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Brown JA, Houghten S, Fogel GB. 2022 IEEE conference on computational intelligence in bioinformatics and computational biology (IEEE CIBCB, 2022). Biosystems 2024; 237:105129. [PMID: 38280445 DOI: 10.1016/j.biosystems.2024.105129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Affiliation(s)
| | | | - Gary B Fogel
- Natural Selection, Inc, San Diego, California, USA.
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Rose R, Feehan A, Lain BN, Ashcraft D, Nolan DJ, Velez-Climent L, Huston C, LaFleur T, Rosenthal S, Fogel GB, Miele L, Pankey G, Garcia-Diaz J, Lamers SL. Whole-genome sequencing of carbapenem-resistant Enterobacterales isolates in southeast Louisiana reveals persistent genetic clusters spanning multiple locations. J Infect Public Health 2023; 16:1911-1917. [PMID: 37866269 DOI: 10.1016/j.jiph.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 10/02/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND We investigated 51 g-negative carbapenem-resistant Enterobacterales (CRE) isolates collected from 22 patients over a five-year period from six health care institutions in the Ochsner Health network in southeast Louisiana. METHODS Short genomic reads were generated using Illumina sequencing and assembled for each isolate. Isolates were classified as Enterobacter spp. (n = 20), Klebsiella spp. (n = 30), and Escherichia coli (n = 1) and grouped into 19 different multi-locus sequence types (MLST). Species and patient-specific core genomes were constructed representing ∼50% of the chromosomal genome. RESULTS We identified two sets of patients with genetically related infections; in both cases, the related isolates were collected > 6 months apart, and in one case, the isolates were collected in different locations. On the other hand, we identified four sets of patients with isolates of the same species collected within 21 days from the same location; however, none had genetically related infections. Genes associated with resistance to carbapenem drugs (blaKPC and/or blaCTX-M-15) were found in 76% of the isolates. We found three blaKPC variants (blaKPC-2, blaKPC-3, and blaKPC-4) associated with four different Enterobacter MLST variants, and two blaKPC variants (blaKPC-2, blaKPC-3) associated with seven different Klebsiella MLST variants. CONCLUSIONS Molecular surveillance is increasingly becoming a powerful tool to understand bacterial spread in both community and clinical settings. This study provides evidence that genetically related infections in clinical settings do not necessarily reflect temporal associations, and vice versa. Our results also highlight the regional genomic and resistance diversity within related bacterial lineages.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts, LLC, Thibodaux, LA, USA; FoxSeq, LLC, Thibodaux, LA, USA.
| | - Amy Feehan
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | - Deborah Ashcraft
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | | | | | | | | | | | - Lucio Miele
- Translational Science and Genetics at LSU Health Science Center, New Orleans, LA, USA
| | - George Pankey
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Julia Garcia-Diaz
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Susanna L Lamers
- BioInfoExperts, LLC, Thibodaux, LA, USA; FoxSeq, LLC, Thibodaux, LA, USA
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Lamers SL, Fogel GB, Liu ES, Nolan DJ, Rose R, McGrath MS. HIV-1 subtypes maintain distinctive physicochemical signatures in Nef domains associated with immunoregulation. Infect Genet Evol 2023; 115:105514. [PMID: 37832752 PMCID: PMC10842591 DOI: 10.1016/j.meegid.2023.105514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND HIV subtype is associated with varied rates of disease progression. The HIV accessory protein, Nef, continues to be present during antiretroviral therapy (ART) where it has numerous immunoregulatory effects. In this study, we analyzed Nef sequences from HIV subtypes A1, B, C, and D using a machine learning approach that integrates functional amino acid information to identify if unique physicochemical features are associated with Nef functional/structural domains in a subtype-specific manner. METHODS 2253 sequences representing subtypes A1, B, C, and D were aligned and domains with known functional properties were scored based on amino acid physicochemical properties. Following feature generation, we used statistical pruning and evolved neural networks (ENNs) to determine if we could successfully classify subtypes. Next, we used ENNs to identify the top five key Nef physicochemical features applied to specific immunoregulatory domains that differentiated subtypes. A signature pattern analysis was performed to the assess amino acid diversity in sub-domains that differentiated each subtype. RESULTS In validation studies, ENNs successfully differentiated each subtype at A1 (87.2%), subtype B (89.5%), subtype C (91.7%), and subtype D (85.1%). Our feature-based domain scoring, followed by t-tests, and a similar ENN identified subtype-specific domain-associated features. Subtype A1 was associated with alterations in Nef CD4 binding domain; subtype B was associated with alterations with the AP-2 Binding domain; subtype C was associated with alterations in a structural Alpha Helix domain; and, subtype D was associated with alterations in a Beta-Sheet domain. CONCLUSIONS Recent studies have focused on HIV Nef as a driver of immunoregulatory disease in those HIV infected and on ART. Nef acts through a complex mixture of interactions that are directly linked to the key features of the subtype-specific domains we identified with the ENN. The study supports the hypothesis that varied Nef subtypes contribute to subtype-specific disease progression.
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Affiliation(s)
| | | | - Enoch S Liu
- Natural Selection, San Diego, California, USA
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Rose R, Nolan DJ, Ashcraft D, Feehan AK, Velez-Climent L, Huston C, Lain B, Rosenthal S, Miele L, Fogel GB, Pankey G, Garcia-Diaz J, Lamers SL. Comparing antimicrobial resistant genes and phenotypes across multiple sequencing platforms and assays for Enterobacterales clinical isolates. BMC Microbiol 2023; 23:225. [PMID: 37596530 PMCID: PMC10436404 DOI: 10.1186/s12866-023-02975-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
INTRODUCTION Whole genome sequencing (WGS) of bacterial isolates can be used to identify antimicrobial resistance (AMR) genes. Previous studies have shown that genotype-based AMR has variable accuracy for predicting carbapenem resistance in carbapenem-resistant Enterobacterales (CRE); however, the majority of these studies used short-read platforms (e.g. Illumina) to generate sequence data. In this study, our objective was to determine whether Oxford Nanopore Technologies (ONT) long-read WGS would improve detection of carbapenem AMR genes with respect to short-read only WGS for nine clinical CRE samples. We measured the minimum inhibitory breakpoint (MIC) using two phenotype assays (MicroScan and ETEST) for six antibiotics, including two carbapenems (meropenem and ertapenem) and four non-carbapenems (gentamicin, ciprofloxacin, cefepime, and trimethoprim/sulfamethoxazole). We generated short-read data using the Illumina NextSeq and long-read data using the ONT MinION. Four assembly methods were compared: ONT-only assembly; ONT-only assembly plus short-read polish; ONT + short-read hybrid assembly plus short-read polish; short-read only assembly. RESULTS Consistent with previous studies, our results suggest that the hybrid assembly produced the highest quality results as measured by gene completeness and contig circularization. However, ONT-only methods had minimal impact on the detection of AMR genes and plasmids compared to short-read methods, although, notably, differences in gene copy number differed between methods. All four assembly methods showed identical presence/absence of the blaKPC-2 carbapenemase gene for all samples. The two phenotype assays showed 100% concordant results for the non-carbapenems, but only 65% concordance for the two carbapenems. The presence/absence of AMR genes was 100% concordant with AMR phenotypes for all four non-carbapenem drugs, although only 22%-50% sensitivity for the carbapenems. CONCLUSIONS Overall, these findings suggest that the lack of complete correspondence between CRE AMR genotype and phenotype for carbapenems, while concerning, is independent of sequencing platform/assembly method.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA.
