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Garey L, Zvolensky MJ, Gallagher MW, Vujanovic A, Kendzor DE, Stephens L, Cheney MK, Cole AB, Kezbers K, Matoska CT, Robison J, Montgomery A, Zappi CV, Businelle MS. A Smartphone-Based Intervention for Anxiety and Depression in Racially and Ethnically Diverse Adults (EASE): Protocol for a Randomized Controlled Trial. JMIR Res Protoc 2022; 11:e40713. [PMID: 36409958 PMCID: PMC9728024 DOI: 10.2196/40713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Clear health disparities have emerged in the rates of COVID-19 exposure, hospitalization, and death among Black, Hispanic, and American Indian (BHAI) individuals, relative to non-Hispanic White (NHW) individuals. BHAI populations have been disproportionately affected by lower behavioral health access and heightened negative mental health outcomes during the pandemic. OBJECTIVE This project directly addresses health disparities in access to behavioral health care during the COVID-19 pandemic among BHAI populations via an adaptation of the established, initially validated, low-cost, mobile app Easing Anxiety Sensitivity for Everyone (EASE) among individuals with symptoms of elevated anxiety or depression or both. METHODS The EASE trial is a 2-arm, prospective, randomized, blinded-assessor study with intention-to-treat analysis. Participants (N=800; n=200, 25%, Black; n=200, 25%, Hispanic; n=200, 25%, American Indian; and n=200, 25%, NHW) are randomized to receive either EASE or an active comparison condition for anxiety and depression. Participants compete an online prescreener, an enrollment call to provide informed consent, a baseline survey, a 6-month intervention period, and 3- and 6-month postbaseline assessments. Select participants also complete a 3- and 6-month postbaseline qualitative interview via phone or an online platform (eg, Zoom). Participants complete 2 scheduled daily ecological momentary assessments (EMAs) during the 6-month study period. These twice-daily EMAs guide a just-in-time approach to immediate, personalized behavioral health care. RESULTS Outcomes include reductions in anxiety and depressive symptoms and functional impairment at 3 and 6 months postrandomization. We also will examine putative mechanisms (eg, anxiety sensitivity [AS] and COVID-19-specific stress and fear) of the intervention effects. Further, as treatment effects may differ across sociocultural factors, perceived discrimination, social support, and socioeconomic status (SES) will be evaluated as potential moderators of treatment effects on the primary outcomes. Process evaluation using data collected during the study, as well as individual interviews with participants, will complement quantitative data. CONCLUSIONS Data from this efficacy trial will determine whether EASE successfully improves symptoms of anxiety and depression and whether these improvements outperform an active comparison control app. If successful, findings from this study have the potential to decrease anxiety and depression symptoms among vulnerable populations determined to be most at risk of exacerbated, long-lasting negative health sequelae. Data from this study may be used to support an implementation and dissemination trial of EASE within real-world behavioral health and social service settings. TRIAL REGISTRATION ClinicalTrials.gov NCT05074693; https://clinicaltrials.gov/ct2/show/NCT05074693. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/40713.
