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Wolf JJ, Xia C, Studstill CJ, Ngo H, Brody SL, Anderson PE, Hahm B. Influenza A virus NS1 induces degradation of sphingosine 1-phosphate lyase to obstruct the host innate immune response. Virology 2021; 558:67-75. [PMID: 33730651 DOI: 10.1016/j.virol.2021.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 11/03/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 12/14/2022]
Abstract
The type I interferon (IFN)-mediated innate immune response is one of the central obstacles influenza A virus (IAV) must overcome in order to successfully replicate within the host. We have previously shown that sphingosine 1-phosphate (S1P) lyase (SPL) enhances IKKϵ-mediated type I IFN responses. Here, we demonstrate that the nonstructural protein 1 (NS1) of IAV counteracts the SPL-mediated antiviral response by inducing degradation of SPL. SPL was ubiquitinated and downregulated upon IAV infection or NS1 expression, whereas NS1-deficient IAV failed to elicit SPL ubiquitination or downregulation. Transiently overexpressed SPL increased phosphorylation of IKKϵ, resulting in enhanced expression of type I IFNs. However, this induction was markedly inhibited by IAV NS1. Collectively, this study reveals a novel strategy employed by IAV to subvert the type I IFN response, providing new insights into the interplay between IAV and host innate immunity.
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Affiliation(s)
- Jennifer J Wolf
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65212, USA
| | - Chuan Xia
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65212, USA; Present Address: State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Caleb J Studstill
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65212, USA
| | - Hanh Ngo
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65212, USA
| | - Steven L Brody
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Paul E Anderson
- Laboratory for Infectious Disease Research, University of Missouri, Columbia, MO, 65212, USA
| | - Bumsuk Hahm
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65212, USA.
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2
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Van Dolah FM, Morey JS, Milne S, Ung A, Anderson PE, Chinain M. Transcriptomic analysis of polyketide synthases in a highly ciguatoxic dinoflagellate, Gambierdiscus polynesiensis and low toxicity Gambierdiscus pacificus, from French Polynesia. PLoS One 2020; 15:e0231400. [PMID: 32294110 PMCID: PMC7159223 DOI: 10.1371/journal.pone.0231400] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/23/2020] [Indexed: 11/18/2022] Open
Abstract
Marine dinoflagellates produce a diversity of polyketide toxins that are accumulated in marine food webs and are responsible for a variety of seafood poisonings. Reef-associated dinoflagellates of the genus Gambierdiscus produce toxins responsible for ciguatera poisoning (CP), which causes over 50,000 cases of illness annually worldwide. The biosynthetic machinery for dinoflagellate polyketides remains poorly understood. Recent transcriptomic and genomic sequencing projects have revealed the presence of Type I modular polyketide synthases in dinoflagellates, as well as a plethora of single domain transcripts with Type I sequence homology. The current transcriptome analysis compares polyketide synthase (PKS) gene transcripts expressed in two species of Gambierdiscus from French Polynesia: a highly toxic ciguatoxin producer, G. polynesiensis, versus a non-ciguatoxic species G. pacificus, each assembled from approximately 180 million Illumina 125 nt reads using Trinity, and compares their PKS content with previously published data from other Gambierdiscus species and more distantly related dinoflagellates. Both modular and single-domain PKS transcripts were present. Single domain β-ketoacyl synthase (KS) transcripts were highly amplified in both species (98 in G. polynesiensis, 99 in G. pacificus), with smaller numbers of standalone acyl transferase (AT), ketoacyl reductase (KR), dehydratase (DH), enoyl reductase (ER), and thioesterase (TE) domains. G. polynesiensis expressed both a larger number of multidomain PKSs, and larger numbers of modules per transcript, than the non-ciguatoxic G. pacificus. The largest PKS transcript in G. polynesiensis encoded a 10,516 aa, 7 module protein, predicted to synthesize part of the polyether backbone. Transcripts and gene models representing portions of this PKS are present in other species, suggesting that its function may be performed in those species by multiple interacting proteins. This study contributes to the building consensus that dinoflagellates utilize a combination of Type I modular and single domain PKS proteins, in an as yet undefined manner, to synthesize polyketides.
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Affiliation(s)
- Frances M. Van Dolah
- Marine Genomics Core, Hollings Marine Laboratory, Charleston, SC, United States of America
- * E-mail:
| | - Jeanine S. Morey
- Marine Genomics Core, Hollings Marine Laboratory, Charleston, SC, United States of America
| | - Shard Milne
- Charleston Computational Genomics Group, Department of Computer Science, College of Charleston, Charleston, SC, United States of America
| | - André Ung
- Laboratoire des Biotoxines Marines, Institut Louis Malardé—UMR 241 EIO, Papeete, Tahiti, French Polynesia
| | - Paul E. Anderson
- Charleston Computational Genomics Group, Department of Computer Science, College of Charleston, Charleston, SC, United States of America
| | - Mireille Chinain
- Laboratoire des Biotoxines Marines, Institut Louis Malardé—UMR 241 EIO, Papeete, Tahiti, French Polynesia
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Chow JC, Anderson PE, Shedlock AM. Sea Turtle Population Genomic Discovery: Global and Locus-Specific Signatures of Polymorphism, Selection, and Adaptive Potential. Genome Biol Evol 2020; 11:2797-2806. [PMID: 31504487 PMCID: PMC6786478 DOI: 10.1093/gbe/evz190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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] [Accepted: 08/29/2019] [Indexed: 12/21/2022] Open
Abstract
In the era of genomics, single-nucleotide polymorphisms (SNPs) have become a preferred molecular marker to study signatures of selection and population structure and to enable improved population monitoring and conservation of vulnerable populations. We apply a SNP calling pipeline to assess population differentiation, visualize linkage disequilibrium, and identify loci with sex-specific genotypes of 45 loggerhead sea turtles (Caretta caretta) sampled from the southeastern coast of the United States, including 42 individuals experimentally confirmed for gonadal sex. By performing reference-based SNP calling in independent runs of Stacks, 3,901–6,998 SNPs and up to 30 potentially sex-specific genotypes were identified. Up to 68 pairs of loci were found to be in complete linkage disequilibrium, potentially indicating regions of natural selection and adaptive evolution. This study provides a valuable SNP diagnostic workflow and a large body of new biomarkers for guiding targeted studies of sea turtle genome evolution and for managing legally protected nonmodel iconic species that have high economic and ecological importance but limited genomic resources.
