America
| | - Donghoon Chung
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, United States of America
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26
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Slomnicki LP, Myers SA, Saraswat Ohri S, Parsh MV, Andres KR, Chariker JH, Rouchka EC, Whittemore SR, Hetman M. Improved locomotor recovery after contusive spinal cord injury in Bmal1 -/- mice is associated with protection of the blood spinal cord barrier. Sci Rep 2020; 10:14212. [PMID: 32848194 PMCID: PMC7450087 DOI: 10.1038/s41598-020-71131-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/10/2020] [Indexed: 11/09/2022] Open
Abstract
The transcription factor BMAL1/ARNTL is a non-redundant component of the clock pathway that regulates circadian oscillations of gene expression. Loss of BMAL1 perturbs organismal homeostasis and usually exacerbates pathological responses to many types of insults by enhancing oxidative stress and inflammation. Surprisingly, we observed improved locomotor recovery and spinal cord white matter sparing in Bmal1-/- mice after T9 contusive spinal cord injury (SCI). While acute loss of neurons and oligodendrocytes was unaffected, Bmal1 deficiency reduced the chronic loss of oligodendrocytes at the injury epicenter 6 weeks post SCI. At 3 days post-injury (dpi), decreased expression of genes associated with cell proliferation, neuroinflammation and disruption of the blood spinal cord barrier (BSCB) was also observed. Moreover, intraspinal extravasation of fibrinogen and immunoglobulins was decreased acutely at dpi 1 and subacutely at dpi 7. Subacute decrease of hemoglobin deposition was also observed. Finally, subacutely reduced levels of the leukocyte marker CD45 and even greater reduction of the pro-inflammatory macrophage receptor CD36 suggest not only lower numbers of those cells but also their reduced inflammatory potential. These data indicate that Bmal1 deficiency improves SCI outcome, in part by reducing BSCB disruption and hemorrhage decreasing cytotoxic neuroinflammation and attenuating the chronic loss of oligodendrocytes.
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Affiliation(s)
- Lukasz P Slomnicki
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, Louisville, KY, 40202, USA
| | - Scott A Myers
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, Louisville, KY, 40202, USA
| | - Sujata Saraswat Ohri
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, 40202, USA.
- Department of Neurological Surgery, University of Louisville, Louisville, KY, 40202, USA.
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 S. Floyd St., MDR616, Louisville, KY, 40292, USA.
| | - Molly V Parsh
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, Louisville, KY, 40202, USA
| | - Kariena R Andres
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, Louisville, KY, 40202, USA
| | - Julia H Chariker
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, 40202, USA
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
| | - Eric C Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, 40202, USA
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
| | - Scott R Whittemore
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, Louisville, KY, 40202, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, 40202, USA
| | - Michal Hetman
- Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, 40202, USA.
- Department of Neurological Surgery, University of Louisville, Louisville, KY, 40202, USA.
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, 40202, USA.
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, 40202, USA.
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 S. Floyd St., MDR616, Louisville, KY, 40292, USA.
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27
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Chariker JH, Sharp M, Ohri SS, Gomes C, Brabazon F, Harman KA, Whittemore SR, Petruska JC, Magnuson DSK, Rouchka EC. RNA-seq data of soleus muscle tissue after spinal cord injury under conditions of inactivity and applied exercise. Data Brief 2020; 28:105056. [PMID: 32226812 PMCID: PMC7093805 DOI: 10.1016/j.dib.2019.105056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/27/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
Reduced muscle mass and increased fatiguability are major complications after spinal cord injury (SCI), and often hinder the rehabilitation efforts of patients. Such detriments to the musculoskeletal system, and the concomitant reduction in level of activity, contribute to secondary complications such as cardiovascular disease, diabetes, bladder dysfunction and liver damage. As a result of decreased weight-bearing capacity after SCI, muscles undergo morphological, metabolic, and contractile changes. Recent studies have shown that exercise after SCI decreases muscle wasting and reduces the burden of secondary complications. Here, we describe RNA sequencing data for detecting chronic transcriptomic changes in the rat soleus after SCI at two levels of injury severity, under conditions of restricted in-cage activity and two methods of applied exercise, swimming or shallow water walking. We demonstrate that the sequenced data are of good quality and show a high alignment rate to the Rattus norvegicus reference assembly (Rn6). The raw data, along with UCSC Genome Browser tracks created to facilitate exploration of gene expression, are available in the NCBI Gene Expression Omnibus (GEO; GSE129694).
