Publications

@article{Ahmad2026b,

title = {Dysregulated host miRNAs with antiviral potential against SARS-CoV-2 identified from COVID-19 patients},

author = {Waqar Ahmad and Bushra Gull and Jasmin Baby and Neena G. Panicker and Thanumol Abdul Khader and Tahir A. Rizvi and Farah Mustafa},

doi = {10.1186/s12967-026-08094-1},

issn = {1479-5876},

year  = {2026},

date = {2026-12-00},

urldate = {2026-12-00},

journal = {J Transl Med},

volume = {24},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {\textbf{Background}

MicroRNAs (miRNAs) are small RNA molecules implicated in controlling most cellular processes by either deadenylating/degrading mRNA transcripts or inhibiting their translation. Viruses and their hosts utilize miRNAs for regulating gene expression, targeting both cellular and viral mRNAs. Since the onset of the COVID-19 pandemic, numerous studies have aimed at elucidating the role of host responses at the molecular and cellular levels in determining disease severity among infected individuals. However, the precise interactions between SARS-CoV-2 and host miRNAs, and their biological impact on virus replication or pathogenesis remains poorly understood.

\textbf{Methods}

Employing miRNAseq and real time PCR, we have previously identified dysregulated host miRNAs in a large cohort of SARS-CoV-2 infected individuals. In this study, we used specialized bioinformatic and computational tools, as well as 3D docking analysis to investigate the ability of the dysregulated miRNAs observed in these COVID-19 patients to target the SARS-CoV-2 genome.

\textbf{Results}

Our analyses reveal that some of the differentially regulated, COVID-19-specific miRNAs had the potential to directly target the SARS-CoV-2 genome or its sub-genomic transcripts essential for virion formation, viral replication, and infection. These included mRNAs for non-structural and structural proteins, suggesting that SARS-CoV-2 may benefit from these miRNAs for its replication or immune evasion. Further miRNA target gene analysis revealed how these miRNAs may also target host cellular pathways, including FoxO, AMPK, mTOR, PI3-Akt, and ErbB, essential for critical cellular functions. Interestingly, these pathways are also disrupted during conditions like diabetes, aging, and neurodegenerative disorders, as well as frequently exploited by viruses to enhance virus replication and pathogenesis.

\textbf{Conclusions}

In summary, this work identifies several endogenous host miRNAs dysregulated during SARS-CoV-2 infection that can be exploited to not only target the virus itself, but also mitigate severe disease during future pandemic(s) with any SARS-CoV-2 variant-of-concern (VOC). Thus, it offers promising new potential molecular targets for therapeutic development, complementing existing antiviral strategies. Coupled with identification of cellular pathways involved in pathogenesis, these findings underscore the profound impact of miRNAs on viral pathogenesis, host metabolism, and immune responses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ahmad2026,

title = {Shaping Cell Identity: Global Transcriptome and Pathway Shifts during Mouse Mammary Epithelial Cell Differentiation},

author = {Waqar Ahmad and Neena Gopinathan Panicker and Tahir A. Rizvi and Farah Mustafa},

doi = {10.34133/csbj.0055},

issn = {2001-0370},

year  = {2026},

date = {2026-03-01},

urldate = {2026-03-01},

journal = {Comput Struct Biotechnol J},

volume = {35},

number = {1},

publisher = {American Association for the Advancement of Science (AAAS)},

abstract = {Mouse mammary epithelial cells possess a remarkable ability to regenerate the entire mammary gland through precisely regulated differentiation, involving complex molecular, morphological, and functional changes. Here, we performed comprehensive transcriptomic profiling of HC11 mouse mammary epithelial cells undergoing lactogenic differentiation using RNA sequencing and integrative bioinformatics. We identified 566 differentially expressed genes, reflecting extensive transcriptional reprogramming and activation of biosynthetic, metabolic, and secretory programs. Strong up-regulation of terminal and lactogenic differentiation markers, including Wap, Csn2, Lpl, Cd36, Lalba, Btn1a1, Xdh, Gata3, and Cebpb, signified maturation into a secretory phenotype. Functional evaluation via gene set enrichment analysis revealed transcriptional enrichment of mTOR, prolactin, insulin, ErbB, and autophagy-associated pathways, consistent with anabolic readiness and terminal differentiation. Conversely, p53, Wnt, and FoxO pathways were down-regulated, marking a transition from proliferation to differentiation. Transcription factors (FoxO1, Zbtb16, and Srebf1) and epigenetic regulators (Gadd45a and Hist1h1e) exhibited dynamic changes, underscoring coordinated transcriptional and chromatin remodeling. Gene set enrichment and protein–protein interaction analyses identified 10 hub genes, Agt, Ccnd1, Igf1, Mki67, Myc, Calm4, Rasgrp1, Cd69, Il6, and Pecam1, as central drivers of differentiation. Clustering of uniquely regulated genes further implicated roles in milk synthesis, protease activity, and lineage stabilization. Together, these findings define a transcriptional framework for lactogenic differentiation in the HC11 cell line model and provide a basis for future mechanistic studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jehad2025b,

title = {Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication},

author = {Mohammad Abdullah Jehad and Lizna M Ali and Vineeta N Pillai and Suresha G Prabhu and Farah Mustafa and Tahir A Rizvi},

editor = {Christian Münz},

doi = {10.1093/femsre/fuaf066},

issn = {1574-6976},

year  = {2026},

date = {2026-01-10},

urldate = {2026-01-10},

journal = {FEMS Microbiology Reviews},

volume = {50},

publisher = {Oxford University Press (OUP)},

abstract = {Retroviruses are exclusive group of positive-sense RNA viruses defined by their ability to reverse transcribe their RNA genome and integrate it into the host’s chromosomal DNA. This distinctive replication strategy enables persistent infection and has profoundly shaped our understanding of molecular biology, gene regulation, and evolution. Retroviruses have contributed to landmark discoveries, including the identification of oncogenes, mechanisms of transcriptional control, and the development of gene therapy vectors. This review provides an updated overview of retroviral molecular biology, emphasizing the coordinated steps of the viral life cycle and emerging insights that are reshaping classical models. It explores virion structure, genome organization, and the interplay of cis-acting sequences and trans-acting factors that govern replication. Special focus is given to recent advances in understanding nuclear trafficking of capsids, spatial dynamics of reverse transcription and integration leading to provirus formation, RNA nuclear export, and selective genome packaging. The structural and functional roles of viral proteins, particularly Gag, are discussed in the context of assembly and maturation. By integrating foundational concepts with new discoveries, this review highlights the molecular sophistication of retroviral replication and identifies outstanding questions that guide future research, with implications extending to antiviral strategies, gene therapy, cancer biology, and evolution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mustafa2025,

title = {miRNA biomarkers for prognosis and therapy monitoring in a multi-ethnic cohort with SARS-CoV-2 infection},

author = {Farah Mustafa and Waqar Ahmad and Bushra Gull and Jasmin Baby and Neena G. Panicker and Thanumol Abdul Khader and Hala Abdul Baki and Erum Rehman and Asif M. Salim and Rubina L. G. Ahmed and Hamda H. Khansaheb and Maya Habous and Laila M. J. A. AlDabal and Soumeya Jaballah and Saif S. Alqassim and Alawi Alsheikh-Ali and Tahir A Rizvi},

doi = {10.1038/s41598-025-15248-6},

issn = {2045-2322},

year  = {2025},

date = {2025-12-00},

urldate = {2025-12-00},

journal = {Sci Rep},

volume = {15},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {This study aimed to identify miRNA-based biomarkers in a multi-ethnic cohort of SARS-CoV-2-infected individuals to enhance preparedness for future variants of concern. A total of 31 healthy controls and 154 infected patients were enrolled, from which 13 matched controls and 38 infected nasal swab samples were analyzed using miRNA sequencing, followed by qRT-PCR validation. Among the 1788 miRNAs detected, 14 differentially expressed miRNAs and four novel miRNAs were identified, with novel-miR-264-5p showing a ≥ 2-fold change. Correlation with clinical markers highlighted several miRNAs as potential prognostic biomarkers. Seven miRNAs, including miR-146b-3p, miR-154-5p, miR-5010-3p, miR-127-3p, miR-335-3p, miR-30c-5p, and miR-202-5p, showed strong prognostic potential. Combined ROC analysis demonstrated that a panel of top-performing miRNAs significantly enhanced diagnostic accuracy (AUC 0.939–0.972; p < 0.0001). Moreover, integrating miRNA biomarkers with clinical parameters further improved performance (AUC = 0.982; p < 0.0001). miR-146b-3p, detected exclusively in infected patients, emerged as a highly specific biomarker. Several nasal miRNAs mirrored blood profiles, highlighting the utility of nasal swabs for non-invasive monitoring. Collectively, these findings suggest that miRNA-based biomarkers, alone or combined with clinical markers, offer a promising platform for COVID-19 prognosis and diagnosis, and lay groundwork for future miRNA-based antiviral strategies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jaballah2025,

title = {Retroviral Vector Technology for Gene Therapy: History, Current Landscape, and Future Prospects},

author = {Soumeya Ali Jaballah and Lizna M Ali and Mohammad Abdullah Jehad and Shaima Akhlaq and Tahir A. Rizvi and Farah Mustafa},

doi = {10.1016/j.jmb.2025.169473},

issn = {0022-2836},

year  = {2025},

date = {2025-12-00},

urldate = {2025-12-00},

journal = {Journal of Molecular Biology},

volume = {437},

number = {24},

publisher = {Elsevier BV},

abstract = {The concept of gene therapy and its practice has been prevalent for over five decades. The first successful retroviral vector-based gene therapy trial took place ∼35 years ago, followed by several setbacks. However, recent years have seen a surge in successes, offering new hope to patients with genetic and other disorders once deemed untreatable. Over the past decade, rapid advancements in molecular biology have led to the development of safer and more effective gene therapy strategies with various gene delivery systems now in use. Among these, viral vectors such as retroviruses, adenoviruses, and adeno-associated viruses are the most widely employed in both research and clinical settings. This is due to their natural efficiency in delivering genetic material into target cells. Among these viral vectors, retroviruses stand out for their unique ability to reverse-transcribe and integrate their genetic material into the host genome, ensuring stable and long-term gene expression. This review highlights advances in retroviral vector development, examining both their therapeutic potential and associated challenges. It also explores strategies for vector production, including transient and stable systems tailored to meet clinical and regulatory demands. Significant progress is discussed in mitigating insertional mutagenesis and vector silencing. As a result, next-generation retroviral vectors with improved safety and efficacy have made it past regulatory approval and are commercially available. Current innovations include replication-competent, non-integrating, integration-retargeted, and hybrid CRISPR/Cas-expressing retroviral vectors undergoing pre-clinical and clinical investigations. This reflects a new era in gene therapy, with retroviral vectors reimagined for greater precision, control, and therapeutic impact.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Khader2024,

title = {Transactivation of the novel 5’ cis-acting element of mouse mammary tumor virus (MMTV) by human retroviral transactivators Tat and Tax},

author = {Thanumol Abdul Khader and Waqar Ahmad and Shaima Akhlaq and Neena Gopinathan Panicker and Bushra Gull and Jasmin Baby and Tahir A. Rizvi and Farah Mustafa},

doi = {10.1038/s42003-024-07139-9},

issn = {2399-3642},

year  = {2024},

date = {2024-12-00},

urldate = {2024-12-00},

journal = {Commun Biol},

volume = {7},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {The mouse mammary tumor virus (MMTV) encodes a 5’ element crucial for transcription of its genome along with the Rem/Rem-responsive element (RmRE) responsible for nuclear export of this unspliced RNA. Whether the 5’ element is Rem-responsive or has any functional interaction with host/viral factors to facilitate MMTV gene expression was tested in this study. Our results reveal that the 5’ element is non-responsive to Rem, but can be transactivated by both HIV Tat and HTLV-1 Tax activators. Reciprocally, MMTV could transactivate not only HIV TAR (similar to HTLV Tax), but also its 5’ element. Furthermore, we reveal involvement of pTEFb, a general elongation factor associated with transactivation by Tat/Tax. This makes MMTV the first betaretrovirus to encode both Rem/RRE and Tat/TAR-Tax/TRE-like transcription regulatory systems. This study should enhance not only our understanding of retrovirus replication and virally-induced cancers/immunodeficiency syndromes, but also development of improved retroviral vectors for human gene therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gull2024,

title = {Identification and characterization of host miRNAs that target the mouse mammary tumour virus (MMTV) genome},

author = {Bushra Gull and Waqar Ahmad and Jasmin Baby and Neena G. Panicker and Thanumol Abdul Khader and Tahir A. Rizvi and Farah Mustafa},

doi = {10.1098/rsob.240203},

issn = {2046-2441},

year  = {2024},

date = {2024-12-00},

urldate = {2024-12-00},

journal = {Open Biol.},

volume = {14},

number = {12},

publisher = {The Royal Society},

abstract = {The intricate interplay between viruses and hosts involves microRNAs (miRNAs) to regulate gene expression by targeting cellular/viral messenger RNAs (mRNAs). Mouse mammary tumour virus (MMTV), the aetiological agent of breast cancer and leukaemia/lymphomas in mice, provides an ideal model to explore how viral and host miRNAs interact to modulate virus replication and tumorigenesis. We previously reported dysregulation of host miRNAs in MMTV-infected mammary glands and MMTV-induced tumours, suggesting a direct interaction between MMTV and miRNAs. To explore this further, we systematically examined all potential interactions between host miRNAs and the MMTV genome using advanced prediction tools. Leveraging miRNA sequencing data from MMTV-expressing cells, we identified dysregulated miRNAs capable of targeting MMTV. Docking analysis validated the interaction of three dysregulated miRNAs with the MMTV genome, followed by confirmation with RNA immunoprecipitation assays. We further identified host targets of these miRNAs using mRNA sequencing data from MMTV-expressing cells. These findings should enhance our understanding of how MMTV replicates and interacts with the host to induce cancer in mice, a model important for cancer research. Given MMTV’s potential zoonosis and association with human breast cancer/lymphomas, if confirmed, our work could further lead to novel miRNA-based antivirals/therapeutics to prevent possible MMTV transmission and associated cancers in humans.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{BABY2024168738,

title = {The Host miR-17-92 Cluster Negatively Regulates Mouse Mammary Tumor Virus (MMTV) Replication Primarily Via Cluster Member miR-92a},

author = {Jasmin Baby and Bushra Gull and Waqar Ahmad and Hala Abdul Baki and Thanumol Abdul Khader and Neena G. Panicker and Shaima Akhlaq and T. A. Rizvi and Farah Mustafa},

url = {https://www.sciencedirect.com/science/article/pii/S0022283624003474},

doi = {https://doi.org/10.1016/j.jmb.2024.168738},

issn = {0022-2836},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Journal of Molecular Biology},