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Affiliation(s)
- Julie C Chow
- Integrative Genetics and Genomics Graduate Group, University of California, Davis
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, Charleston, South Carolina.,Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA 93407
| | - Andrew M Shedlock
- Department of Biology, College of Charleston, Charleston, South Carolina.,College of Graduate Studies, Medical University of South Carolina.,Marine Genomics Division, Hollings Marine Laboratory, Charleston, South Carolina
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4
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Anderson PE, Olson RM, Willix JL, Anderson DM. Standardized Method for Aerosol Challenge of Rodents with Yersinia pestis for Modeling Primary Pneumonic Plague. Methods Mol Biol 2020; 2010:29-39. [PMID: 31177429 DOI: 10.1007/978-1-4939-9541-7_3] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Primary pneumonic plague occurs when Yersinia pestis is inhaled into the lower respiratory tract where it invades the alveoli and grows. Rapid bacterial growth eventually elicits a neutrophilic inflammatory response that is ineffective and damaging, leading to accelerated progression of disease. In the laboratory, modeling of primary pneumonic plague can be accomplished by instillation of bacterial culture in the nares of anesthetized mice and rats. Although primary pneumonic plague can develop from this method, variability in dosing and side effects of anesthesia can complicate data interpretation. In contrast, aerosol challenge models allow for well-controlled studies of pneumonic plague with minimal experimental bias and unwanted side effects. For these reasons, antibiotic testing and the licensing of new treatments depend on efficacy data generated from aerosol delivery of Y. pestis in order to more accurately model transmission and the early stages of human pneumonic plague. In order to meet this need, we have extensively characterized pneumonic plague in mice and rats challenged by nose-only exposure to Yersinia pestis. With this approach, simultaneous challenge of large cohorts of animals, gently restrained and not anesthetized, assures safe, well-controlled, unbiased, and uniform infection. In this chapter, we present a standardized method for reproducible aerosol delivery of wild-type Y. pestis to rodents for experimental models of primary pneumonic plague.
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Affiliation(s)
- Paul E Anderson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
- The Laboratory for Infectious Disease Research, University of Missouri, Columbia, MO, USA
| | - Rachel M Olson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
- The Laboratory for Infectious Disease Research, University of Missouri, Columbia, MO, USA
| | - Joshua L Willix
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
- The Laboratory for Infectious Disease Research, University of Missouri, Columbia, MO, USA
| | - Deborah M Anderson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA.
- The Laboratory for Infectious Disease Research, University of Missouri, Columbia, MO, USA.
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Turner CA, Jacobs AD, Marques CK, Oates JC, Kamen DL, Anderson PE, Obeid JS. Word2Vec inversion and traditional text classifiers for phenotyping lupus. BMC Med Inform Decis Mak 2017; 17:126. [PMID: 28830409 PMCID: PMC5568290 DOI: 10.1186/s12911-017-0518-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [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: 01/30/2017] [Accepted: 08/03/2017] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Identifying patients with certain clinical criteria based on manual chart review of doctors' notes is a daunting task given the massive amounts of text notes in the electronic health records (EHR). This task can be automated using text classifiers based on Natural Language Processing (NLP) techniques along with pattern recognition machine learning (ML) algorithms. The aim of this research is to evaluate the performance of traditional classifiers for identifying patients with Systemic Lupus Erythematosus (SLE) in comparison with a newer Bayesian word vector method. METHODS We obtained clinical notes for patients with SLE diagnosis along with controls from the Rheumatology Clinic (662 total patients). Sparse bag-of-words (BOWs) and Unified Medical Language System (UMLS) Concept Unique Identifiers (CUIs) matrices were produced using NLP pipelines. These matrices were subjected to several different NLP classifiers: neural networks, random forests, naïve Bayes, support vector machines, and Word2Vec inversion, a Bayesian inversion method. Performance was measured by calculating accuracy and area under the Receiver Operating Characteristic (ROC) curve (AUC) of a cross-validated (CV) set and a separate testing set. RESULTS We calculated the accuracy of the ICD-9 billing codes as a baseline to be 90.00% with an AUC of 0.900, the shallow neural network with CUIs to be 92.10% with an AUC of 0.970, the random forest with BOWs to be 95.25% with an AUC of 0.994, the random forest with CUIs to be 95.00% with an AUC of 0.979, and the Word2Vec inversion to be 90.03% with an AUC of 0.905. CONCLUSIONS Our results suggest that a shallow neural network with CUIs and random forests with both CUIs and BOWs are the best classifiers for this lupus phenotyping task. The Word2Vec inversion method failed to significantly beat the ICD-9 code classification, but yielded promising results. This method does not require explicit features and is more adaptable to non-binary classification tasks. The Word2Vec inversion is hypothesized to become more powerful with access to more data. Therefore, currently, the shallow neural networks and random forests are the desirable classifiers.
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Affiliation(s)
- Clayton A. Turner
- Department of Computer Science, College of Charleston, 66 George Street, Charleston, 29424 USA
| | - Alexander D. Jacobs
- Department of Computer Science, College of Charleston, 66 George Street, Charleston, 29424 USA
| | - Cassios K. Marques
- Department of Computer Science, College of Charleston, 66 George Street, Charleston, 29424 USA
| | - James C. Oates
- Department of Public Health Sciences, Medical University of South Carolina, 135 Cannon Street, Charleston, 29425 USA
| | - Diane L. Kamen
- Department of Public Health Sciences, Medical University of South Carolina, 135 Cannon Street, Charleston, 29425 USA
| | - Paul E. Anderson
- Department of Computer Science, College of Charleston, 66 George Street, Charleston, 29424 USA
| | - Jihad S. Obeid
- Department of Public Health Sciences, Medical University of South Carolina, 135 Cannon Street, Charleston, 29425 USA
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Labuzzetta CJ, Antonio ML, Watson PM, Wilson RC, Laboissonniere LA, Trimarchi JM, Genc B, Ozdinler PH, Watson DK, Anderson PE. Complementary feature selection from alternative splicing events and gene expression for phenotype prediction. Bioinformatics 2017; 32:i421-i429. [PMID: 27587658 PMCID: PMC6276944 DOI: 10.1093/bioinformatics/btw430] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION A central task of bioinformatics is to develop sensitive and specific means of providing medical prognoses from biomarker patterns. Common methods to predict phenotypes in RNA-Seq datasets utilize machine learning algorithms trained via gene expression. Isoforms, however, generated from alternative splicing, may provide a novel and complementary set of transcripts for phenotype prediction. In contrast to gene expression, the number of isoforms increases significantly due to numerous alternative splicing patterns, resulting in a prioritization problem for many machine learning algorithms. This study identifies the empirically optimal methods of transcript quantification, feature engineering and filtering steps using phenotype prediction accuracy as a metric. At the same time, the complementary nature of gene and isoform data is analyzed and the feasibility of identifying isoforms as biomarker candidates is examined. RESULTS Isoform features are complementary to gene features, providing non-redundant information and enhanced predictive power when prioritized and filtered. A univariate filtering algorithm, which selects up to the N highest ranking features for phenotype prediction is described and evaluated in this study. An empirical comparison of pipelines for isoform quantification is reported by performing cross-validation prediction tests with datasets from human non-small cell lung cancer (NSCLC) patients, human patients with chronic obstructive pulmonary disease (COPD) and amyotrophic lateral sclerosis (ALS) transgenic mice, each including samples of diseased and non-diseased phenotypes. AVAILABILITY AND IMPLEMENTATION https://github.com/clabuzze/Phenotype-Prediction-Pipeline.git CONTACT clabuzze@iastate.edu, antoniom@bc.edu, watsondk@musc.edu, andersonpe2@cofc.edu.