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Affiliation(s)
- Julia H. Chariker
- Department of Neuroscience Training, University of Louisville, 522 East Gray St., Louisville, KY, 40202, USA
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, 522 East Gray St., Louisville, KY, 40202, USA
| | - Morgan Sharp
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
| | - Sujata Saraswat Ohri
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
| | - Cynthia Gomes
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
| | - Fiona Brabazon
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
| | - Kathryn A. Harman
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Health & Sport Sciences, University of Louisville, 2100 South Floyd Street, Louisville, KY, 40208, USA
| | - Scott R. Whittemore
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
| | - Jeffrey C. Petruska
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
| | - David SK. Magnuson
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
| | - Eric C. Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, 522 East Gray St., Louisville, KY, 40202, USA
- Department of Computer and Engineering Science, Speed School of Engineering, University of Louisville, Duthie Center for Engineering, 2301 South 3rd St., Louisville, KY, 40292, USA
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28
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Scalf CS, Chariker JH, Rouchka EC, Ashley NT. Transcriptomic analysis of immune response to bacterial lipopolysaccharide in zebra finch (Taeniopygia guttata). BMC Genomics 2019; 20:647. [PMID: 31412766 PMCID: PMC6693190 DOI: 10.1186/s12864-019-6016-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 08/05/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Despite the convergence of rapid technological advances in genomics and the maturing field of ecoimmunology, our understanding of the genes that regulate immunity in wild populations is still nascent. Previous work to assess immune function has relied upon relatively crude measures of immunocompetence. However, with next-generation RNA-sequencing, it is now possible to create a profile of gene expression in response to an immune challenge. In this study, captive zebra finch (Taeniopygia guttata; adult males) were challenged with bacterial lipopolysaccharide (LPS) or vehicle to stimulate the innate immune system. 2 hours after injection, birds were euthanized and hypothalami, spleen, and red blood cells (RBCs) were collected. Taking advantage of the fully sequenced genome of zebra finch, total RNA was isolated, sequenced, and partially annotated in these tissue/cells. RESULTS In hypothalamus, there were 707 significantly upregulated transcripts, as well as 564 and 144 in the spleen and RBCs, respectively, relative to controls. Also, 155 transcripts in the hypothalamus, 606 in the spleen, and 61 in the RBCs were significantly downregulated. More specifically, a number of immunity-related transcripts (e.g., IL-1β, RSAD2, SOCS3) were upregulated among tissues/cells. Additionally, transcripts involved in metabolic processes (APOD, LRAT, RBP4) were downregulated. CONCLUSIONS These results suggest a potential trade-off in expression of genes that regulate immunity and metabolism in birds challenged with LPS. This finding is consistent with a hypothermic response to LPS treatment in small birds. Unlike mammals, birds have nucleated RBCs, and these results support a novel transcriptomic response of avian RBCs to immune challenge.
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Affiliation(s)
- Cassandra S Scalf
- Department of Biology, Western Kentucky University, Bowling Green, KY, 42101-1800, USA
| | - Julia H Chariker
- Department of Neuroscience Training, University of Louisville, Louisville, KY, 40292, USA
| | - Eric C Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, 40292, USA
| | - Noah T Ashley
- Department of Biology, Western Kentucky University, Bowling Green, KY, 42101-1800, USA.
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29
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Chariker JH, Ohri SS, Gomes C, Brabazon F, Harman KA, DeVeau KM, Magnuson DSK, Hetman M, Petruska JC, Whittemore SR, Rouchka EC. Activity/exercise-induced changes in the liver transcriptome after chronic spinal cord injury. Sci Data 2019; 6:88. [PMID: 31197156 PMCID: PMC6565704 DOI: 10.1038/s41597-019-0087-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/29/2019] [Indexed: 01/01/2023] Open
Abstract
Multi-organ dysfunction is a major complication after spinal cord injury (SCI). In addition to local injury within the spinal cord, SCI causes major disruption to the peripheral organ innervation and regulation. The liver contains sympathetic, parasympathetic, and small sensory axons. The bi-directional signaling of sensory dorsal root ganglion (DRG) neurons that provide both efferent and afferent information is of key importance as it allows sensory neurons and peripheral organs to affect each other. SCI-induced liver inflammation precedes and may exacerbate intraspinal inflammation and pathology after SCI, which may be modulated by activity and exercise. In this study, we collected comprehensive gene expression data through RNA sequencing of liver tissue from rats with chronic SCI to determine the effects of activity and exercise on those expression patterns. The sequenced data are of high quality and show a high alignment rate to the Rn6 genome. Gene expression is demonstrated for genes associated with known liver pathologies. UCSC Genome Browser expression tracks are provided with the data to facilitate exploration of the samples.
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Affiliation(s)
- Julia H Chariker
- Department of Neuroscience Training, University of Louisville, 522 East Gray St., Louisville, KY, 40202, USA
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, 522 East Gray St., Louisville, Kentucky, 40202, USA
| | - Sujata Saraswat Ohri
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
| | - Cynthia Gomes
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
| | - Fiona Brabazon
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
- Wiley Publishing, Hoboken, NJ, 07030, USA
| | - Kathryn A Harman
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Health & Sport Sciences, University of Louisville, 2100 South Floyd Street, Louisville, KY, 40208, USA
| | - Kathryn M DeVeau
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
| | - David S K Magnuson
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
| | - Michal Hetman
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
| | - Jeffrey C Petruska
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
| | - Scott R Whittemore
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA.
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA.
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA.
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, 522 East Gray St., Louisville, Kentucky, 40202, USA.
- Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Duthie Center for Engineering, 2301 South 3rd St., Louisville, Kentucky, 40292, USA.