- FoxSeq, LLC, Thibodaux, LA, USA.
| | - David J Nolan
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Deborah Ashcraft
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Amy K Feehan
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | | | - Benjamin Lain
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Simon Rosenthal
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Lucio Miele
- Translational Science and Genetics at Louisiana State University Health Science Center, New Orleans, LA, USA
| | | | - George Pankey
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Julia Garcia-Diaz
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Susanna L Lamers
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
- FoxSeq, LLC, Thibodaux, LA, USA
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Nolan DJ, Rose R, Zhang R, Leong A, Fogel GB, Scholte LLS, Bethony JM, Bracci P, Lamers SL, McGrath MS. The Persistence of HIV Diversity, Transcription, and Nef Protein in Kaposi's Sarcoma Tumors during Antiretroviral Therapy. Viruses 2022; 14:v14122774. [PMID: 36560778 PMCID: PMC9782636 DOI: 10.3390/v14122774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Epidemic Kaposi's sarcoma (KS), defined by co-infection with Human Herpes Virus 8 (HHV-8) and the Human Immunodeficiency Virus (HIV), is a major cause of mortality in sub-Saharan Africa. Antiretroviral therapy (ART) significantly reduces the risk of developing KS, and for those with KS, tumors frequently resolve with ART alone. However, for unknown reasons, a significant number of KS cases do not resolve and can progress to death. To explore how HIV responds to ART in the KS tumor microenvironment, we sequenced HIV env-nef found in DNA and RNA isolated from plasma, peripheral blood mononuclear cells, and tumor biopsies, before and after ART, in four Ugandan study participants who had unresponsive or progressive KS after 180-250 days of ART. We performed immunohistochemistry experiments to detect viral proteins in matched formalin-fixed tumor biopsies. Our sequencing results showed that HIV diversity and RNA expression in KS tumors are maintained after ART, despite undetectable plasma viral loads. The presence of spliced HIV transcripts in KS tumors after ART was consistent with a transcriptionally active viral reservoir. Immunohistochemistry staining found colocalization of HIV Nef protein and tissue-resident macrophages in the KS tumors. Overall, our results demonstrated that even after ART reduced plasma HIV viral load to undetectable levels and restored immune function, HIV in KS tumors continues to be transcriptionally and translationally active, which could influence tumor maintenance and progression.
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Affiliation(s)
- David J. Nolan
- Bioinfoexperts, LLC, Thibodaux, LA 70301, USA
- Correspondence:
| | | | - Rongzhen Zhang
- Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, CA 94110, USA
| | - Alan Leong
- Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, CA 94110, USA
| | | | - Larissa L. S. Scholte
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC 20037, USA
| | - Jeffrey M. Bethony
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC 20037, USA
| | - Paige Bracci
- The AIDS and Cancer Specimen Resource, San Francisco, CA 94110, USA
| | | | - Michael S. McGrath
- Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, CA 94110, USA
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Ruz GA, Ashlock D, Allmendinger R, Fogel GB. Editorial: 2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2020). Biosystems 2022; 218:104698. [PMID: 35568273 DOI: 10.1016/j.biosystems.2022.104698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Gonzalo A Ruz
- Facultad de Ingenier´ıa y Ciencias, Universidad Adolfo Ib´an˜ez Santiago, Chile; Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.
| | - Daniel Ashlock
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | | | - Gary B Fogel
- Natural Selection, Inc., 6480 Weathers Place, Suite 350, San Diego, CA 92121, USA
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Sutton G, Fogel GB, Abramson B, Brinkac L, Michael T, Liu ES, Thomas S. Horizontal transfer and evolution of wall teichoic acid gene cassettes in Bacillus subtilis. F1000Res 2022; 10:354. [PMID: 35035886 PMCID: PMC8753576 DOI: 10.12688/f1000research.51874.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Wall teichoic acid (WTA) genes are essential for production of cell walls in gram-positive bacteria and necessary for survival and variability in the cassette has led to recent antibiotic resistance acquisition in pathogenic bacteria. Methods: Using a pan-genome approach, we examined the evolutionary history of WTA genes in
Bacillus subtilis ssp.
subtilis. Results: Our analysis reveals an interesting pattern of evolution from the type-strain WTA gene cassette possibly resulting from horizontal acquisition from organisms with similar gene sequences. The WTA cassettes have a high level of variation which may be due to one or more independent horizontal transfer events during the evolution of
Bacillus subtilis ssp.
subtilis. This swapping of entire WTA cassettes and smaller regions within the WTA cassettes is an unusual feature in the evolution of the
Bacillus subtilis genome and highlights the importance of horizontal transfer of gene cassettes through homologous recombination within
B. subtilis or other bacterial species. Conclusions: Reduced sequence conservation of these WTA cassettes may indicate a modified function like the previously documented WTA ribitol/glycerol variation. An improved understanding of high-frequency recombination of gene cassettes has ramifications for synthetic biology and the use of
B. subtilis in industry.
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Affiliation(s)
- Granger Sutton
- J. Craig Venter Institute, Rockville, Maryland, 20850, USA
| | - Gary B Fogel
- Natural Selection, Inc., San Diego, CA, 92121, USA
| | - Bradley Abramson
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Todd Michael
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Enoch S Liu
- Natural Selection, Inc., San Diego, CA, 92121, USA
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Sutton G, Fogel GB, Abramson B, Brinkac L, Michael T, Liu ES, Thomas S. A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes. F1000Res 2021; 10:286. [PMID: 34113437 PMCID: PMC8156514 DOI: 10.12688/f1000research.51873.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/17/2021] [Indexed: 11/22/2022] Open
Abstract
Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. Methods: We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. Results: We show that the core regions determined by our method contain all or almost all essential genes. This demonstrates the accuracy of our method as essential genes should be core genes. We show that we outperform previous methods by this measure. We also explain why there are exceptions to this rule for our method. Conclusions: We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.
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Affiliation(s)
- Granger Sutton
- J. Craig Venter Institute, Rockville, Maryland, 20850, USA
| | - Gary B Fogel
- Natural Selection, Inc., San Diego, CA, 92121, USA
| | | | | | - Todd Michael
- J. Craig Venter Institute, Rockville, Maryland, 20850, USA
| | - Enoch S Liu
- Natural Selection, Inc., San Diego, CA, 92121, USA
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Sutton G, Fogel GB, Abramson B, Brinkac L, Michael T, Liu ES, Thomas S. A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes. F1000Res 2021; 10:286. [DOI: 10.12688/f1000research.51873.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/31/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. Methods: We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. Results: We show that the core regions determined by our method contain all or almost all essential genes. This demonstrates the accuracy of our method as essential genes should be core genes. We show that we outperform previous methods by this measure. We also explain why there are exceptions to this rule for our method. Conclusions: We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.