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Affiliation(s)
| | | | - Patricia M Watson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, NC 29425, USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, NC 29425, USA
| | - Lauren A Laboissonniere
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Jeffrey M Trimarchi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Baris Genc
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - P Hande Ozdinler
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Dennis K Watson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, NC 29425, USA
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, Charleston, SC 29424, USA
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7
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Morey JS, Neely MG, Lunardi D, Anderson PE, Schwacke LH, Campbell M, Van Dolah FM. RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins. BMC Genomics 2016; 17:720. [PMID: 27608714 PMCID: PMC5016863 DOI: 10.1186/s12864-016-3020-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 04/09/2016] [Accepted: 08/16/2016] [Indexed: 11/30/2022] Open
Abstract
Background The blood transcriptome can reflect both systemic exposures and pathological changes in other organs of the body because immune cells recirculate through the blood, lymphoid tissues, and affected sites. In human and veterinary medicine, blood transcriptome analysis has been used successfully to identify markers of disease or pathological conditions, but can be confounded by large seasonal changes in expression. In comparison, the use of transcriptomic based analyses in wildlife has been limited. Here we report a longitudinal study of four managed bottlenose dolphins located in Waikoloa, Hawaii, serially sampled (approximately monthly) over the course of 1 year to establish baseline information on the content and variation of the dolphin blood transcriptome. Results Illumina based RNA-seq analyses were carried out using both the Ensembl dolphin genome and a de novo blood transcriptome as guides. Overall, the blood transcriptome encompassed a wide array of cellular functions and processes and was relatively stable within and between animals over the course of 1 year. Principal components analysis revealed moderate clustering by sex associated with the variation among global gene expression profiles (PC1, 22 % of variance). Limited seasonal change was observed, with < 2.5 % of genes differentially expressed between winter and summer months (FDR < 0.05). Among the differentially expressed genes, cosinor analysis identified seasonal rhythmicity for the observed changes in blood gene expression, consistent with studies in humans. While the proportion of seasonally variant genes in these dolphins is much smaller than that reported in humans, the majority of those identified in dolphins were also shown to vary with season in humans. Gene co-expression network analysis identified several gene modules with significant correlation to age, sex, or hematological parameters. Conclusions This longitudinal analysis of healthy managed dolphins establishes a preliminary baseline for blood transcriptome analysis in this species. Correlations with hematological parameters, distinct from muted seasonal effects, suggest that the otherwise relatively stable blood transcriptome may be a useful indicator of health and exposure. A robust database of gene expression in free-ranging and managed dolphins across seasons with known adverse health conditions or contaminant exposures will be needed to establish predictive gene expression profiles suitable for biomonitoring. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3020-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeanine S Morey
- National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC, 29412, USA.
| | - Marion G Neely
- National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC, 29412, USA
| | - Denise Lunardi
- Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44121, Ferrara, Italy
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, Charleston, SC, 29424, USA
| | - Lori H Schwacke
- National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC, 29412, USA
| | | | - Frances M Van Dolah
- National Centers for Coastal Ocean Sciences, National Ocean Service, NOAA, 331 Fort Johnson Rd, Charleston, SC, 29412, USA. .,Present Address: Graduate Program in Marine Biology, University of Charleston, Charleston, SC, 29412, USA.
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8
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Paul MR, Levitt NP, Moore DE, Watson PM, Wilson RC, Denlinger CE, Watson DK, Anderson PE. Multivariate models from RNA-Seq SNVs yield candidate molecular targets for biomarker discovery: SNV-DA. BMC Genomics 2016; 17:263. [PMID: 27029813 PMCID: PMC4815211 DOI: 10.1186/s12864-016-2542-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 09/01/2015] [Accepted: 02/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has recently been shown that significant and accurate single nucleotide variants (SNVs) can be reliably called from RNA-Seq data. These may provide another source of features for multivariate predictive modeling of disease phenotype for the prioritization of candidate biomarkers. The continuous nature of SNV allele fraction features allows the concurrent investigation of several genomic phenomena, including allele specific expression, clonal expansion and/or deletion, and copy number variation. RESULTS The proposed software pipeline and package, SNV Discriminant Analysis (SNV-DA), was applied on two RNA-Seq datasets with varying sample sizes sequenced at different depths: a dataset containing primary tumors from twenty patients with different disease outcomes in lung adenocarcinoma and a larger dataset of primary tumors representing two major breast cancer subtypes, estrogen receptor positive and triple negative. Predictive models were generated using the machine learning algorithm, sparse projections to latent structures discriminant analysis. Training sets composed of RNA-Seq SNV features limited to genomic regions of origin (e.g. exonic or intronic) and/or RNA-editing sites were shown to produce models with accurate predictive performances, were discriminant towards true label groupings, and were able to produce SNV rankings significantly different from than univariate tests. Furthermore, the utility of the proposed methodology is supported by its comparable performance to traditional models as well as the enrichment of selected SNVs located in genes previously associated with cancer and genes showing allele-specific expression. As proof of concept, we highlight the discovery of a previously unannotated intergenic locus that is associated with epigenetic regulatory marks in cancer and whose significant allele-specific expression is correlated with ER+ status; hereafter named ER+ associated hotspot (ERPAHS). CONCLUSION The use of models from RNA-Seq SNVs to identify and prioritize candidate molecular targets for biomarker discovery is supported by the ability of the proposed method to produce significantly accurate predictive models that are discriminant towards true label groupings. Importantly, the proposed methodology allows investigation of mutations outside of exonic regions and identification of interesting expressed loci not included in traditional gene annotations. An implementation of the proposed methodology is provided that allows the user to specify SNV filtering criteria and cross-validation design during model creation and evaluation.
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Affiliation(s)
- Matt R Paul
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA. .,Department of Cancer Biology, University of Pennsylvania, 421 Curie Blvd, Philadelphia, PA, USA.
| | - Nicholas P Levitt
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
| | - David E Moore
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
| | - Patricia M Watson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Robert C Wilson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Chadrick E Denlinger
- Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Surgery, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Dennis K Watson
- Hollings Cancer Center, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA.,Department of Pathology, Medical University of South Carolina, 165 Canon St., Charleston, SC, USA
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, 66 George St., Charleston, SC, USA
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Abstract
Developmental testing of high explosives for military applications involves small-scale formulation, safety testing, and finally detonation performance tests to verify theoretical calculations. small-scale For newly developed formulations, the process begins with small-scale mixes, thermal testing, and impact and friction sensitivity. Only then do subsequent larger scale formulations proceed to detonation testing, which will be covered in this paper. Recent advances in characterization techniques have led to unparalleled precision in the characterization of early-time evolution of detonations. The new technique of photo-Doppler velocimetry (PDV) for the measurement of detonation pressure and velocity will be shared and compared with traditional fiber-optic detonation velocity and plate-dent calculation of detonation pressure. In particular, the role of aluminum in explosive formulations will be discussed. Recent developments led to the development of explosive formulations that result in reaction of aluminum very early in the detonation product expansion. This enhanced reaction leads to changes in the detonation velocity and pressure due to reaction of the aluminum with oxygen in the expanding gas products.