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30
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Chariker JH, Gomes C, Brabazon F, Harman KA, Ohri SS, Magnuson DSK, Whittemore SR, Petruska JC, Rouchka EC. Transcriptome of dorsal root ganglia caudal to a spinal cord injury with modulated behavioral activity. Sci Data 2019; 6:83. [PMID: 31175296 PMCID: PMC6555821 DOI: 10.1038/s41597-019-0088-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/29/2019] [Indexed: 12/30/2022] Open
Abstract
Spinal cord injury (SCI) is a devastating clinical condition resulting in significant disabilities. Apart from local injury within the spinal cord, SCI patients develop a myriad of complications including multi-organ dysfunction. Some of the dysfunctions may be directly or indirectly related to the sensory neurons of the dorsal root ganglia (DRG), which signal to both the spinal cord and the peripheral organs. After SCI, some classes of DRG neurons exhibit sensitization and undergo axonal sprouting both peripherally and centrally. Such physiological and anatomical re-organization after SCI contributes to both adaptive and maladaptive plasticity processes, which may be modulated by activity and exercise. In this study, we collected comprehensive gene expression data in whole DRG below the levels of the injury to compare the effects of SCI with and without two different forms of exercise in rats.
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Affiliation(s)
- Julia H Chariker
- Department of Neuroscience Training, University of Louisville, 522 East Gray Street, Louisville, Kentucky, 40202, USA
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, 522 East Gray Street, Louisville, Kentucky, 40202, USA
| | - Cynthia Gomes
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
| | - Fiona Brabazon
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
- Wiley Publishing, Hoboken, NJ, 07030, USA
| | - Kathryn A Harman
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Health & Sport Sciences, University of Louisville, 2100 South Floyd Street, Louisville, KY, 40208, USA
| | - Sujata Saraswat Ohri
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
| | - David S K Magnuson
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
| | - Scott R Whittemore
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA
| | - Jeffrey C Petruska
- Department of Anatomical Sciences and Neurobiology, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA.
- Kentucky Spinal Cord Injury Research Center, University of Louisville, 511 South Floyd St., Louisville, KY, 40202, USA.
- Department of Neurological Surgery, University of Louisville, 220 Abraham Flexner Way, Suite 1500, Louisville, KY, 40202, USA.
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, 522 East Gray Street, Louisville, Kentucky, 40202, USA.
- Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Duthie Center for Engineering, 2301 South 3rd St., Louisville, Kentucky, 40292, USA.
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31
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Harrison BJ, Park JW, Gomes C, Petruska JC, Sapio MR, Iadarola MJ, Chariker JH, Rouchka EC. Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs. Front Genet 2019; 10:182. [PMID: 30915105 PMCID: PMC6422928 DOI: 10.3389/fgene.2019.00182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/19/2019] [Indexed: 01/08/2023] Open
Abstract
The length of untranslated regions at the 3' end of transcripts (3'UTRs) is regulated by alternate polyadenylation (APA). 3'UTRs contain regions that harbor binding motifs for regulatory molecules. However, the mechanisms that coordinate the 3'UTR length of specific groups of transcripts are not well-understood. We therefore developed a method, CSI-UTR, that models 3'UTR structure as tandem segments between functional alternative-polyadenylation sites (termed cleavage site intervals-CSIs). This approach facilitated (1) profiling of 3'UTR isoform expression changes and (2) statistical enrichment of putative regulatory motifs. CSI-UTR analysis is UTR-annotation independent and can interrogate legacy data generated from standard RNA-Seq libraries. CSI-UTR identified a set of CSIs in human and rodent transcriptomes. Analysis of RNA-Seq datasets from neural tissue identified differential expression events within 3'UTRs not detected by standard gene-based differential expression analyses. Further, in many instances 3'UTR and CDS from the same gene were regulated differently. This modulation of motifs for RNA-interacting molecules with potential condition-dependent and tissue-specific RNA binding partners near the polyA signal and CSI junction may play a mechanistic role in the specificity of alternative polyadenylation. Source code, CSI BED files and example datasets are available at: https://github.com/UofLBioinformatics/CSI-UTR.