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Affiliation(s)
- Lorra Garey
- HEALTH Institute, University of Houston, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, United States
| | - Michael J Zvolensky
- HEALTH Institute, University of Houston, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, United States
- Department of Behavioral Science, MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Matthew W Gallagher
- HEALTH Institute, University of Houston, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, United States
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, United States
| | - Anka Vujanovic
- HEALTH Institute, University of Houston, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, United States
| | - Darla E Kendzor
- TSET Health Promotion Research Center, Stephenson Cancer Center, Oklahoma City, OK, United States
- Department of Family and Preventive Medicine, Health Sciences Center, University of Oklahoma, Oklahoma City, OK, United States
| | - Lancer Stephens
- College of Public Health, Health Sciences Center, University of Oklahoma, Oklahoma City, OK, United States
- Oklahoma Shared Clinical and Translational Research Resources, Health Sciences Center, University of Oklahoma, Oklahoma City, OK, United States
| | - Marshall K Cheney
- Department of Health and Exercise Science, University of Oklahoma, Norman, OK, United States
| | - Ashley B Cole
- Department of Psychology, Oklahoma State University, Stillwater, OK, United States
| | - Krista Kezbers
- TSET Health Promotion Research Center, Stephenson Cancer Center, Oklahoma City, OK, United States
| | - Cameron T Matoska
- HEALTH Institute, University of Houston, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, United States
| | - Jillian Robison
- TSET Health Promotion Research Center, Stephenson Cancer Center, Oklahoma City, OK, United States
| | - Audrey Montgomery
- TSET Health Promotion Research Center, Stephenson Cancer Center, Oklahoma City, OK, United States
| | - Christopher V Zappi
- HEALTH Institute, University of Houston, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, United States
| | - Michael S Businelle
- TSET Health Promotion Research Center, Stephenson Cancer Center, Oklahoma City, OK, United States
- Department of Family and Preventive Medicine, Health Sciences Center, University of Oklahoma, Oklahoma City, OK, United States
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Compaore TR, Soubeiga ST, Ouattara AK, Tchelougou D, Bisseye C, Bakouan DR, Compaore I, Dembele A, Yonli AT, Obiri-Yeboah D, Djigma WF, Simpore J. APOBEC3G expression and HIV-1 infection in Burkina Faso. J Public Health Afr 2018; 9:907. [PMID: 30687488 PMCID: PMC6326155 DOI: 10.4081/jphia.2018.907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/14/2018] [Indexed: 11/23/2022] Open
Abstract
APOBEC3G is a potent inhibitor of HIV-1 replication, and act by deaminating cytidines in uracil on the negative strand of the viral cDNA. In this case-control study, APOBEC3G expression in subjects' naïve to HAART infected by HIV-1 and the effect of APOBEC3G polymorphism on its expression were evaluated. The results show that the HIV-1 infected carriers of the G minor alleles of the variant rs8177832 had a higher expression of APOBEC3G mRNA than the controls carriers of the G minor allele. APOBEC3G polymorphisms could play an important role in the modulation of the HIV-1 dissemination.
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Affiliation(s)
- Tegwinde Rebeca Compaore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Serge Theophile Soubeiga
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Abdoul Karim Ouattara
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Damehan Tchelougou
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Cyrille Bisseye
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Didier Romuald Bakouan
- Permanent Secretary Against Aids and Sexually Transmitted Diseases, Ouagadougou, Burkina Faso
| | - Issaka Compaore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Augustine Dembele
- Permanent Secretary Against Aids and Sexually Transmitted Diseases, Ouagadougou, Burkina Faso
| | - Albert Theophane Yonli
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
| | - Dorcas Obiri-Yeboah
- Microbiology Department, School of Medical Sciences, University of Cape Coast, Ghana
| | | | - Jacques Simpore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/LABIOGENE, University of Ouagadougou, Burkina Faso
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Abstract
APOBEC3s (A3) are endogenous DNA-editing enzymes that are expressed in immune cells including T lymphocytes. A3s target and mutate the genomes of retroviruses that infect immune tissues such as the human immunodeficiency virus (HIV). Therefore, A3s were classically defined as host anti-viral innate immune factors. In contrast, we and others showed that A3s can also benefit the virus by mediating escape from adaptive immune recognition and drugs. Crucially, whether A3-mediated mutations help or hinder HIV, is not up to chance. Rather, the virus has evolved multiple mechanisms to actively and maximally subvert A3 activity. More recently, extensive A3 mutational footprints in tumor genomes have been observed in many different cancers. This suggests a role for A3s in cancer initiation and progression. On the other hand, multiple anti-tumor activities of A3s have also come to light, including impact on immune checkpoint molecules and possible generation of tumor neo-antigens. Here, we review the studies that reshaped the view of A3s from anti-viral innate immune agents to host factors exploited by HIV to escape from immune recognition. Viruses and tumors share many attributes, including rapid evolution and adeptness at exploiting mutations. Given this parallel, we then discuss the pro- and anti-tumor roles of A3s, and suggest that lessons learned from studying A3s in the context of anti-viral immunity can be applied to tumor immunotherapy.