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Fogel GB. [Conference Calendar]. IEEE COMPUT INTELL M 2020. [DOI: 10.1109/mci.2019.2954682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Lamers SL, Fogel GB, Nolan DJ, Barbier AE, Rose R, Singer EJ, Gonzalez-Perez MP, McGrath MS. Emerging Patterns in HIV-1 gp120 Variable Domains in Anatomical Tissues in the Absence of a Plasma Viral Load. AIDS Res Hum Retroviruses 2019; 35:588-596. [PMID: 30793919 PMCID: PMC6588100 DOI: 10.1089/aid.2018.0267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV envelope protein contains five hypervariable domains (V1-V5) that are fundamental for cell entry. We contrasted modifications in the variable domains derived from a panel of 24 tissues from 7 subjects with no measurable plasma viral load (NPVL) to variable domains from 76 tissues from 15 subjects who had a detectable plasma viral load (PVL) at death. NPVL subject's V1 and V2 domains were usually highly length variable, whereas length variation in PVL sequences was more conserved. Longer V1s contained more charged residues, whereas longer V2s were more glycosylated. Structural analysis demonstrated V1/V2 charge, and N-site additions/subtractions were localized to the CD4 binding pocket. Diversified envelopes in tissues during therapy may represent a mechanism for HIV persistence in tissues, as binding pocket complexity is associated with HIV that may escape neutralization, whereas shorter envelopes are associated with increased infectivity. Further analysis of tissue-derived envelope sequences may enable better understanding of potential immunological approaches targeting the persistent HIV reservoir.
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Affiliation(s)
| | | | | | | | | | - Elyse J. Singer
- The National Neurological AIDS Bank, University of California, Los Angeles, California
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine and Olive View-UCLA Medical Center, Los Angeles, California
| | - Maria Paz Gonzalez-Perez
- Program in Molecular Medicine, The University of Massachusetts Medical School, Worcester, Massachusetts
| | - Michael S. McGrath
- Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, California
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Fogel GB. [Conference Calendar]. IEEE COMPUT INTELL M 2019. [DOI: 10.1109/mci.2019.2901100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abbass HA, Fogel GB, Fidock J. Corrections to “Guest Editorial: Special Issue on Human–Machine Symbiosis”. IEEE Trans Emerg Top Comput Intell 2018. [DOI: 10.1109/tetci.2018.2867053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Lamers SL, Fogel GB, Liu ES, Barbier AE, Rodriguez CW, Singer EJ, Nolan DJ, Rose R, McGrath MS. Brain-specific HIV Nef identified in multiple patients with neurological disease. J Neurovirol 2017; 24:1-15. [PMID: 29063512 DOI: 10.1007/s13365-017-0586-0] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/28/2017] [Accepted: 10/03/2017] [Indexed: 12/11/2022]
Abstract
HIV-1 Nef is a flexible, multifunctional protein with several cellular targets that is required for pathogenicity of the virus. This protein maintains a high degree of genetic variation among intra- and inter-host isolates. HIV Nef is relevant to HIV-associated neurological diseases (HAND) in patients treated with combined antiretroviral therapy because of the protein's role in promoting survival and migration of infected brain macrophages. In this study, we analyzed 2020 HIV Nef sequences derived from 22 different tissues and 31 subjects using a novel computational approach. This approach combines statistical regression and evolved neural networks (ENNs) to classify brain sequences based on the physical and chemical characteristics of functional Nef domains. Based on training, testing, and validation data, the method successfully classified brain Nef sequences at 84.5% and provided informative features for further examination. These included physicochemical features associated with the Src-homology-3 binding domain, the Nef loop (including the AP-2 Binding region), and a cytokine-binding domain. Non-brain sequences from patients with HIV-associated neurological disease were frequently classified as brain, suggesting that the approach could indicate neurological risk using blood-derived virus or for the development of biomarkers for use in assay systems aimed at drug efficacy studies for the treatment of HIV-associated neurological diseases.
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Lamers SL, Fogel GB, Liu ES, Nolan DJ, Salemi M, Barbier AE, Rose R, Singer EJ, McGrath MS. Predicted coreceptor usage at end-stage HIV disease in tissues derived from subjects on antiretroviral therapy with an undetectable plasma viral load. Infect Genet Evol 2017; 51:194-197. [PMID: 28392467 DOI: 10.1016/j.meegid.2017.04.004] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 01/05/2023]
Abstract
HIV cure research is increasingly focused on anatomical tissues as sites for residual HIV replication during combined antiretroviral therapy (cART). Tissue-based HIV could contribute to low-level immune activation and viral rebound over the course of infection and could also influence the development of diseases, such as atherosclerosis, neurological disorders and cancers. cART-treated subjects have a decreased and irregular presence of HIV among tissues, which has resulted in a paucity of actual evidence concerning how or if HIV persists, replicates and evolves in various anatomical sites during therapy. In this study, we pooled 1806 HIV envelope V3 loop sequences from twenty-six tissue types (seventy-one total tissues) of six pre-cART subjects, four subjects with an unknown cART history who died with profound AIDS, and five subjects who died while on cART with an undetectable plasma viral load. A computational approach was used to assess sequences for their ability to utilize specific cellular coreceptors (R5, R5 and X4, or X4). We found that autopsied tissues obtained from virally suppressed cART+ subjects harbored both integrated and expressed viruses with similar coreceptor usage profiles to subjects with no or ineffective cART therapy (i.e., significant plasma viral load at death). The study suggests that tissue microenvironments provide a sanctuary for the continued evolution of HIV despite cART.
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Affiliation(s)
- S L Lamers
- Bioinfoexperts, LLC, Thibodaux, LA, USA.
| | - G B Fogel
- Natural Selection, Inc., San Diego, CA, USA
| | - E S Liu
- Natural Selection, Inc., San Diego, CA, USA
| | - D J Nolan
- Bioinfoexperts, LLC, Thibodaux, LA, USA; The University of Florida Emerging Pathogens Institute and the Department of Pathology and Laboratory Medicine, Gainesville, FL, USA
| | - M Salemi
- The University of Florida Emerging Pathogens Institute and the Department of Pathology and Laboratory Medicine, Gainesville, FL, USA
| | | | - R Rose
- Bioinfoexperts, LLC, Thibodaux, LA, USA
| | - E J Singer
- The National Neurological AIDS Bank, University of California, Los Angeles, CA, USA; David Geffen School of Medicine and Olive View-UCLA Medical Center, Department of Pathology and Laboratory Medicine, Los Angeles, USA
| | - M S McGrath
- The AIDS and Cancer Specimen Resource, San Francisco, CA, USA; The University of California Department of Medicine, San Francisco, CA, USA
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Alotaibi M, Reyes BD, Le T, Luong P, Valafar F, Metzger RP, Fogel GB, Hecht D. Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution. J Mol Graph Model 2017; 71:135-153. [PMID: 27914300 PMCID: PMC5203806 DOI: 10.1016/j.jmgm.2016.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 04/25/2016] [Revised: 10/04/2016] [Accepted: 10/10/2016] [Indexed: 12/15/2022]
Abstract
Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database. We used these alignments to compare active site and non-active site conservation in terms of amino acid residues, secondary structure and amino acid residue class. With respect to amino acid sequences and residue classes, active-site positions in both plasmid and chromosomal DHFR are significantly more conserved than non-active site positions. Secondary structure conservation was similar for active site and non-active site positions. Plasmid-encoded DHFR proteins have greater degree of sequence and residue class conservation, particularly in sequence positions associated with a network of concerted protein motions, than chromosomal-encoded DHFR proteins. These structure-based were used to build DHFR specific phylogenetic trees from which evidence for horizontal gene transfer was identified.