volume = {436},

number = {20},

pages = {168738},

abstract = {The mouse mammary tumor virus (MMTV) is a well-known causative agent of breast cancer in mice. Previously, we have shown that MMTV dysregulates expression of the host miR-17-92 cluster in MMTV-infected mammary glands and MMTV-induced tumors. This cluster, better known as oncomiR-1, is frequently dysregulated in cancers, particularly breast cancer. In this study, our aim was to uncover a functional interaction between MMTV and the cluster. Our results reveal that MMTV expression led to dysregulation of the cluster in both mammary epithelial HC11 and HEK293T cells with the expression of miR-92a cluster member being affected the most. Conversely, overexpression of the whole or partial cluster significantly repressed MMTV expression. Notably, overexpression of cluster member miR-92a alone repressed MMTV expression to the same extent as overexpression of the complete/partial cluster. Inhibition of miR-92a led to nearly a complete restoration of MMTV expression, while deletion/substitution of the miR-92a seed sequence rescued MMTV expression. Dual luciferase assays identified MMTV genomic RNA as the potential target of miR-92a. These results show that the miR-17-92 cluster acts as part of the cell’s well-known miRNA-based anti-viral response to thwart incoming MMTV infection. Thus, this study provides the first evidence highlighting the biological significance of host miRNAs in regulating MMTV replication and potentially influencing tumorigenesis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1371/journal.pbio.3002827,

title = {MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals},

author = {Suresha G. Prabhu and Vineeta N. Pillai and Lizna Mohamed Ali and Valérie Vivet-Boudou and Akhil Chameettachal and Serena Bernacchi and Farah Mustafa and Roland Marquet and T. A. Rizvi},

url = {https://doi.org/10.1371/journal.pbio.3002827},

doi = {10.1371/journal.pbio.3002827},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {PLOS Biology},

volume = {22},

number = {10},

pages = {1-34},

publisher = {Public Library of Science},

abstract = {The packaging of genomic RNA (gRNA) into retroviral particles relies on the specific recognition by the Gag precursor of packaging signals (Psi), which maintain a complex secondary structure through long-range interactions (LRIs). However, it remains unclear whether the binding of Gag to Psi alone is enough to promote RNA packaging and what role LRIs play in this process. Using mouse mammary tumor virus (MMTV), we investigated the effects of mutations in 4 proposed LRIs on gRNA structure and function. Our findings revealed the presence of an unsuspected extended LRI, and hSHAPE revealed that maintaining a wild-type–like Psi structure is crucial for efficient packaging. Surprisingly, filter-binding assays demonstrated that most mutants, regardless of their packaging capability, exhibited significant binding to Pr77Gag, suggesting that Gag binding to Psi is insufficient for efficient packaging. Footprinting experiments indicated that efficient RNA packaging is promoted when Pr77Gag binds to 2 specific sites within Psi, whereas binding elsewhere in Psi does not lead to efficient packaging. Taken together, our results suggest that the 3D structure of the Psi/Pr77Gag complex regulates the assembly of viral particles around gRNA, enabling effective discrimination against other viral and cellular RNAs that may also bind Gag efficiently.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Krishnan2023,

title = {Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging},

author = {A. Krishnan and L. M. Ali and Suresha G Prabhu and V. N. Pillai and A. Chameettachal and Valérie Vivet-Boudou and Serena Bernacchi and F. Mustafa and Roland Marquet and T. A. Rizvi},

doi = {10.1261/rna.079840.123},

issn = {1469-9001},

year  = {2024},

date = {2024-01-00},

urldate = {2024-01-00},

journal = {RNA},

volume = {30},

number = {1},

pages = {68--88},

publisher = {Cold Spring Harbor Laboratory},

abstract = {The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous regions within the 5′ end of the gRNA that assumes a higher order structure harboring several structural motifs. To better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ sequences using genetic, biochemical, and structure–function relationship approaches. Our mutational analysis revealed that the unpaired U85CUG88 stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput selective 2′ hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences, with substitutions in the U85CUG88 stretch, revealed that these mutations had limited structural impact and maintained nucleotides 80–92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our data suggest that the single-stranded U85CUG88 sequence is important during FIV RNA packaging. Filter-binding assays performed using purified FIV Pr50Gag on WT and mutant U85CUG88 ψ RNAs led to reduced levels of Pr50Gag binding to mutant U85CUG88 ψ RNAs, indicating that the U85CUG88 stretch is crucial for ψ RNA–Pr50Gag interactions. Delineating sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of FIV-based vectors for human gene therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tay2023,

title = {HLA class I associations with the severity of COVID-19 disease in the United Arab Emirates},

author = {Guan K. Tay and Halima Alnaqbi and Sarah Chehadeh and Braulio Peramo and Farah Mustafa and Tahir A. Rizvi and Bassam H. Mahboub and Maimunah Uddin and Nawal Alkaabi and Eman Alefishat and Herbert F. Jelinek and Habiba Alsafar and },

editor = {Engin Berber},

doi = {10.1371/journal.pone.0285712},

issn = {1932-6203},

year  = {2023},

date = {2023-09-14},

journal = {PLoS ONE},

volume = {18},

number = {9},

publisher = {Public Library of Science (PLoS)},

abstract = {SARS-CoV-2 appears to induce diverse innate and adaptive immune responses, resulting in different clinical manifestations of COVID-19. Due to their function in presenting viral peptides and initiating the adaptive immune response, certain Human Leucocyte Antigen (HLA) alleles may influence the susceptibility to severe SARS-CoV-2 infection. In this study, 92 COVID-19 patients from 15 different nationalities, with mild (n = 30), moderate (n = 35), and severe (n = 27) SARS-CoV-2 infection, living in the United Arab Emirates (UAE) were genotyped for the Class I HLA -A, -C, and -B alleles using next-generation sequencing (NGS) between the period of May 2020 to June 2020. Alleles and inferred haplotype frequencies in the hospitalized patient group (those with moderate to severe disease, n = 62) were compared to non-hospitalized patients (mild or asymptomatic, n = 30). An interesting trend was noted between the severity of COVID-19 and the HLA-C*04 (P = 0.0077) as well as HLA-B*35 (P = 0.0051) alleles. The class I haplotype HLA-C*04-B*35 was also significantly associated (P = 0.0049). The involvement of inflammation, HLA-C*04, and HLA-B*35 in COVID-19 severity highlights the potential roles of both the adaptive and innate immune responses against SARS-CoV-2. Both alleles have been linked to several respiratory diseases, including pulmonary arterial hypertension along with infections caused by the coronavirus and influenza. This study, therefore, supports the potential use of HLA testing in prioritizing public healthcare interventions for patients at risk of COVID-19 infection and disease progression, in addition to providing personalized immunotherapeutic targets.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37145095,

title = {Differentially-regulated miRNAs in COVID-19: A systematic review},

author = {Waqar Ahmad and Bushra Gull and Jasmin Baby and Neena G Panicker and Thanumol A Khader and Shaima Akhlaq and T. A. Rizvi and F. Mustafa},

doi = {10.1002/rmv.2449},

issn = {1099-1654},

year  = {2023},

date = {2023-07-01},

urldate = {2023-07-01},

journal = {Rev Med Virol},

volume = {33},

number = {4},

pages = {e2449},

abstract = {Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for coronavirus disease of 2019 (COVID-19) that infected more than 760 million people worldwide with over 6.8 million deaths to date. COVID-19 is one of the most challenging diseases of our times due to the nature of its spread, its effect on multiple organs, and an inability to predict disease prognosis, ranging from being completely asymptomatic to death. Upon infection, SARS-CoV-2 alters the host immune response by changing host-transcriptional machinery. MicroRNAs (miRNAs) are regarded as post-transcriptional regulators of gene expression that can be perturbed by invading viruses. Several in vitro and in vivo studies have reported such dysregulation of host miRNA expression upon SARS-CoV-2 infection. Some of this could occur as an anti-viral response of the host to the viral infection. Viruses themselves can counteract that response by mounting their own pro-viral response that facilitates virus infection, an aspect which may cause pathogenesis. Thus, miRNAs could serve as possible disease biomarkers in infected people. In the current review, we have summarised and analysed the existing data about miRNA dysregulation in patients infected with SARS-CoV-2 to determine their concordance between studies, and identified those that could serve as potential biomarkers during infection, disease progression, and death, even in people with other co-morbidities. Having such biomarkers can be vital in not only predicting COVID-19 prognosis, but also the development of novel miRNA-based anti-virals and therapeutics which can become invaluable in case of the emergence of new viral variants with pandemic potential in the future.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37243196,

title = {Global Down-regulation of Gene Expression Induced by Mouse Mammary Tumor Virus (MMTV) in Normal Mammary Epithelial Cells},

author = {Waqar Ahmad and Neena G Panicker and Shaima Akhlaq and Bushra Gull and Jasmin Baby and Thanumol A Khader and T. A. Rizvi and F. Mustafa},

doi = {10.3390/v15051110},

issn = {1999-4915},

year  = {2023},

date = {2023-05-01},

urldate = {2023-05-01},

journal = {Viruses},

volume = {15},

number = {5},

abstract = {Mouse mammary tumor virus (MMTV) is a  that causes breast cancer in mice. The mouse mammary epithelial cells are the most permissive cells for MMTV, expressing the highest levels of virus upon infection and being the ones later transformed by the virus due to repeated rounds of infection/superinfection and integration, leading eventually to mammary tumors. The aim of this study was to identify genes and molecular pathways dysregulated by MMTV expression in mammary epithelial cells. Towards this end, mRNAseq was performed on normal mouse mammary epithelial cells stably expressing MMTV, and expression of host genes was analyzed compared with cells in its absence. The identified differentially expressed genes (DEGs) were grouped on the basis of gene ontology and relevant molecular pathways. Bioinformatics analysis identified 12 hub genes, of which 4 were up-regulated (Angp2, Ccl2, Icam, and Myc) and 8 were down-regulated (Acta2, Cd34, Col1a1, Col1a2, Cxcl12, Eln, Igf1, and Itgam) upon MMTV expression. Further screening of these DEGs showed their involvement in many diseases, especially in breast cancer progression when compared with available data. Gene Set Enrichment Analysis (GSEA) identified 31 molecular pathways dysregulated upon MMTV expression, amongst which the PI3-AKT-mTOR was observed to be the central pathway down-regulated by MMTV. Many of the DEGs and 6 of the 12 hub genes identified in this study showed expression profile similar to that observed in the PyMT mouse model of breast cancer, especially during tumor progression. Interestingly, a global down-regulation of gene expression was observed, where nearly 74% of the DEGs in HC11 cells were repressed by MMTV expression, an observation similar to what was observed in the PyMT mouse model during tumor progression, from hyperplasia to adenoma to early and late carcinomas. Comparison of our results with the Wnt1 mouse model revealed further insights into how MMTV expression could lead to activation of the Wnt1 pathway independent of insertional mutagenesis. Thus, the key pathways, DEGs, and hub genes identified in this study can provide important clues to elucidate the molecular mechanisms involved in MMTV replication, escape from cellular anti-viral response, and potential to cause cell transformation. These data also validate the use of the MMTV-infected HC11 cells as an important model to study early transcriptional changes that could lead to mammary cell transformation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN25,

title = {Understanding Retroviral Life Cycle and its Genomic RNA Packaging},

author = {A. Chameettachal and F. Mustafa and T. A. Rizvi},

doi = {10.1016/j.jmb.2022.167924},

issn = {0022-2836},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {J Mol Biol},

volume = {435},

number = {3},

pages = {167924},

abstract = {Members of the family Retroviridae are important animal and human pathogens. Being obligate parasites, their replication involves a series of steps during which the virus hijacks the cellular machinery. Additionally, many of the steps of retrovirus replication are unique among viruses, including reverse transcription, integration, and specific packaging of their genomic RNA (gRNA) as a dimer. Progress in retrovirology has helped identify several molecular mechanisms involved in each of these steps, but many are still unknown or remain controversial. This review summarizes our present understanding of the molecular mechanisms involved in various stages of retrovirus replication. Furthermore, it provides a comprehensive analysis of our current understanding of how different retroviruses package their gRNA into the assembling virions. RNA packaging in retroviruses holds a special interest because of the uniqueness of packaging a dimeric genome. Dimerization and packaging are highly regulated and interlinked events, critical for the virus to decide whether its unspliced RNA will be packaged as a "genome" or translated into proteins. Finally, some of the outstanding areas of exploration in the field of RNA packaging are highlighted, such as the role of epitranscriptomics, heterogeneity of transcript start sites, and the necessity of functional polyA sequences. An in-depth knowledge of mechanisms that interplay between viral and cellular factors during virus replication is critical in understanding not only the virus life cycle, but also its pathogenesis, and development of new antiretroviral compounds, vaccines, as well as retroviral-based vectors for human gene therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN115,

title = {Expression, purification, and functional characterization of soluble recombinant full-length simian immunodeficiency virus (SIV) Pr55(Gag)},

author = {V. N. Pillai and L. M. Ali and S. G. Prabhu and A. Krishnan and S. Tariq and F. Mustafa and T. A. Rizvi},

doi = {10.1016/j.heliyon.2023.e12892},

issn = {2405-8440 (Print) 2405-8440},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Heliyon},

volume = {9},

number = {1},

pages = {e12892},

abstract = {The simian immunodeficiency virus (SIV) precursor polypeptide Pr55(Gag) drives viral assembly and facilitates specific recognition and packaging of the SIV genomic RNA (gRNA) into viral particles. While several studies have tried to elucidate the role of SIV Pr55(Gag) by expressing its different components independently, studies using full-length SIV Pr55(Gag) have not been conducted, primarily due to the unavailability of purified and biologically active full-length SIV Pr55(Gag). We successfully expressed soluble, full-length SIV Pr55(Gag) with His(6)-tag in bacteria and purified it using affinity and gel filtration chromatography. In the process, we identified within Gag, a second in-frame start codon downstream of a putative Shine-Dalgarno-like sequence resulting in an additional truncated form of Gag. Synonymously mutating this sequence allowed expression of full-length Gag in its native form. The purified Gag assembled into virus-like particles (VLPs) in vitro in the presence of nucleic acids, revealing its biological functionality. In vivo experiments also confirmed formation of functional VLPs, and quantitative reverse transcriptase PCR demonstrated efficient packaging of SIV gRNA by these VLPs. The methodology we employed ensured the availability of >95% pure, biologically active, full-length SIV Pr55(Gag) which should facilitate future studies to understand protein structure and RNA-protein interactions involved during SIV gRNA packaging.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN23,

title = {Detection of SARS-CoV-2 in COVID-19 Patient Nasal Swab Samples Using Signal Processing},

author = {M. A. Ahmad and L. J. A. Olule and M. Meetani and F. A. Sheikh and R. A. Blooshi and N. G. Panicker and F. Mustafa and T. A. Rizvi},

doi = {10.1109/jstsp.2021.3134073},

issn = {1932-4553 (Print) 1932-4553},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {IEEE J Sel Top Signal Process},