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Affiliation(s)
- Rodger Cornell
- Detonation Physics Branch, US Army ARDEC, Picatinny Arsenal
| | - Erik Wrobel
- Detonation Physics Branch, US Army ARDEC, Picatinny Arsenal
| | - Paul E Anderson
- Explosives Research Branch, US Army ARDEC, Picatinny Arsenal;
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10
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Johnson JG, Paul MR, Kniffin CD, Anderson PE, Burnett LE, Burnett KG. High CO2 alters the hypoxia response of the Pacific whiteleg shrimp (Litopenaeus vannamei) transcriptome including known and novel hemocyanin isoforms. Physiol Genomics 2015; 47:548-58. [DOI: 10.1152/physiolgenomics.00031.2015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/17/2015] [Indexed: 01/19/2023] Open
Abstract
Acclimation to low O2 in many organisms involves changes at the level of the transcriptome. Here we used high-throughput RNA sequencing (RNA-Seq) to explore the global transcriptomic response and specific involvement of a suite of hemocyanin (Hc) subunits to low O2 alone and in combination with high CO2, which naturally co-occurs with low O2. Hepatopancreas mRNA of juvenile L. vannamei exposed to air-saturated water, low O2, or low O2/high CO2 for 4 or 24 h was pooled, sequenced (HiSeq 2500) and assembled (Trinity: 52,190 contigs) to create a deep strand-specific reference transcriptome. Annotation of the assembly revealed sequences encoding the previously described small Hc subunit (HcS), and three full-length isoforms of the large subunit (HcL1-3). In addition to this, a previously unidentified full-length Hc subunit was discovered. Phylogenetic analysis demonstrated the subunit to be a β-type Hc subunit (denoted HcB), making this the first report of a β-type hemocyanin subunit in the Penaeoidea. RNAs of individual shrimp were sequenced; regulated genes identified from pairwise comparisons demonstrated a distinct pattern of regulation between prolonged low O2 and low O2/high CO2 treatments by GO term enrichment analysis (Roff-Bentzen, P < 0.0001), showcasing the stabilization of energetically costly translational machinery, mobilization of energy stores, and downregulation of the ubiquitin/proteasomal degradation machinery. Exposure to hypoxia for 24 h resulted in an increase in all of the full-length hemocyanin subunits (HcS, HcL1, HcL2, HcL3, and HcB). The addition of CO2 to hypoxia muted the transcriptomic response of all the Hc subunits to low O2, except for the β-type subunit.
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Affiliation(s)
- Jillian G. Johnson
- Grice Marine Laboratory, College of Charleston, Hollings Marine Laboratory, Charleston, South Carolina; and
| | - Matthew R. Paul
- Grice Marine Laboratory, College of Charleston, Hollings Marine Laboratory, Charleston, South Carolina; and
| | - Casey D. Kniffin
- Grice Marine Laboratory, College of Charleston, Hollings Marine Laboratory, Charleston, South Carolina; and
| | - Paul E. Anderson
- Department of Computer Science, College of Charleston, Charleston, South Carolina
| | - Louis E. Burnett
- Grice Marine Laboratory, College of Charleston, Hollings Marine Laboratory, Charleston, South Carolina; and
| | - Karen G. Burnett
- Grice Marine Laboratory, College of Charleston, Hollings Marine Laboratory, Charleston, South Carolina; and
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11
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Sullivan CV, Chapman RW, Reading BJ, Anderson PE. Transcriptomics of mRNA and egg quality in farmed fish: Some recent developments and future directions. Gen Comp Endocrinol 2015; 221:23-30. [PMID: 25725305 DOI: 10.1016/j.ygcen.2015.02.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 02/14/2015] [Accepted: 02/18/2015] [Indexed: 11/29/2022]
Abstract
Maternal mRNA transcripts deposited in growing oocytes regulate early development and are under intensive investigation as determinants of egg quality. The research has evolved from single gene studies to microarray and now RNA-Seq analyses in which mRNA expression by virtually every gene can be assessed and related to gamete quality. Such studies have mainly focused on genes changing two- to several-fold in expression between biological states, and have identified scores of candidate genes and a few gene networks whose functioning is related to successful development. However, ever-increasing yields of information from high throughput methods for detecting transcript abundance have far outpaced progress in methods for analyzing the massive quantities of gene expression data, and especially for meaningful relation of whole transcriptome profiles to gamete quality. We have developed a new approach to this problem employing artificial neural networks and supervised machine learning with other novel bioinformatics procedures to discover a previously unknown level of ovarian transcriptome function at which minute changes in expression of a few hundred genes is highly predictive of egg quality. In this paper, we briefly review the progress in transcriptomics of fish egg quality and discuss some future directions for this field of study.
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Affiliation(s)
- Craig V Sullivan
- Department of Biology, North Carolina State University, Raleigh, NC 27695-7617, USA; Carolina AquaGyn, P.O. Box 12914, Raleigh, NC 27605, USA(1).
| | - Robert W Chapman
- Marine Resources Division, South Carolina Department of Natural Resources, Charleston, SC 29412, USA
| | - Benjamin J Reading
- Department of Biology, North Carolina State University, Raleigh, NC 27695-7617, USA; Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695-7617, USA(1)
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, Charleston, SC 29424, USA
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Scheiber MN, Watson PM, Rumboldt T, Stanley C, Wilson RC, Findlay VJ, Anderson PE, Watson DK. FLI1 expression is correlated with breast cancer cellular growth, migration, and invasion and altered gene expression. Neoplasia 2014; 16:801-13. [PMID: 25379017 PMCID: PMC4212256 DOI: 10.1016/j.neo.2014.08.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 07/09/2014] [Accepted: 08/15/2014] [Indexed: 12/21/2022] Open
Abstract
ETS factors have been shown to be dysregulated in breast cancer. ETS factors control the expression of genes involved in many biological processes, such as cellular proliferation, differentiation, and apoptosis. FLI1 is an ETS protein aberrantly expressed in retrovirus-induced hematological tumors, but limited attention has been directed towards elucidating the role of FLI1 in epithelial-derived cancers. Using data mining, we show that loss of FLI1 expression is associated with shorter survival and more aggressive phenotypes of breast cancer. Gain and loss of function cellular studies indicate the inhibitory effect of FLI1 expression on cellular growth, migration, and invasion. Using Fli1 mutant mice and both a transgenic murine breast cancer model and an orthotopic injection of syngeneic tumor cells indicates that reduced Fli1 contributes to accelerated tumor growth. Global expression analysis and RNA-Seq data from an invasive human breast cancer cell line with over expression of either FLI1 and another ETS gene, PDEF, shows changes in several cellular pathways associated with cancer, such as the cytokine-cytokine receptor interaction and PI3K-Akt signaling pathways. This study demonstrates a novel role for FLI1 in epithelial cells. In addition, these results reveal that FLI1 down-regulation in breast cancer may promote tumor progression.