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Affiliation(s)
- Faezeh Borzooee
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mahdi Asgharpour
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Emma Quinlan
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Michael D Grant
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
| | - Mani Larijani
- a Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine , Memorial University of Newfoundland , St. John's, Newfoundland A1B 3V6 , Canada
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Chen Q, Xiao X, Wolfe A, Chen XS. The in vitro Biochemical Characterization of an HIV-1 Restriction Factor APOBEC3F: Importance of Loop 7 on Both CD1 and CD2 for DNA Binding and Deamination. J Mol Biol 2016; 428:2661-70. [PMID: 27063502 DOI: 10.1016/j.jmb.2016.03.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 12/11/2015] [Revised: 03/27/2016] [Accepted: 03/28/2016] [Indexed: 10/22/2022]
Abstract
APOBEC3F (A3F) is a member of the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) family of proteins that can deaminate cytosine (C) to uracil (U) on nucleic acids. A3F is one of the four APOBEC members with two Zn-coordinated homologous cytosine deaminase (CD) domains, with the others being A3G, A3D, and A3B. Here we report the in vitro characterization of DNA binding and deaminase activities using purified wild-type and various mutant proteins of A3F from an Escherichia coli expression system. We show that even though CD1 is catalytically inactive and CD2 is the active deaminase domain, presence of CD1 on the N-terminus of CD2 enhances the deaminase activity by over an order of magnitude. This enhancement of CD2 catalytic activity is mainly through the increase of substrate single-stranded (ss) DNA binding by the N-terminal CD1 domain. We further show that the loop 7 of both CD1 and CD2 of A3F plays an important role for ssDNA binding for each individual domain, as well as for the deaminase activity of CD2 domain in the full-length A3F.
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Affiliation(s)
- Qihan Chen
- Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiao Xiao
- Genetic, Molecular and Cellular Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron Wolfe
- Genetic, Molecular and Cellular Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center; University of Southern California, Los Angeles, CA 90089, USA.
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Compaore TR, Soubeiga ST, Ouattara AK, Obiri-Yeboah D, Tchelougou D, Maiga M, Assih M, Bisseye C, Bakouan D, Compaore IP, Dembele A, Martinson J, Simpore J. APOBEC3G Variants and Protection against HIV-1 Infection in Burkina Faso. PLoS One 2016; 11:e0146386. [PMID: 26741797 PMCID: PMC4704832 DOI: 10.1371/journal.pone.0146386] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 09/07/2015] [Accepted: 12/16/2015] [Indexed: 01/27/2023] Open
Abstract
Studies on host factors, particularly the APOBEC3G gene, have previously found an association with AIDS progression in some populations and against some HIV-1 strains but not others. Our study had two main objectives: firstly, to screen a population from Burkina Faso for three variants of APOBEC3G previously described, and secondly to analyze the effect of these three variants and their haplotypes on HIV-1 infection with Circulating Recombinant Forms (CRFs) present in Burkina Faso. This case control study involved 708 seropositive and seronegative individuals. Genotyping was done by the TaqMan allelic discrimination method. Minor allele frequencies of rs6001417 (p<0.05), rs8177832 (P<0.05), and rs35228531 (P<0.001) were higher in seronegative subjects. The rs6001417 and rs8177832 SNPs were associated with HIV-1 infection in an additive model (P<0.01). Furthermore the SNP rs35228531 was also associated with HIV-1 infection in a dominant model (P<0.001). Odds ratio analysis of genotypes and alleles of the different APOBEC3G variants showed that there is a strong association between the minor genetic variants, genotype of the three SNPs, and HIV-1 status. Haplotype analysis demonstrated that rs6001417, rs8177832, and rs35228531 are in linkage disequilibrium. The haplotype GGT from the rs6001417, rs8177832 and rs35228531 respectively has a protective effect OR = 0.54 [0.43-0.68] with P<0.001. There was also associations between the haplotypes GGC OR = 1.6 [1.1;-2.3] P<0.05, and CGC OR = 5.21 [2.4-11.3] P<0.001, which increase the risk of infection by HIV-1 from almost two (2) to five (5) fold. This study demonstrates an association of rs6001417, rs8177832, and rs35228531 of APOBEC3G with HIV-1 infection in a population from Burkina Faso.