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Affiliation(s)
- Mona Alotaibi
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; King Saud University, P.O. Box 245714, Riyadh 11312, Saudi Arabia.
| | - Ben Delos Reyes
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Tin Le
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Phuong Luong
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Faramarz Valafar
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, CA 92182-7720, USA.
| | - Robert P Metzger
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA.
| | - Gary B Fogel
- Natural Selection, Inc., 6480 Weathers Place, Suite 350, San Diego, CA 92121, USA.
| | - David Hecht
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; Department of Chemistry, Southwestern College, 900 Otay Lakes Rd., Chula Vista, CA 91910, USA.
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17
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Lamers SL, Rose R, Maidji E, Agsalda-Garcia M, Nolan DJ, Fogel GB, Salemi M, Garcia DL, Bracci P, Yong W, Commins D, Said J, Khanlou N, Hinkin CH, Sueiras MV, Mathisen G, Donovan S, Shiramizu B, Stoddart CA, McGrath MS, Singer EJ. HIV DNA Is Frequently Present within Pathologic Tissues Evaluated at Autopsy from Combined Antiretroviral Therapy-Treated Patients with Undetectable Viral Loads. J Virol 2016; 90:8968-83. [PMID: 27466426 PMCID: PMC5044815 DOI: 10.1128/jvi.00674-16] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [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] [Received: 04/11/2016] [Accepted: 07/20/2016] [Indexed: 01/05/2023] Open
Abstract
UNLABELLED HIV infection treatment strategies have historically defined effectiveness through measuring patient plasma HIV RNA. While combined antiretroviral therapy (cART) can reduce plasma viral load (pVL) to undetectable levels, the degree that HIV is eliminated from other anatomical sites remains unclear. We investigated the HIV DNA levels in 229 varied autopsy tissues from 20 HIV-positive (HIV(+)) cART-treated study participants with low or undetectable plasma VL and cerebrospinal fluid (CSF) VL prior to death who were enrolled in the National Neurological AIDS Bank (NNAB) longitudinal study and autopsy cohort. Extensive medical histories were obtained for each participant. Autopsy specimens, including at least six brain and nonbrain tissues per participant, were reviewed by study pathologists. HIV DNA, measured in tissues by quantitative and droplet digital PCR, was identified in 48/87 brain tissues and 82/142 nonbrain tissues at levels >200 HIV copies/million cell equivalents. No participant was found to be completely free of tissue HIV. Parallel sequencing studies from some tissues recovered intact HIV DNA and RNA. Abnormal histological findings were identified in all participants, especially in brain, spleen, lung, lymph node, liver, aorta, and kidney. All brain tissues demonstrated some degree of pathology. Ninety-five percent of participants had some degree of atherosclerosis, and 75% of participants died with cancer. This study assists in characterizing the anatomical locations of HIV, in particular, macrophage-rich tissues, such as the central nervous system (CNS) and testis. Additional studies are needed to determine if the HIV recovered from tissues promotes the pathogenesis of inflammatory diseases, such as HIV-associated neurocognitive disorders, cancer, and atherosclerosis. IMPORTANCE It is well-known that combined antiretroviral therapy (cART) can reduce plasma HIV to undetectable levels; however, cART cannot completely clear HIV infection. An ongoing question is, "Where is HIV hiding?" A well-studied HIV reservoir is "resting" T cells, which can be isolated from blood products and succumb to cART once activated. Less-studied reservoirs are anatomical tissue samples, which have unknown cART penetration, contain a comparably diverse spectrum of potentially HIV-infected immune cells, and are important since <2% of body lymphocytes actually reside in blood. We examined 229 varied autopsy specimens from 20 HIV(+) participants who died while on cART and identified that >50% of tissues were HIV infected. Additionally, we identified considerable pathology in participants' tissues, especially in brain, spleen, lung, lymph node, liver, aorta, and kidney. This study substantiates that tissue-associated HIV is present despite cART and can inform future studies into HIV persistence.
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Affiliation(s)
| | | | - Ekaterina Maidji
- Division of Experimental Medicine, Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California, USA
| | - Melissa Agsalda-Garcia
- The University of Hawaii, Department of Tropical Medicine, Medical Microbiology & Pharmacology and Hawaii Center for AIDS, Honolulu, Hawaii, USA
| | - David J Nolan
- Bioinfoexperts, LLC, Thibodaux, Louisiana, USA The University of Florida Emerging Pathogens Institute, Department of Pathology and Laboratory Medicine, Gainesville, Florida, USA
| | - Gary B Fogel
- Natural Selection, Inc., San Diego, California, USA
| | - Marco Salemi
- The University of Florida Emerging Pathogens Institute, Department of Pathology and Laboratory Medicine, Gainesville, Florida, USA
| | - Debra L Garcia
- The AIDS and Cancer Specimen Resource, San Francisco, California, USA University of California, San Francisco, Department of Medicine, San Francisco, California, USA
| | - Paige Bracci
- The AIDS and Cancer Specimen Resource, San Francisco, California, USA University of California, San Francisco, Department of Medicine, San Francisco, California, USA
| | - William Yong
- National Neurological AIDS Bank, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA David Geffen School of Medicine and Olive View-UCLA Medical Center, Department of Pathology and Laboratory Medicine, Los Angeles, California, USA
| | - Deborah Commins
- University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - Jonathan Said
- National Neurological AIDS Bank, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA David Geffen School of Medicine and Olive View-UCLA Medical Center, Department of Pathology and Laboratory Medicine, Los Angeles, California, USA
| | - Negar Khanlou
- National Neurological AIDS Bank, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA David Geffen School of Medicine and Olive View-UCLA Medical Center, Department of Pathology and Laboratory Medicine, Los Angeles, California, USA
| | - Charles H Hinkin
- National Neurological AIDS Bank, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA UCLA School of Medicine, Department of Psychiatry & Biobehavioral Sciences, Los Angeles, California, USA
| | - Miguel Valdes Sueiras
- National Neurological AIDS Bank, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA David Geffen School of Medicine and Olive View-UCLA Medical Center, Department of Neurology, Los Angeles, California, USA
| | - Glenn Mathisen
- National Neurological AIDS Bank, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Suzanne Donovan
- National Neurological AIDS Bank, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
| | - Bruce Shiramizu
- The University of Hawaii, Department of Tropical Medicine, Medical Microbiology & Pharmacology and Hawaii Center for AIDS, Honolulu, Hawaii, USA
| | - Cheryl A Stoddart
- Division of Experimental Medicine, Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California, USA
| | - Michael S McGrath
- The AIDS and Cancer Specimen Resource, San Francisco, California, USA University of California, San Francisco, Department of Medicine, San Francisco, California, USA
| | - Elyse J Singer
- National Neurological AIDS Bank, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA David Geffen School of Medicine and Olive View-UCLA Medical Center, Department of Neurology, Los Angeles, California, USA
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Tyrrell AM, Lones MA, Smith SL, Fogel GB. 2015 Information Processing in Cells and Tissues (IPCAT 2015). Biosystems 2016; 146:1-2. [PMID: 27616167 DOI: 10.1016/j.biosystems.2016.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andy M Tyrrell
- Intelligent Systems Group, University of York, York YO10 5DD, England, UK.
