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Pavicic M, Walker AM, Sullivan KA, Lagergren J, Cliff A, Romero J, Streich J, Garvin MR, Pestian J, McMahon B, Oslin DW, Beckham JC, Kimbrel NA, Jacobson DA. Using iterative random forest to find geospatial environmental and Sociodemographic predictors of suicide attempts. Front Psychiatry 2023; 14:1178633. [PMID: 37599888 PMCID: PMC10433206 DOI: 10.3389/fpsyt.2023.1178633] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/21/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Despite a recent global decrease in suicide rates, death by suicide has increased in the United States. It is therefore imperative to identify the risk factors associated with suicide attempts to combat this growing epidemic. In this study, we aim to identify potential risk factors of suicide attempt using geospatial features in an Artificial intelligence framework. Methods We use iterative Random Forest, an explainable artificial intelligence method, to predict suicide attempts using data from the Million Veteran Program. This cohort incorporated 405,540 patients with 391,409 controls and 14,131 attempts. Our predictive model incorporates multiple climatic features at ZIP-code-level geospatial resolution. We additionally consider demographic features from the American Community Survey as well as the number of firearms and alcohol vendors per 10,000 people to assess the contributions of proximal environment, access to means, and restraint decrease to suicide attempts. In total 1,784 features were included in the predictive model. Results Our results show that geographic areas with higher concentrations of married males living with spouses are predictive of lower rates of suicide attempts, whereas geographic areas where males are more likely to live alone and to rent housing are predictive of higher rates of suicide attempts. We also identified climatic features that were associated with suicide attempt risk by age group. Additionally, we observed that firearms and alcohol vendors were associated with increased risk for suicide attempts irrespective of the age group examined, but that their effects were small in comparison to the top features. Discussion Taken together, our findings highlight the importance of social determinants and environmental factors in understanding suicide risk among veterans.
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Affiliation(s)
- Mirko Pavicic
- Oak Ridge National Laboratory, Computational and Predictive Biology, Oak Ridge, TN, United States
| | - Angelica M. Walker
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Kyle A. Sullivan
- Oak Ridge National Laboratory, Computational and Predictive Biology, Oak Ridge, TN, United States
| | - John Lagergren
- Oak Ridge National Laboratory, Computational and Predictive Biology, Oak Ridge, TN, United States
| | - Ashley Cliff
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Jonathon Romero
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, United States
| | - Jared Streich
- Oak Ridge National Laboratory, Computational and Predictive Biology, Oak Ridge, TN, United States
| | - Michael R. Garvin
- Oak Ridge National Laboratory, Computational and Predictive Biology, Oak Ridge, TN, United States
| | - John Pestian
- Oak Ridge National Laboratory, Computational and Predictive Biology, Oak Ridge, TN, United States
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, United States
| | - Benjamin McMahon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - David W. Oslin
- VISN 4 Mental Illness Research, Education, and Clinical Center, Center of Excellence, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jean C. Beckham
- Durham Veterans Affairs Health Care System, Durham, NC, United States
- VA Mid-Atlantic Mental Illness, Research, Education, and Clinical Center, Seattle, WA, United States
- Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, United States
| | - Nathan A. Kimbrel
- Durham Veterans Affairs Health Care System, Durham, NC, United States
- VA Mid-Atlantic Mental Illness, Research, Education, and Clinical Center, Seattle, WA, United States
- Duke University School of Medicine, Duke University, Durham, NC, United States
- VA Health Services Research and Development Center of Innovation to Accelerate Discovery and Practice Transformation, Durham, NC, United States
| | - Daniel A. Jacobson
- Oak Ridge National Laboratory, Computational and Predictive Biology, Oak Ridge, TN, United States
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Dennehy R, Duggan N, Dignam S, McCormack S, Dillon E, Molony J, Romano M, Hou Y, Ardill L, Whelan MVX, Drulis‐Kawa Z, Ó'Cróinín T, Valvano MA, Berisio R, McClean S. Protein with negative surface charge distribution, Bnr1, shows characteristics of a DNA-mimic protein and may be involved in the adaptation of Burkholderia cenocepacia. Microbiologyopen 2022; 11:e1264. [PMID: 35212475 PMCID: PMC9060813 DOI: 10.1002/mbo3.1264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/14/2022] [Indexed: 11/11/2022] Open
Abstract
Adaptation of opportunistic pathogens to their host environment requires reprogramming of a vast array of genes to facilitate survival in the host. Burkholderia cenocepacia, a Gram-negative bacterium with a large genome of ∼8 Mb that colonizes environmental niches, is exquisitely adaptable to the hypoxic environment of the cystic fibrosis lung and survives in macrophages. We previously identified an immunoreactive acidic protein encoded on replicon 3, BCAS0292. Deletion of the BCAS0292 gene significantly altered the abundance of 979 proteins by 1.5-fold or more; 19 proteins became undetectable while 545 proteins showed ≥1.5-fold reduced abundance, suggesting the BCAS0292 protein is a global regulator. Moreover, the ∆BCAS0292 mutant showed a range of pleiotropic effects: virulence and host-cell attachment were reduced, antibiotic susceptibility was altered, and biofilm formation enhanced. Its growth and survival were impaired in 6% oxygen. In silico prediction of its three-dimensional structure revealed BCAS0292 presents a dimeric β-structure with a negative surface charge. The ΔBCAS0292 mutant displayed altered DNA supercoiling, implicated in global regulation of gene expression. Three proteins were identified in pull-downs with FLAG-tagged BCAS0292, including the Histone H1-like protein, HctB, which is recognized as a global transcriptional regulator. We propose that BCAS0292 protein, which we have named Burkholderia negatively surface-charged regulatory protein 1 (Bnr1), acts as a DNA-mimic and binds to DNA-binding proteins, altering DNA topology and regulating the expression of multiple genes, thereby enabling the adaptation of B. cenocepacia to highly diverse environments.
