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Article ; Online: The Influence of Angler Values, Involvement, Catch Orientation, Satisfaction, Agency Trust, and Demographics on Support for Habitat Protection and Restoration Versus Stocking in Publicly Managed Waters.

Schroeder, Susan A / Fulton, David C / Altena, Eric / Baird, Heather / Dieterman, Douglas / Jennings, Martin

2018 Volume 62, Issue 4, Page(s) 665–677

Abstract: Resource managers benefit from knowledge of angler support for fisheries management strategies. Factors including angler values (protection, utilitarian, and dominance), involvement (attraction, centrality, social, identity affirmation, and expression), ... ...

Abstract	Resource managers benefit from knowledge of angler support for fisheries management strategies. Factors including angler values (protection, utilitarian, and dominance), involvement (attraction, centrality, social, identity affirmation, and expression), catch-related motivations (catching some, many, and big fish, and keeping fish), satisfaction, agency trust, and demographics may relate to fisheries management preferences. Using results from a mail survey of Minnesota resident anglers, we explored how these factors were related to budget support for fish stocking relative to habitat protection/restoration. Results suggest that values, angler involvement, catch orientation, satisfaction, total and recent years fishing, age, and education influence relative support for stocking versus habitat protection/restoration. Utilitarian values, angling centrality, an orientation to catch many fish, satisfaction with the number of fish caught, number of recent years fishing, and age positively related to support for stocking over habitat management, while protection values, attraction to angling, total years fishing, and education level were negatively related to relative support for stocking.
MeSH term(s)	Animals ; Conservation of Water Resources/methods ; Ecosystem ; Fisheries/organization & administration ; Health Knowledge, Attitudes, Practice ; Minnesota ; Personal Satisfaction ; Population Dynamics
Language	English
Publishing date	2018-05-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	1478932-2
ISSN	1432-1009 ; 0364-152X
ISSN (online)	1432-1009
ISSN	0364-152X
DOI	10.1007/s00267-018-1067-9
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Article ; Online: Enrichment of intersubtype HIV-1 recombinants in a dual infection system using HIV-1 strain-specific siRNAs

Abraha Awet / Dudley Dawn M / Baird Heather / Nelson Kenneth N / Abreha Measho / Gao Yong / Arts Eric J

Retrovirology, Vol 8, Iss 1, p

2011 Volume 5

Abstract: Abstract Background Intersubtype HIV-1 recombinants in the form of unique or stable circulating recombinants forms (CRFs) are responsible for over 20% of infections in the worldwide epidemic. Mechanisms controlling the generation, selection, and ... ...

Abstract	Abstract Background Intersubtype HIV-1 recombinants in the form of unique or stable circulating recombinants forms (CRFs) are responsible for over 20% of infections in the worldwide epidemic. Mechanisms controlling the generation, selection, and transmission of these intersubtype HIV-1 recombinants still require further investigation. All intersubtype HIV-1 recombinants are generated and evolve from initial dual infections, but are difficult to identify in the human population. In vitro studies provide the most practical system to study mechanisms, but the recombination rates are usually very low in dual infections with primary HIV-1 isolates. This study describes the use of HIV-1 isolate-specific siRNAs to enrich intersubtype HIV-1 recombinants and inhibit the parental HIV-1 isolates from a dual infection. Results Following a dual infection with subtype A and D primary HIV-1 isolates and two rounds of siRNA treatment, nearly 100% of replicative virus was resistant to a siRNA specific for an upstream target sequence in the subtype A envelope ( env ) gene as well as a siRNA specific for a downstream target sequence in the subtype D env gene. Only 20% (10/50) of the replicating virus had nucleotide substitutions in the siRNA-target sequence whereas the remaining 78% (39/50) harbored a recombination breakpoint that removed both siRNA target sequences, and rendered the intersubtype D/A recombinant virus resistant to the dual siRNA treatment. Since siRNAs target the newly transcribed HIV-1 mRNA, the siRNAs only enrich intersubtype env recombinants and do not influence the recombination process during reverse transcription. Using this system, a strong bias is selected for recombination breakpoints in the C2 region, whereas other HIV-1 env regions, most notably the hypervariable regions, were nearly devoid of intersubtype recombination breakpoints. Sequence conservation plays an important role in selecting for recombination breakpoints, but the lack of breakpoints in many conserved env regions suggest that other mechanisms are at play. Conclusion These findings show that siRNAs can be used as an efficient in vitro tool for enriching recombinants, to facilitate further study on mechanisms of intersubytpe HIV-1 recombination, and to generate replication-competent intersubtype recombinant proteins with a breadth in HIV-1 diversity for future vaccine studies.
Keywords	Medicine (General) ; R5-920 ; Medicine ; R ; DOAJ:Medicine (General) ; DOAJ:Health Sciences ; Immunologic diseases. Allergy ; RC581-607
Subject code	570
Language	English
Publishing date	2011-01-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
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Article ; Online: Enrichment of intersubtype HIV-1 recombinants in a dual infection system using HIV-1 strain-specific siRNAs.