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Affiliation(s)
- Benjamin J Harrison
- Department of Biomedical Sciences, Center for Excellence in the Neurosciences, College of Osteopathic Medicine, University of New England, Biddeford, ME, United States.,Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States
| | - Juw Won Park
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States.,Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Louisville, KY, United States
| | - Cynthia Gomes
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States
| | - Jeffrey C Petruska
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, United States.,Department of Neurological Surgery, University of Louisville, Louisville, KY, United States
| | - Matthew R Sapio
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Julia H Chariker
- Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, KY, United States.,Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, Louisville, KY, United States.,Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Louisville, KY, United States
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Zahin M, Dean WL, Ghim SJ, Joh J, Gray RD, Khanal S, Bossart GD, Mignucci-Giannoni AA, Rouchka EC, Jenson AB, Trent JO, Chaires JB, Chariker JH. Identification of G-quadruplex forming sequences in three manatee papillomaviruses. PLoS One 2018; 13:e0195625. [PMID: 29630682 PMCID: PMC5891072 DOI: 10.1371/journal.pone.0195625] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/25/2018] [Indexed: 11/30/2022] Open
Abstract
The Florida manatee (Trichechus manatus latirotris) is a threatened aquatic mammal in United States coastal waters. Over the past decade, the appearance of papillomavirus-induced lesions and viral papillomatosis in manatees has been a concern for those involved in the management and rehabilitation of this species. To date, three manatee papillomaviruses (TmPVs) have been identified in Florida manatees, one forming cutaneous lesions (TmPV1) and two forming genital lesions (TmPV3 and TmPV4). We identified DNA sequences with the potential to form G-quadruplex structures (G4) across the three genomes. G4 were located on both DNA strands and across coding and non-coding regions on all TmPVs, offering multiple targets for viral control. Although G4 have been identified in several viral genomes, including human PVs, most research has focused on canonical structures comprised of three G-tetrads. In contrast, the vast majority of sequences we identified would allow the formation of non-canonical structures with only two G-tetrads. Our biophysical analysis confirmed the formation of G4 with parallel topology in three such sequences from the E2 region. Two of the structures appear comprised of multiple stacked two G-tetrad structures, perhaps serving to increase structural stability. Computational analysis demonstrated enrichment of G4 sequences on all TmPVs on the reverse strand in the E2/E4 region and on both strands in the L2 region. Several G4 sequences occurred at similar regional locations on all PVs, most notably on the reverse strand in the E2 region. In other cases, G4 were identified at similar regional locations only on PVs forming genital lesions. On all TmPVs, G4 sequences were located in the non-coding region near putative E2 binding sites. Together, these findings suggest that G4 are possible regulatory elements in TmPVs.
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Affiliation(s)
- Maryam Zahin
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - William L. Dean
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Shin-je Ghim
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Joongho Joh
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Robert D. Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Sujita Khanal
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
| | - Gregory D. Bossart
- Georgia Aquarium, Atlanta, Georgia, United States of America
- Division of Comparative Pathology, Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | | | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Duthie Center for Engineering, Louisville, Kentucky, United States of America
- KBRIN Bioinformatics Core, University of Louisville, Louisville, Kentucky, United States of America
| | - Alfred B. Jenson
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - John O. Trent
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
| | - Julia H. Chariker
- KBRIN Bioinformatics Core, University of Louisville, Louisville, Kentucky, United States of America
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, Kentucky, United States of America
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Melikishvili M, Chariker JH, Rouchka EC, Fondufe-Mittendorf YN. Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis. Cell Discov 2017; 3:17043. [PMID: 29387452 PMCID: PMC5787697 DOI: 10.1038/celldisc.2017.43] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 10/23/2017] [Indexed: 12/25/2022] Open
Abstract
Recent studies implicate Poly (ADP-ribose) polymerase 1 (PARP1) in alternative splicing regulation, and PARP1 may be an RNA-binding protein. However, detailed knowledge of RNA targets and the RNA-binding region for PARP1 are unknown. Here we report the first global study of PARP1–RNA interactions using PAR–CLIP in HeLa cells. We identified a largely overlapping set of 22 142 PARP1–RNA-binding peaks mapping to mRNAs, with 20 484 sites located in intronic regions. PARP1 preferentially bound RNA containing GC-rich sequences. Using a Bayesian model, we determined positional effects of PARP1 on regulated exon-skipping events: PARP1 binding upstream and downstream of the skipped exons generally promotes exon inclusion, whereas binding within the exon of interest and intronic regions closer to the skipped exon promotes exon skipping. Using truncation mutants, we show that removal of the Zn1Zn2 domain switches PARP1 from a DNA binder to an RNA binder. This study represents a first step into understanding the role of PARP1–RNA interaction. Continued identification and characterization of the functional interplay between PARPs and RNA may provide important insights into the role of PARPs in RNA regulation.
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Affiliation(s)
- Manana Melikishvili
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Julia H Chariker
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY, USA.,Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, 522 East Gray Street, Louisville, KY, USA
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, 522 East Gray Street, Louisville, KY, USA.,Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, USA
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Rouchka EC, Chariker JH, Tieri DA, Park JW, Rajurkar S, Singh V, Verma NK, Cui Y, Farman M, Condon B, Moore N, Jaromczyk J, Jaromczyk J, Harris D, Calie P, Shin EK, Davis RL, Shaban-Nejad A, Mitchell JM, Flight RM, Wang QJ, Higashi RM, Fan TWM, Lane AN, Moseley HNB, Lu L, Daigle BJ, Chen X, Smelter A, Moseley HNB, Jaromczyk JW, Farman M, Chen L, Moore N, Phan BK, Serpico NJ, Toney EG, Melton CE, Mandel JR, Daigle BJ, Chen H, Zaman KI, Homayouni R, Trainor PJ, Carlisle SM, DeFilippis AP, Rai SN. Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics. BMC Bioinformatics 2017. [PMCID: PMC5647556 DOI: 10.1186/s12859-017-1781-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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35
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Chariker JH, Zhang Y, Pani JR, Rouchka EC. Identification of successful mentoring communities using network-based analysis of mentor-mentee relationships across Nobel laureates. Scientometrics 2017; 111:1733-1749. [PMID: 28596628 PMCID: PMC5438421 DOI: 10.1007/s11192-017-2364-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Indexed: 11/18/2022]
Abstract
Skills underlying scientific innovation and discovery generally develop within an academic community, often beginning with a graduate mentor’s laboratory. In this paper, a network analysis of doctoral student-dissertation advisor relationships in The Academic Family Tree indicates the pattern of Nobel laureate mentoring relationships is non-random. Nobel laureates had a greater number of Nobel laureate ancestors, descendants, mentees/grandmentees, and local academic family, supporting the notion that assortative processes occur in the selection of mentors and mentees. Subnetworks composed entirely of Nobel laureates extended across as many as four generations. Several successful mentoring communities in high-level science were identified, as measured by number of Nobel laureates within the community. These communities centered on Cambridge University in the latter nineteenth century and Columbia University in the early twentieth century. The current practice of building web-based academic networks, extended to include a wider variety of measures of academic success, would allow for the identification of modern successful scientific communities and should be promoted.