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Affiliation(s)
- Ruth Dennehy
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
| | - Niamh Duggan
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Simon Dignam
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
| | - Sarah McCormack
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Eugene Dillon
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Jessica Molony
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Maria Romano
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Yueran Hou
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Laura Ardill
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Matthew V. X. Whelan
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Zuzanna Drulis‐Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and MicrobiologyUniversity of WroclawWroclawPoland
| | - Tadhg Ó'Cróinín
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Miguel A. Valvano
- School of Medicine, Dentistry and Biomedical Sciences, Wellcome‐Wolfson Institute for Experimental MedicineQueen's University BelfastBelfastUK
| | - Rita Berisio
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Siobhán McClean
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
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Liao YT, Lin SJ, Ko TP, Liu CY, Hsu KC, Wang HC. Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases. Int J Biol Macromol 2020; 160:903-914. [PMID: 32502608 DOI: 10.1016/j.ijbiomac.2020.05.267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/27/2020] [Accepted: 05/31/2020] [Indexed: 12/14/2022]
Abstract
Uracil-DNA glycosylases (UDGs) are conserved DNA-repair enzymes that can be found in many species, including herpesviruses. Since they play crucial roles for efficient viral DNA replication in herpesviruses, they have been considered as potential antiviral targets. In our previous work, Staphylococcus aureus SAUGI was identified as a DNA mimic protein that targets UDGs from S. aureus, human, Herpes simplex virus (HSV) and Epstein-Barr virus (EBV). Interestingly, SAUGI has the strongest inhibitory effects with EBVUDG. Here, we determined complex structures of SAUGI with EBVUDG and another γ-herpesvirus UDG from Kaposi's sarcoma-associated herpesvirus (KSHVUDG), which SAUGI fails to effectively inhibit. Structural analysis of the SAUGI/EBVUDG complex suggests that the additional interaction between SAUGI and the leucine loop may explain why SAUGI shows the highest binding capacity with EBVUDG. In contrast, SAUGI appears to make only partial contacts with the key components responsible for the compression and stabilization of the DNA backbone in the leucine loop extension of KSHVUDG. The findings in this study provide a molecular explanation for the differential inhibitory effects and binding strengths that SAUGI has on these two UDGs, and the structural basis of the differences should be helpful in developing inhibitors that would interfere with viral DNA replication.
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Affiliation(s)
- Yi-Ting Liao
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 115, Taiwan; Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan.
| | - Shin-Jen Lin
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Chang-Yi Liu
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 115, Taiwan; Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan.
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan; Biomedical Commercialization Center, Taipei Medical University, Taipei 110, Taiwan.
| | - Hao-Ching Wang
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 115, Taiwan; Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan.
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Corvaglia V, Carbajo D, Prabhakaran P, Ziach K, Mandal PK, Santos VD, Legeay C, Vogel R, Parissi V, Pourquier P, Huc I. Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: artificial analogues of DNA mimic proteins. Nucleic Acids Res 2019; 47:5511-5521. [PMID: 31073604 PMCID: PMC6582331 DOI: 10.1093/nar/gkz352] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
Inspired by DNA mimic proteins, we have introduced aromatic foldamers bearing phosphonate groups as synthetic mimics of the charge surface of B-DNA and competitive inhibitors of some therapeutically relevant DNA-binding enzymes: the human DNA Topoisomerase 1 (Top1) and the human HIV-1 integrase (HIV-1 IN). We now report on variants of these anionic foldamers bearing carboxylates instead of phosphonates. Several new monomers have been synthesized with protecting groups suitable for solid phase synthesis (SPS). Six hexadecaamides have been prepared using SPS. Proof of their resemblance to B-DNA was brought by the first crystal structure of one of these DNA-mimic foldamers in its polyanionic form. While some of the foldamers were found to be as active as, or even more active than, the original phosphonate oligomers, others had no activity at all or could even stimulate enzyme activity in vitro. Some foldamers were found to have differential inhibitory effects on the two enzymes. These results demonstrate a strong dependence of inhibitory activity on foldamer structure and charge distribution. They open broad avenues for the development of new classes of derivatives that could inhibit the interaction of specific proteins with their DNA target thereby influencing the cellular pathways in which they are involved.