volume = {16},

number = {2},

pages = {164-174},

abstract = {This work presents an opto-electrical method that measures the viral nucleocapsid protein and anti-N antibody interactions to differentiate between SARS-CoV-2 negative and positive nasal swab samples. Upon light exposure of the patient nasal swab sample mixed with the anti-N antibody, charge transfer (CT) transitions within the altered protein folds are initiated between the charged amino acids side chain moieties and the peptide backbone that play the role of donor and acceptor groups. A Figure of Merit (FOM) was introduced to correlate the relative variations of the samples with and without antibody at two different voltages. Empirically, SARS-CoV-2 in patient nasal swab samples was detected within two minutes, if an extracted FOM threshold of >1 was achieved; otherwise, the sample wasconsidered negative.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN63,

title = {Impact of the Sinopharm's BBIBP-CorV vaccine in preventing hospital admissions and death in infected vaccinees: Results from a retrospective study in the emirate of Abu Dhabi, United Arab Emirates (UAE)},

author = {F. Ismail AlHosani and A. Eduardo Stanciole and B. Aden and A. Timoshkin and O. Najim and W. Abbas Zaher and F. AlSayedsaleh AlDhaheri and S. Al Mazrouie and T. A. Rizvi and F. Mustafa},

doi = {10.1016/j.vaccine.2022.02.039},

issn = {0264-410X (Print) 0264-410x},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Vaccine},

volume = {40},

number = {13},

pages = {2003-2010},

abstract = {BACKGROUND: This is a community-based, retrospective, observational study conducted to determine effectiveness of the BBIBP-CorV inactivated vaccine in the real-world setting against hospital admissions and death. STUDY DESIGN: Study participants were selected from 214,940 PCR-positive cases of COVID-19 reported to the Department of Health, Abu Dhabi Emirate, United Arab Emirates (UAE) between September 01, 2020 and May 1, 2021. Of these, 176,640 individuals were included in the study who were aged ≥ 15 years with confirmed COVID-19 positive status who had records linked to their vaccination status. Those with incomplete or missing records were excluded (n = 38,300). Study participants were divided into three groups depending upon their vaccination status: fully vaccinated (two doses), partially vaccinated (single dose), and non-vaccinated. Study outcomes included COVID-19-related admissions to hospital general and critical care wards and death. Vaccine effectiveness for each outcome was based on the incidence density per 1000 person-years. RESULTS: The fully-, partially- and non-vaccinated groups included 62,931, 21,768 and 91,941 individuals, respectively. Based on the incidence rate ratios, the vaccine effectiveness in fully vaccinated individuals was 80%, 92%, and 97% in preventing COVID-19-related hospital admissions, critical care admissions, and death, respectively, when compared to the non-vaccinated group. No protection was observed for critical and non-critical care hospital admissions for the partially vaccinated group, while some protection against death was apparent, although statistically insignificant. CONCLUSIONS: In a COVID-19 pandemic, use of the Sinopharm BBIBP-CorV inactivated vaccine is effective in preventing severe disease and death in a two-dose regimen. Lack of protection with the single dose may be explained by insufficient seroconversion and/or neutralizing antibody responses, behavioral factors (i.e., false sense of protection), and/or other biological factors (emergence of variants, possibility of reinfection, duration of vaccine protection, etc.).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hamouda2021,

title = {Wastewater surveillance for SARS-CoV-2: Lessons learnt from recent studies to define future applications},

author = {Mohamed Hamouda and Farah Mustafa and Munjed Maraqa and Tahir A Rizvi and Ashraf Aly Hassan},

doi = {10.1016/j.scitotenv.2020.143493},

issn = {0048-9697},

year  = {2021},

date = {2021-03-00},

urldate = {2021-03-00},

journal = {Science of The Total Environment},

volume = {759},

publisher = {Elsevier BV},

abstract = {Wastewater-based epidemiology (WBE) is successful in the detection of the spread of SARS-CoV-2. This review examines the methods used and results of recent studies on the quantification of SARS-CoV-2 in wastewater. WBE becomes essential, especially with virus transmission path uncertainty, limitations on the number of clinical tests that could be conducted, and a relatively long period for infected people to show symptoms. Wastewater surveillance was used to show the effect of lockdown on the virus spread. A WBE framework tailored for SARS-CoV-2 that incorporates lessons learnt from the reviewed studies was developed. Results of the review helped outline challenges facing the detection of SARS-CoV-2 in wastewater samples. A comparison between the various studies with regards to sample concentration and virus quantification was conducted. Five different primers sets were used for qPCR quantification; however, due to limited data availability, there is no consensus on the most sensitive primer. Correlating the slope of the relationship between the number of gene copies vs. the cumulative number of infections normalized to the total population served with the average new cases, suggests that qPCR results could help estimating the number of new infections. The correlation is improved when a lag period was introduced to account for asymptomatic infections. Based on lessons learnt from recent studies, it is recommended that future applications should consider the following: 1) ensuring occupational safety in managing sewage collection and processing, 2) evaluating the effectiveness of greywater disinfection, 3) measuring viral RNA decay due to biological and chemical activities during collection and treatment, 4) assessing the effectiveness of digital PCR, and 5) conducting large scale international studies that follow standardized protocols.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN14,

title = {Optical Detection of SARS-CoV-2 Utilizing Antigen-Antibody Binding Interactions},

author = {M. A. Ahmad and F. Mustafa and N. Panicker and T. A. Rizvi},

doi = {10.3390/s21196596},

issn = {1424-8220},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Sensors (Basel)},

volume = {21},

number = {19},

abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease (COVID-19) pandemic, is sweeping the world today. This study investigates the optical detection of SARS-CoV-2, utilizing the antigen-antibody binding interactions utilizing a light source from a smart phone and a portable spectrophotometer. The proof-of-concept is shown by detecting soluble preparations of spike protein subunits from SARS-CoV-2, followed by detection of the actual binding potential of the SARS-CoV-2 proteins with their corresponding antigens. The measured binding interactions for RBD and NCP proteins with their corresponding antibodies under different conditions have been measured and analyzed. Based on these observations, a "hump or spike" in light intensity is observed when a specific molecular interaction takes place between two proteins. The optical responses could further be analyzed using the principle component analysis technique to enhance and allows precise detection of the specific target in a multi-protein mixture.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN40,

title = {A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag},

author = {A. Chameettachal and V. Vivet-Boudou and F. N. N. Pitchai and V. N. Pillai and L. M. Ali and A. Krishnan and S. Bernacchi and F. Mustafa and R. Marquet and T. A. Rizvi},

doi = {10.1093/nar/gkab223},

issn = {0305-1048 (Print) 0305-1048},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Nucleic Acids Res},

volume = {49},

number = {8},

pages = {4668-4688},

abstract = {Retroviral RNA genome (gRNA) harbors cis-acting sequences that facilitate its specific packaging from a pool of other viral and cellular RNAs by binding with high-affinity to the viral Gag protein during virus assembly. However, the molecular intricacies involved during selective gRNA packaging are poorly understood. Binding and footprinting assays on mouse mammary tumor virus (MMTV) gRNA with purified Pr77Gag along with in cell gRNA packaging study identified two Pr77Gag binding sites constituting critical, non-redundant packaging signals. These included: a purine loop in a bifurcated stem-loop containing the gRNA dimerization initiation site, and the primer binding site (PBS). Despite these sites being present on both unspliced and spliced RNAs, Pr77Gag specifically bound to unspliced RNA, since only that could adopt the native bifurcated stem-loop structure containing looped purines. These results map minimum structural elements required to initiate MMTV gRNA packaging, distinguishing features that are conserved amongst divergent retroviruses from those perhaps unique to MMTV. Unlike purine-rich motifs frequently associated with packaging signals, direct involvement of PBS in gRNA packaging has not been documented in retroviruses. These results enhance our understanding of retroviral gRNA packaging/assembly, making it not only a target for novel therapeutic interventions, but also development of safer gene therapy vectors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN38,

title = {A Stretch of Unpaired Purines in the Leader Region of Simian Immunodeficiency Virus (SIV) Genomic RNA is Critical for its Packaging into Virions},

author = {V. N. Pillai and L. M. Ali and S. G. Prabhu and A. Krishnan and A. Chameettachal and F. N. N. Pitchai and F. Mustafa and T. A. Rizvi},

doi = {10.1016/j.jmb.2021.167293},

issn = {0022-2836},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {J Mol Biol},

volume = {433},

number = {23},

pages = {167293},

abstract = {Simian immunodeficiency virus (SIV) is an important lentivirus used as a non-human primate model to study HIV replication, and pathogenesis of human AIDS, as well as a potential vector for human gene therapy. This study investigated the role of single-stranded purines (ssPurines) as potential genomic RNA (gRNA) packaging determinants in SIV replication. Similar ssPurines have been implicated as important motifs for gRNA packaging in many retroviruses like, HIV-1, MPMV, and MMTV by serving as Gag binding sites during virion assembly. In examining the secondary structure of the SIV 5' leader region, as recently deduced using SHAPE methodology, we identified four specific stretches of ssPurines (I-IV) in the region that harbors major packaging determinants of SIV. The significance of these ssPurine motifs were investigated by mutational analysis coupled with a biologically relevant single round of replication assay. These analyses revealed that while ssPurine II was essential, the others (ssPurines I, III, & IV) did not significantly contribute to SIV gRNA packaging. Any mutation in the ssPurine II, such as its deletion or substitution, or other mutations that caused base pairing of ssPurine II loop resulted in near abrogation of RNA packaging, further substantiating the crucial role of ssPurine II and its looped conformation in SIV gRNA packaging. Structure prediction analysis of these mutants further corroborated the biological results and further revealed that the unpaired nature of ssPurine II is critical for its function during SIV RNA packaging perhaps by enabling it to function as a specific binding site for SIV Gag.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN19,

title = {Identification of Pr78(Gag) Binding Sites on the Mason-Pfizer Monkey Virus Genomic RNA Packaging Determinants},

author = {F. N. N. Pitchai and A. Chameettachal and V. Vivet-Boudou and L. M. Ali and V. N. Pillai and A. Krishnan and S. Bernacchi and F. Mustafa and R. Marquet and T. A. Rizvi},

doi = {10.1016/j.jmb.2021.166923},

issn = {0022-2836},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {J Mol Biol},

volume = {433},

number = {10},

pages = {166923},

abstract = {How retroviral Gag proteins recognize the packaging signals (Psi) on their genomic RNA (gRNA) is a key question that we addressed here using Mason-Pfizer monkey virus (MPMV) as a model system by combining band-shift assays and footprinting experiments. Our data show that Pr78(Gag) selects gRNA against spliced viral RNA by simultaneously binding to two single stranded loops on the MPMV Psi RNA: (1) a large purine loop (ssPurines), and (2) a loop which partially overlaps with a mostly base-paired purine repeat (bpPurines) and extends into a GU-rich binding motif. Importantly, this second Gag binding site is located immediately downstream of the major splice donor (mSD) and is thus absent from the spliced viral RNAs. Identifying elements crucial for MPMV gRNA packaging should help in understanding not only the mechanism of virion assembly by retroviruses, but also facilitate construction of safer retroviral vectors for human gene therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN36,

title = {Role of Purine-Rich Regions in Mason-Pfizer Monkey Virus (MPMV) Genomic RNA Packaging and Propagation},

author = {L. M. Ali and F. N. N. Pitchai and V. Vivet-Boudou and A. Chameettachal and A. Jabeen and V. N. Pillai and F. Mustafa and R. Marquet and T. A. Rizvi},

doi = {10.3389/fmicb.2020.595410},

issn = {1664-302X (Print) 1664-302x},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Front Microbiol},

volume = {11},

pages = {595410},

abstract = {A distinguishing feature of the Mason-Pfizer monkey virus (MPMV) packaging signal RNA secondary structure is a single-stranded purine-rich sequence (ssPurines) in close vicinity to a palindromic stem loop (Pal SL) that functions as MPMV dimerization initiation site (DIS). However, unlike other retroviruses, MPMV contains a partially base-paired repeat sequence of ssPurines (bpPurines) in the adjacent region. Both purine-rich sequences have earlier been proposed to act as potentially redundant Gag binding sites to initiate the process of MPMV genomic RNA (gRNA) packaging. The objective of this study was to investigate the biological significance of ssPurines and bpPurines in MPMV gRNA packaging by systematic mutational and biochemical probing analyses. Deletion of either ssPurines or bpPurines individually had no significant effect on MPMV gRNA packaging, but it was severely compromised when both sequences were deleted simultaneously. Selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) analysis of the mutant RNAs revealed only mild effects on structure by deletion of either ssPurines or bpPurines, while the structure was dramatically affected by the two simultaneous deletions. This suggests that ssPurines and bpPurines play a redundant role in MPMV gRNA packaging, probably as Gag binding sites to facilitate gRNA capture and encapsidation. Interestingly, the deletion of bpPurines revealed an additional severe defect on RNA propagation that was independent of the presence or absence of ssPurines or the gRNA structure of the region. These findings further suggest that the bpPurines play an additional role in the early steps of MPMV replication cycle that is yet to be identified.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN22,

title = {Electrical detection of blood cells in urine},

author = {N. Nasir and S. Raji and F. Mustafa and T. A. Rizvi and Z. Al Natour and A. Hilal-Alnaqbi and M. Al Ahmad},

doi = {10.1016/j.heliyon.2019.e03102},

issn = {2405-8440 (Print) 2405-8440},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Heliyon},

volume = {6},

number = {1},

pages = {e03102},

abstract = {Available methods for detecting blood in the urine (hematuria) can be problematic since results can be influenced by many factors in patients and in the lab settings, resulting in false positive or false negative results. This necessitates the development of new, accurate and easy-access methods that save time and effort. This study demonstrates a label-free and accurate method for detecting the presence of red and white blood cells (RBCs and WBCs) in urine by measuring the changes in the dielectric properties of urine upon increasing concentrations of both cell types. The current method could detect changes in the electrical properties of fresh urine over a short time interval, making this method suitable for detecting changes that cannot be recognized by conventional methods. Correcting for these changes enabled the detection of a minimum cell concentration of 10(2) RBCs per ml which is not possible by conventional methods used in the labs except for the semi-quantitative method that can detect 50 RBCs per ml, but it is a lengthy and involved procedure, not suitable for high volume labs. This ability to detect very small amount of both types of cells makes the proposed technique an attractive tool for detecting hematuria, the presence of which is indicative of problems in the excretory system.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN41,

title = {The Large Action of Chlorpromazine: Translational and Transdisciplinary Considerations in the Face of COVID-19},

author = {E. Stip and T. A. Rizvi and F. Mustafa and S. Javaid and S. Aburuz and N. N. Ahmed and K. Abdel Aziz and D. Arnone and A. Subbarayan and F. Al Mugaddam and G. Khan},

doi = {10.3389/fphar.2020.577678},

issn = {1663-9812 (Print) 1663-9812},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Front Pharmacol},

