Our Technophile
Matthew B
Past PhD student
Matthew T Browning (1997-2001): Defended his doctoral thesis entitled, “Cross-packaging among retroviruses and characterization of the feline immunodeficiency virus (FIV) packaging signal: Implications for the development of FIV-based gene transfer systems”. His thesis related work resulted in several publications in the leading journals of the field (Browning et al., J. Virol., 2001; Browning et al., J. Gen. Virol., 2003; Browning et al., Virus Research, 2003). Matt pivoted himself from being an active scientist to becoming a patent lawyer. Currently, Matt is working as an intellectual property lawyer in Houston, TX USA.
Publications
2004
Mustafa, F.; Lew, K. A.; Schmidt, R. D.; Browning, M. T.; Rizvi, T. A.
Mutational analysis of the predicted secondary RNA structure of the Mason-Pfizer monkey virus packaging signal Journal Article
In: Virus Res, vol. 99, no. 1, pp. 35-46, 2004, ISSN: 0168-1702 (Print) 0168-1702.
@article{RN140,
title = {Mutational analysis of the predicted secondary RNA structure of the Mason-Pfizer monkey virus packaging signal},
author = {F. Mustafa and K. A. Lew and R. D. Schmidt and M. T. Browning and T. A. Rizvi},
doi = {10.1016/j.virusres.2003.09.012},
issn = {0168-1702 (Print) 0168-1702},
year = {2004},
date = {2004-01-01},
urldate = {2004-01-01},
journal = {Virus Res},
volume = {99},
number = {1},
pages = {35-46},
abstract = {The 5' end of the Mason-Pfizer monkey virus (MPMV) genomic RNA has been predicted to fold into a complex stem/loop structure that is thought to play a role in specific RNA encapsidation. In this study, we used a set of mutations that either abrogated or recreated the first four stem loops predicted within the 5' untranslated region (5' UTR) for effects on RNA packaging. Test of these mutations in our biological assay revealed that only stem loop 1 (SL1) was important for the packaging potential of MPMV, while mutations in none of the other stem loops affected packaging significantly. Interestingly, it was the primary sequence of SL1 RNA and not its secondary structure that affected packaging since compensatory mutations that reformed SL1 were unable to restore the packaging efficiency of the retroviral vector. Additionally, our mutational analysis reveals that stem loop 4, predicted to be the major packaging determinant of MPMV, does not seem to have a significant role in packaging. Finally, results of the biological effects of the structural mutations are discussed in relation to their effects on the folding potential of the various stem loops.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The 5' end of the Mason-Pfizer monkey virus (MPMV) genomic RNA has been predicted to fold into a complex stem/loop structure that is thought to play a role in specific RNA encapsidation. In this study, we used a set of mutations that either abrogated or recreated the first four stem loops predicted within the 5' untranslated region (5' UTR) for effects on RNA packaging. Test of these mutations in our biological assay revealed that only stem loop 1 (SL1) was important for the packaging potential of MPMV, while mutations in none of the other stem loops affected packaging significantly. Interestingly, it was the primary sequence of SL1 RNA and not its secondary structure that affected packaging since compensatory mutations that reformed SL1 were unable to restore the packaging efficiency of the retroviral vector. Additionally, our mutational analysis reveals that stem loop 4, predicted to be the major packaging determinant of MPMV, does not seem to have a significant role in packaging. Finally, results of the biological effects of the structural mutations are discussed in relation to their effects on the folding potential of the various stem loops.
2003
Browning, M. T.; Mustafa, F.; Schmidt, R. D.; Lew, K. A.; Rizvi, T. A.
Delineation of sequences important for efficient packaging of feline immunodeficiency virus RNA Journal Article
In: J Gen Virol, vol. 84, no. Pt 3, pp. 621-627, 2003, ISSN: 0022-1317 (Print) 0022-1317.
@article{RN141,
title = {Delineation of sequences important for efficient packaging of feline immunodeficiency virus RNA},
author = {M. T. Browning and F. Mustafa and R. D. Schmidt and K. A. Lew and T. A. Rizvi},
doi = {10.1099/vir.0.18886-0},
issn = {0022-1317 (Print) 0022-1317},
year = {2003},
date = {2003-01-01},
urldate = {2003-01-01},
journal = {J Gen Virol},
volume = {84},
number = {Pt 3},
pages = {621-627},
abstract = {We have used systematic deletion analysis of the 5' untranslated region (UTR) of the feline immunodeficiency virus (FIV) genome, both in the presence and absence of various amounts of gag, to define the cis-acting sequences responsible for efficient RNA packaging. Our analyses revealed that the primary FIV packaging signal consists of two essential core elements located within the first 90-120 bp of the 5'UTR and the first 90 bp of the gag gene. Interestingly, the region between the major splice donor (SD) and gag, including approximately 130-160 bp upstream of the SD, is dispensable for encapsidation. Finally, other determinants of packaging were found to be present in the viral LTR and/or within the 3' end of the viral genome. Taken together, our results suggest that the primary packaging determinants of FIV are multipartite and discontinuous, composed of two elements within the 5'UTR and gag gene.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We have used systematic deletion analysis of the 5' untranslated region (UTR) of the feline immunodeficiency virus (FIV) genome, both in the presence and absence of various amounts of gag, to define the cis-acting sequences responsible for efficient RNA packaging. Our analyses revealed that the primary FIV packaging signal consists of two essential core elements located within the first 90-120 bp of the 5'UTR and the first 90 bp of the gag gene. Interestingly, the region between the major splice donor (SD) and gag, including approximately 130-160 bp upstream of the SD, is dispensable for encapsidation. Finally, other determinants of packaging were found to be present in the viral LTR and/or within the 3' end of the viral genome. Taken together, our results suggest that the primary packaging determinants of FIV are multipartite and discontinuous, composed of two elements within the 5'UTR and gag gene.