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Affiliation(s)
- Valentina Corvaglia
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, München 81377, Germany.,Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Daniel Carbajo
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Panchami Prabhakaran
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Krzysztof Ziach
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Pradeep Kumar Mandal
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, München 81377, Germany.,Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | | | - Carole Legeay
- Sanofi recherche & développement, Montpellier 34184, France
| | - Rachel Vogel
- Sanofi recherche & développement, Montpellier 34184, France
| | - Vincent Parissi
- Université de Bordeaux, CNRS, Laboratoire de Microbiologie Fondamentale et Pathogénicité (UMR 5234), Bordeaux 33146, France
| | - Philippe Pourquier
- INSERM U1194, Institut de Recherche en Cancérologie de Montpellier & Université de Montpellier, Montpellier 34298, France
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, München 81377, Germany.,Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
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Liao YT, Lin SS, Lin SJ, Sun WT, Shen BN, Cheng HP, Lin CP, Ko TP, Chen YF, Wang HC. Structural insights into the interaction between phytoplasmal effector causing phyllody 1 and MADS transcription factors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:706-719. [PMID: 31323156 DOI: 10.1111/tpj.14463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/24/2019] [Accepted: 07/02/2019] [Indexed: 05/21/2023]
Abstract
Phytoplasmas are bacterial plant pathogens which can induce severe symptoms including dwarfism, phyllody and virescence in an infected plant. Because phytoplasmas infect many important crops such as peanut and papaya they have caused serious agricultural losses. The phytoplasmal effector causing phyllody 1 (PHYL1) is an important phytoplasmal pathogenic factor which affects the biological function of MADS transcription factors by interacting with their K (keratin-like) domain, thus resulting in abnormal plant developments such as phyllody. Until now, lack of information on the structure of PHYL1 has prevented a detailed understanding of the binding mechanism between PHYL1 and the MADS transcription factors. Here, we present the crystal structure of PHYL1 from peanut witches'-broom phytoplasma (PHYL1PnWB ). This protein was found to fold into a unique α-helical hairpin with exposed hydrophobic residues on its surface that may play an important role in its biological function. Using proteomics approaches, we propose a binding mode of PHYL1PnWB with the K domain of the MADS transcription factor SEPALLATA3 (SEP3_K) and identify the residues of PHYL1PnWB that are important for this interaction. Furthermore, using surface plasmon resonance we measure the binding strength of PHYL1PnWB proteins to SEP3_K. Lastly, based on confocal images, we found that α-helix 2 of PHYL1PnWB plays an important role in PHYL1-mediated degradation of SEP3. Taken together, these results provide a structural understanding of the specific binding mechanism between PHYL1PnWB and SEP3_K.
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Affiliation(s)
- Yi-Ting Liao
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
- Center of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
| | - Shin-Jen Lin
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Wan-Ting Sun
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Bing-Nan Shen
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Han-Pin Cheng
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Chan-Pin Lin
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Department of Plant Pathology and Microbiology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Fan Chen
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Hao-Ching Wang
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
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Wang H, Chou C, Hsu K, Lee C, Wang AH. New paradigm of functional regulation by DNA mimic proteins: Recent updates. IUBMB Life 2018; 71:539-548. [DOI: 10.1002/iub.1992] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Hao‐Ching Wang
- Graduate Institute of Translational MedicineCollege of Medical Science and Technology, Taipei Medical University Taipei 110 Taiwan
| | - Chia‐Cheng Chou
- National Center for High‐performance ComputingNational Applied Research Laboratories Hsinchu 300 Taiwan
| | - Kai‐Cheng Hsu
- Graduate Institute of Cancer Molecular Biology and Drug DiscoveryCollege of Medical Science and Technology, Taipei Medical University Taipei 110 Taiwan
| | - Chi‐Hua Lee
- Institute of Biological Chemistry, Academia Sinica Taipei 115 Taiwan
| | - Andrew H.‐J. Wang
- Graduate Institute of Translational MedicineCollege of Medical Science and Technology, Taipei Medical University Taipei 110 Taiwan
- Institute of Biological Chemistry, Academia Sinica Taipei 115 Taiwan
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