volume = {11},

pages = {577678},

abstract = {Coronavirus disease 2019 (COVID-19) is a severe acute respiratory syndrome (SARS) in humans that is caused by SARS-associated coronavirus type 2 (SARS-CoV-2). In the context of COVID-19, several aspects of the relations between psychiatry and the pandemic due to the coronavirus have been described. Some drugs used as antiviral medication have neuropsychiatric side effects, and conversely some psychotropic drugs have antiviral properties. Chlorpromazine (CPZ, Largactil(®)) is a well-established antipsychotic medication that has recently been proposed to have antiviral activity against SARS-CoV-2. This review aims to 1) inform health care professionals and scientists about the history of CPZ use in psychiatry and its potential anti- SARS-CoV-2 activities 2) inform psychiatrists about its potential anti-SARS-CoV-2 activities, and 3) propose a research protocol for investigating the use of CPZ in the treatment of COVID-19 during the potential second wave. The history of CPZ's discovery and development is described in addition to the review of literature from published studies within the discipline of virology related to CPZ. The early stages of infection with coronavirus are critical events in the course of the viral cycle. In particular, viral entry is the first step in the interaction between the virus and the cell that can initiate, maintain, and spread the infection. The possible mechanism of action of CPZ is related to virus cell entry via clathrin-mediated endocytosis. Therefore, CPZ could be useful to treat COVID-19 patients provided that its efficacy is evaluated in adequate and well-conducted clinical trials. Interestingly, clinical trials of very good quality are in progress. However, more information is still needed about the appropriate dosage regimen. In short, CPZ repositioning is defined as a new use beyond the field of psychiatry.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN9,

title = {SARS-CoV-2/COVID-19: Viral Genomics, Epidemiology, Vaccines, and Therapeutic Interventions},

author = {M. Uddin and F. Mustafa and T. A. Rizvi and T. Loney and H. A. Suwaidi and A. H. H. Al-Marzouqi and A. K. Eldin and N. Alsabeeha and T. E. Adrian and C. Stefanini and N. Nowotny and A. Alsheikh-Ali and A. C. Senok},

doi = {10.3390/v12050526},

issn = {1999-4915},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Viruses},

volume = {12},

number = {5},

abstract = {The COVID-19 pandemic is due to infection caused by the novel SARS-CoV-2 virus that impacts the lower respiratory tract. The spectrum of symptoms ranges from asymptomatic infections to mild respiratory symptoms to the lethal form of COVID-19 which is associated with severe pneumonia, acute respiratory distress, and fatality. To address this global crisis, up-to-date information on viral genomics and transcriptomics is crucial for understanding the origins and global dispersion of the virus, providing insights into viral pathogenicity, transmission, and epidemiology, and enabling strategies for therapeutic interventions, drug discovery, and vaccine development. Therefore, this review provides a comprehensive overview of COVID-19 epidemiology, genomic etiology, findings from recent transcriptomic map analysis, viral-human protein interactions, molecular diagnostics, and the current status of vaccine and novel therapeutic intervention development. Moreover, we provide an extensive list of resources that will help the scientific community access numerous types of databases related to SARS-CoV-2 OMICs and approaches to therapeutics related to COVID-19 treatment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Krishnan2019,

title = {Purification and Functional Characterization of a Biologically Active Full-Length Feline Immunodeficiency Virus (FIV) Pr50Gag},

author = {A. Krishnan and Vineeta N. Pillai and Akhil Chameettachal and Lizna Mohamed Ali and Fathima Nuzra Nagoor Pitchai and Saeed Tariq and Farah Mustafa and Roland Marquet and Tahir A. Rizvi},

doi = {10.3390/v11080689},

issn = {1999-4915},

year  = {2019},

date = {2019-08-00},

urldate = {2019-08-00},

journal = {Viruses},

volume = {11},

number = {8},

publisher = {MDPI AG},

abstract = {<jats:p>The feline immunodeficiency virus (FIV) full-length Pr50Gag precursor is a key player in the assembly of new viral particles. It is also a critical component of the efficient selection and packaging of two copies of genomic RNA (gRNA) into the newly formed virus particles from a wide pool of cellular and spliced viral RNA. To understand the molecular mechanisms involved during FIV gRNA packaging, we expressed the His6-tagged and untagged recombinant FIV Pr50Gag protein both in eukaryotic and prokaryotic cells. The recombinant Pr50Gag-His6-tag fusion protein was purified from soluble fractions of prokaryotic cultures using immobilized metal affinity chromatography (IMAC). This purified protein was able to assemble in vitro into virus-like particles (VLPs), indicating that it preserved its ability to oligomerize/multimerize. Furthermore, VLPs formed in eukaryotic cells by the FIV full-length Pr50Gag both in the presence and absence of His6-tag could package FIV sub-genomic RNA to similar levels, suggesting that the biological activity of the recombinant full-length Pr50Gag fusion protein was retained in the presence of His6-tag at the carboxy terminus. Successful expression and purification of a biologically active, recombinant full-length Pr50Gag-His6-tag fusion protein will allow study of the intricate RNA-protein interactions involved during FIV gRNA encapsidation.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN53,

title = {Stabilizing role of structural elements within the 5´ Untranslated Region (UTR) and gag sequences in Mason-Pfizer monkey virus (MPMV) genomic RNA packaging},

author = {R. M. Kalloush and V. Vivet-Boudou and L. M. Ali and V. N. Pillai and F. Mustafa and R. Marquet and T. A. Rizvi},

doi = {10.1080/15476286.2019.1572424},

issn = {1547-6286 (Print) 1547-6286},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {RNA Biol},

volume = {16},

number = {5},

pages = {612-625},

abstract = {The Mason-Pfizer monkey virus (MPMV) genomic RNA (gRNA) packaging signal is a highly-structured element with several stem-loops held together by two phylogenetically conserved long-range interactions (LRIs) between U5 and gag complementary sequences. These LRIs play a critical role in maintaining the structure of the 5´ end of the MPMV gRNA. Thus, one could hypothesize that the overall RNA secondary structure of this region is further architecturally held together by three other stem loops (SL3, Gag SL1, and Gag SL2) comprising of sequences from the distal parts of the 5´untranslated region (5' UTR) to ~ 120 nucleotides into gag, excluding gag sequences involved in forming the U5-Gag LRIs. To provide functional evidence for the biological significance of these stem loops during gRNA encapsidation, these structural motifs were mutated and their effects on MPMV RNA packaging and propagation were tested in a single round trans-complementation assay. The mutant RNA structures were further studied by high throughput SHAPE (hSHAPE) assay. Our results reveal that sequences involved in forming these three stem loops do not play crucial roles at an individual level during MPMV gRNA packaging or propagation. Further structure-function analysis indicates that the U5-Gag LRIs have a more important architectural role in stabilizing the higher order structure of the 5´ UTR than the three stem loops which have a more secondary and perhaps indirect role in stabilizing the overall RNA secondary structure of the region. Our work provides a better understanding of the molecular interactions that take place during MPMV gRNA packaging.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN32,

title = {A cis-Acting Element Downstream of the Mouse Mammary Tumor Virus Major Splice Donor Critical for RNA Elongation and Stability},

author = {S. Akhlaq and N. G. Panicker and P. S. Philip and L. M. Ali and J. P. Dudley and T. A. Rizvi and F. Mustafa},

doi = {10.1016/j.jmb.2018.08.025},

issn = {0022-2836 (Print) 0022-2836},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {J Mol Biol},

volume = {430},

number = {21},

pages = {4307-4324},

abstract = {BACKGROUND: The mouse mammary tumor virus (MMTV) encodes a functional signal peptide, a cleavage product of envelope and Rem proteins. Signal peptide interacts with a 3' cis-acting RNA element, the Rem-responsive element (RmRE), to facilitate expression of both unspliced genomic (gRNA) and spliced mRNAs. An additional RmRE has been proposed at the 5' end of the genome, facilitating nuclear export of the unspliced gRNA, whereas the 3' RmRE could facilitate translation of all other mRNAs, including gRNA. RESULTS: To address this hypothesis, a series of mutations were introduced into a 24-nt region found exclusively in the unspliced gRNA. Mutant clones using MMTV or human cytomegalovirus promoters were tested in both transient and stable transfections to determine their effect on gRNA nuclear export, stability, and translation. Nuclear export of the gRNA was affected only in a small mutant subset in stably transfected Jurkat T cells. Quantitative real-time RT-PCR of actinomycin D-treated cells expressing MMTV revealed that multiple mutants were severely compromised for RNA expression and stability. Both genomic and spliced nuclear RNAs were reduced, leading to abrogation of Gag and Env protein expressed from unspliced and spliced mRNAs, respectively. RT-PCRs with multiple primer pairs indicated failure to elongate genomic MMTV transcripts beyond ~500 nt compared to the wild type in a cell line-dependent manner. CONCLUSIONS: MMTV contains a novel cis-acting element downstream of the major splice donor critical for facilitating MMTV gRNA elongation and stability. Presence of a mirror repeat within the element may represent important viral/host factor binding site(s) within MMTV gRNA.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN88,

title = {Biochemical and Functional Characterization of Mouse Mammary Tumor Virus Full-Length Pr77(Gag) Expressed in Prokaryotic and Eukaryotic Cells},

author = {A. Chameettachal and V. N. Pillai and L. M. Ali and F. N. N. Pitchai and M. T. Ardah and F. Mustafa and R. Marquet and T. A. Rizvi},

doi = {10.3390/v10060334},

issn = {1999-4915},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {Viruses},

volume = {10},

number = {6},

abstract = {The mouse mammary tumor virus (MMTV) Pr77(Gag) polypeptide is an essential retroviral structural protein without which infectious viral particles cannot be formed. This process requires specific recognition and packaging of dimerized genomic RNA (gRNA) by Gag during virus assembly. Most of the previous work on retroviral assembly has used either the nucleocapsid portion of Gag, or other truncated Gag derivatives—not the natural substrate for virus assembly. In order to understand the molecular mechanism of MMTV gRNA packaging process, we expressed and purified full-length recombinant Pr77(Gag)-His₆-tag fusion protein from soluble fractions of bacterial cultures. We show that the purified Pr77(Gag)-His₆-tag protein retained the ability to assemble virus-like particles (VLPs) in vitro with morphologically similar immature intracellular particles. The recombinant proteins (with and without His₆-tag) could both be expressed in prokaryotic and eukaryotic cells and had the ability to form VLPs in vivo. Most importantly, the recombinant Pr77(Gag)-His₆-tag fusion proteins capable of making VLPs in eukaryotic cells were competent for packaging sub-genomic MMTV RNAs. The successful expression and purification of a biologically active, full-length MMTV Pr77(Gag) should lay down the foundation towards performing RNA–protein interaction(s), especially for structure-function studies and towards understanding molecular intricacies during MMTV gRNA packaging and assembly processes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN90,

title = {The bifurcated stem loop 4 (SL4) is crucial for efficient packaging of mouse mammary tumor virus (MMTV) genomic RNA},

author = {F. Mustafa and V. Vivet-Boudou and A. Jabeen and L. M. Ali and R. M. Kalloush and R. Marquet and T. A. Rizvi},

doi = {10.1080/15476286.2018.1486661},

issn = {1547-6286 (Print) 1547-6286},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {RNA Biol},

volume = {15},

number = {8},

pages = {1047-1059},

abstract = {Packaging the mouse mammary tumor virus (MMTV) genomic RNA (gRNA) requires the entire 5' untranslated region (UTR) in conjunction with the first 120 nucleotides of the gag gene. This region includes several palindromic (pal) sequence(s) and stable stem loops (SLs). Among these, stem loop 4 (SL4) adopts a bifurcated structure consisting of three stems, two apical loops, and an internal loop. Pal II, located in one of the apical loops, mediates gRNA dimerization, a process intricately linked to packaging. We thus hypothesized that the bifurcated SL4 structure could constitute the major gRNA packaging determinant. To test this hypothesis, the two apical loops and the flanking sequences forming the bifurcated SL4 were individually mutated. These mutations all had deleterious effects on gRNA packaging and propagation. Next, single and compensatory mutants were designed to destabilize then recreate the bifurcated SL4 structure. A structure-function analysis using bioinformatics predictions and RNA chemical probing revealed that mutations that led to the loss of the SL4 bifurcated structure abrogated RNA packaging and propagation, while compensatory mutations that recreated the native SL4 structure restored RNA packaging and propagation to wild type levels. Altogether, our results demonstrate that SL4 constitutes the principal packaging determinant of MMTV gRNA. Our findings further suggest that SL4 acts as a structural switch that can not only differentiate between RNA for translation versus packaging/dimerization, but its location also allows differentiation between spliced and unspliced RNAs during gRNA encapsidation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN51,

title = {Expression, purification, and characterization of biologically active full-length Mason-Pfizer monkey virus (MPMV) Pr78(Gag)},

author = {F. N. N. Pitchai and L. Ali and V. N. Pillai and A. Chameettachal and S. S. Ashraf and F. Mustafa and R. Marquet and T. A. Rizvi},

doi = {10.1038/s41598-018-30142-0},

issn = {2045-2322},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {Sci Rep},

volume = {8},

number = {1},

pages = {11793},

abstract = {MPMV precursor polypeptide Pr78(Gag) orchestrates assembly and packaging of genomic RNA (gRNA) into virus particles. Therefore, we have expressed recombinant full-length Pr78(Gag) either with or without His(6)-tag in bacterial as well as eukaryotic cultures and purified the recombinant protein from soluble fractions of the bacterial cultures. The recombinant Pr78(Gag) protein has the intrinsic ability to assemble in vitro to form virus like particles (VLPs). Consistent with this observation, the recombinant protein could form VLPs in both prokaryotes and eukaryotes. VLPs formed in eukaryotic cells by recombinant Pr78(Gag) with or without His(6)-tag can encapsidate MPMV transfer vector RNA, suggesting that the inclusion of the His(6)-tag to the full-length Pr78(Gag) did not interfere with its expression or biological function. This study demonstrates the expression and purification of a biologically active, recombinant Pr78(Gag), which should pave the way to study RNA-protein interactions involved in the MPMV gRNA packaging process.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{AlAhmad2018b,

title = {Electrical Characterization of Normal and Cancer Cells},

author = {Mahmoud Al Ahmad and Zeina Al Natour and Farah Mustafa and Tahir A. Rizvi},

doi = {10.1109/access.2018.2830883},

issn = {2169-3536},

year  = {2018},

date = {2018-00-00},

urldate = {2018-00-00},

journal = {IEEE Access},

volume = {6},

pages = {25979--25986},

publisher = {Institute of Electrical and Electronics Engineers (IEEE)},

abstract = {In this paper, we characterize and discriminate between normal and cancer cells from three different tissue types, liver, lung, and breast, using capacitance–voltage-based extracted set of parameters. Cells from each type of cancer cell line were suspended in a liquid media either individually or as mixtures with their normal counterparts. Empirically, normal cells were observed to exhibit higher dielectric constants when compared to cancer cells from the same tissue. Moreover, adding cancer cells to normal cells was observed to increase the capacitance of normal cells, and the extent of this increase varied with the type of tissue tested with the lung cells causing the greatest change. This shows that the cancer cells of different cell origin possess their own signature electrical parameters, especially when compared with their normal counterparts, and that cancer cell seems to affect normal cells in a different manner, depending upon the tissue type. It was also noticed that the cells (both cancer and normal) exhibited a higher dielectric value as per the following order (from least to most): breast, lung, and liver. The changes in electrical parameters from normal to cancer state were explained not only by the modification of its physiological and biochemical properties but also by the morphological changes. This approach paves the way for exploring unique electrical signatures of normal and their corresponding cancer cells to enable their detection and discrimination.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{AlAhmad2018,