Browning, M. T.; Mustafa, F.; Schmidt, R. D.; Lew, K. A.; Rizvi, T. A.
Sequences within the gag gene of feline immunodeficiency virus (FIV) are important for efficient RNA encapsidation Journal Article
In: Virus Res, vol. 93, no. 2, pp. 199-209, 2003, ISSN: 0168-1702 (Print) 0168-1702.
@article{RN145,
title = {Sequences within the gag gene of feline immunodeficiency virus (FIV) are important for efficient RNA encapsidation},
author = {M. T. Browning and F. Mustafa and R. D. Schmidt and K. A. Lew and T. A. Rizvi},
doi = {10.1016/s0168-1702(03)00098-4},
issn = {0168-1702 (Print) 0168-1702},
year = {2003},
date = {2003-01-01},
urldate = {2003-01-01},
journal = {Virus Res},
volume = {93},
number = {2},
pages = {199-209},
abstract = {Feline immunodeficiency virus (FIV)-based retroviral vector systems are being developed for human gene therapy. Consequently, it has become important to know the precise sequence requirements for the packaging of FIV genome so that such sequences can be eliminated from transfer vectors post-transduction for improved safety. Recently, we have shown that sequences both within the 5'-untranslated leader region (UTR) and the 5'-end of gag are required for efficient packaging and transduction of FIV-based vectors. However, the extent of gag sequence important in the encapsidation process is not clear as well as their relative contribution to packaging. In this study, using a biologically relevant packaging system, we demonstrate that at the most 100 bp of gag sequences are sufficient for efficient RNA packaging in conjunction with the 5'-UTR and no other sequences within the next 600 bp of gag exist that affect packaging. In addition, we show that sequences within gag do not simply act as spatial elements to stabilize other structural determinants of packaging located within the 5'-UTR, but are important in themselves for the encapsidation process.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Feline immunodeficiency virus (FIV)-based retroviral vector systems are being developed for human gene therapy. Consequently, it has become important to know the precise sequence requirements for the packaging of FIV genome so that such sequences can be eliminated from transfer vectors post-transduction for improved safety. Recently, we have shown that sequences both within the 5'-untranslated leader region (UTR) and the 5'-end of gag are required for efficient packaging and transduction of FIV-based vectors. However, the extent of gag sequence important in the encapsidation process is not clear as well as their relative contribution to packaging. In this study, using a biologically relevant packaging system, we demonstrate that at the most 100 bp of gag sequences are sufficient for efficient RNA packaging in conjunction with the 5'-UTR and no other sequences within the next 600 bp of gag exist that affect packaging. In addition, we show that sequences within gag do not simply act as spatial elements to stabilize other structural determinants of packaging located within the 5'-UTR, but are important in themselves for the encapsidation process.
Schmidt, R. D.; Mustafa, F.; Lew, K. A.; Browning, M. T.; Rizvi, T. A.
Sequences within both the 5' untranslated region and the gag gene are important for efficient encapsidation of Mason-Pfizer monkey virus RNA Journal Article
In: Virology, vol. 309, no. 1, pp. 166-78, 2003, ISSN: 0042-6822 (Print) 0042-6822.