| | - Michael A Lones
- Intelligent Systems Group, University of York, York YO10 5DD, England, UK
| | - Stephen L Smith
- Intelligent Systems Group, University of York, York YO10 5DD, England, UK
| | - Gary B Fogel
- Intelligent Systems Group, University of York, York YO10 5DD, England, UK
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19
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Lamers SL, Fogel GB, Liu ES, Salemi M, McGrath MS. On the Physicochemical and Structural Modifications Associated with HIV-1 Subtype B Tropism Transition. AIDS Res Hum Retroviruses 2016; 32:829-40. [PMID: 27071630 DOI: 10.1089/aid.2015.0373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
HIV-1 enters immune cells via binding the viral envelope to a host cell CD4 receptor, and then a secondary co-receptor, usually CCR5 (R5) or CXCR4 (X4), and some HIV can utilize both co-receptors (R5X4). Although a small set of amino-acid properties such as charge and sequence length applied to HIV-1 envelope V3 loop sequence data can be used to predict co-receptor usage, we sought to expand the fundamental understanding of the physiochemical basis of tropism by analyzing many, perhaps less obvious, amino-acid properties over a diverse array of HIV sequences. We examined 74 amino-acid physicochemical scales over 1,559 V3 loop sequences with biologically tested tropisms downloaded from the Los Alamos HIV sequence database. Linear regressions were then calculated for each feature relative to three tropism transitions (R5→X4; R5→R5X4; R5X4→X4). Independent correlations were rank ordered to determine informative features. A structural analysis of the V3 loop was performed to better interpret these findings relative to HIV tropism states. Similar structural changes are required for R5 and R5X4 to transition to X4, thus suggesting that R5 and R5X4 types are more similar than either phenotype is to X4. Overall, the analysis suggests a continuum of viral tropism that is only partially related to charge; in fact, the analysis suggests that charge modification may be primarily attributed to decreased R5 usage, and further structural changes, particularly those associated with β-sheet structure, are likely required for full X4 usage.
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Affiliation(s)
| | | | | | - Marco Salemi
- Department of Pathology and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Michael S. McGrath
- Department of Laboratory Medicine, Pathology, and Medicine, and the AIDS and Cancer Specimen Resource, University of California, San Francisco, California
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20
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Hinton A, Hunter SE, Afrikanova I, Jones GA, Lopez AD, Fogel GB, Hayek A, King CC. sRNA-seq analysis of human embryonic stem cells and definitive endoderm reveals differentially expressed microRNAs and novel IsomiRs with distinct targets. Stem Cells 2015; 32:2360-72. [PMID: 24805944 DOI: 10.1002/stem.1739] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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: 06/13/2012] [Revised: 03/30/2014] [Accepted: 04/09/2014] [Indexed: 11/06/2022]
Abstract
MicroRNAs (miRNAs) are noncoding, regulatory RNAs expressed dynamically during differentiation of human embryonic stem cells (hESCs) into defined lineages. Mapping developmental expression of miRNAs during transition from pluripotency to definitive endoderm (DE) should help to elucidate the mechanisms underlying lineage specification and ultimately enhance differentiation protocols. In this report, next generation sequencing was used to build upon our previous analysis of miRNA expression in human hESCs and DE. From millions of sequencing reads, 747 and 734 annotated miRNAs were identified in pluripotent and DE cells, respectively, including 77 differentially expressed miRNAs. Among these, four of the top five upregulated miRNAs were previously undetected in DE. Furthermore, the stem-loop for miR-302a, an important miRNA for both hESCs self-renewal and endoderm specification, produced several highly expressed miRNA species (isomiRs). Overall, isomiRs represented >10% of sequencing reads in >40% of all detected stem-loop arms, suggesting that the impact of these abundant miRNA species may have been overlooked in previous studies. Because of their relative abundance, the role of differential isomiR targeting was studied using the miR-302 cluster as a model system. A miRNA mimetic for miR-302a-5p, but not miR-302a-5p(+3), decreased expression of orthodenticle homeobox 2 (OTX2). Conversely, isomiR 302a-5p(+3) selectively decreased expression of tuberous sclerosis protein 1, but not OTX2, indicating nonoverlapping specificity of miRNA processing variants. Taken together, our characterization of miRNA expression, which includes novel miRNAs and isomiRs, helps establish a foundation for understanding the role of miRNAs in DE formation and selective targeting by isomiRs.
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Affiliation(s)
- Andrew Hinton
- Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, California, USA
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21
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Lamers SL, Fogel GB, Nolan DJ, McGrath MS, Salemi M. HIV-associated neuropathogenesis: a systems biology perspective for modeling and therapy. Biosystems 2014; 119:53-61. [PMID: 24732754 DOI: 10.1016/j.biosystems.2014.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 02/23/2014] [Revised: 04/03/2014] [Accepted: 04/04/2014] [Indexed: 12/19/2022]
Abstract
Despite the development of powerful antiretroviral drugs, HIV-1 associated neurological disorders (HAND) will affect approximately half of those infected with HIV-1. Combined anti-retroviral therapy (cART) targets viral replication and increases T-cell counts, but it does not always control macrophage polarization, brain infection or inflammation. Moreover, it remains difficult to identify those at risk for HAND. New therapies that focus on modulating host immune response by making use of biological pathways could prove to be more effective than cART for the treatment of neuroAIDS. Additionally, while numerous HAND biomarkers have been suggested, they are of little use without methods for appropriate data integration and a systems-level interpretation. Machine learning, could be used to develop multifactorial computational models that provide clinicians and researchers with the ability to identify which factors (in what combination and relative importance) are considered important to outcome.
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Affiliation(s)
| | - Gary B Fogel
- Natural Selection, Inc., 5910 Pacific Center Blvd Suite 315, San Diego, CA 92121, USA.
| | - David J Nolan
- University of Florida, 2055 Mowry Road, Department of Pathology and Laboratory Medicine, Gainesville, FL 32610, USA.
| | - Michael S McGrath
- University of California, 1001 Potrero Avenue, Building 20, 4(th) Floor, Room 2407, San Francisco, CA 94110-3518, USA.
| | - Marco Salemi
- University of Florida, 2055 Mowry Road, Department of Pathology and Laboratory Medicine, Gainesville, FL 32610, USA.
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22
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Ruz GA, Goles E, Montalva M, Fogel GB. Dynamical and topological robustness of the mammalian cell cycle network: a reverse engineering approach. Biosystems 2013; 115:23-32. [PMID: 24212100 DOI: 10.1016/j.biosystems.2013.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 12/11/2022]
Abstract
A common gene regulatory network model is the threshold Boolean network, used for example to model the Arabidopsis thaliana floral morphogenesis network or the fission yeast cell cycle network. In this paper, we analyze a logical model of the mammalian cell cycle network and its threshold Boolean network equivalent. Firstly, the robustness of the network was explored with respect to update perturbations, in particular, what happened to the attractors for all the deterministic updating schemes. Results on the number of different limit cycles, limit cycle lengths, basin of attraction size, for all the deterministic updating schemes were obtained through mathematical and computational tools. Secondly, we analyzed the topology robustness of the network, by reconstructing synthetic networks that contained exactly the same attractors as the original model by means of a swarm intelligence approach. Our results indicate that networks may not be very robust given the great variety of limit cycles that a network can obtain depending on the updating scheme. In addition, we identified an omnipresent network with interactions that match with the original model as well as the discovery of new interactions. The techniques presented in this paper are general, and can be used to analyze other logical or threshold Boolean network models of gene regulatory networks.