title = {Detection of Mouse Mammary Tumor Virus (MMTV) Particles in an Immortalized T Cell Line Based on Electrical Parameters},

author = {Mahmoud Al Ahmad and Shaima Akhlaq and Tahir A. Rizvi and Farah Mustafa},

doi = {10.1109/access.2018.2874987},

issn = {2169-3536},

year  = {2018},

date = {2018-00-00},

urldate = {2018-00-00},

journal = {IEEE Access},

volume = {6},

pages = {63597--63605},

publisher = {Institute of Electrical and Electronics Engineers (IEEE)},

abstract = {Label-free detection and characterization of cells producing virus particles is a highly desirable property that can pave the way for direct detection of virally infected cells in body fluids, tissues, and eventually in infected individuals. Identification of such properties can also provide a better understanding of the growth and/or evolution of virally infected cells in real-time experimental setups. This paper takes a closer look at the electrical properties of an immortalized T cell line capable of producing virus particles along with its non-virus producing control cell line using capacitance-voltage (C-V) measurements. In addition, two other important control cell lines were also included in which the ability of the cells to produce virus particles was abrogated by using genetic mutations. The conducted C-V measurements revealed that it is possible to electrically differentiate between these different cell lines. The cells producing wild-type (WT) virus particles could be distinguished from the control cells in which no DNA was introduced and, hence, were incapable of producing any virus particles. Interestingly, the cells in which two mutant DNAs were introduced that abrogated their ability to produce virus particles showed a similar electrical profile to each other, yet distinct from that of the cells producing the WT virus. These results clearly demonstrate that the electrical technique was able to distinguish between cells expressing virus particles versus cells that do not express virus particles. Data analysis revealed a twofold difference in the interaction capacitance between WT and mutant cells. Characterizing cells using electrical parameters are not laborious and lengthy, as is the case with conventional biochemical methods that typically take several days. Together, these data suggest that it is possible to electrically characterize and differentiate virally infected cells from uninfected cells. It is our hope that eventually these observations co...},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN18,

title = {Electrical characterization of DNA supported on nitrocellulose membranes},

author = {M. A. Ahmad and R. M. Milhem and N. G. Panicker and T. A. Rizvi and F. Mustafa},

doi = {10.1038/srep29089},

issn = {2045-2322},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Sci Rep},

volume = {6},

pages = {29089},

abstract = {Integrated DNA-based nanoscale electronic devices will enable the continued realization of Moore's Law at the level of functional devices and systems. In this work, the electrical characterization of single and complementary base paired DNA has been directly measured and investigated via the use of nitrocellulose membranes. A radio frequency DAKS-3.5 was used to measure the reflection coefficients of different DNA solutions dotted onto nitrocellulose membranes. Each DNA solution was exposed to a radio frequency signal with a power of 10 dBm and with a sweep from 200 MHz up to 13.6 GHz. The conducted measurements show some distinctions between the homomeric and complementary bases due to their different electrical polarization. As revealed from the measurements conducted, with the addition of DNA oligonucleotides, the measured capacitance increased when compared with buffer medium alone. The DNA molecules could be modeled as dielectric material that can hold electrical charges. Furthermore, the complementary paired DNA molecule-based inks solutions had a higher capacitance value compared with single DNA molecules (A, C, G and T) solutions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN101,

title = {Electrical detection and quantification of single and mixed DNA nucleotides in suspension},

author = {M. A. Ahmad and N. G. Panicker and T. A. Rizvi and F. Mustafa},

doi = {10.1038/srep34016},

issn = {2045-2322},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Sci Rep},

volume = {6},

pages = {34016},

abstract = {High speed sequential identification of the building blocks of DNA, (deoxyribonucleotides or nucleotides for short) without labeling or processing in long reads of DNA is the need of the hour. This can be accomplished through exploiting their unique electrical properties. In this study, the four different types of nucleotides that constitute a DNA molecule were suspended in a buffer followed by performing several types of electrical measurements. These electrical parameters were then used to quantify the suspended DNA nucleotides. Thus, we present a purely electrical counting scheme based on the semiconductor theory that allows one to determine the number of nucleotides in a solution by measuring their capacitance-voltage dependency. The nucleotide count was observed to be similar to the multiplication of the corresponding dopant concentration and debye volume after de-embedding the buffer contribution. The presented approach allows for a fast and label-free quantification of single and mixed nucleotides in a solution.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN15,

title = {Cross- and Co-Packaging of Retroviral RNAs and Their Consequences},

author = {L. M. Ali and T. A. Rizvi and F. Mustafa},

doi = {10.3390/v8100276},

issn = {1999-4915},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Viruses},

volume = {8},

number = {10},

abstract = {Retroviruses belong to the family Retroviridae and are ribonucleoprotein (RNP) particles that contain a dimeric RNA genome. Retroviral particle assembly is a complex process, and how the virus is able to recognize and specifically capture the genomic RNA (gRNA) among millions of other cellular and spliced retroviral RNAs has been the subject of extensive investigation over the last two decades. The specificity towards RNA packaging requires higher order interactions of the retroviral gRNA with the structural Gag proteins. Moreover, several retroviruses have been shown to have the ability to cross-/co-package gRNA from other retroviruses, despite little sequence homology. This review will compare the determinants of gRNA encapsidation among different retroviruses, followed by an examination of our current understanding of the interaction between diverse viral genomes and heterologous proteins, leading to their cross-/co-packaging. Retroviruses are well-known serious animal and human pathogens, and such a cross-/co-packaging phenomenon could result in the generation of novel viral variants with unknown pathogenic potential. At the same time, however, an enhanced understanding of the molecular mechanisms involved in these specific interactions makes retroviruses an attractive target for anti-viral drugs, vaccines, and vectors for human gene therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN77,

title = {Packaging of Mason-Pfizer monkey virus (MPMV) genomic RNA depends upon conserved long-range interactions (LRIs) between U5 and gag sequences},

author = {R. M. Kalloush and V. Vivet-Boudou and L. M. Ali and F. Mustafa and R. Marquet and T. A. Rizvi},

doi = {10.1261/rna.055731.115},

issn = {1355-8382 (Print) 1355-8382},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Rna},

volume = {22},

number = {6},

pages = {905-19},

abstract = {MPMV has great potential for development as a vector for gene therapy. In this respect, precisely defining the sequences and structural motifs that are important for dimerization and packaging of its genomic RNA (gRNA) are of utmost importance. A distinguishing feature of the MPMV gRNA packaging signal is two phylogenetically conserved long-range interactions (LRIs) between U5 and gag complementary sequences, LRI-I and LRI-II. To test their biological significance in the MPMV life cycle, we introduced mutations into these structural motifs and tested their effects on MPMV gRNA packaging and propagation. Furthermore, we probed the structure of key mutants using SHAPE (selective 2'hydroxyl acylation analyzed by primer extension). Disrupting base-pairing of the LRIs affected gRNA packaging and propagation, demonstrating their significance to the MPMV life cycle. A double mutant restoring a heterologous LRI-I was fully functional, whereas a similar LRI-II mutant failed to restore gRNA packaging and propagation. These results demonstrate that while LRI-I acts at the structural level, maintaining base-pairing is not sufficient for LRI-II function. In addition, in vitro RNA dimerization assays indicated that the loss of RNA packaging in LRI mutants could not be attributed to the defects in dimerization. Our findings suggest that U5-gag LRIs play an important architectural role in maintaining the structure of the 5' region of the MPMV gRNA, expanding the crucial role of LRIs to the nonlentiviral group of retroviruses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN21,

title = {Label-free capacitance-based identification of viruses},

author = {M. Al Ahmad and F. Mustafa and L. M. Ali and J. V. Karakkat and T. A. Rizvi},

doi = {10.1038/srep09809},

issn = {2045-2322},

year  = {2015},

date = {2015-01-01},

urldate = {2015-01-01},

journal = {Sci Rep},

volume = {5},

pages = {9809},

abstract = {This study was undertaken to quantitate a single virus suspension in culture medium without any pre-processing. The electrical capacitance per virus particle was used to identify the kind of virus present by measuring the suspension (virus plus medium) capacitance, de-embedding the medium contribution, and dividing by the virus count. The proposed technique is based on finding the single virus effective dielectric constant which is directly related to the virus composition. This value was used to identify the virus type accordingly. Two types of viruses thus tested were further quantified by a biochemical technique to validate the results. Furthermore, non-organic nanoparticles with known concentration and capacitance per particle were identified using the proposed method. The selectivity of the method was demonstrated by performing electrical measurements on a third virus, revealing that the proposed technique is specific and sensitive enough to permit detection of a few hundred virus particles per milliliter within a few minutes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN59,

title = {Structural basis of genomic RNA (gRNA) dimerization and packaging determinants of mouse mammary tumor virus (MMTV)},

author = {S. J. Aktar and V. Vivet-Boudou and L. M. Ali and A. Jabeen and R. M. Kalloush and D. Richer and F. Mustafa and R. Marquet and T. A. Rizvi},

doi = {10.1186/s12977-014-0096-6},

issn = {1742-4690},

year  = {2014},

date = {2014-01-01},

urldate = {2014-01-01},

journal = {Retrovirology},

volume = {11},

pages = {96},

abstract = {BACKGROUND: One of the hallmarks of retroviral life cycle is the efficient and specific packaging of two copies of retroviral gRNA in the form of a non-covalent RNA dimer by the assembling virions. It is becoming increasingly clear that the process of dimerization is closely linked with gRNA packaging, and in some retroviruses, the latter depends on the former. Earlier mutational analysis of the 5' end of the MMTV genome indicated that MMTV gRNA packaging determinants comprise sequences both within the 5' untranslated region (5' UTR) and the beginning of gag. RESULTS: The RNA secondary structure of MMTV gRNA packaging sequences was elucidated employing selective 2'hydroxyl acylation analyzed by primer extension (SHAPE). SHAPE analyses revealed the presence of a U5/Gag long-range interaction (U5/Gag LRI), not predicted by minimum free-energy structure predictions that potentially stabilizes the global structure of this region. Structure conservation along with base-pair covariations between different strains of MMTV further supported the SHAPE-validated model. The 5' region of the MMTV gRNA contains multiple palindromic (pal) sequences that could initiate intermolecular interaction during RNA dimerization. In vitro RNA dimerization, SHAPE analysis, and structure prediction approaches on a series of pal mutants revealed that MMTV RNA utilizes a palindromic point of contact to initiate intermolecular interactions between two gRNAs, leading to dimerization. This contact point resides within pal II (5' CGGCCG 3') at the 5' UTR and contains a canonical "GC" dyad and therefore likely constitutes the MMTV RNA dimerization initiation site (DIS). Further analyses of these pal mutants employing in vivo genetic approaches indicate that pal II, as well as pal sequences located in the primer binding site (PBS) are both required for efficient MMTV gRNA packaging. CONCLUSIONS: Employing structural prediction, biochemical, and genetic approaches, we show that pal II functions as a primary point of contact between two MMTV RNAs, leading to gRNA dimerization and its subsequent encapsidation into the assembling virus particles. The results presented here enhance our understanding of the MMTV gRNA dimerization and packaging processes and the role of structural motifs with respect to RNA-RNA and possibly RNA-protein interactions that might be taking place during MMTV life cycle.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN24,

title = {Virus detection and quantification using electrical parameters},

author = {M. Al Ahmad and F. Mustafa and L. M. Ali and T. A. Rizvi},

doi = {10.1038/srep06831},

issn = {2045-2322},

year  = {2014},

date = {2014-01-01},

urldate = {2014-01-01},

journal = {Sci Rep},

volume = {4},

pages = {6831},

abstract = {Here we identify and quantitate two similar viruses, human and feline immunodeficiency viruses (HIV and FIV), suspended in a liquid medium without labeling, using a semiconductor technique. The virus count was estimated by calculating the impurities inside a defined volume by observing the change in electrical parameters. Empirically, the virus count was similar to the absolute value of the ratio of the change of the virus suspension dopant concentration relative to the mock dopant over the change in virus suspension Debye volume relative to mock Debye volume. The virus type was identified by constructing a concentration-mobility relationship which is unique for each kind of virus, allowing for a fast (within minutes) and label-free virus quantification and identification. For validation, the HIV and FIV virus preparations were further quantified by a biochemical technique and the results obtained by both approaches corroborated well. We further demonstrate that the electrical technique could be applied to accurately measure and characterize silica nanoparticles that resemble the virus particles in size. Based on these results, we anticipate our present approach to be a starting point towards establishing the foundation for label-free electrical-based identification and quantification of an unlimited number of viruses and other nano-sized particles.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN80,

title = {SHAPE analysis of the 5' end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization},

author = {S. J. Aktar and A. Jabeen and L. M. Ali and V. Vivet-Boudou and R. Marquet and T. A. Rizvi},

doi = {10.1261/rna.040931.113},

issn = {1355-8382 (Print) 1355-8382},

year  = {2013},

date = {2013-01-01},

urldate = {2013-01-01},

journal = {Rna},

volume = {19},

number = {12},

pages = {1648-58},

abstract = {Earlier genetic and structural prediction analyses revealed that the packaging determinants of Mason Pfizer monkey virus (MPMV) include two discontinuous core regions at the 5' end of its genomic RNA. RNA secondary structure predictions suggested that these packaging determinants fold into several stem-loops (SLs). To experimentally validate this structural model, we employed selective 2' hydroxyl acylation analyzed by primer extension (SHAPE), which examines the flexibility of the RNA backbone at each nucleotide position. Our SHAPE data validated several predicted structural motifs, including U5/Gag long-range interactions (LRIs), a stretch of single-stranded purine (ssPurine)-rich region, and a distinctive G-C-rich palindromic (pal) SL. Minimum free-energy structure predictions, phylogenetic, and in silico modeling analyses of different MPMV strains revealed that the U5 and gag sequences involved in the LRIs differ minimally within strains and maintain a very high degree of complementarity. Since the pal SL forms a helix loop containing a canonical "GC" dyad, it may act as a RNA dimerization initiation site (DIS), enabling the virus to package two copies of its genome. Analyses of wild-type and pal mutant RNAs revealed that disruption of pal sequence strongly affected RNA dimerization. However, when in vitro transcribed trans-complementary pal mutants were incubated together showed RNA dimerization was restored authenticating that the pal loop (5'-CGGCCG-3') functions as DIS.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN35,

title = {Bioenergetics of murine lungs infected with respiratory syncytial virus},