Gao, Yong / Abreha, Measho / Nelson, Kenneth N / Baird, Heather / Dudley, Dawn M / Abraha, Awet / Arts, Eric J

Retrovirology

2011 Volume 8, Issue 1, Page(s) 5

Abstract: Background: Intersubtype HIV-1 recombinants in the form of unique or stable circulating recombinants forms (CRFs) are responsible for over 20% of infections in the worldwide epidemic. Mechanisms controlling the generation, selection, and transmission of ...

Abstract	Background: Intersubtype HIV-1 recombinants in the form of unique or stable circulating recombinants forms (CRFs) are responsible for over 20% of infections in the worldwide epidemic. Mechanisms controlling the generation, selection, and transmission of these intersubtype HIV-1 recombinants still require further investigation. All intersubtype HIV-1 recombinants are generated and evolve from initial dual infections, but are difficult to identify in the human population. In vitro studies provide the most practical system to study mechanisms, but the recombination rates are usually very low in dual infections with primary HIV-1 isolates. This study describes the use of HIV-1 isolate-specific siRNAs to enrich intersubtype HIV-1 recombinants and inhibit the parental HIV-1 isolates from a dual infection. Results: Following a dual infection with subtype A and D primary HIV-1 isolates and two rounds of siRNA treatment, nearly 100% of replicative virus was resistant to a siRNA specific for an upstream target sequence in the subtype A envelope (env) gene as well as a siRNA specific for a downstream target sequence in the subtype D env gene. Only 20% (10/50) of the replicating virus had nucleotide substitutions in the siRNA-target sequence whereas the remaining 78% (39/50) harbored a recombination breakpoint that removed both siRNA target sequences, and rendered the intersubtype D/A recombinant virus resistant to the dual siRNA treatment. Since siRNAs target the newly transcribed HIV-1 mRNA, the siRNAs only enrich intersubtype env recombinants and do not influence the recombination process during reverse transcription. Using this system, a strong bias is selected for recombination breakpoints in the C2 region, whereas other HIV-1 env regions, most notably the hypervariable regions, were nearly devoid of intersubtype recombination breakpoints. Sequence conservation plays an important role in selecting for recombination breakpoints, but the lack of breakpoints in many conserved env regions suggest that other mechanisms are at play. Conclusion: These findings show that siRNAs can be used as an efficient in vitro tool for enriching recombinants, to facilitate further study on mechanisms of intersubytpe HIV-1 recombination, and to generate replication-competent intersubtype recombinant proteins with a breadth in HIV-1 diversity for future vaccine studies.
MeSH term(s)	Base Sequence ; Drug Resistance, Viral ; HIV Infections/virology ; HIV-1/genetics ; HIV-1/isolation & purification ; HIV-1/physiology ; Humans ; Molecular Sequence Data ; RNA, Small Interfering/genetics ; Recombination, Genetic ; Sequence Alignment ; Virus Replication ; env Gene Products, Human Immunodeficiency Virus/genetics
Chemical Substances	RNA, Small Interfering ; env Gene Products, Human Immunodeficiency Virus
Language	English
Publishing date	2011-01-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1742-4690
ISSN (online)	1742-4690
DOI	10.1186/1742-4690-8-5
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Article: Cryopreserved cell monolayers for rapid detection of herpes simplex virus and influenza virus.

Huang, Yung T / Yan, Huimin / Sun, Yan / Jollick, Joseph A / Baird, Heather

Journal of clinical microbiology

2001 Volume 40, Issue 11, Page(s) 4301–4303

Abstract: Cryopreserved cell monolayers are a new cell culture technology intended to ensure the availability of cells in the laboratory for virus detection. Two cryopreserved cell monolayers, ELVIS for the detection of herpes simplex virus (HSV) and R-Mix for the ...