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Affiliation(s)
- Julia H Chariker
- Department of Psychological and Brain Sciences, University of Louisville, Life Sciences Building, Room 317, Louisville, KY 40292 USA.,KBRIN Bioinformatics Core, University of Louisville, 522 East Gray Street, Louisville, KY 40202 USA
| | - Yihang Zhang
- KBRIN Bioinformatics Core, University of Louisville, 522 East Gray Street, Louisville, KY 40202 USA
| | - John R Pani
- Department of Psychological and Brain Sciences, University of Louisville, Life Sciences Building, Room 317, Louisville, KY 40292 USA
| | - Eric C Rouchka
- KBRIN Bioinformatics Core, University of Louisville, 522 East Gray Street, Louisville, KY 40202 USA.,Department of Computer Engineering and Computer Science, Duthie Center for Engineering, University of Louisville, Room 208, Louisville, KY 40292 USA
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Chariker JH, Miller DM, Rouchka EC. Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends. PLoS One 2016; 11:e0165101. [PMID: 27776185 PMCID: PMC5077116 DOI: 10.1371/journal.pone.0165101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/06/2016] [Indexed: 12/17/2022] Open
Abstract
G-quadruplex structures (G4) are found throughout the human genome and are known to play a regulatory role in a variety of molecular processes. Structurally, they have many configurations and can form from one or more DNA strands. At the gene level, they regulate gene expression and protein synthesis. In this paper, chromosomal-level patterns of distribution are analyzed on the human genome to identify high-level distribution patterns potentially related to global functional processes. Here we show unique high density banding patterns on individual chromosomes that are highly correlated, appearing in a mirror pattern, across forward and reverse DNA strands. The highest density of G4 sequences occurs within four megabases of one end of most chromosomes and contains G4 motifs that bind with zinc finger proteins. These findings suggest that G4 may play a role in global chromosomal processes such as those found in meiosis.
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Affiliation(s)
- Julia H. Chariker
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY, United States of America
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, KY, United States of America
| | - Donald M. Miller
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, United States of America
- Department of Medicine, University of Louisville, Louisville, KY, United States of America
| | - Eric C. Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, KY, United States of America
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville KY, United States of America
- * E-mail:
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Rouchka EC, Chariker JH, Harrison BJ, Park JW, Cao X, Pounds S, Raimondi S, Downing J, Ribeiro R, Rubnitz J, Lamba J, Daigle BJ, Burgess D, Gehrlich S, Carmen JC, Johnson N, Emani C, Gehrlich S, Burgess D, Carmen JC, De Silva K, Heaton MP, Kalbfleisch TS, Viangteeravat T, Mudunuri R, Ajayi O, Şen F, Huang EY, Mohebbi M, Florian L, Jackson DJ, Naber JF, Sabbir AKM, Ellingson SR, Lu Y, Phillips CA, Langston MA, Sevakula RK, Thirukovalluru R, Verma NK, Cui Y, Sayed M, Park JW, Wang J, Liu Q, Shyr Y, Zhang X, Ellingson SR, Prodduturi N, Oliver GR, Grill D, Na J, Eckel-Passow J, Klee EW, Goodin MM, Farman M, Inocencio H, Jang C, Jaromczyk JW, Moore N, Sovacool K, Dent L, Izban M, Mandape S, Sakhare S, Pratap S, Marshall D, DePriest MS, MacLeod JN, Kalbfleisch TS, Emani C, Adam H, Blandford E, Campbell J, Castlen J, Dixon B, Gilbert G, Hall A, Kreisle P, Lasher J, Oakes B, Speer A, Valentine M, Nagisetty NSVR, Jose R, Viangteeravat T, Rooney R, Hains D. Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016. BMC Bioinformatics 2016; 17:297. [PMID: 28166713 PMCID: PMC5001208 DOI: 10.1186/s12859-016-1154-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
I1 Proceedings of the Fifteenth Annual UT- KBRIN Bioinformatics Summit 2016 Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park P1 CC-PROMISE: Projection onto the Most Interesting Statistical Evidence (PROMISE) with Canonical Correlation to integrate gene expression and methylation data with multiple pharmacologic and clinical endpoints Xueyuan Cao, Stanley Pounds, Susana Raimondi, James Downing, Raul Ribeiro, Jeffery Rubnitz, Jatinder Lamba P2 Integration of microRNA-mRNA interaction networks with gene expression data to increase experimental power Bernie J Daigle, Jr. P3 Designing and writing software for in silico subtractive hybridization of large eukaryotic genomes Deborah Burgess, Stephanie Gehrlich, John C Carmen P4 Tracking the molecular evolution of Pax gene Nicholas Johnson; Chandrakanth Emani P5 Identifying genetic differences in thermally dimorphic and state specific fungi using in silico genomic comparison Stephanie Gehrlich, Deborah Burgess, John C Carmen P6 Identification of conserved genomic regions and variation therein amongst Cetartiodactyla species using next generation sequencing Kalpani De Silva, Michael P Heaton, Theodore S Kalbfleisch P7 Mining physiological data to identify patients with similar medical events and phenotypes Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun Ajayi, Fatih Şen, Eunice Y Huang P8 Smart brief for home health monitoring Mohammad Mohebbi, Luaire Florian, Douglas J Jackson, John F Naber P9 Side-effect term matching for