author = {A. R. Alsuwaidi and S. Benedict and J. Kochiyil and F. Mustafa and S. M. Hartwig and S. Almarzooqi and A. Albawardi and T. A. Rizvi and S. M. Varga and A. K. Souid},

doi = {10.1186/1743-422x-10-22},

issn = {1743-422x},

year  = {2013},

date = {2013-01-01},

urldate = {2013-01-01},

journal = {Virol J},

volume = {10},

pages = {22},

abstract = {BACKGROUND: Cellular bioenergetics (cellular respiration and accompanying ATP synthesis) is a highly sensitive biomarker of tissue injury and may be altered following infection. The status of cellular mitochondrial O(2) consumption of the lung in pulmonary RSV infection is unknown. METHODS: In this study, lung fragments from RSV-infected BALB/c mice were evaluated for cellular O(2) consumption, ATP content and caspase activity. The disease was induced by intranasal inoculation with the RSV strain A2 and lung specimens were analyzed on days 2-15 after inoculation. A phosphorescence O(2) analyzer that measured dissolved O(2) concentration as a function of time was used to monitor respiration. The caspase-3 substrate analogue N-acetyl-asp-glu-val-asp-7-amino-4-methylcoumarin (Ac-DEVD-AMC) was used to monitor intracellular caspases. RESULTS: O(2) concentration declined linearly with time when measured in a sealed vial containing lung fragment and glucose as a respiratory substrate, revealing its zero-order kinetics. O(2) consumption was inhibited by cyanide, confirming the oxidation occurred in the respiratory chain. Cellular respiration increased by 1.6-fold (p<0.010) and ATP content increased by 3-fold in the first week of RSV infection. Both parameters returned to levels found in uninfected lungs in the second week of RSV infection. Intracellular caspase activity in infected lungs was similar to uninfected lungs throughout the course of disease. CONCLUSIONS: Lung tissue bioenergetics is transiently enhanced in RSV infection. This energy burst, triggered by the virus or virus-induced inflammation, is an early biomarker of the disease and may be targeted for therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN58,

title = {NDM-2 carbapenemase-producing Acinetobacter baumannii in the United Arab Emirates},

author = {A. Ghazawi and A. Sonnevend and R. A. Bonnin and L. Poirel and P. Nordmann and R. Hashmey and T. A. Rizvi and B. Hamadeh M and T. Pál},

doi = {10.1111/j.1469-0691.2011.03726.x},

issn = {1198-743x},

year  = {2012},

date = {2012-01-01},

urldate = {2012-01-01},

journal = {Clin Microbiol Infect},

volume = {18},

number = {2},

pages = {E34-6},

abstract = {Screening 155 carbapenem non-susceptible Acinetobacter baumannii strains recovered in Abu Dhabi hospitals identified two metallo-ß-lactamase bla(NDM) gene-carrying isolates. They were isolated 4 months apart from the urine of a cancer patient previously treated in Egypt, Lebanon and in the United Arab Emirates. They were clonally related and carried the bla(NDM-2) gene recently identified in A. baumannii in Egypt and Israel. Sequences surrounding the bla(NDM-2) gene showed significant similarities with those associated with bla(NDM-1) in Enterobacteriaceae and A. baumannii. Repeated isolation of bla(NDM-2)-positive A. baumannii in the Middle East raises the possibility of the local emergence and spread of a unique clone.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN89,

title = {Sequences within both the 5' UTR and Gag are required for optimal in vivo packaging and propagation of mouse mammary tumor virus (MMTV) genomic RNA},

author = {F. Mustafa and D. Al Amri and F. Al Ali and N. Al Sari and S. Al Suwaidi and P. Jayanth and P. S. Philips and T. A. Rizvi},

doi = {10.1371/journal.pone.0047088},

issn = {1932-6203},

year  = {2012},

date = {2012-01-01},

urldate = {2012-01-01},

journal = {PLoS One},

volume = {7},

number = {10},

pages = {e47088},

abstract = {BACKGROUND: This study mapped regions of genomic RNA (gRNA) important for packaging and propagation of mouse mammary tumor virus (MMTV). MMTV is a type B betaretrovirus which preassembles intracellularly, a phenomenon distinct from retroviruses that assemble the progeny virion at cell surface just before budding such as the type C human and feline immunodeficiency viruses (HIV and FIV). Studies of FIV and Mason-Pfizer monkey virus (MPMV), a type D betaretrovirus with similar intracellular virion assembly processes as MMTV, have shown that the 5' untranslated region (5' UTR) and 5' end of gag constitute important packaging determinants for gRNA. METHODOLOGY: Three series of MMTV transfer vectors containing incremental amounts of gag or 5' UTR sequences, or incremental amounts of 5' UTR in the presence of 400 nucleotides (nt) of gag were constructed to delineate the extent of 5' sequences that may be involved in MMTV gRNA packaging. Real time PCR measured the packaging efficiency of these vector RNAs into MMTV particles generated by co-transfection of MMTV Gag/Pol, vesicular stomatitis virus envelope glycoprotein (VSV-G Env), and individual transfer vectors into human 293T cells. Transfer vector RNA propagation was monitored by measuring transduction of target HeLaT4 cells following infection with viral particles containing a hygromycin resistance gene expression cassette on the packaged RNA. PRINCIPAL FINDINGS: MMTV requires the entire 5' UTR and a minimum of ~120 nucleotide (nt) at the 5' end of gag for not only efficient gRNA packaging but also propagation of MMTV-based transfer vector RNAs. Vector RNAs without the entire 5' UTR were defective for both efficient packaging and propagation into target cells. CONCLUSIONS/SIGNIFICANCE: These results reveal that the 5' end of MMTV genome is critical for both gRNA packaging and propagation, unlike the recently delineated FIV and MPMV packaging determinants that have been shown to be of bipartite nature.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN70,

title = {Reciprocal cross-packaging of primate lentiviral (HIV-1 and SIV) RNAs by heterologous non-lentiviral MPMV proteins},

author = {I. R. Al Shamsi and N. S. Al Dhaheri and P. S. Phillip and F. Mustafa and T. A. Rizvi},

doi = {10.1016/j.virusres.2010.09.018},

issn = {0168-1702},

year  = {2011},

date = {2011-01-01},

urldate = {2011-01-01},

journal = {Virus Res},

volume = {155},

number = {1},

pages = {352-7},

abstract = {Retroviral RNA packaging signal (ψ) allows the preferential packaging of genomic RNA into virus particles through its interaction with the nucleocapsid protein. The specificity of this interaction came into question when it was shown that primate retroviruses, such as HIV-1, could cross-package RNA from its simian cousin, SIV, and vice versa and that feline retrovirus, FIV could cross-package RNA from a distantly related primate retrovirus, MPMV. To study the generality of this phenomenon further, we determined whether there is a greater packaging restriction between the lentiviral class of retroviruses (HIV-1 and SIV) and a non-lentivirus, MPMV. Our results revealed that primate lentiviral RNAs can be cross-packaged by primate non-lentiviral particles reciprocally, but the cross-packaged RNAs could not be propagated by the heterologous particles. Packaging of RNA in the context of both retroviral vectors as well as non-retroviral RNA containing SIV, HIV, and MPMV packaging determinants by each others proteins further confirmed the specificity of cross-packaging conferred by the packaging sequences. These results reveal the promiscuous nature of retroviral packaging determinants and raise caution against their wide spread presence on retroviral vectors to be used for human gene therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN47,

title = {Eugenol enhances the chemotherapeutic potential of gemcitabine and induces anticarcinogenic and anti-inflammatory activity in human cervical cancer cells},

author = {A. Hussain and K. Brahmbhatt and A. Priyani and M. Ahmed and T. A. Rizvi and C. Sharma},

doi = {10.1089/cbr.2010.0925},

issn = {1084-9785},

year  = {2011},

date = {2011-01-01},

urldate = {2011-01-01},

journal = {Cancer Biother Radiopharm},

volume = {26},

number = {5},

pages = {519-27},

abstract = {Administration of natural or synthetic agents to inhibit, delay, block, or reverse the initiation and promotional events associated with carcinogenesis opens a new avenue for cancer prevention and treatment to reduce cancer morbidity and mortality. Eugenol, a potential chemopreventive agent, is a component of clove and several other spices such as basil, cinnamon, and bay leaves. A number of reports have shown that eugenol possesses antiseptic, analgesic, antibacterial, and anticancer properties. The present study was undertaken to evaluate the chemopreventive potential of eugenol alone and in combination with a chemotherapeutic agent such as gemcitabine. Eugenol showed dose-dependent selective cytotoxicity toward HeLa cells in comparison to normal cells, pointing to its safe cytotoxicity profile. A combination of eugenol and gemcitabine induced growth inhibition and apoptosis at lower concentrations, compared with the individual drugs. The analysis of the data using a combination index showed combination index values of <1 indicating strong synergistic interaction. The combination thus may enhance the efficacy of gemcitabine at lower doses and minimize the toxicity on normal cells. In addition, the expression analysis of genes involved in apoptosis and inflammation revealed significant downregulation of Bcl-2, COX-2, and IL-1β on treatment with eugenol. Thus, the results suggest that eugenol exerts its anticancer activities via apoptosis induction and anti-inflammatory properties and also provide the first evidence demonstrating synergism between eugenol and gemcitabine, which may enhance the therapeutic index of prevention and/or treatment of cervical cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN67,

title = {SHAPE analysis of the FIV Leader RNA reveals a structural switch potentially controlling viral packaging and genome dimerization},

author = {J. C. Kenyon and S. J. Tanner and M. Legiewicz and P. S. Phillip and T. A. Rizvi and S. F. Le Grice and A. M. Lever},

doi = {10.1093/nar/gkr252},

issn = {0305-1048 (Print) 0305-1048},

year  = {2011},

date = {2011-01-01},

urldate = {2011-01-01},

journal = {Nucleic Acids Res},

volume = {39},

number = {15},

pages = {6692-704},

abstract = {Feline immunodeficiency virus (FIV) infects many species of cat, and is related to HIV, causing a similar pathology. High-throughput selective 2' hydroxyl acylation analysed by primer extension (SHAPE), a technique that allows structural interrogation at each nucleotide, was used to map the secondary structure of the FIV packaging signal RNA. Previous studies of this RNA showed four conserved stem-loops, extensive long-range interactions (LRIs) and a small, palindromic stem-loop (SL5) within the gag open reading frame (ORF) that may act as a dimerization initiation site (DIS), enabling the virus to package two copies of its genome. Our analyses of wild-type (wt) and mutant RNAs suggest that although the four conserved stem-loops are static structures, the 5' and 3' regions previously shown to form LRI also adopt an alternative, yet similarly conserved conformation, in which the putative DIS is occluded, and which may thus favour translational and splicing functions over encapsidation. SHAPE and in vitro dimerization assays were used to examine SL5 mutants. Dimerization contacts appear to be made between palindromic loop sequences in SL5. As this stem-loop is located within the gag ORF, recognition of a dimeric RNA provides a possible mechanism for the specific packaging of genomic over spliced viral RNAs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN123,

title = {Ectopic myelinating oligodendrocytes in the dorsal spinal cord as a consequence of altered semaphorin 6D signaling inhibit synapse formation},

author = {J. R. Leslie and F. Imai and K. Fukuhara and N. Takegahara and T. A. Rizvi and R. H. Friedel and F. Wang and A. Kumanogoh and Y. Yoshida},

doi = {10.1242/dev.066076},

issn = {0950-1991 (Print) 0950-1991},

year  = {2011},

date = {2011-01-01},

urldate = {2011-01-01},

journal = {Development},

volume = {138},

number = {18},

pages = {4085-95},

abstract = {Different types of sensory neurons in the dorsal root ganglia project axons to the spinal cord to convey peripheral information to the central nervous system. Whereas most proprioceptive axons enter the spinal cord medially, cutaneous axons typically do so laterally. Because heavily myelinated proprioceptive axons project to the ventral spinal cord, proprioceptive axons and their associated oligodendrocytes avoid the superficial dorsal horn. However, it remains unclear whether their exclusion from the superficial dorsal horn is an important aspect of neural circuitry. Here we show that a mouse null mutation of Sema6d results in ectopic placement of the shafts of proprioceptive axons and their associated oligodendrocytes in the superficial dorsal horn, disrupting its synaptic organization. Anatomical and electrophysiological analyses show that proper axon positioning does not seem to be required for sensory afferent connectivity with motor neurons. Furthermore, ablation of oligodendrocytes from Sema6d mutants reveals that ectopic oligodendrocytes, but not proprioceptive axons, inhibit synapse formation in Sema6d mutants. Our findings provide new insights into the relationship between oligodendrocytes and synapse formation in vivo, which might be an important element in controlling the development of neural wiring in the central nervous system.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN42,

title = {A G-C-rich palindromic structural motif and a stretch of single-stranded purines are required for optimal packaging of Mason-Pfizer monkey virus (MPMV) genomic RNA},

author = {S. A. Jaballah and S. J. Aktar and J. Ali and P. S. Phillip and N. S. Al Dhaheri and A. Jabeen and T. A. Rizvi},

doi = {10.1016/j.jmb.2010.06.043},

issn = {0022-2836},

year  = {2010},

date = {2010-01-01},

urldate = {2010-01-01},

journal = {J Mol Biol},

volume = {401},

number = {5},

pages = {996-1014},

abstract = {During retroviral RNA packaging, two copies of genomic RNA are preferentially packaged into the budding virus particles whereas the spliced viral RNAs and the cellular RNAs are excluded during this process. Specificity towards retroviral RNA packaging is dependent upon sequences at the 5' end of the viral genome, which at times extend into Gag sequences. It has earlier been suggested that the Mason-Pfizer monkey virus (MPMV) contains packaging sequences within the 5' untranslated region (UTR) and Gag. These studies have also suggested that the packaging determinants of MPMV that lie in the UTR are bipartite and are divided into two regions both upstream and downstream of the major splice donor. However, the precise boundaries of these discontinuous regions within the UTR and the role of the intervening sequences between these dipartite sequences towards MPMV packaging have not been investigated. Employing a combination of genetic and structural prediction analyses, we have shown that region "A", immediately downstream of the primer binding site, is composed of 50 nt, whereas region "B" is composed of the last 23 nt of UTR, and the intervening 55 nt between these two discontinuous regions do not contribute towards MPMV RNA packaging. In addition, we have identified a 14-nt G-C-rich palindromic sequence (with 100% autocomplementarity) within region A that has been predicted to fold into a structural motif and is essential for optimal MPMV RNA packaging. Furthermore, we have also identified a stretch of single-stranded purines (ssPurines) within the UTR and 8 nt of these ssPurines are duplicated in region B. The native ssPurines or its repeat in region B when predicted to refold as ssPurines has been shown to be essential for RNA packaging, possibly functioning as a potential nucleocapsid binding site. Findings from this study should enhance our understanding of the steps involved in MPMV replication including RNA encapsidation process.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN49,