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Affiliation(s)
- Gonzalo A Ruz
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Av. Diagonal Las Torres 2640, Santiago, Chile.
| | - Eric Goles
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Av. Diagonal Las Torres 2640, Santiago, Chile
| | - Marco Montalva
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Av. Diagonal Las Torres 2640, Santiago, Chile
| | - Gary B Fogel
- Natural Selection, Inc., 5910 Pacific Center Boulevard, Suite 315, San Diego, CA 92121, USA
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23
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Fogel GB. [Conference Calendar]. IEEE COMPUT INTELL M 2013. [DOI: 10.1109/mci.2013.2278944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Lamers SL, Nolan DJ, Strickland SL, Prosperi M, Fogel GB, Goodenow MM, Salemi M. Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS. J Gen Virol 2013; 94:2469-2479. [PMID: 23963535 DOI: 10.1099/vir.0.055335-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Human immunodeficiency virus intra-host recombination has never been studied in vivo both during early infection and throughout disease progression. The CD8-depleted rhesus macaque model of neuroAIDS was used to investigate the impact of recombination from early infection up to the onset of neuropathology in animals inoculated with a simian immunodeficiency virus (SIV) swarm. Several lymphoid and non-lymphoid tissues were collected longitudinally at 21 days post-infection (p.i.), 61 days p.i. and necropsy (75-118 days p.i.) from four macaques that developed SIV-encephalitis or meningitis, as well as from two animals euthanized at 21 days p.i. The number of recombinant sequences and breakpoints in different tissues and over time from each primate were compared. Breakpoint locations were mapped onto predicted RNA and protein secondary structures. Recombinants were found at each time point and in each primate as early as 21 days p.i. No association was found between recombination rates and specific tissue of origin. Several identical breakpoints were identified in sequences derived from different tissues in the same primate and among different primates. Breakpoints predominantly mapped to unpaired nucleotides or pseudoknots in RNA secondary structures, and proximal to glycosylation sites and cysteine residues in protein sequences, suggesting selective advantage in the emergence of specific recombinant sequences. Results indicate that recombinant sequences can become fixed very early after infection with a heterogeneous viral swarm. Features of RNA and protein secondary structure appear to play a role in driving the production of recombinants and their selection in the rapid disease model of neuroAIDS.
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Affiliation(s)
| | - David J Nolan
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA.,Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Samantha L Strickland
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA.,Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mattia Prosperi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA.,Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Gary B Fogel
- Natural Selection Inc., San Diego, CA 92121, USA
| | - Maureen M Goodenow
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA.,Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
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25
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Fogel GB. [Conference Calendar]. IEEE COMPUT INTELL M 2013. [DOI: 10.1109/mci.2013.2264574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Abstract
Combined anti-retroviral therapy (cART) has significantly reduced the number of AIDS-associated illnesses and changed the course of HIV-1 disease in developed countries. Despite the ability of cART to maintain high CD4+ T-cell counts, a number of macrophage-mediated diseases can still occur in HIV-infected subjects. These diseases include lymphoma, metabolic diseases, and HIV-associated neurological disorders. Within macrophages, the HIV-1 regulatory protein "Nef" can modulate surface receptors, interact with signaling pathways, and promote specific environments that contribute to each of these pathologies. Moreover, genetic variation in Nef may also guide the macrophage response. Herein, we review findings relating to the Nef-macrophage interaction and how this relationship contributes to disease pathogenesis.
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27
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Fogel GB. [Conference Calendar]. IEEE COMPUT INTELL M 2013. [DOI: 10.1109/mci.2013.2247899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Fogel GB. A Report on the IEEE Life Sciences Grand Challenges Conference [Conference Report]. IEEE COMPUT INTELL M 2013. [DOI: 10.1109/mci.2013.2247821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Fogel GB. [Conference Calendar]. IEEE COMPUT INTELL M 2013. [DOI: 10.1109/mci.2012.2228602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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30
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Abstract
Plasmodium falciparum, the causal agent of malaria, continues to evolve resistance to frontline therapeutics such as chloroquine and sulfadoxine-pyrimethamine. Here we study the amino acid replacements in dihydrofolate reductase (DHFR) that confer resistance to pyrimethamine while still binding the natural DHFR substrate, 7,8-dihydrofolate, and cofactor, NADPH. The chain of amino acid replacements that has led to resistance can be inferred in a computer, leading to a broader understanding of the coevolution between the drug and target. This in silico approach suggests that only a small set of specific active site replacements in the proper order could have led to the resistant strains in the wild today. A similar approach can be used on any target of interest to anticipate likely pathways of future resistance for more effective drug development.
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Affiliation(s)
- David Hecht
- Southwestern College, 900 Otay Lakes Rd., Chula Vista, CA 91910, USA
| | - Gary B. Fogel
- Natural Selection, Inc., 9330 Scranton Rd., San Diego, CA 92121, USA
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31
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32
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Fogel GB, Schwartz AW. Lynn Margulis (1938–2011). Biosystems 2012; 107:65. [DOI: 10.1016/j.biosystems.2011.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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33
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Hinton A, Hunter S, Reyes G, Fogel GB, King CC. From pluripotency to islets: miRNAs as critical regulators of human cellular differentiation. Adv Genet 2012; 79:1-34. [PMID: 22989764 DOI: 10.1016/b978-0-12-394395-8.00001-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) actively regulate differentiation as pluripotent cells become cells of pancreatic endocrine lineage, including insulin-producing β cells. The process is dynamic; some miRNAs help maintain pluripotency, while others drive cell fate decisions. Here, we survey the current literature and describe the biological role of selected miRNAs in maintenance of both mouse and human embryonic stem cell (ESC) pluripotency. Subsequently, we review the increasing evidence that miRNAs act at selected points in differentiation to regulate decisions about early cell fate (definitive endoderm and mesoderm), formation of pancreatic precursor cells, endocrine cell function, as well as epithelial to mesenchymal transition.