computational adverse drug reaction predictions AKM Sabbir, Sally R Ellingson P10 Enrichment vs robustness: A comparison of transcriptomic data clustering metrics Yuping Lu, Charles A Phillips, Michael A Langston P11 Deep neural networks for transcriptome-based cancer classification Rahul K Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui P12 Motif discovery using K-means clustering Mohammed Sayed, Juw Won Park P13 Large scale discovery of active enhancers from nascent RNA sequencing Jing Wang, Qi Liu, Yu Shyr P14 Computationally characterizing genomic pipelines and benchmarking results using GATK best practices on the high performance computing cluster at the University of Kentucky Xiaofei Zhang, Sally R Ellingson P15 Development of approaches enabling the identification of abnormal gene expression from RNA-Seq in personalized oncology Naresh Prodduturi, Gavin R Oliver, Diane Grill, Jie Na, Jeanette Eckel-Passow, Eric W Klee P16 Processing RNA-Seq data of plants infected with coffee ringspot virus Michael M Goodin, Mark Farman, Harrison Inocencio, Chanyong Jang, Jerzy W Jaromczyk, Neil Moore, Kelly Sovacool P17 Comparative transcriptomics of three Acinetobacter baumanii clinical isolates with different antibiotic resistance patterns Leon Dent, Mike Izban, Sammed Mandape, Shruti Sakhare, Siddharth Pratap, Dana Marshall P18 Metagenomic assessment of possible microbial contamination in the equine reference genome assembly M Scotty DePriest, James N MacLeod, Theodore S Kalbfleisch P19 Molecular evolution of cancer driver genes Chandrakanth Emani, Hanady Adam, Ethan Blandford, Joel Campbell, Joshua Castlen, Brittany Dixon, Ginger Gilbert, Aaron Hall, Philip Kreisle, Jessica Lasher, Bethany Oakes, Allison Speer, Maximilian Valentine P20 Biorepository Laboratory Information Management System Naga Satya V Rao Nagisetty, Rony Jose, Teeradache Viangteeravat, Robert Rooney, David Hains
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Abstract
Branching tubular structures are prevalent in many different organic and synthetic settings. From trees and vegetation in nature, to vascular structures throughout human and animal biology, these structures are always candidates for new methods of graphical and visual expression. We present a modeling tool for the creation and interactive modification of these structures. Parameters such as thickness and position of branching structures can be modified, while geometric constraints ensure that the resulting mesh will have an accurate anatomical structure by not having inconsistent geometry. We apply this method to the creation of accurate representations of the different types of retinal cells in the human eye. This method allows a user to quickly produce anatomically accurate structures with low polygon counts that are suitable for rendering at interactive rates on commodity computers and mobile devices.
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Affiliation(s)
- William A Mattingly
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky USA
| | - Julia H Chariker
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, Kentucky USA
| | - Richard Paris
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky USA
| | - Dar-Jen Chang
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky USA
| | - John R Pani
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, Kentucky USA
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Mattingly WA, Kelley RR, Chariker JH, Weimken T, Ramirez J. An iterative workflow for creating biomedical visualizations using Inkscape and D3.js. BMC Bioinformatics 2015. [PMCID: PMC4625097 DOI: 10.1186/1471-2105-16-s15-p10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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40
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Rouchka EC, Chariker JH, Harrison BJ. Proceedings of the Fourteenth Annual UT- KBRIN Bioinformatics Summit 2015. BMC Bioinformatics 2015; 16 Suppl 15:I1-P21. [PMID: 26510995 PMCID: PMC4625115 DOI: 10.1186/1471-2105-16-s15-i1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Mattingly WA, Kelley RR, Wiemken TL, Chariker JH, Peyrani P, Guinn BE, Binford LE, Buckner K, Ramirez J. Real-Time Enrollment Dashboard For Multisite Clinical Trials. Contemp Clin Trials Commun 2015; 1:17-21. [PMID: 26878068 PMCID: PMC4746719 DOI: 10.1016/j.conctc.2015.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
OBJECTIVE Achieving patient recruitment goals are critical for the successful completion of a clinical trial. We designed and developed a web-based dashboard for assisting in the management of clinical trial screening and enrollment. MATERIALS AND METHODS We use the dashboard to assist in the management of two observational studies of community-acquired pneumonia. Clinical research associates and managers using the dashboard were surveyed to determine its effectiveness as compared with traditional direct communication. RESULTS The dashboard has been in use since it was first introduced in May of 2014. Of the 23 staff responding to the survey, 77% felt that it was easier or much easier to use the dashboard for communication than to use direct communication. CONCLUSION We have designed and implemented a visualization dashboard for managing multi-site clinical trial enrollment in two community acquired pneumonia studies. Information dashboards are a useful tool for clinical trial management. They can be used as a standalone trial information tool or included into a larger management system.