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Key Words
- Ad-FLI1, Ad-GFP-FLI1
- EMT, Epithelial-mesenchymal transition
- ER, Estrogen receptor
- FLI1, Friend leukemia virus integration 1
- GAPDH, Glyceraldehyde-3-phosphate dehydrogenase
- GEO, Gene Expression Omnibus
- GOBO, Gene expression-based Outcome for Breast cancer Online
- IDC, Invasive ductal carcinoma
- IHC, Immunohistochemistry
- ILC, Invasive lobular carcinoma
- N, Normal Breast Tissue
- PDEF, Prostate-derived ETS factor
- PyVT, FVB/N-Tg(MMTV-PyVT)634Mul/J
- Rb, Retinoblastoma
- T, Tumor
- uPA, Urokinase plasminogen activator
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Affiliation(s)
- Melissa N Scheiber
- Department of Pathology and Laboratory Medicine, The James E. Clyburn Research Center, Medical University of South Carolina, 68 President Street, Charleston, SC 29425
| | - Patricia M Watson
- Department of Medicine, Division of Hematology/Oncology, The James E. Clyburn Research Center, Medical University of South Carolina, 68 President Street, Charleston, SC 29425
| | - Tihana Rumboldt
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Children's Hospital, 171 Ashley Avenue, Charleston, SC 29425
| | - Connor Stanley
- Department of Computer Science, College of Charleston, Charleston, SC 29424
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, The James E. Clyburn Research Center, Medical University of South Carolina, 68 President Street, Charleston, SC 29425
| | - Victoria J Findlay
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Walton Research Building, 39 Sabin Street, Charleston, SC 29425
| | - Paul E Anderson
- Department of Computer Science, College of Charleston, Charleston, SC 29424
| | - Dennis K Watson
- Department of Pathology and Laboratory Medicine, The James E. Clyburn Research Center, Medical University of South Carolina, 68 President Street, Charleston, SC 29425
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Caflin KC, Anderson PE. In-situ Remediation of Hydrogen Fluoride During a Detonation Event. Propellants, Explosives, Pyrotechnics 2014. [DOI: 10.1002/prep.201400100] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Coate EA, Kocsis AG, Peters KN, Anderson PE, Ellersieck MR, Fine DM, Anderson DM. Remote monitoring of the progression of primary pneumonic plague in Brown Norway rats in high-capacity, high-containment housing. Pathog Dis 2014; 71:265-75. [PMID: 24719212 DOI: 10.1111/2049-632x.12176] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 03/05/2014] [Accepted: 03/31/2014] [Indexed: 01/25/2023] Open
Abstract
Development of new vaccines, diagnostics, and therapeutics for biodefense or other relatively rare infectious diseases is hindered by the lack of naturally occurring human disease on which to conduct clinical trials of efficacy. To overcome this experimental gap, the U.S. Food and Drug Administration established the Animal Rule, in which efficacy testing in two well-characterized animal models that closely resemble human disease may be accepted in lieu of large-scale clinical trials for diseases with limited natural human incidence. In this report, we evaluated the Brown Norway rat as a model for pneumonic plague and describe the natural history of clinical disease following inhalation exposure to Yersinia pestis. In high-capacity, high-containment housing, we monitored temperature, activity, heart rate, and rhythm by capturing electronic impulses transmitted from abdominal telemeter implants. Using this system, we show that reduced activity and development of fever are sensitive indications of disease progression. Furthermore, we identified heart arrhythmias as contributing factors to the rapid progression to lethality following the fever response. Together, these data validate the Brown Norway rat as an experimental model for human pneumonic plague and provide new insight that may ultimately lead to novel approaches in postexposure treatment of this devastating infection.
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Affiliation(s)
- Eric A Coate
- Department of Veterinary Pathobiology, Regional Biocontainment Laboratory, University of Missouri, Columbia, MO, USA
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Anderson PE, Cook P, Davis A, Mychajlonka K, Mileham M. Silicon Fuel in High Performance Explosives. Propellants, Explosives, Pyrotechnics 2013. [DOI: 10.1002/prep.201300077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Anderson PE, Cook P, Davis A, Mychajlonka K. The Effect of Binder Systems on Early Aluminum Reaction in Detonations. Propellants, Explosives, Pyrotechnics 2013. [DOI: 10.1002/prep.201200104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Gater ST, Peters KN, Kocsis AG, Dhariwala MO, Anderson DM, Anderson PE. Host stress and immune responses during aerosol challenge of Brown Norway rats with Yersinia pestis. Front Cell Infect Microbiol 2012; 2:147. [PMID: 23226684 PMCID: PMC3510485 DOI: 10.3389/fcimb.2012.00147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/08/2012] [Indexed: 01/25/2023] Open
Abstract
Inhalation exposure models are becoming the preferred method for the comparative study of respiratory infectious diseases due to their resemblance to the natural route of infection. To enable precise delivery of pathogen to the lower respiratory tract in a manner that imposes minimal biosafety risk, nose-only exposure systems have been developed. Early inhalation exposure technology for infectious disease research grew out of technology used in asthma research where predominantly the Collison nebulizer is used to generate an aerosol by beating a liquid sample against glass. Although infectious aerosol droplets of 1–5 μm in size can be generated, the Collison often causes loss of viability. In this work, we evaluate a gentler method for aerosolization of living cells and describe the use of the Sparging Liquid Aerosol Generator (SLAG) in a rat pneumonic plague model. The SLAG creates aerosols by continuous dripping of liquid sample on a porous metal disc. We show the generation of 0.5–1 μm Yersinia pestis aerosol particles using the SLAG with spray factors typically ranging from 10−7 to 10−8 with no detectable loss of bacterial viability. Delivery of these infectious particles via nose-only exposure led to the rapid development of lethal pneumonic plague. Further, we evaluated the effect of restraint-stress imposed by the nose-only exposure chamber on early inflammatory responses and bacterial deposition. Elevated serum corticosterone which peaked at 2 h post-procedure indicated the animals experienced stress as a result of restraint in the nose-only chamber. However, we observed no correlation between elevated corticosterone and the amount of bacterial deposition or inflammation in the lungs. Together these data demonstrate the utility of the SLAG and the nose-only chamber for aerosol challenge of rodents by Y. pestis.
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Affiliation(s)
- Susan T Gater
- Laboratory for Infectious Disease Research, University of Missouri Columbia, MO, USA
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Anderson PE, Raymer ML, Kelly BJ, Reo NV, DelRaso NJ, Doom TE. Characterization of 1H NMR spectroscopic data and the generation of synthetic validation sets. ACTA ACUST UNITED AC 2009; 25:2992-3000. [PMID: 19759199 DOI: 10.1093/bioinformatics/btp540] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Common contemporary practice within the nuclear magnetic resonance (NMR) metabolomics community is to evaluate and validate novel algorithms on empirical data or simplified simulated data. Empirical data captures the complex characteristics of experimental data, but the optimal or most correct analysis is unknown a priori; therefore, researchers are forced to rely on indirect performance metrics, which are of limited value. In order to achieve fair and complete analysis of competing techniques more exacting metrics are required. Thus, metabolomics researchers often evaluate their algorithms on simplified simulated data with a known answer. Unfortunately, the conclusions obtained on simulated data are only of value if the data sets are complex enough for results to generalize to true experimental data. Ideally, synthetic data should be indistinguishable from empirical data, yet retain a known best analysis. RESULTS We have developed a technique for creating realistic synthetic metabolomics validation sets based on NMR spectroscopic data. The validation sets are developed by characterizing the salient distributions in sets of empirical spectroscopic data. Using this technique, several validation sets are constructed with a variety of characteristics present in 'real' data. A case study is then presented to compare the relative accuracy of several alignment algorithms using the increased precision afforded by these synthetic data sets. AVAILABILITY These data sets are available for download at http://birg.cs.wright.edu/nmr_synthetic_data_sets.