@article{RN131,
title = {Sequences within both the 5' untranslated region and the gag gene are important for efficient encapsidation of Mason-Pfizer monkey virus RNA},
author = {R. D. Schmidt and F. Mustafa and K. A. Lew and M. T. Browning and T. A. Rizvi},
doi = {10.1016/s0042-6822(02)00101-0},
issn = {0042-6822 (Print) 0042-6822},
year = {2003},
date = {2003-01-01},
urldate = {2003-01-01},
journal = {Virology},
volume = {309},
number = {1},
pages = {166-78},
abstract = {It has previously been shown that the 5' untranslated leader region (UTR), including about 495 bp of the gag gene, is sufficient for the efficient encapsidation and propagation of Mason-Pfizer monkey virus (MPMV) based retroviral vectors. In addition, a deletion upstream of the major splice donor, SD, has been shown to adversely affect MPMV RNA packaging. However, the precise sequence requirement for the encapsidation of MPMV genomic RNA within the 5' UTR and gag remains largely unknown. In this study, we have used a systematic deletion analysis of the 5' UTR and gag gene to define the cis-acting sequences responsible for efficient MPMV RNA packaging. Using an in vivo packaging and transduction assay, our results reveal that the MPMV packaging signal is primarily found within the first 30 bp immediately downstream of the primer binding site. However, its function is dependent upon the presence of the last 23 bp of the 5' UTR and approximately the first 100 bp of the gag gene. Thus, sequences that affect MPMV RNA packaging seem to reside both upstream and downstream of the major splice donor with the downstream region responsible for the efficient functioning of the upstream primary packaging determinant.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
It has previously been shown that the 5' untranslated leader region (UTR), including about 495 bp of the gag gene, is sufficient for the efficient encapsidation and propagation of Mason-Pfizer monkey virus (MPMV) based retroviral vectors. In addition, a deletion upstream of the major splice donor, SD, has been shown to adversely affect MPMV RNA packaging. However, the precise sequence requirement for the encapsidation of MPMV genomic RNA within the 5' UTR and gag remains largely unknown. In this study, we have used a systematic deletion analysis of the 5' UTR and gag gene to define the cis-acting sequences responsible for efficient MPMV RNA packaging. Using an in vivo packaging and transduction assay, our results reveal that the MPMV packaging signal is primarily found within the first 30 bp immediately downstream of the primer binding site. However, its function is dependent upon the presence of the last 23 bp of the 5' UTR and approximately the first 100 bp of the gag gene. Thus, sequences that affect MPMV RNA packaging seem to reside both upstream and downstream of the major splice donor with the downstream region responsible for the efficient functioning of the upstream primary packaging determinant.
2001
Browning, M. T.; Schmidt, R. D.; Lew, K. A.; Rizvi, T. A.
Primate and feline lentivirus vector RNA packaging and propagation by heterologous lentivirus virions Journal Article
In: J Virol, vol. 75, no. 11, pp. 5129-40, 2001, ISSN: 0022-538X (Print) 0022-538x.
@article{RN114,
title = {Primate and feline lentivirus vector RNA packaging and propagation by heterologous lentivirus virions},
author = {M. T. Browning and R. D. Schmidt and K. A. Lew and T. A. Rizvi},
doi = {10.1128/jvi.75.11.5129-5140.2001},
issn = {0022-538X (Print) 0022-538x},
year = {2001},
date = {2001-01-01},
urldate = {2001-01-01},
journal = {J Virol},
volume = {75},
number = {11},
pages = {5129-40},
abstract = {Development of safe and effective gene transfer systems is critical to the success of gene therapy protocols for human diseases. Currently, several primate lentivirus-based gene transfer systems, such as those based on human and simian immunodeficiency viruses (HIV/SIV), are being tested; however, their use in humans raises safety concerns, such as the generation of replication-competent viruses through recombination with related endogenous retroviruses or retrovirus-like elements. Due to the greater phylogenetic distance from primate lentiviruses, feline immunodeficiency virus (FIV) is becoming the lentivirus of choice for human gene transfer systems. However, the safety of FIV-based vector systems has not been tested experimentally. Since lentiviruses such as HIV-1 and SIV have been shown to cross-package their RNA genomes, we tested the ability of FIV RNA to get cross-packaged into primate lentivirus particles such as HIV-1 and SIV, as well as a nonlentiviral retrovirus such as Mason-Pfizer monkey virus (MPMV), and vice versa. Our results reveal that FIV RNA can be cross-packaged by primate lentivirus particles such as HIV-1 and SIV and vice versa; however, a nonlentivirus particle such as MPMV is unable to package FIV RNA. Interestingly, FIV particles can package MPMV RNA but cannot propagate the vector RNA further for other steps of the retrovirus life cycle. These findings reveal that diverse retroviruses are functionally more similar than originally thought and suggest that upon coinfection of the same host, cross- or copackaging may allow distinct retroviruses to generate chimeric variants with unknown pathogenic potential.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Development of safe and effective gene transfer systems is critical to the success of gene therapy protocols for human diseases. Currently, several primate lentivirus-based gene transfer systems, such as those based on human and simian immunodeficiency viruses (HIV/SIV), are being tested; however, their use in humans raises safety concerns, such as the generation of replication-competent viruses through recombination with related endogenous retroviruses or retrovirus-like elements. Due to the greater phylogenetic distance from primate lentiviruses, feline immunodeficiency virus (FIV) is becoming the lentivirus of choice for human gene transfer systems. However, the safety of FIV-based vector systems has not been tested experimentally. Since lentiviruses such as HIV-1 and SIV have been shown to cross-package their RNA genomes, we tested the ability of FIV RNA to get cross-packaged into primate lentivirus particles such as HIV-1 and SIV, as well as a nonlentiviral retrovirus such as Mason-Pfizer monkey virus (MPMV), and vice versa. Our results reveal that FIV RNA can be cross-packaged by primate lentivirus particles such as HIV-1 and SIV and vice versa; however, a nonlentivirus particle such as MPMV is unable to package FIV RNA. Interestingly, FIV particles can package MPMV RNA but cannot propagate the vector RNA further for other steps of the retrovirus life cycle. These findings reveal that diverse retroviruses are functionally more similar than originally thought and suggest that upon coinfection of the same host, cross- or copackaging may allow distinct retroviruses to generate chimeric variants with unknown pathogenic potential.