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Affiliation(s)
- William A. Mattingly
- Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, KY, USA
- Corresponding author. William A Mattingly, PhD, Division of Infectious Diseases, Department of Medicine, University of Louisville, 501 East Broadway, Suite 140B, Louisville, Kentucky 40202, USA.
| | - Robert R. Kelley
- Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Timothy L. Wiemken
- Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Julia H. Chariker
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY, USA
| | - Paula Peyrani
- Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Brian E. Guinn
- Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Laura E. Binford
- Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Kimberley Buckner
- Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Julio Ramirez
- Division of Infectious Diseases, Department of Medicine, University of Louisville, Louisville, KY, USA
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Rouchka EC, Chariker JH. Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014. BMC Bioinformatics 2015; 15 Suppl 10:I1. [PMID: 25571995 PMCID: PMC4196018 DOI: 10.1186/1471-2105-15-s10-i1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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43
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Pani JR, Chariker JH, Naaz F, Mattingly W, Roberts J, Sephton SE. Learning with interactive computer graphics in the undergraduate neuroscience classroom. Adv Health Sci Educ Theory Pract 2014; 19:507-28. [PMID: 24449123 PMCID: PMC4107209 DOI: 10.1007/s10459-013-9483-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 11/17/2013] [Indexed: 05/26/2023]
Abstract
Instruction of neuroanatomy depends on graphical representation and extended self-study. As a consequence, computer-based learning environments that incorporate interactive graphics should facilitate instruction in this area. The present study evaluated such a system in the undergraduate neuroscience classroom. The system used the method of adaptive exploration, in which exploration in a high fidelity graphical environment is integrated with immediate testing and feedback in repeated cycles of learning. The results of this study were that students considered the graphical learning environment to be superior to typical classroom materials used for learning neuroanatomy. Students managed the frequency and duration of study, test, and feedback in an efficient and adaptive manner. For example, the number of tests taken before reaching a minimum test performance of 90 % correct closely approximated the values seen in more regimented experimental studies. There was a wide range of student opinion regarding the choice between a simpler and a more graphically compelling program for learning sectional anatomy. Course outcomes were predicted by individual differences in the use of the software that reflected general work habits of the students, such as the amount of time committed to testing. The results of this introduction into the classroom are highly encouraging for development of computer-based instruction in biomedical disciplines.
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Affiliation(s)
- John R Pani
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY, 40292, USA,
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Abstract
A study was conducted to test the hypothesis that instruction with graphically integrated representations of whole and sectional neuroanatomy is especially effective for learning to recognize neural structures in sectional imagery (such as MRI images). Neuroanatomy was taught to two groups of participants using computer graphical models of the human brain. Both groups learned whole anatomy first with a three-dimensional model of the brain. One group then learned sectional anatomy using two-dimensional sectional representations, with the expectation that there would be transfer of learning from whole to sectional anatomy. The second group learned sectional anatomy by moving a virtual cutting plane through the three-dimensional model. In tests of long-term retention of sectional neuroanatomy, the group with graphically integrated representation recognized more neural structures that were known to be challenging to learn. This study demonstrates the use of graphical representation to facilitate a more elaborated (deeper) understanding of complex spatial relations.
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Affiliation(s)
- Farah Naaz
- Department of Psychological and Brain Sciences, University of Louisville
| | - Julia H Chariker
- Department of Psychological and Brain Sciences, University of Louisville
| | - John R Pani
- Department of Psychological and Brain Sciences, University of Louisville
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45
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Pani JR, Chariker JH, Naaz F. Computer-based learning: interleaving whole and sectional representation of neuroanatomy. Anat Sci Educ 2013; 6:11-8. [PMID: 22761001 PMCID: PMC4399858 DOI: 10.1002/ase.1297] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 05/23/2012] [Indexed: 05/17/2023]
Abstract
The large volume of material to be learned in biomedical disciplines requires optimizing the efficiency of instruction. In prior work with computer-based instruction of neuroanatomy, it was relatively efficient for learners to master whole anatomy and then transfer to learning sectional anatomy. It may, however, be more efficient to continuously integrate learning of whole and sectional anatomy. A study of computer-based learning of neuroanatomy was conducted to compare a basic transfer paradigm for learning whole and sectional neuroanatomy with a method in which the two forms of representation were interleaved (alternated). For all experimental groups, interactive computer programs supported an approach to instruction called adaptive exploration. Each learning trial consisted of time-limited exploration of neuroanatomy, self-timed testing, and graphical feedback. The primary result of this study was that interleaved learning of whole and sectional neuroanatomy was more efficient than the basic transfer method, without cost to long-term retention or generalization of knowledge to recognizing new images (Visible Human and MRI).