Abstract	Cryopreserved cell monolayers are a new cell culture technology intended to ensure the availability of cells in the laboratory for virus detection. Two cryopreserved cell monolayers, ELVIS for the detection of herpes simplex virus (HSV) and R-Mix for the detection of influenza virus, were evaluated. The results indicated that fresh and cryopreserved cell monolayers are comparable in sensitivity for the detection of HSV and influenza virus. The cells retain the same level of sensitivity for up to 4 months at -80 degrees C.
MeSH term(s)	Animals ; Cells, Cultured ; Cryopreservation ; Herpes Simplex/virology ; Herpesvirus 1, Human/growth & development ; Herpesvirus 1, Human/isolation & purification ; Humans ; Influenza A virus/growth & development ; Influenza A virus/isolation & purification ; Influenza B virus/growth & development ; Influenza B virus/isolation & purification ; Influenza, Human/virology ; Reagent Kits, Diagnostic ; Sensitivity and Specificity ; Time Factors ; Virus Cultivation/methods
Chemical Substances	Reagent Kits, Diagnostic
Language	English
Publishing date	2001-10-13
Publishing country	United States
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.40.11.4301-4303.2002
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Article: Sequence determinants of breakpoint location during HIV-1 intersubtype recombination

Baird, Heather A / Galetto, RomÃ¡n / Gao, Yong / Simon-Loriere, Etienne / Abreha, Measho / Archer, John / Fan, Jun / Robertson, David L / Arts, Eric J / Negroni, Matteo

Nucleic acids research. 2006 Oct., v. 34, no. 18

2006

Abstract: Retroviral recombination results from strand switching, during reverse transcription, between the two copies of genomic RNA present in the virus. We analysed recombination in part of the envelope gene, between HIV-1 subtype A and D strains. After a ... ...

Abstract	Retroviral recombination results from strand switching, during reverse transcription, between the two copies of genomic RNA present in the virus. We analysed recombination in part of the envelope gene, between HIV-1 subtype A and D strains. After a single infection cycle, breakpoints clustered in regions corresponding to the constant portions of Env. With some exceptions, a similar distribution was observed after multiple infection cycles, and among recombinant sequences in the HIV Sequence Database. We compared the experimental data with computer simulations made using a program that only allows recombination to occur whenever an identical base is present in the aligned parental RNAs. Experimental recombination was more frequent than expected on the basis of simulated recombination when, in a region spanning 40 nt from the 5' border of a breakpoint, no more than two discordant bases between the parental RNAs were present. When these requirements were not fulfilled, breakpoints were distributed randomly along the RNA, closer to the distribution predicted by computer simulation. A significant preference for recombination was also observed for regions containing homopolymeric stretches. These results define, for the first time, local sequence determinants for recombination between divergent HIV-1 isolates.
Keywords	Human immunodeficiency virus 1 ; RNA ; computer simulation ; databases ; genes ; reverse transcription ; transcription (genetics) ; viruses
Language	English
Dates of publication	2006-10
Size	p. 5203-5216.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkl669
Database	NAL-Catalogue (AGRICOLA)

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Article: Monitoring processed, mature Human Immunodeficiency Virus type 1 particles immediately following treatment with a protease inhibitor-containing treatment regimen.

Baird, Heather A / Marozsan, Andre J / Lederman, Michael M / Landay, Alan / Mildvan, Donna / Kuritzkes, Daniel R / Kessler, Harold A / Arts, Eric J

AIDS research and therapy

2005 Volume 2, Issue 1, Page(s) 2

Abstract: Protease inhibitors (PIs) block HIV-1 maturation into an infectious virus particle by inhibiting the protease processing of gag and gag-pol precursor proteins. We have used a simple anti-HIV-1 p24 Western blot to monitor the processing of p55gag ... ...

Abstract	Protease inhibitors (PIs) block HIV-1 maturation into an infectious virus particle by inhibiting the protease processing of gag and gag-pol precursor proteins. We have used a simple anti-HIV-1 p24 Western blot to monitor the processing of p55gag precursor into the mature p24 capsid immediately following the first dosage of a PI-containing treatment regimen. Evidence of PI activity was observed in plasma virus as early as 72 hours post treatment-initiation and was predictive of plasma viral RNA decrease at 4 weeks.
Language	English
Publishing date	2005-04-12
Publishing country	England
Document type	Journal Article
ISSN	1742-6405
ISSN	1742-6405
DOI	10.1186/1742-6405-2-2
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Article ; Online: Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination

Abreha Measho / Giacomoni Véronique / Anthony Reshma M / Lalonde Matthew / Galetto Román / Gao Yong / Baird Heather A / Destefano Jeffrey J / Negroni Matteo / Arts Eric J

Retrovirology, Vol 3, Iss 1, p

2006 Volume 91

Abstract: Abstract Background HIV-1 recombination between different subtypes has a major impact on the global epidemic. The generation of these intersubtype recombinants follows a defined set of events starting with dual infection of a host cell, heterodiploid ... ...