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Affiliation(s)
- Paul E Anderson
- Department of Computer Science and Engineering, Dayton, OH 45435, USA
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Affiliation(s)
- J Levy
- Eye Department, Royal Infirmary, Edinburgh
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20
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Smith JQ, Anderson PE, Liverani S. Separation measures and the geometry of Bayes factor selection for classification. J R Stat Soc Series B Stat Methodol 2008. [DOI: 10.1111/j.1467-9868.2008.00664.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JCW, Lynn JR, Straume M, Smith JQ, Millar AJ. FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell 2006; 18:639-50. [PMID: 16473970 PMCID: PMC1383639 DOI: 10.1105/tpc.105.038315] [Citation(s) in RCA: 225] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Temperature compensation contributes to the accuracy of biological timing by preventing circadian rhythms from running more quickly at high than at low temperatures. We previously identified quantitative trait loci (QTL) with temperature-specific effects on the circadian rhythm of leaf movement, including a QTL linked to the transcription factor FLOWERING LOCUS C (FLC). We have now analyzed FLC alleles in near-isogenic lines and induced mutants to eliminate other candidate genes. We showed that FLC lengthened the circadian period specifically at 27 degrees C, contributing to temperature compensation of the circadian clock. Known upstream regulators of FLC expression in flowering time pathways similarly controlled its circadian effect. We sought to identify downstream targets of FLC regulation in the molecular mechanism of the circadian clock using genome-wide analysis to identify FLC-responsive genes and 3503 transcripts controlled by the circadian clock. A Bayesian clustering method based on Fourier coefficients allowed us to discriminate putative regulatory genes. Among rhythmic FLC-responsive genes, transcripts of the transcription factor LUX ARRHYTHMO (LUX) correlated in peak abundance with the circadian period in flc mutants. Mathematical modeling indicated that the modest change in peak LUX RNA abundance was sufficient to cause the period change due to FLC, providing a molecular target for the crosstalk between flowering time pathways and circadian regulation.
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Affiliation(s)
- Kieron D Edwards
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3JH United Kingdom
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23
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Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JCW, Lynn JR, Straume M, Smith JQ, Millar AJ. FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell 2006; 18:639-650. [PMID: 16473970 DOI: 10.1105/tpc.105.038315.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Temperature compensation contributes to the accuracy of biological timing by preventing circadian rhythms from running more quickly at high than at low temperatures. We previously identified quantitative trait loci (QTL) with temperature-specific effects on the circadian rhythm of leaf movement, including a QTL linked to the transcription factor FLOWERING LOCUS C (FLC). We have now analyzed FLC alleles in near-isogenic lines and induced mutants to eliminate other candidate genes. We showed that FLC lengthened the circadian period specifically at 27 degrees C, contributing to temperature compensation of the circadian clock. Known upstream regulators of FLC expression in flowering time pathways similarly controlled its circadian effect. We sought to identify downstream targets of FLC regulation in the molecular mechanism of the circadian clock using genome-wide analysis to identify FLC-responsive genes and 3503 transcripts controlled by the circadian clock. A Bayesian clustering method based on Fourier coefficients allowed us to discriminate putative regulatory genes. Among rhythmic FLC-responsive genes, transcripts of the transcription factor LUX ARRHYTHMO (LUX) correlated in peak abundance with the circadian period in flc mutants. Mathematical modeling indicated that the modest change in peak LUX RNA abundance was sufficient to cause the period change due to FLC, providing a molecular target for the crosstalk between flowering time pathways and circadian regulation.
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Affiliation(s)
- Kieron D Edwards
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3JH United Kingdom
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24
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Anderson PE, Jensen HJ. Network properties, species abundance and evolution in a model of evolutionary ecology. J Theor Biol 2005; 232:551-8. [PMID: 15588635 DOI: 10.1016/j.jtbi.2004.03.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Revised: 02/20/2004] [Accepted: 03/18/2004] [Indexed: 11/22/2022]
Abstract
We study the evolution of the network properties of a populated network embedded in a genotype space characterized by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution produces two distinct types of network. When a specific genotype is only able to influence a few other genotypes, the ecosystem consists of separate non-interacting clusters (i.e. isolated compartments) in genotype space. When different types may influence a large number of other sites, the network becomes one large interconnected cluster. The distribution of interaction strengths--but not the number of connections--changes significantly with time. We find that the species abundance is only realistic for a high level of species connectivity. This suggests that real ecosystems form one interconnected whole in which selection leads to stronger interactions between the different types. Analogies with niche and neutral theory and assembly models are also considered.
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Affiliation(s)
- Paul E Anderson
- Department of Mathematics, Imperial College, 180 Queen's Gate, London, SW7 2AZ, UK
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25
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Anderson PE, Badlani RN, Mayer J, Mabrouk PA. Electrochemical synthesis and characterization of conducting polymers in supercritical carbon dioxide. J Am Chem Soc 2002; 124:10284-5. [PMID: 12197723 DOI: 10.1021/ja026494c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This contribution reports the first synthesis of conducting polymers (CPs), specifically, polyaniline (PAn) and polypyrrole (PPy), in supercritical carbon dioxide (scCO2). CPs synthesized electrochemically in scCO2 were characterized with cyclic voltammetry (CV), four-point probe conductivity, scanning electron microscopy (SEM), and UV-vis spectroscopy. Preliminary data indicate that CPs synthesized by this method exhibit novel morphology and high conductivity comparable to that synthesized by traditional methods.
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Affiliation(s)
- Paul E Anderson
- Department of Chemistry, Northeastern University, 111 Hurtig Hall, 360 Huntington Avenue, Boston, Massachusetts 02115, USA
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Anderson PE, Gober JW. FlbT, the post-transcriptional regulator of flagellin synthesis in Caulobacter crescentus, interacts with the 5' untranslated region of flagellin mRNA. Mol Microbiol 2000. [PMID: 11029689 DOI: 10.1046/j.1365-2958.2000.02108.x.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Flagellar gene expression' in Caulobacter crescentus is regulated by a complex trans-acting hierarchy, in which the assembly of early structural proteins is required for the expression of later structural proteins. The flagellins that comprise the filament are regulated at both the transcriptional and the post-transcriptional levels. Post-transcriptional regulation is sensitive to the assembly of the flagellar basal body and hook structures. In mutant strains lacking these structures, flagellin genes are transcribed, but not translated. Mutations in the flagellar regulatory gene, flbT, restore flagellin translation in the absence of flagellar assembly. In this report, we investigate the mechanism of FlbT-mediated post-transcriptional regulation. We show that FlbT is associated with the 5' untranslated region (UTR) of fljK (25 kDa flagellin) mRNA and that this association requires a predicted loop structure in the transcript. Mutations within this loop abolished FlbT association and resulted in increased mRNA stability, indicating that FlbT promotes the degradation of flagellin mRNA by associating with the 5' UTR. We also assayed the effects on gene expression using mutant transcripts fused to lacZ. Interestingly, the mutant transcript that failed to associate with FlbT in vitro was still repressed in mutants defective in flagellum assembly, suggesting that other factors in addition to FlbT couple assembly to translation.