title = {Optimal packaging of FIV genomic RNA depends upon a conserved long-range interaction and a palindromic sequence within gag},

author = {T. A. Rizvi and J. C. Kenyon and J. Ali and S. J. Aktar and P. S. Phillip and A. Ghazawi and F. Mustafa and A. M. L. Lever},

doi = {10.1016/j.jmb.2010.08.019},

issn = {0022-2836 (Print) 0022-2836},

year  = {2010},

date = {2010-01-01},

urldate = {2010-01-01},

journal = {J Mol Biol},

volume = {403},

number = {1},

pages = {103-119},

abstract = {The feline immunodeficiency virus (FIV) is a lentivirus that is related to human immunodeficiency virus (HIV), causing a similar pathology in cats. It is a potential small animal model for AIDS and the FIV-based vectors are also being pursued for human gene therapy. Previous studies have mapped the FIV packaging signal (ψ) to two or more discontinuous regions within the 5' 511 nt of the genomic RNA and structural analyses have determined its secondary structure. The 5' and 3' sequences within ψ region interact through extensive long-range interactions (LRIs), including a conserved heptanucleotide interaction between R/U5 and gag. Other secondary structural elements identified include a conserved 150 nt stem-loop (SL2) and a small palindromic stem-loop within gag open reading frame that might act as a viral dimerization initiation site. We have performed extensive mutational analysis of these sequences and structures and ascertained their importance in FIV packaging using a trans-complementation assay. Disrupting the conserved heptanucleotide LRI to prevent base pairing between R/U5 and gag reduced packaging by 2.8-5.5 fold. Restoration of pairing using an alternative, non-wild type (wt) LRI sequence restored RNA packaging and propagation to wt levels, suggesting that it is the structure of the LRI, rather than its sequence, that is important for FIV packaging. Disrupting the palindrome within gag reduced packaging by 1.5-3-fold, but substitution with a different palindromic sequence did not restore packaging completely, suggesting that the sequence of this region as well as its palindromic nature is important. Mutation of individual regions of SL2 did not have a pronounced effect on FIV packaging, suggesting that either it is the structure of SL2 as a whole that is necessary for optimal packaging, or that there is redundancy within this structure. The mutational analysis presented here has further validated the previously predicted RNA secondary structure of FIV ψ.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN94,

title = {Role of a heterologous retroviral transport element in the development of genetic complementation assay for mouse mammary tumor virus (MMTV) replication},

author = {T. A. Rizvi and J. Ali and P. S. Phillip and A. Ghazawi and P. Jayanth and F. Mustafa},

doi = {10.1016/j.virol.2008.12.027},

issn = {0042-6822},

year  = {2009},

date = {2009-01-01},

urldate = {2009-01-01},

journal = {Virology},

volume = {385},

number = {2},

pages = {464-72},

abstract = {The mouse mammary tumor virus (MMTV) is a type B retrovirus that is unique from other retroviruses in having multiple "tissue specific" and "hormone inducible" promoters. This unique feature has lead to the increasing interest in studying the biology of MMTV replication with the ultimate goal of developing MMTV based vectors for potentially targeted human gene therapy. In this report, we describe, for the first time, the establishment of an in vivo genetic complementation assay to study various aspects of MMTV replication. In the assay described here, the function of MMTV Rem/RmRE regulatory pathway has been successfully substituted by a heterologous retroviral constitutive transport element (CTE) from Mason Pfizer Monkey Virus (MPMV) for mature MMTV particle production. Our results revealed that in the absence of MPMV CTE or Rem/RmRE, RNA transcribed from MMTV Gag-Pol expression plasmids were efficiently transported to the cytoplasm. However, the presence of CTE was indispensable for Gag-Pol protein expression. In addition, we report the development of MMTV based vectors in which the packageable RNA was transcribed either from MMTV LTR or from a chimeric LTR, which could successfully be packaged and propagated by particles produced from MMTV Gag-Pol expression plasmids containing a heterologous transport element. The role of MPMV CTE in the transport of MMTV transfer vector RNA was not found to be significant. Development of such an assay should not only shed light on how MMTV regulates its gene expression, but also should provide additional molecular tools for delineating the packaging determinants for MMTV, which is imperative for the development of novel vectors for targeted and inducible gene therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN66,

title = {Cross-packaging of genetically distinct mouse and primate retroviral RNAs},

author = {N. S. Al Dhaheri and P. S. Phillip and A. Ghazawi and J. Ali and E. Beebi and S. A. Jaballah and T. A. Rizvi},

doi = {10.1186/1742-4690-6-66},

issn = {1742-4690},

year  = {2009},

date = {2009-01-01},

urldate = {2009-01-01},

journal = {Retrovirology},

volume = {6},

pages = {66},

abstract = {BACKGROUND: The mouse mammary tumor virus (MMTV) is unique from other retroviruses in having multiple viral promoters, which can be regulated by hormones in a tissue specific manner. This unique property has lead to increased interest in studying MMTV replication with the hope of developing MMTV based vectors for human gene therapy. However, it has recently been reported that related as well as unrelated retroviruses can cross-package each other's genome raising safety concerns towards the use of candidate retroviral vectors for human gene therapy. Therefore, using a trans complementation assay, we looked at the ability of MMTV RNA to be cross-packaged and propagated by an unrelated primate Mason-Pfizer monkey virus (MPMV) that has intracellular assembly process similar to that of MMTV. RESULTS: Our results revealed that MMTV and MPMV RNAs could be cross-packaged by the heterologous virus particles reciprocally suggesting that pseudotyping between two genetically distinct retroviruses can take place at the RNA level. However, the cross-packaged RNAs could not be propagated further indicating a block at post-packaging events in the retroviral life cycle. To further confirm that the specificity of cross-packaging was conferred by the packaging sequences (psi), we cloned the packaging sequences of these viruses on expression plasmids that generated non-viral RNAs. Test of these non-viral RNAs confirmed that the reciprocal cross-packaging was primarily due to the recognition of psi by the heterologous virus proteins. CONCLUSION: The results presented in this study strongly argue that MPMV and MMTV are promiscuous in their ability to cross-package each other's genome suggesting potential RNA-protein interactions among divergent retroviral RNAs proposing that these interactions are more complicated than originally thought. Furthermore, these observations raise the possibility that MMTV and MPMV genomes could also co-package providing substrates for exchanging genetic information.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN60,

title = {The secondary structure of the 5' end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem-loop},

author = {J. C. Kenyon and A. Ghazawi and W. K. Cheung and P. S. Phillip and T. A. Rizvi and A. M. Lever},

doi = {10.1261/rna.1284908},

issn = {1355-8382 (Print) 1355-8382},

year  = {2008},

date = {2008-01-01},

urldate = {2008-01-01},

journal = {Rna},

volume = {14},

number = {12},

pages = {2597-608},

abstract = {Feline immunodeficiency virus (FIV) is a lentivirus that infects cats and is related to human immunodeficiency virus (HIV). Although it is a common worldwide infection, and has potential uses as a human gene therapy vector and as a nonprimate model for HIV infection, little detail is known of the viral life cycle. Previous experiments have shown that its packaging signal includes two or more regions within the first 511 nucleotides of the genomic RNA. We have undertaken a secondary structural analysis of this RNA by minimal free-energy structural prediction, biochemical mapping, and phylogenetic analysis, and show that it contains five conserved stem-loops and a conserved long-range interaction between heptanucleotide sequences 5'-CCCUGUC-3' in R/U5 and 5'-GACAGGG-3' in gag. This long-range interaction is similar to that seen in primate lentiviruses where it is thought to be functionally important. Along with strains that infect domestic cats, this heptanucleotide interaction can also occur in species-specific FIV strains that infect pumas, lions, and Pallas' cats where the heptanucleotide sequences involved vary. We have analyzed spliced and genomic FIV RNAs and see little structural change or sequence conservation within single-stranded regions of the 5' UTR that are important for viral packaging, suggesting that FIV may employ a cotranslational packaging mechanism.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN118,

title = {Both the 5' and 3' LTRs of FIV contain minor RNA encapsidation determinants compared to the two core packaging determinants within the 5' untranslated region and gag},

author = {A. Ghazawi and F. Mustafa and P. S. Phillip and P. Jayanth and J. Ali and T. A. Rizvi},

doi = {10.1016/j.micinf.2005.09.015},

issn = {1286-4579 (Print) 1286-4579},

year  = {2006},

date = {2006-01-01},

urldate = {2006-01-01},

journal = {Microbes Infect},

volume = {8},

number = {3},

pages = {767-78},

abstract = {This study was undertaken to address the role of feline immunodeficiency virus (FIV) long terminal repeats (LTR) as potential packaging determinants. A number of studies in the recent past have clearly demonstrated that the core packaging determinants of FIV reside within at least two distinct regions at the 5' end of the viral genome, from R in the 5' LTR to approximately 150 bp within the 5' untranslated region (5' UTR) and within the first 100 bp of gag; however, there have been conflicting observations as to the role of the LTR regions in packaging and whether they contain the principal packaging determinants of FIV. Using a semi-quantitative RT-PCR approach on heterologous non-viral vector RNAs in an in vivo packaging assay, this study demonstrates that the principal packaging determinants of FIV reside within the first 150 bp of 5' UTR and 100 bp of gag (the two core regions) and not the viral 5' LTR. Furthermore, it shows that in addition to the 5' LTR, the 3' LTR also contains packaging determinants, but of a less significant nature compared to the core packaging determinants. This study defines the relative contribution of the various regions implicated in FIV genomic RNA packaging, and reveals that like other primate lentiviruses, the packaging determinants of FIV are multipartite and spread out, an observation that has implications for safer and more streamlined design of FIV-based gene transfer vectors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN121,

title = {Sequences intervening between the core packaging determinants are dispensable for maintaining the packaging potential and propagation of feline immunodeficiency virus transfer vector RNAs},

author = {F. Mustafa and A. Ghazawi and P. Jayanth and P. S. Phillip and J. Ali and T. A. Rizvi},

doi = {10.1128/jvi.79.21.13817-13821.2005},

issn = {0022-538X (Print) 0022-538x},

year  = {2005},

date = {2005-01-01},

urldate = {2005-01-01},

journal = {J Virol},

volume = {79},

number = {21},

pages = {13817-21},

abstract = {The packaging determinants of feline immunodeficiency virus (FIV) consist of two discontinuous core regions, extending from R to approximately 150 bp of the 5' untranslated region and the first approximately 100 bp of gag. However, the role of sequences intervening between the core regions in packaging has not been clear. A mutational analysis was conducted to determine whether the intervening sequences played a role in FIV RNA packaging, using an in vivo packaging assay complemented with semiquantitative reverse transcriptase PCR. Our analyses reveal that the intervening sequences are dispensable not only for vector RNA packaging but also for propagation, confirming the discontinuous nature of the FIV packaging signal.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN139,

title = {Relative activity of the feline immunodeficiency virus promoter in feline and primate cell lines},

author = {F. Mustafa and P. Jayanth and P. S. Phillip and A. Ghazawi and R. D. Schmidt and K. A. Lew and T. A. Rizvi},

doi = {10.1016/j.micinf.2004.10.015},

issn = {1286-4579 (Print) 1286-4579},

year  = {2005},

date = {2005-01-01},

urldate = {2005-01-01},

journal = {Microbes Infect},

volume = {7},

number = {2},

pages = {233-9},

abstract = {The feline immunodeficiency virus (FIV) long terminal repeat (LTR), compared with some primate lentiviral LTRs, is quite a strong basal promoter. However, it seems to be highly species-specific in function and generally not very efficient in cells of non-feline origin. This study systematically explored the function of the FIV LTR in simian Cos cells compared with its activity in feline and human cells. Our studies, using biologically relevant two- and three-plasmid trans complementation assays followed by semi-quantitative reverse transcriptase PCR, show that the FIV LTR is functional in Cos cells. The results of the Cos experiment are different from previously reported literature and suggest that the strain specificity of the FIV LTR is an important determinant of whether the LTR will be functional in a particular cell type.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN143,

title = {Close proximity of the MPMV CTE to the polyadenylation sequences is important for efficient function in the subgenomic context},

author = {F. Mustafa and P. S. Phillip and P. Jayanth and A. Ghazawi and K. A. Lew and R. D. Schmidt and T. A. Rizvi},

doi = {10.1016/j.virusres.2004.06.014},

issn = {0168-1702 (Print) 0168-1702},

year  = {2004},

date = {2004-01-01},

urldate = {2004-01-01},

journal = {Virus Res},

volume = {105},

number = {2},

pages = {209-18},

abstract = {The constitutive transport element (CTE) of Mason-Pfizer monkey virus (MPMV) is a short cis-acting sequence element critical for virus gene expression. Analogous to the Rev/Rev Responsive Element (RRE) of primate lentiviruses, CTE allows the nucleocytoplasmic transport of unspliced viral mRNAs. In fact, CTE can functionally replace Rev/RRE in the genomic context and has been used successfully in the expression of viral and cellular genes from expression vectors as well. However, unlike RRE, CTE accomplishes this by interacting with cellular factors, making CTE function independent of co-expressed trans factors. Thus, CTE has proven to be a valuable tool in the expression of heterologous genes. Our previous studies have shown that close proximity of CTE to the polyadenylation sequences is important for CTE function in the genomic context. However, it is controversial whether CTE needs to be located spatially close to the polyadenylation sequences in the subgenomic context. Since CTE is being frequently used in expression vectors, we investigated the position dependency of CTE in the heterologous, subgenomic background using both genetic and structural analyses. Our results reveal that similar to the genomic situation, close proximity of CTE to the polyadenylation sequences is important for its function in the heterologous subgenomic context.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{RN96,

title = {Postnatal passive immunization of neonatal macaques with a triple combination of human monoclonal antibodies against oral simian-human immunodeficiency virus challenge},

author = {R. Hofmann-Lehmann and J. Vlasak and R. A. Rasmussen and B. A. Smith and T. W. Baba and V. Liska and F. Ferrantelli and D. C. Montefiori and H. M. McClure and D. C. Anderson and B. J. Bernacky and T. A. Rizvi and R. Schmidt and L. R. Hill and M. E. Keeling and H. Katinger and G. Stiegler and L. A. Cavacini and M. R. Posner and T. C. Chou and J. Andersen and R. M. Ruprecht},