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Affiliation(s)
- Tegwinde Rebeca Compaore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Serge Theophile Soubeiga
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Abdoul Karim Ouattara
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Dorcas Obiri-Yeboah
- University of Cape Coast, School of Medical Sciences, Microbiology Department, Cape Coast, Ghana
| | - Damehan Tchelougou
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Mamoudou Maiga
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Maleki Assih
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Cyrille Bisseye
- Laboratory of Molecular and Cellular Biology, University of Sciences and Techniques of Masuku (USTM), Franceville, Gabon
| | - Didier Bakouan
- Permanent Secretary against AIDS and Sexually Transmitted Diseases, Ouagadougou, Burkina Faso
| | - Issaka Pierre Compaore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
| | - Augustine Dembele
- Permanent Secretary against AIDS and Sexually Transmitted Diseases, Ouagadougou, Burkina Faso
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacques Simpore
- Pietro Annigoni Biomolecular Research Centre (CERBA)/ LABIOGENE, University of Ouagadougou, Ouagadougou, Burkina Faso
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Zhou X, Han X, Zhao K, Du J, Evans SL, Wang H, Li P, Zheng W, Rui Y, Kang J, Yu XF. Dispersed and conserved hydrophobic residues of HIV-1 Vif are essential for CBFβ recruitment and A3G suppression. J Virol 2014; 88:2555-63. [PMID: 24352440 DOI: 10.1128/JVI.03604-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED CBFβ was recently found to be a key regulator of the ability of human immunodeficiency virus type 1 (HIV-1) Vif to overcome host antiviral APOBEC3 proteins. However, the detailed molecular requirements for the Vif-CBFβ interaction are still not clear. Here, we mapped the minimum Vif domain required for CBFβ binding. In terms of CBFβ binding, the Vif N terminus was very sensitive to deletions. We determined that the Vif fragment from residues 5 to 126 was sufficient to form a stable complex with CBFβ in vitro. We also observed that ionic interactions were not the main contributor to the interaction between Vif and CBFβ. Instead, hydrophobic interactions were important for maintaining the Vif-CBFβ complex, since it could be disrupted by nonionic detergent. Site-directed mutagenesis of conserved hydrophobic amino acids revealed novel residues in Vif that were important for CBFβ binding and APOBEC3 inactivation. At least part of the well-characterized HCCH domain (residues 108 to 139) was required to form a stable Vif-CBFβ complex. Thus, the HCCH motif may have a dual role in binding both Cul5 and CBFβ. Considering the importance of Vif in HIV-1 infection, this unique Vif-CBFβ interaction represents an attractive pharmacological intervention target against HIV-1. IMPORTANCE Vif-induced APOBEC3 protein degradation was the first host antiviral mechanism against HIV-1/simian immunodeficiency virus to be revealed, yet details regarding which proteins are degraded are not fully demonstrated. Recently, host cellular factor CBFβ was found to be essential for Vif to function and promote viral infectivity. In this study, we present more critical information on the Vif-CBFβ interaction by revealing that hydrophobicity contributes the most to the Vif-CBFβ interaction and locating several novel hydrophobic sites (tryptophans and phenylalanines) that are conserved among Vif proteins from different lentiviruses and essential for Vif binding to CBFβ. Mutations on these sites result in a reduced/abolished Vif-CBFβ interaction, leading to the attenuated potency of Vif on both inducing the degradation of antiviral factors like APOBEC3G and promoting HIV-1 infectivity. Therefore, information from this study will help people to further understand how Vif acts against host antiviral mechanism, which is important for novel anti-HIV-1 drug development.