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Affiliation(s)
- P E Anderson
- Department of Microbiology and Molecular Genetics, University of California, Los Angeles, CA 90095-1569, USA
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Anderson PE, Gober JW. FlbT, the post-transcriptional regulator of flagellin synthesis in Caulobacter crescentus, interacts with the 5' untranslated region of flagellin mRNA. Mol Microbiol 2000; 38:41-52. [PMID: 11029689 DOI: 10.1046/j.1365-2958.2000.02108.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [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] [Indexed: 11/20/2022]
Abstract
Flagellar gene expression' in Caulobacter crescentus is regulated by a complex trans-acting hierarchy, in which the assembly of early structural proteins is required for the expression of later structural proteins. The flagellins that comprise the filament are regulated at both the transcriptional and the post-transcriptional levels. Post-transcriptional regulation is sensitive to the assembly of the flagellar basal body and hook structures. In mutant strains lacking these structures, flagellin genes are transcribed, but not translated. Mutations in the flagellar regulatory gene, flbT, restore flagellin translation in the absence of flagellar assembly. In this report, we investigate the mechanism of FlbT-mediated post-transcriptional regulation. We show that FlbT is associated with the 5' untranslated region (UTR) of fljK (25 kDa flagellin) mRNA and that this association requires a predicted loop structure in the transcript. Mutations within this loop abolished FlbT association and resulted in increased mRNA stability, indicating that FlbT promotes the degradation of flagellin mRNA by associating with the 5' UTR. We also assayed the effects on gene expression using mutant transcripts fused to lacZ. Interestingly, the mutant transcript that failed to associate with FlbT in vitro was still repressed in mutants defective in flagellum assembly, suggesting that other factors in addition to FlbT couple assembly to translation.
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Affiliation(s)
- P E Anderson
- Department of Microbiology and Molecular Genetics, University of California, Los Angeles, CA 90095-1569, USA
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Johnstone BH, Handler AA, Chao DK, Nguyen V, Smith M, Ryu SY, Simons EL, Anderson PE, Simons RW. The widely conserved Era G-protein contains an RNA-binding domain required for Era function in vivo. Mol Microbiol 1999; 33:1118-31. [PMID: 10510227 DOI: 10.1046/j.1365-2958.1999.01553.x] [Citation(s) in RCA: 38] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Era is a small G-protein widely conserved in eubacteria and eukaryotes. Although essential for bacterial growth and implicated in diverse cellular processes, its actual function remains unclear. Several lines of evidence suggest that Era may be involved in some aspect of RNA biology. The GTPase domain contains features in common with all G-proteins and is required for Era function in vivo. The C-terminal domain (EraCTD) bears scant similarity to proteins outside the Era subfamily. On the basis of sequence comparisons, we argue that the EraCTD is similar to, but distinct from, the KH RNA-binding domain. Although both contain the consensus VIGxxGxxI RNA-binding motif, the protein folds are probably different. We show that bacterial Era binds RNA in vitro and can form higher-order RNA-protein complexes. Mutations in the VIGxxGxxI motif and other conserved residues of the Escherichia coli EraCTD decrease RNA binding in vitro and have corresponding effects on Era function in vivo, including previously described effects on cell division and chromosome partitioning. Importantly, mutations in L-66, located in the predicted switch II region of the E. coli Era GTPase domain, also perturb binding, leading us to propose that the GTPase domain regulates RNA binding in response to unknown cellular cues. The possible biological significance of Era RNA binding is discussed.
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Affiliation(s)
- B H Johnstone
- Department of Microbiology and Molecular Genetics and the Molecular Biology Institute, 1602 Molecular Sciences, University of California, Los Angeles, CA 90095, USA
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Watson CG, Davenport E, Anderson PE, Mendez CM, Gearhart LP. The relationships between premilitary school record data and risk for posttraumatic stress disorder among Vietnam war veterans. J Nerv Ment Dis 1998; 186:338-44. [PMID: 9653417 DOI: 10.1097/00005053-199806000-00003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The purpose of this study was to determine whether Vietnam veterans' risk for posttraumatic stress disorder (PTSD) was correlated with their premilitary school performance. The authors compared both primary and secondary school record data on hospitalized chemically dependent PTSD patients with those of both non-PTSD, chemically dependent and community controls. All participants were male Vietnam war combat veterans. The comparisons were made with MANCOVA analyses with the effects of combat and age differences between groups controlled. For the most part, primary-school grade point average, absenteeism, and tardiness data on three groups did not differ significantly. However, the mean secondary school grade points of the future PTSD patients were generally substantially lower than those of controls. Additionally, more secondary school absenteeism and tardiness were reported among future PTSD patients than in the controls. The groups did not differ significantly on number of extracurricular activities. Academic weakness, absenteeism, and tardiness in secondary school appear to be moderately strong predictors of vulnerability to PTSD after traumatization. It also supports the claim that chronic PTSD is, in part, the result of weaknesses present before exposure to trauma.
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Affiliation(s)
- C G Watson
- Department of Veteran Affairs Medical Research Service, St. Cloud, Minnesota 56303, USA
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Lydiatt WM, Anderson PE, Bazzana T, Casale M, Hughes CJ, Huvos AG, Lydiatt DD, Schantz SP. Molecular support for field cancerization in the head and neck. Cancer 1998; 82:1376-80. [PMID: 9529031] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Two competing concepts, field cancerization and micrometastatic lesions, have been postulated to account for the high frequency of second primary tumors and multicentric dysplasia in patients with head and neck carcinoma. METHODS To provide insight into this process, the authors examined histologically normal mucosa and dysplastic tissue adjacent to invasive tumor for loss of heterozygosity (LOH) at three commonly deleted loci. Tissues from 21 patients with carcinoma of the oral cavity and oropharynx were identified and verified by a pathologist to contain histologically normal mucosa, dysplasia, and adjacent invasive squamous cell carcinoma. Each specimen was analyzed for LOH at D9S171 (9p21), D3S1007 (3p21.3-22), and D3S1228 (3p14). RESULTS Of the 21 patients, 19 had adequate DNA for analysis. Seventeen patients were heterozygous at one or both of the 3p sites and LOH occurred in 6 of 17 invasive tumor specimens, 1 of 17 dysplasia specimens, and in none of the mucosal specimens. LOH at 9p21 occurred in 11 of 13 informative specimens of invasive tumor, 8 of 13 dysplasia specimens, and 6 of 13 normal mucosa specimens. However, one case that did not have 9p deletion in the tumor demonstrated LOH in the mucosa and two cases had LOH in both the tumor and mucosa but with deletion of the opposite allele. CONCLUSIONS These data suggest that 9p21 but not 3p14 or 3p21 deletions occur in the absence of histologic changes. In two cases preinvasive and invasive lesions that apparently were an example of histologic progression contained disparate genetic events, calling into question the use of adjacent dysplasia as a model for premalignant lesions.
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Affiliation(s)
- W M Lydiatt
- Otolaryngology-Head and Neck Surgery, University of Nebraska Medical Center and Nebraska Methodist Hospital, Omaha 68198-1225, USA
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Mulcahy MM, Cohen JI, Anderson PE, Ditamasso J, Schmidt W. Relative accuracy of fine-needle aspiration and frozen section in the diagnosis of well-differentiated thyroid cancer. Laryngoscope 1998; 108:494-6. [PMID: 9546258 DOI: 10.1097/00005537-199804000-00006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The need for and extent of thyroid surgery for a thyroid nodule is usually primarily based on fine-needle aspiration (FNA) and frozen section diagnosis. The relative role of these modalities in 66 patients who had undergone FNA and subsequent thyroidectomy with frozen section was investigated. Cases that demonstrated discordance between FNA and frozen section (n = 22; 33%) were identified, and all slides were re-reviewed by a cytopathologist using current established cytologic criteria. A change in diagnosis was made in 13 cases with an increase in accuracy of FNA from 71% to 88%. The accuracy of frozen section (92%) did not change appreciably with re-review (94%). The accuracy of FNA and frozen section combined was found to be 98%. The rate of discordance decreased from 33% to 13% with re-review. When strict histologic and cytologic criteria are applied, FNA and frozen section are accurate and complementary methods that help in determining the operative management of thyroid masses. However, when FNA yields a diagnosis of "follicular neoplasm," frozen section is unlikely to change this diagnosis.