Abstract	Abstract Background HIV-1 recombination between different subtypes has a major impact on the global epidemic. The generation of these intersubtype recombinants follows a defined set of events starting with dual infection of a host cell, heterodiploid virus production, strand transfers during reverse transcription, and then selection. In this study, recombination frequencies were measured in the C1-C4 regions of the envelope gene in the presence (using a multiple cycle infection system) and absence (in vitro reverse transcription and single cycle infection systems) of selection for replication-competent virus. Ugandan subtypes A and D HIV-1 env sequences (115-A, 120-A, 89-D, 122-D, 126-D) were employed in all three assay systems. These subtypes co-circulate in East Africa and frequently recombine in this human population. Results Increased sequence identity between viruses or RNA templates resulted in increased recombination frequencies, with the exception of the 115-A virus or RNA template. Analyses of the recombination breakpoints and mechanistic studies revealed that the presence of a recombination hotspot in the C3/V4 env region, unique to 115-A as donor RNA, could account for the higher recombination frequencies with the 115-A virus/template. Single-cycle infections supported proportionally less recombination than the in vitro reverse transcription assay but both systems still had significantly higher recombination frequencies than observed in the multiple-cycle virus replication system. In the multiple cycle assay, increased replicative fitness of one HIV-1 over the other in a dual infection dramatically decreased recombination frequencies. Conclusion Sequence variation at specific sites between HIV-1 isolates can introduce unique recombination hotspots, which increase recombination frequencies and skew the general observation that decreased HIV-1 sequence identity reduces recombination rates. These findings also suggest that the majority of intra- or intersubtype A/D HIV-1 recombinants, generated with each round of infection, are not replication-competent and do not survive in the multiple-cycle system. Ability of one HIV-1 isolate to outgrow the other leads to reduced co-infections, heterozygous virus production, and recombination frequencies.
Keywords	Medicine (General) ; R5-920 ; Medicine ; R ; DOAJ:Medicine (General) ; DOAJ:Health Sciences ; Immunologic diseases. Allergy ; RC581-607
Subject code	570
Language	English
Publishing date	2006-12-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
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Article: Relationships between infectious titer, capsid protein levels, and reverse transcriptase activities of diverse human immunodeficiency virus type 1 isolates.

Marozsan, Andre J / Fraundorf, Erika / Abraha, Awet / Baird, Heather / Moore, Dawn / Troyer, Ryan / Nankja, Immaculate / Arts, Eric J

Journal of virology

2004 Volume 78, Issue 20, Page(s) 11130–11141

Abstract: Most studies on human immunodeficiency virus type 1 (HIV-1) replication kinetics or fitness must rely on a particular assay to initially standardize inocula from virus stocks. The most accurate measure of infectious HIV-1 titers involves a limiting ... ...

Abstract	Most studies on human immunodeficiency virus type 1 (HIV-1) replication kinetics or fitness must rely on a particular assay to initially standardize inocula from virus stocks. The most accurate measure of infectious HIV-1 titers involves a limiting dilution-infection assay and a calculation of the dose required for 50% infectivity of susceptible cells in tissue culture (TCID(50)). Surrogate assays are now commonly used to measure the amount of p24 capsid, the endogenous reverse transcriptase (RT) activity, or the amount of viral genomic RNA in virus particles. However, a direct comparison of these surrogate assays and actual infectious HIV-1 titers from TCID(50) assays has not been performed with even the most conserved laboratory strains, let alone the highly divergent primary HIV-1 isolates of different subtypes. This study indicates that endogenous RT activity, not p24 content or viral RNA load, is the best surrogate measure of infectious HIV-1 titer in both cell-free supernatants and viruses purified on sucrose cushions. Sequence variation between HIV-1 subtypes did not appear to affect the function or activity of the RT enzyme in this endogenous assay but did affect the detection of p24 capsid by both enzyme immunoassays and Western blots. Clear groupings of non-syncytium-inducing (NSI), CCR5-tropic (R5), and SI/CXCR4-tropic (X4) HIV-1 isolates were observed when we compared the slopes derived from correlations of RT activity with infectious titers. Finally, the replication efficiency or fitness of both the NSI/R5 and SI/X4 HIV-1 isolates was not linked to the titers of the virus stocks.
MeSH term(s)	Blotting, Western ; HIV Core Protein p24/metabolism ; HIV Reverse Transcriptase/metabolism ; HIV-1/enzymology ; HIV-1/metabolism ; HIV-1/pathogenicity ; Humans ; Immunoenzyme Techniques ; Leukocytes, Mononuclear/virology ; RNA, Viral/blood ; Viral Load ; Virus Replication
Chemical Substances	HIV Core Protein p24 ; RNA, Viral ; HIV Reverse Transcriptase (EC 2.7.7.49)
Language	English
Publishing date	2004-10
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.78.20.11130-11141.2004
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Article ; Online: Monitoring processed, mature Human Immunodeficiency Virus type 1 particles immediately following treatment with a protease inhibitor-containing treatment regimen