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Affiliation(s)
- Andrew Hinton
- Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
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34
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Dillman RO, Fogel GB, Cornforth AN, Selvan SR, Schiltz PM, DePriest C. Features associated with survival in metastatic melanoma patients treated with patient-specific dendritic cell vaccines. Cancer Biother Radiopharm 2011; 26:407-15. [PMID: 21812653 DOI: 10.1089/cbr.2011.0973] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Previously, a 54% 5-year survival was reported for metastatic melanoma patients treated with patient-specific vaccines consisting of autologous dendritic cells loaded with antigens from autologous proliferating tumor cells. This study attempted to determine which clinical and laboratory factors best explained long-term survival in this group of patients. Univariate analyses were used to identify factors associated with continuous survival after initiating vaccine therapy. Multivariate logistic regression was used to identify independent factors to classify survival at 3.5 years. Survivors were followed a minimum of 3.7 years (median: 5.7). Univariate analyses identified eight features associated with improved survival: Eastern Cooperative Oncology Group (ECOG) performance status (PS) of 0, no measurable disease at study entry, receiving 8 vaccinations, age <50 years, normal baseline lactate dehydrogenase, no history of visceral metastases, anergy to standard skin tests, and failure of interferon-gamma (IFN-γ) to induce apoptosis in autologous tumor cells. After examining 54 variables for which complete information was available over all patients, the best multivariate regression for survival at 3.5 years utilized six features: prior radiation therapy, younger age, male gender, ECOG PS 0, higher numbers of cells administered during the first 3 injections, and lower numbers of viable cells administered during the first 3 injections. This model correctly classified survival for 28 of 32 patients (87%) and death for 20 of 22 (91%). When features with incomplete information were included in the analysis, addition of IFN-γ-induced apoptosis (n=49) improved predictive accuracy to 27 of 29 (93%) for survival and 19 of 20 (95%) for death. Dependencies between variables were common, but these multivariate linear models yielded high classification accuracy for survival at 3.5 years and identified two features of the vaccine itself as being of independent significance.
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Affiliation(s)
- Robert O Dillman
- Hoag Cancer Institute; One Hoag Drive, Newport Beach, CA 92658, USA.
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Fogel GB, Fogel DB. Simulating natural selection as a culling mechanism on finite populations with the hawk-dove game. Biosystems 2011; 104:57-62. [PMID: 21219966 DOI: 10.1016/j.biosystems.2011.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 12/30/2010] [Accepted: 01/02/2011] [Indexed: 11/27/2022]
Abstract
The behaviors of individuals and species are often explained in terms of evolutionary stable strategies (ESSs). The analysis of ESSs determines which, if any, combinations of behaviors cannot be invaded by alternative strategies. Two assumptions required to generate an ESS (i.e., an infinite population and payoffs described only on the average) do not hold under natural conditions. Previous experiments indicated that under more realistic conditions of finite populations and stochastic payoffs, populations may evolve in trajectories that are unrelated to an ESS, even in very simple games. The simulations offered here extend earlier research by employing truncation selection with random parental selection in a hawk-dove game. Payoffs are determined in pairwise contests using either the expected outcome, or the result of a random variable. In each case, however, the mean fraction of hawks over many generations and across many independent trials does not conform to the expected ESS. Implications of these results and philosophical underpinnings of ESS theory are offered.
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Affiliation(s)
- Gary B Fogel
- Natural Selection Inc., 9330 Scranton Rd., San Diego, CA 92121, USA.
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L. Lamers S, B. Fogel G, C. Huysentruyt L, S. McGrath M. HIV-1 Nef Protein Visits B-Cells via Macrophage Nanotubes: A Mechanism for AIDS-Related Lymphoma Pathogenesis? Curr HIV Res 2010; 8:638-40. [DOI: 10.2174/157016210794088209] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 11/11/2010] [Indexed: 11/22/2022]
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Lamers SL, Fogel GB, Huysentruyt L, Poon A, McGrath MS. The HIV nef protein within ARL is genetically and structurally distinct from those in the brain of patients with HAD. Infect Agent Cancer 2010. [PMCID: PMC3002740 DOI: 10.1186/1750-9378-5-s1-a77] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Anand A, Pugalenthi G, Fogel GB, Suganthan P. Identification and analysis of transcription factor family-specific features derived from DNA and protein information. Pattern Recognit Lett 2010. [DOI: 10.1016/j.patrec.2009.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Anand A, Pugalenthi G, Fogel GB, Suganthan PN. An approach for classification of highly imbalanced data using weighting and undersampling. Amino Acids 2010; 39:1385-91. [DOI: 10.1007/s00726-010-0595-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 04/07/2010] [Indexed: 10/19/2022]
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40
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Abstract
Genes are often classified into biologically related groups so that inferences on their functions can be made. This paper demonstrates that the di-codon usage is a useful feature for gene classification and gives better classification accuracy than the codon usage. Our experiments with different classifiers show that support vector machines performs better than other classifiers in classifying genes by using di-codon usage as features. The method is illustrated on 1841 HLA sequences which are classified into two major classes, HLA-I and HLA-II, and further classified into the subclasses of major classes. By using both codon and di-codon features, we show near perfect accuracies in the classification of HLA molecules into major classes and their sub-classes.
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Affiliation(s)
- David Hecht
- Southwestern College, 900 Otay Lakes Road, Chula Vista, California 91910, and Natural Selection, Inc., 9330 Scranton Road, Suite 150, San Diego, California 92121
| | - Gary B. Fogel
- Southwestern College, 900 Otay Lakes Road, Chula Vista, California 91910, and Natural Selection, Inc., 9330 Scranton Road, Suite 150, San Diego, California 92121
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Lamers SL, Salemi M, Galligan DC, de Oliveira T, Fogel GB, Granier SC, Zhao L, Brown JN, Morris A, Masliah E, McGrath MS. Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology. PLoS One 2009; 4:e5065. [PMID: 19333384 PMCID: PMC2659430 DOI: 10.1371/journal.pone.0005065] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 02/12/2009] [Indexed: 11/19/2022] Open
Abstract
There is evidence that immune-activated macrophages infected with the Human Immunodeficiency Virus (HIV) are associated with tissue damage and serve as a long-lived viral reservoir during therapy. In this study, we analyzed 780 HIV genetic sequences generated from 53 tissues displaying normal and abnormal histopathology. We found up to 50% of the sequences from abnormal lymphoid and macrophage rich non-lymphoid tissues were intra-host viral recombinants. The presence of extensive recombination, especially in non-lymphoid tissues, implies that HIV-1 infected macrophages may significantly contribute to the generation of elusive viral genotypes in vivo. Because recombination has been implicated in immune evasion, the acquisition of drug-resistance mutations, and alterations of viral co-receptor usage, any attempt towards the successful eradication of HIV-1 requires therapeutic approaches targeting tissue macrophages.
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Affiliation(s)
| | - Marco Salemi
- BioInfoExperts, Thibodaux, Louisiana, United States of America
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Derek C. Galligan
- Department of Laboratory Medicine, Positive Health Program, University of California San Francisco, San Francisco, California, United States of America
| | - Tulio de Oliveira
- BioInfoExperts, Thibodaux, Louisiana, United States of America
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Gary B. Fogel
- Natural Selection, Inc., San Diego, California, United States of America
| | - Sara C. Granier
- BioInfoExperts, Thibodaux, Louisiana, United States of America
| | - Li Zhao
- The Department of Toxicology, Shandong University, Jinan, China
| | - Joseph N. Brown
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Alanna Morris
- Department of Laboratory Medicine, Positive Health Program, University of California San Francisco, San Francisco, California, United States of America
| | - Eliezer Masliah
- Department of Pathology, School of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Michael S. McGrath
- Department of Laboratory Medicine, Positive Health Program, University of California San Francisco, San Francisco, California, United States of America
- Pathologica Inc., Burlingame, California, United States of America
- AIDS and Cancer Specimen Resource, San Francisco, California, United States of America
- * E-mail:
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Fogel GB, Porto VW, Varga G, Dow ER, Craven AM, Powers DM, Harlow HB, Su EW, Onyia JE, Su C. Evolutionary computation for discovery of composite transcription factor binding sites. Nucleic Acids Res 2008; 36:e142. [PMID: 18927103 PMCID: PMC2588514 DOI: 10.1093/nar/gkn738] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [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: 07/07/2008] [Revised: 09/05/2008] [Accepted: 10/02/2008] [Indexed: 12/02/2022] Open
Abstract
Previous research demonstrated the use of evolutionary computation for the discovery of transcription factor binding sites (TFBS) in promoter regions upstream of coexpressed genes. However, it remained unclear whether or not composite TFBS elements, commonly found in higher organisms where two or more TFBSs form functional complexes, could also be identified by using this approach. Here, we present an important refinement of our previous algorithm and test the identification of composite elements using NFAT/AP-1 as an example. We demonstrate that by using appropriate existing parameters such as window size, novel-scoring methods such as central bonusing and methods of self-adaptation to automatically adjust the variation operators during the evolutionary search, TFBSs of different sizes and complexity can be identified as top solutions. Some of these solutions have known experimental relationships with NFAT/AP-1. We also indicate that even after properly tuning the model parameters, the choice of the appropriate window size has a significant effect on algorithm performance. We believe that this improved algorithm will greatly augment TFBS discovery.