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Affiliation(s)
- John R Pani
- Laboratory for Visual-Spatial Learning, Department of Psychological and Brain Sciences, College of Arts and Sciences, University of Louisville, Louisville, KY 40292, USA.
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46
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Chariker JH, Naaz F, Pani JR. Item difficulty in the evaluation of computer-based instruction: an example from neuroanatomy. Anat Sci Educ 2012; 5:63-75. [PMID: 22231801 PMCID: PMC3394676 DOI: 10.1002/ase.1260] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/13/2011] [Accepted: 12/14/2011] [Indexed: 05/15/2023]
Abstract
This article reports large item effects in a study of computer-based learning of neuroanatomy. Outcome measures of the efficiency of learning, transfer of learning, and generalization of knowledge diverged by a wide margin across test items, with certain sets of items emerging as particularly difficult to master. In addition, the outcomes of comparisons between instructional methods changed with the difficulty of the items to be learned. More challenging items better differentiated between instructional methods. This set of results is important for two reasons. First, it suggests that instruction may be more efficient if sets of consistently difficult items are the targets of instructional methods particularly suited to them. Second, there is wide variation in the published literature regarding the outcomes of empirical evaluations of computer-based instruction. As a consequence, many questions arise as to the factors that may affect such evaluations. The present article demonstrates that the level of challenge in the material that is presented to learners is an important factor to consider in the evaluation of a computer-based instructional system.
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Affiliation(s)
- Julia H. Chariker
- Visual Cognition Laboratory, Department of Psychological and Brain Sciences, College of Art and Sciences, University of Louisville, Louisville, Kentucky
| | - Farah Naaz
- Visual Cognition Laboratory, Department of Psychological and Brain Sciences, College of Art and Sciences, University of Louisville, Louisville, Kentucky
| | - John R. Pani
- Visual Cognition Laboratory, Department of Psychological and Brain Sciences, College of Art and Sciences, University of Louisville, Louisville, Kentucky
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Abstract
A longitudinal experiment was conducted to evaluate the effectiveness of new methods for learning neuroanatomy with computer-based instruction. Using a 3D graphical model of the human brain, and sections derived from the model, tools for exploring neuroanatomy were developed to encourage adaptive exploration. This is an instructional method which incorporates graphical exploration in the context of repeated testing and feedback. With this approach, 72 participants learned either sectional anatomy alone or whole anatomy followed by sectional anatomy. Sectional anatomy was explored either with perceptually continuous navigation through the sections or with discrete navigation (as in the use of an anatomical atlas). Learning was measured longitudinally to a high performance criterion. Subsequent tests examined transfer of learning to the interpretation of biomedical images and long-term retention. There were several clear results of this study. On initial exposure to neuroanatomy, whole anatomy was learned more efficiently than sectional anatomy. After whole anatomy was mastered, learners demonstrated high levels of transfer of learning to sectional anatomy and from sectional anatomy to the interpretation of complex biomedical images. Learning whole anatomy prior to learning sectional anatomy led to substantially fewer errors overall than learning sectional anatomy alone. Use of continuous or discrete navigation through sectional anatomy made little difference to measured outcomes. Efficient learning, good long-term retention, and successful transfer to the interpretation of biomedical images indicated that computer-based learning using adaptive exploration can be a valuable tool in instruction of neuroanatomy and similar disciplines.
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Affiliation(s)
- Julia H Chariker
- Department of Psychological and Brain Sciences, University of Louisville
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Pani JR, Chariker JH, Dawson TE, Johnson N. Acquiring new spatial intuitions: Learning to reason about rotations☆. Cogn Psychol 2005; 51:285-333. [PMID: 16165120 DOI: 10.1016/j.cogpsych.2005.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Revised: 01/18/2005] [Accepted: 06/12/2005] [Indexed: 10/25/2022]
Abstract
There are certain simple rotations of objects that most people cannot reason about accurately. Reliable gaps in the understanding of a fundamental physical domain raise the question of how learning to reason in that domain might proceed. Using virtual reality techniques, this project investigated the nature of learning to reason across the domain of simple rotations. Learning consisted of the acquisition of spatial intuitions: there was encoding of useful spatiotemporal information in specific problem types and a gradual accumulation of this understanding across the domain. This pattern of learning through the accumulation of intuitions is especially interesting for rotational motion, in which an elegant domain-wide kinematics is available to support insightful learning. Individual ability to reason about rotations correlated highly with mastery motivation, skill in fluid reasoning, and skill in reasoning about spatial transformations. Thus, general cognitive advantages aided the understanding of individual rotations without guaranteeing immediate generalization across the domain.
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Affiliation(s)
- John R Pani
- Department of Psychological and Brain Sciences, University of Louisville, KY 40292, USA.
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Abstract
There is a broad effort underway to reduce the frequency of medical error. This effort will be facilitated by understanding the causes of human error and the methods that serve to reduce it in settings comparable to medical practice. To serve this end, this article is a review of cognitive psychology as it relates to the origins of human error and an application of that material to issues that arise in medical practice.
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Affiliation(s)
- John R Pani
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, Kentucky 40292, USA.
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