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Affiliation(s)
- M M Mulcahy
- Department of Otolaryngology--Head and Neck Surgery, Oregon Health Sciences University, Portland 97201, USA
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32
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Anderson PE. Fee increases? 'Just do it'! Dent Econ 1997; 87:24, 26, 28-30 passim. [PMID: 9452560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Anderson PE. Staff-related costs on the rise. Dent Econ 1997; 87:68, 70, 72 passim. [PMID: 9452556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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34
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Anderson PE. Staff salaries continue to rise, but employee numbers level. Dent Econ 1996; 86:42-7. [PMID: 9242076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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35
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Anderson PE. Dentists respond to annual practice survey. Dent Econ 1996; 86:30-2, 34, 36 passim. [PMID: 9242058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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36
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Anderson PE. Latest fee survey shows more dentists advertising. Dent Econ 1996; 86:52-3. [PMID: 9020665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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37
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Anderson PE. Are your fees keeping pace? Dent Econ 1996; 86:26-8, 30, 32 passion. [PMID: 9020628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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38
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Anderson PE. Are changes in dentistry compromising ethics?--Part II. Dent Econ 1996; 86:50-5, 57. [PMID: 9020670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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39
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Anderson PE. Are changes in the profession compromising dental ethics? Dent Econ 1996; 86:49-52, 54, 56 passim. [PMID: 9020637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Abstract
The Escherichia coli rnc-era-recO operon encodes ribonuclease III (RNase III; a dsRNA endonuclease involved in rRNA and mRNA processing and decay), Era (an essential G-protein of unknown functions and RecO (involved in the RecF homologous recombination pathway). Expression of the rnc and era genes is negatively autoregulated: RNase III cleaves the rncO 'operator' in the untranslated leader, destabilizing the operon mRNA. As part of a larger effort to understand RNase III and Era structure and function, we characterized rnc operon structure, function and regulation in the closely related bacterium Salmonella typhimurium. Construction of a S typhimurium strain conditionally defective for RNase III and Era expression showed that Era is essential for cell growth. This mutant strain also enabled selection of recombinant clones containing the intact S typhimurium rnc-era-recO operon, whose nucleotide sequence, predicted protein sequence, and predicted rncO RNA secondary structure were all highly conserved with those of E coli. Furthermore, genetic and biochemical analysis revealed that S typhimurium rnc gene expression is negatively autoregulated by a mechanism very similar or identical to that in E coli, and that the cleavage specificities of RNase IIIs.t. and RNase IIIE.c. are indistinguishable with regard to rncO cleavage and S typhimurium 23S rRNA fragmentation in vivo.
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Affiliation(s)
- P E Anderson
- Department of Microbiology and Molecular Genetics, University of California, Los Angeles 90095, USA
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Abstract
We compared the frequencies with which PTSD patients, psychiatric controls, and hospital employee controls reported that their fathers, mothers, and oldest siblings of each sex had been incarcerated or had received psychiatric/psychological treatment. We also compared estimates of the number of psychiatric hospitalizations, incarcerations, courses of outpatient treatment, treatment sessions, and days of institutionalization undergone by the relatives. Only a chance number of significant differences appeared, which suggests that general psychosocial maladjustment in one's family of origin does not appear to increase trauma survivors' risk for PTSD.
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Affiliation(s)
- C G Watson
- Research Service, Department of Veterans Affairs Medical Center, ST. Cloud, MN 56303, USA
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Anderson PE. Salaries big bite of overhead pie. Dent Econ 1995; 85:30, 32, 34, 36. [PMID: 8631434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Goh KL, Parasakthi N, Peh SC, Anderson PE, Tan KK. Prolonged treatment with omeprazole does not improve the eradication rate of Helicobacter pylori infection--a short report [corrected]. Singapore Med J 1995; 36:619-20. [PMID: 8781634] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Omeprazole has been shown to have a suppressive effect on Helicobacter pylori. The aim of this study was to determine if prolonged treatment with omeprazole would result in a higher eradication rate than short course treatment. Twenty patients with endoscopy proven duodenal ulcers and unequivocal evidence of Helicobacter pylori (HP) infection based on culture, histology, urease test and Gram's stain of a fresh tissue smear were treated with omeprazole 40 mg om for 2-4 weeks. Following ulcer healing, patients received either maintenance omeprazole 20 mg om or placebo for up to one year. All 20 patients had healed ulcers following a 2-4 week course of omeprazole 40 mg om.. All were negative for HP at the end of treatment. Thirteen patients received short course therapy with omeprazole only, followed by placebo. On follow-up endoscopy at 3 months, only one of 13 (7.7%) had eradicated the bacteria. Seven patients received maintenance treatment with omeprazole 20mg om for one year. Following completion of treatment, patients were followed up at 1, 3 and 6 months. Only one of 7 (14.3%) patients had eradicated the infection on long term follow-up. The eradication rates of HP with both short and long course omeprazole monotherapy were low.
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Affiliation(s)
- K L Goh
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Anderson PE. More staff, higher salaries sum up staffing patterns. Dent Econ 1995; 85:56-62, 64. [PMID: 9515312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Anderson PE. High-income dentists see more patients. Dent Econ 1995; 85:54. [PMID: 8612909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Anderson PE. Dentists more optimistic in 1995 practice survey. Dent Econ 1995; 85:34-8, 42, 44. [PMID: 8612908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Abstract
Posttraumatic stress disorder (PTSD) patients, psychiatric controls, and hospital employee controls rated their father, mother, and oldest sibling of each sex on 14 PTSD Interview (PTSD-I) symptom ratings. The stress disorder patients assigned their relatives significantly higher PTSD-I ratings than the control group members did in 35 of 120 comparisons. The number of significant differences was nearly identical in the fathers, mothers, sisters, and brothers. Differences were particularly frequent on items pertaining to intrusive thoughts, impoverished relationships, and guilt. The results suggest that a trauma survivor's risk for PTSD may be related to his family's history for PTSD-like behaviors.
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Affiliation(s)
- C G Watson
- Research Service, Department of Veterans Affairs Medical Center, St. Cloud, Minnesota 56303, USA
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Anderson PE. Dental fees keep pace with low inflation rate. Dent Econ 1995; 85:36-8, 42,44-51. [PMID: 8612926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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MacDonald DA, Anderson PE, Tsagarakis CI, Holland CJ. Correlations between the Myers-Briggs Type Indicator and the Neo Personality Inventory facets. Psychol Rep 1995; 76:449-50. [PMID: 7667455 DOI: 10.2466/pr0.1995.76.2.449] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Using data obtained from 48 male and 161 female undergraduate students in psychology, correlations between scores on the scales of the Myers-Briggs Type Indicator and the facets of the Neuroticism, Extraversion, and Openness domains of the NEO Personality Inventory were low to moderate.
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Affiliation(s)
- D A MacDonald
- Department of Psychology, University of Windsor, Ontario Canada
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Anderson PE. Auxiliary pay continues to rise. Dent Econ 1994; 84:45-8, 50, 52 passim. [PMID: 8612889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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