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Rios A, Quesada J, Anderson D, Goldstein A, Fossum T, Colby-Germinario S, Wainberg MA. Complete inactivation of HIV-1 using photo-labeled non-nucleoside reverse transcriptase inhibitors. Virus Res 2011; 155:189-94. [DOI: 10.1016/j.virusres.2010.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 09/28/2010] [Accepted: 10/05/2010] [Indexed: 12/28/2022]
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Cca A, Cc I, Lu A, Jc E, Pjc N, Fn O. HIV/AIDS selective infectivity–report of two peculiar cases. ASIAN PAC J TROP MED 2010; 3:1006-8. [DOI: 10.1016/s1995-7645(11)60020-5] [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: 11/24/2022] Open
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Abstract
The human cytidine deaminase APOBEC3G (A3G) is an innate restriction factor that inhibits human immunodeficiency virus, type 1 (HIV-1) replication. Regulation of A3G gene expression plays an important role in this suppression. Currently, an understanding of the mechanism of this gene regulation is largely unknown. Here, we have identified and characterized a TATA-less core promoter with an NFAT/IRF-4 composite binding site that confers cell type-specific transcriptional regulation. We found that A3G expression is critically dependent on NFATc1/NFATc2 and IRF-4. When either NFATc1 or NFATc2 and IRF-4 were co-expressed, A3G promoter activity was observed in cells that normally lack A3G expression and expression was not detected in the presence of the individual factors. This induced A3G expression allowed normally permissive CEMss cells to adopt a nonpermissive state, able to resist an HIV-1Δvif challenge. This represents the first reporting of manipulating the restrictive state of a cell type via gene regulation. Identification of NFAT and IRF family members as critical regulators of A3G expression offers important insight into the transcriptional control mechanisms that regulate innate immune responses and identifies specific targets for therapeutic intervention aimed at effectively boosting our natural immunity, in the form of a host defensive factor, against HIV-1.
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Affiliation(s)
- Melissa A Farrow
- Department of Biology, College of the Holy Cross, Worcester, Massachusetts 01610, USA
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Romani B, Engelbrecht S, Glashoff RH. Antiviral roles of APOBEC proteins against HIV-1 and suppression by Vif. Arch Virol 2009; 154:1579-88. [DOI: 10.1007/s00705-009-0481-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 07/22/2009] [Indexed: 01/18/2023]
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Kim MS, Jang SY, Park CS, Lee KM, Lee DH, Lee CH. Timing and evolution of the most recent common ancestor of the Korean clade HIV subtype B based on nef and vif sequences. J Microbiol 2009; 47:85-90. [PMID: 19229495 DOI: 10.1007/s12275-008-0240-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 12/05/2008] [Indexed: 01/26/2023]
Abstract
Molecular phylogenetic studies of the HIV-1 isolated from Koreans have suggested the presence of the so-called "Korean clade", which can be defined as a cluster free of foreign isolates. The Korean clade accounts for more than 60% of Korean isolates and exerts characteristic amino acid sequences. Thus, it is merited to estimate when this Korean clade first emerged in order to understand the evolutionary pattern of the Korean clade. We analyzed and reconstructed the most recent common ancestor (MRCA) sequences from nef (n=229) and vif (n=179) Korean clade sequences. Linear regression analyses of sequence divergence estimates were plotted against sampling years to infer the year in which there was zero divergence from the MRCA sequences. MRCA sequences suggested the Korean clade was first emerged around 1984, before the first detection of HIV-1 in Korea in 1985. Further studies on synonymous and nonsynonymous substitution rates suggested positive selection event for the Korean clade, while other subtype B had undergone negative to neutral evolution.
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