Kuritzkes Daniel R / Mildvan Donna / Landay Alan / Lederman Michael M / Marozsan Andre J / Baird Heather A / Kessler Harold A / Arts Eric J

AIDS Research and Therapy, Vol 2, Iss 1, p

2005 Volume 2

Abstract: Abstract Protease inhibitors (PIs) block HIV-1 maturation into an infectious virus particle by inhibiting the protease processing of gag and gag-pol precursor proteins. We have used a simple anti-HIV-1 p24 Western blot to monitor the processing of p55 ... ...

Abstract	Abstract Protease inhibitors (PIs) block HIV-1 maturation into an infectious virus particle by inhibiting the protease processing of gag and gag-pol precursor proteins. We have used a simple anti-HIV-1 p24 Western blot to monitor the processing of p55 gag precursor into the mature p24 capsid immediately following the first dosage of a PI-containing treatment regimen. Evidence of PI activity was observed in plasma virus as early as 72 hours post treatment-initiation and was predictive of plasma viral RNA decrease at 4 weeks.
Keywords	Protease inhibitors ; HIV-1 ; p24 antigen capture ; Immunologic diseases. Allergy ; RC581-607 ; Specialties of internal medicine ; RC581-951 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Allergy and Immunology ; DOAJ:Medicine (General) ; DOAJ:Health Sciences ; Medicine (General) ; R5-920
Language	English
Publishing date	2005-04-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination.

Baird, Heather A / Gao, Yong / Galetto, Román / Lalonde, Matthew / Anthony, Reshma M / Giacomoni, Véronique / Abreha, Measho / Destefano, Jeffrey J / Negroni, Matteo / Arts, Eric J

Retrovirology

2006 Volume 3, Page(s) 91

Abstract: Background: HIV-1 recombination between different subtypes has a major impact on the global epidemic. The generation of these intersubtype recombinants follows a defined set of events starting with dual infection of a host cell, heterodiploid virus ... ...

Abstract	Background: HIV-1 recombination between different subtypes has a major impact on the global epidemic. The generation of these intersubtype recombinants follows a defined set of events starting with dual infection of a host cell, heterodiploid virus production, strand transfers during reverse transcription, and then selection. In this study, recombination frequencies were measured in the C1-C4 regions of the envelope gene in the presence (using a multiple cycle infection system) and absence (in vitro reverse transcription and single cycle infection systems) of selection for replication-competent virus. Ugandan subtypes A and D HIV-1 env sequences (115-A, 120-A, 89-D, 122-D, 126-D) were employed in all three assay systems. These subtypes co-circulate in East Africa and frequently recombine in this human population. Results: Increased sequence identity between viruses or RNA templates resulted in increased recombination frequencies, with the exception of the 115-A virus or RNA template. Analyses of the recombination breakpoints and mechanistic studies revealed that the presence of a recombination hotspot in the C3/V4 env region, unique to 115-A as donor RNA, could account for the higher recombination frequencies with the 115-A virus/template. Single-cycle infections supported proportionally less recombination than the in vitro reverse transcription assay but both systems still had significantly higher recombination frequencies than observed in the multiple-cycle virus replication system. In the multiple cycle assay, increased replicative fitness of one HIV-1 over the other in a dual infection dramatically decreased recombination frequencies. Conclusion: Sequence variation at specific sites between HIV-1 isolates can introduce unique recombination hotspots, which increase recombination frequencies and skew the general observation that decreased HIV-1 sequence identity reduces recombination rates. These findings also suggest that the majority of intra- or intersubtype A/D HIV-1 recombinants, generated with each round of infection, are not replication-competent and do not survive in the multiple-cycle system. Ability of one HIV-1 isolate to outgrow the other leads to reduced co-infections, heterozygous virus production, and recombination frequencies.
MeSH term(s)	Base Sequence ; Cell Line ; Chromosome Mapping ; Genes, env ; HIV-1/genetics ; HIV-1/isolation & purification ; HIV-1/physiology ; Humans ; RNA, Viral/chemistry ; Recombination, Genetic ; Uganda ; Virus Replication
Chemical Substances	RNA, Viral
Language	English
Publishing date	2006-12-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1742-4690
ISSN (online)	1742-4690
DOI	10.1186/1742-4690-3-91
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