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Affiliation(s)
- Gary B. Fogel
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121 and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - V. William Porto
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121 and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Gabor Varga
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121 and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Ernst R. Dow
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121 and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Andrew M. Craven
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121 and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - David M. Powers
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121 and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Harry B. Harlow
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121 and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Eric W. Su
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121 and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Jude E. Onyia
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121 and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Chen Su
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121 and Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
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Lamers SL, Salemi M, McGrath MS, Fogel GB. Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks. IEEE/ACM Trans Comput Biol Bioinform 2008; 5:291-300. [PMID: 18451438 PMCID: PMC3523352 DOI: 10.1109/tcbb.2007.1074] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The HIV-1 genome is highly heterogeneous. This variation affords the virus a wide range of molecular properties, including the ability to infect cell types, such as macrophages and lymphocytes, expressing different chemokine receptors on the cell surface. In particular, R5 HIV-1 viruses use CCR5 as co-receptor for viral entry, X4 viruses use CXCR4, whereas some viral strains, known as R5X4 or D-tropic, have the ability to utilize both co-receptors. X4 and R5X4 viruses are associated with rapid disease progression to AIDS. R5X4 viruses differ in that they have yet to be characterized by the examination of the genetic sequence of HIV-1 alone. In this study, a series of experiments was performed to evaluate different strategies of feature selection and neural network optimization. We demonstrate the use of artificial neural networks trained via evolutionary computation to predict viral co-receptor usage. The results indicate identification of R5X4 viruses with predictive accuracy of 75.5%.
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Affiliation(s)
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida (UF-COM) Gainesville, 1600 S.W. Archer Road, Gainesville, FL 32610
| | - Michael S. McGrath
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143-0874
| | - Gary B. Fogel
- Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121
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Fogel GB, Cheung M, Pittman E, Hecht D. In silico screening against wild-type and mutant Plasmodium falciparum dihydrofolate reductase. J Mol Graph Model 2008; 26:1145-52. [DOI: 10.1016/j.jmgm.2007.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 10/11/2007] [Accepted: 10/11/2007] [Indexed: 12/21/2022]
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Hecht D, Cheung M, Fogel GB. QSAR using evolved neural networks for the inhibition of mutant PfDHFR by pyrimethamine derivatives. Biosystems 2008; 92:10-5. [DOI: 10.1016/j.biosystems.2007.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 10/25/2007] [Accepted: 10/29/2007] [Indexed: 10/22/2022]
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Davis N, Biddlecom N, Hecht D, Fogel GB. On the relationship between GC content and the number of predicted microRNA binding sites by MicroInspector. Comput Biol Chem 2008; 32:222-6. [PMID: 18407791 DOI: 10.1016/j.compbiolchem.2008.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Revised: 02/15/2008] [Accepted: 02/16/2008] [Indexed: 10/22/2022]
Abstract
MicroRNA GC content and length is believed to play a role in the prediction of putative microRNA targets. MicroInspector was evaluated to determine the extent to which these characteristics of microRNAs play a role in binding site predictive accuracy. A strong bias towards under predicting the number of expected bindings sites for low GC content sequences was observed, especially for microRNAs with <50% GC content. Researchers working with organisms with unusually low GC content should be aware of this bias.
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Affiliation(s)
- Nicole Davis
- Southwestern College, 900 Otay Lakes Road, Chula Vista, CA 91910, USA
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Fogel GB, Bullinger E, Su SF, Azuaje F. Special section on machine intelligence approaches to systems biology. IEEE Trans Syst Man Cybern B Cybern 2008; 38:2-4. [PMID: 18270077 DOI: 10.1109/tsmcb.2007.910577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The three papers in this special section focus on machine intelligence approaches to systems biology.
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Fogel GB, Weekes DG, Varga G, Dow ER, Craven AM, Harlow HB, Su EW, Onyia JE, Su C. A statistical analysis of the TRANSFAC database. Biosystems 2005; 81:137-54. [PMID: 15941617 DOI: 10.1016/j.biosystems.2005.03.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [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: 03/16/2005] [Revised: 03/16/2005] [Indexed: 11/18/2022]
Abstract
Transcription factors are key regulatory elements that control gene expression. The TRANSFAC database represents the largest repository for experimentally derived transcription factor binding sites (TFBS). Understanding TFBS, which are typically conserved during evolution, helps us identify genomic regions related to human health and disease, and regions that might be predictive of patient outcomes. Here we present a statistical analysis of all TFBS in the TRANSFAC database. Our analysis suggests that current definition of TFBS core regions in TRANSFAC should be re-examined so as to capture a more precise notion of "cores." We offer insight into more appropriate definitions of TFBS consensus sequences and core regions. These revised definitions provide a better understanding of the nature of transcription factor-DNA binding and assist with developing algorithms for de novo TFBS discovery as well as finding novel variants of known TFBS.
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Affiliation(s)
- Gary B Fogel
- Natural Selection, Inc., 3333 N. Torrey Pines Ct., Suite 200, La Jolla, CA 92037, USA
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Lesnik EA, Fogel GB, Weekes D, Henderson TJ, Levene HB, Sampath R, Ecker DJ. Identification of conserved regulatory RNA structures in prokaryotic metabolic pathway genes. Biosystems 2004; 80:145-54. [PMID: 15823413 DOI: 10.1016/j.biosystems.2004.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [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: 09/08/2004] [Revised: 11/04/2004] [Accepted: 11/05/2004] [Indexed: 11/24/2022]
Abstract
A combination of algorithms to search RNA sequence for the potential for secondary structure formation, and search large numbers of sequences for structural similarity, were used to search the 5'UTRs of annotated genes in the Escherichia coli genome for regulatory RNA structures. Using this approach, similar RNA structures that regulate genes in the thiamin metabolic pathway were identified. In addition, several putative regulatory structures were discovered upstream of genes involved in other metabolic pathways including glycerol metabolism and ethanol fermentation. The results demonstrate that this computational approach is a powerful tool for discovery of important RNA structures within prokaryotic organisms.
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