doi = {10.1128/jvi.75.16.7470-7480.2001},

issn = {0022-538X (Print) 0022-538x},

year  = {2001},

date = {2001-01-01},

urldate = {2001-01-01},

journal = {J Virol},

volume = {75},

number = {16},

pages = {7470-80},

abstract = {To develop prophylaxis against mother-to-child human immunodeficiency virus (HIV) transmission, we established a simian-human immunodeficiency virus (SHIV) infection model in neonatal macaques that mimics intrapartum mucosal virus exposure (T. W. Baba et al., AIDS Res. Hum. Retroviruses 10:351-357, 1994). Using this model, neonates were protected from mucosal SHIV-vpu(+) challenge by pre- and postnatal treatment with a combination of three human neutralizing monoclonal antibodies (MAbs), F105, 2G12, and 2F5 (Baba et al., Nat. Med. 6:200-206, 2000). In the present study, we used this MAb combination only postnatally, thereby significantly reducing the quantity of antibodies necessary and rendering their potential use in humans more practical. We protected two neonates with this regimen against oral SHIV-vpu(+) challenge, while four untreated control animals became persistently infected. Thus, synergistic MAbs protect when used as immunoprophylaxis without the prenatal dose. We then determined in vitro the optimal MAb combination against the more pathogenic SHIV89.6P, a chimeric virus encoding env of the primary HIV89.6. Remarkably, the most potent combination included IgG1b12, which alone does not neutralize SHIV89.6P. We administered the combination of MAbs IgG1b12, 2F5, and 2G12 postnatally to four neonates. One of the four infants remained uninfected after oral challenge with SHIV89.6P, and two infants had no or a delayed CD4(+) T-cell decline. In contrast, all control animals had dramatic drops in their CD4(+) T cells by 2 weeks postexposure. We conclude that our triple MAb combination partially protected against mucosal challenge with the highly pathogenic SHIV89.6P. Thus, combination immunoprophylaxis with passively administered synergistic human MAbs may play a role in the clinical prevention of mother-to-infant transmission of HIV type 1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN125,

title = {Intravirion display of a peptide corresponding to the dimer structure of protease attenuates HIV-1 replication},

author = {M. Cartas and S. P. Singh and D. Serio and T. A. Rizvi and V. S. Kalyanaraman and C. S. Goldsmith and S. R. Zaki and I. T. Weber and A. Srinivasan},

doi = {10.1089/104454901753438615},

issn = {1044-5498 (Print) 1044-5498},

year  = {2001},

date = {2001-01-01},

urldate = {2001-01-01},

journal = {DNA Cell Biol},

volume = {20},

number = {12},

pages = {797-805},

abstract = {Current treatment of HIV-1-infected individuals involves the administration of several drugs, all of which target either the reverse transcriptase or the protease activity of the virus. Unfortunately, the benefits of such treatments are compromised by the emergence of viruses exhibiting resistance to the drugs. This situation warrants new approaches for interfering with virus replication. Considering the activation of protease in the virus particles, a novel strategy to inhibit HIV-1 replication was tested targeting the dimerization domain of the protease. To test this idea, we have selected four residues from the C terminus of HIV-1 protease that map to the dimer interface region of the enzyme. We have exploited Vpr to display the peptides in the virus particles. The chimeric Vpr exhibited expression and virion incorporation similar to wildtype Vpr. The virus derived from the HIV-1 proviral DNA containing chimeric Vpr sequences registered a reduced level of replication in CEM and CEM X 174 cells in comparison with viruses containing wildtype Vpr. Similar results were observed in a single-round replication assay. These results suggest that the intravirion display of peptides targeting viral proteins is a powerful approach for developing antiviral agents and for dissecting the dynamic interactions between structural proteins during virus assembly and disassembly.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN128,

title = {Virion-associated HIV-1 Vpr: variable amount in virus particles derived from cells upon virus infection or proviral DNA transfection},

author = {S. P. Singh and P. Tungaturthi and M. Cartas and B. Tomkowicz and T. A. Rizvi and S. A. Khan and V. S. Kalyanaraman and A. Srinivasan},

doi = {10.1006/viro.2001.0849},

issn = {0042-6822 (Print) 0042-6822},

year  = {2001},

date = {2001-01-01},

urldate = {2001-01-01},

journal = {Virology},

volume = {283},

number = {1},

pages = {78-83},

abstract = {Human immunodeficiency virus type-1 (HIV-1) Vpr is a virion-associated protein implicated to have a role in AIDS pathogenesis. In regard to the amount of Vpr incorporated into virus particles, the published data vary widely. To address this, we quantitated Vpr in virus particles derived from diverse sources that are used to evaluate the biological effect of Vpr. Virus particles from infected cells showed only a small amount of Vpr. Interestingly, virus particles from cells cotransfected with HIV-1 proviral DNA lacking Vpr coding sequences (NLDeltaVpr) and a Vpr expression plasmid showed a drastic increase (29.4-fold) in the incorporation of Vpr. Furthermore, cotransfection involving NLDeltaVpr and different concentrations of Vpr expression plasmid resulted in virus particles containing Vpr in proportion to the Vpr expression plasmid used. The differences in virus particles with respect to Vpr as revealed by these studies should be taken into account in assessing the effect of Vpr.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN64,

title = {Enhancement of mucosal immune response against HIV-1 Gag by DNA immunization},

author = {I. Yoshizawa and Y. Soda and T. Mizuochi and S. Yasuda and T. A. Rizvi and T. Takemori and Y. Tsunetsugu-Yokota},

doi = {10.1016/s0264-410x(00)00539-9},

issn = {0264-410X (Print) 0264-410x},

year  = {2001},

date = {2001-01-01},

urldate = {2001-01-01},

journal = {Vaccine},

volume = {19},

number = {20-22},

pages = {2995-3003},

abstract = {In order to examine the feasibility of Gag-expression DNA as a potential candidate for HIV vaccine using a mouse model, we injected DNA into mice either intramuscularly or by using a gene gun. Both methods induced a low level of antibody production. However, after booster immunization with p24 protein emulsified with complete Freund's adjuvant via a footpad, we found that only the preceding intramuscular DNA immunization induced an anti-Gag Th1-type (IgG(2a)) antibody response, in addition to the enhancement of a Th2-type (IgG(1)) antibody response. Importantly, when mice were boosted intranasally with p24 and cholera toxin, intramuscular DNA injection was found to enhance both systemic and mucosal Gag-specific immune responses. These results indicate that intramuscular DNA immunization confers the inducibility of memory cells, which circulate around various mucosal tissues. Therefore, intramuscular DNA priming, followed by a mucosal booster immunization, could be considered as a regimen applicable to HIV vaccine.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN112,

title = {Human neutralizing monoclonal antibodies of the IgG1 subtype protect against mucosal simian-human immunodeficiency virus infection},

author = {T. W. Baba and V. Liska and R. Hofmann-Lehmann and J. Vlasak and W. Xu and S. Ayehunie and L. A. Cavacini and M. R. Posner and H. Katinger and G. Stiegler and B. J. Bernacky and T. A. Rizvi and R. Schmidt and L. R. Hill and M. E. Keeling and Y. Lu and J. E. Wright and T. C. Chou and R. M. Ruprecht},

doi = {10.1038/72309},

issn = {1078-8956 (Print) 1078-8956},

year  = {2000},

date = {2000-01-01},

urldate = {2000-01-01},

journal = {Nat Med},

volume = {6},

number = {2},

pages = {200-6},

abstract = {Although maternal human immunodeficiency virus type 1 (HIV-1) transmission occurs during gestation, intrapartum and postpartum (by breast-feeding), 50-70% of all infected children seem to acquire HIV-1 shortly before or during delivery. Epidemiological evidence indicates that mucosal exposure is an important aspect of intrapartum HIV transmission. A simian immunodeficiency virus (SIV) macaque model has been developed that mimics the mucosal exposure that can occur during intrapartum HIV-1 transmission. To develop immunoprophylaxis against intrapartum HIV-1 transmission, we used SHIV-vpu+ (refs. 5,6), a chimeric simian-human virus that encodes the env gene of HIV-IIIB. Several combinations of human monoclonal antibodies against HIV-1 have been identified that neutralize SHIV-vpu+ completely in vitro through synergistic interaction. Here, we treated four pregnant macaques with a triple combination of the human IgG1 monoclonal antibodies F105, 2G12 and 2F5. All four macaques were protected against intravenous SHIV-vpu+ challenge after delivery. The infants received monoclonal antibodies after birth and were challenged orally with SHIV-vpu+ shortly thereafter. We found no evidence of infection in any infant during 6 months of follow-up. This demonstrates that IgG1 monoclonal antibodies protect against mucosal lentivirus challenge in neonates. We conclude that epitopes recognized by the three monoclonal antibodies are important determinants for achieving substantial protection, thus providing a rational basis for AIDS vaccine development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Baba1999,

title = {Human Monoclonal Antibodies Protect Neonatal and Adult Rhesus Monkeys from Mucosal or Parenteral Immunodeficiency Virus Exposure},

author = {Timothy W Baba and Vladimir Liska and Regina Hoffman-Lehmann and Josef Vlasak and Marshall R Posner and Lisa A Cavacini and Hermann Katinger and Bruce J Bernacky and Tahir A Rizvi and Michale Keeling and Russell Schmidt and Ruth M Ruprecht},

doi = {10.1203/00006450-199904020-00924},

issn = {1530-0447},

year  = {1999},

date = {1999-04-00},

urldate = {1999-04-00},

journal = {Pediatr Res},

volume = {45},

number = {4, Part 2 of 2},

pages = {156A--156A},

publisher = {Springer Science and Business Media LLC},

abstract = {We developed a primate animal model to investigate whether infusion of a triple combination of broadly neutralizing human anti-HIV-1 monoclonal antibodies (mAb) could protect rhesus monkey neonates and their mothers from infection with SHIV-vpu+, a chimeric simian/human immunodeficiency virus that expresses the HIV-1 gp120 and gp41 envelope glycoproteins. We infused 4 pregnant rhesus monkeys with a triple human mAb cocktail 5 days prior to cesarean section delivery. Neutralizing antibody levels were detected in cord blood, demonstrating transport of human IgG1 antibodies across the macaque placenta. An infusion of this mAb cocktail was given to the 4 neonates, followed by oral exposure to SHIV-vpu+. A final infusion of mAbs was given to the neonates 8 days later. Animals were evaluated for evidence of infection by virus culture, PCR and immunoblot analysis over a six month period. In contrast to the 4 positive control animals that became infected, sterilizing immunity that resulted in complete protection was achieved in each of the 4 mAb-treated neonates that we exposed mucosally to SHIV-vpu+ (p=0.028). In a parallel study, all 4 of the adult rhesus monkeys that received mAb therapy were completely protected against intravenous (i.v.) challenge with SHIV-vpu+. In contrast, all 5 positive control animals became infected (p=0.016). In sum, passive administration of broadly neutralizing human IgG1 mAbs resulted in sterilizing immunity and completely protected rhesus monkeys against either i.v. or mucosal virus challenge. These results demonstrates that the three antigenic epitopes recognized by these human mAbs are critical determinants for achieving sterilizing immunity against immunodeficiency virus infection that results from either i.v. or mucosal exposure and provide a focus for future AIDS vaccine development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN111,

title = {Neutralizing antibody-independent containment of immunodeficiency virus challenges by DNA priming and recombinant pox virus booster immunizations},

author = {H. L. Robinson and D. C. Montefiori and R. P. Johnson and K. H. Manson and M. L. Kalish and J. D. Lifson and T. A. Rizvi and S. Lu and S. L. Hu and G. P. Mazzara and D. L. Panicali and J. G. Herndon and R. Glickman and M. A. Candido and S. L. Lydy and M. S. Wyand and H. M. McClure},

doi = {10.1038/8406},

issn = {1078-8956 (Print) 1078-8956},

year  = {1999},

date = {1999-01-01},

urldate = {1999-01-01},

journal = {Nat Med},

volume = {5},

number = {5},

pages = {526-34},

abstract = {Eight different protocols were compared for their ability to raise protection against immunodeficiency virus challenges in rhesus macaques. The most promising containment of challenge infections was achieved by intradermal DNA priming followed by recombinant fowl pox virus booster immunizations. This containment did not require neutralizing antibody and was active for a series of challenges ending with a highly virulent virus with a primary isolate envelope heterologous to the immunizing strain.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN39,

title = {Oral transmission of primate lentiviruses},

author = {R. M. Ruprecht and T. W. Baba and V. Liska and N. B. Ray and L. N. Martin and M. Murphey-Corb and T. A. Rizvi and B. J. Bernacky and M. E. Keeling and H. M. McClure and J. Andersen},

doi = {10.1086/314794},

issn = {0022-1899 (Print) 0022-1899},

year  = {1999},

date = {1999-01-01},

urldate = {1999-01-01},

journal = {J Infect Dis},

volume = {179 Suppl 3},

pages = {S408-12},

abstract = {Oral transmission of human immunodeficiency virus type 1 (HIV-1) is well documented in children who become infected postnatally through breast milk. In contrast, epidemiologic surveys have yielded conflicting data regarding oral HIV-1 transmission among adults, even though case reports have described seroconversion and the development of AIDS in adults whose only risk was oral-genital contact. To study oral virus transmission in primate models, we exposed rhesus macaques of various ages to cell-free simian immunodeficiency virus (SIV), including uncloned and molecularly cloned viruses. In neonates, viremia and AIDS developed after nontraumatic oral exposure to several SIV strains. Furthermore, chimeric simian human immunodeficiency viruses containing the HIV-1 envelope can also cross intact upper gastrointestinal mucosal surfaces in neonates. In adult macaques, infection and AIDS have resulted from well-controlled, nontraumatic, experimental oral exposure to different strains of SIV. These findings have implications for the risks of HIV-1 transmission during oral-genital contact.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN55,

title = {HIV-1 Gag shares a signature motif with annexin (Anx7), which is required for virus replication},

author = {M. Srivastava and M. Cartas and T. A. Rizvi and S. P. Singh and D. Serio and V. S. Kalyanaraman and H. B. Pollard and A. Srinivasan},

doi = {10.1073/pnas.96.6.2704},

issn = {0027-8424 (Print) 0027-8424},

year  = {1999},

date = {1999-01-01},

urldate = {1999-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {96},

number = {6},

pages = {2704-9},

abstract = {Genetic and biochemical analyses of the Gag protein of HIV-1 indicate a crucial role for this protein in several functions related to viral replication, including viral assembly. It has been suggested that Gag may fulfill some of the functions by recruiting host cellular protein(s). In our effort to identify structural and functional homologies between Gag and cellular cytoskeletal and secretory proteins involved in transport, we observed that HIV-1 Gag contains a unique PGQM motif in the capsid region. This motif was initially noted in the regulatory domain of synexin the membrane fusion protein of Xenopus laevis. To evaluate the functional significance of the highly conserved PGQM motif, we introduced alanine (A) in place of individual residues of the PGQM and deleted the motif altogether in a Gag expression plasmid and in an HIV-1 proviral DNA. The proviral DNA containing mutations in the PGQM motif showed altered expression, assembly, and release of viral particles in comparison to parental (NL4-3) DNA. When tested in multiple- and single-round replication assays, the mutant viruses exhibited distinct replication phenotypes; the viruses containing the A for the G and Q residues failed to replicate, whereas A in place of the P and M residues did not inhibit viral replication. Deletion of the tetrapeptide also resulted in the inhibition of replication. These results suggest that the PGQM motif may play an important role in the infection process of HIV-1 by facilitating protein-protein interactions between viral and/or viral and cellular proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN150,

title = {Oral SIV, SHIV, and HIV type 1 infection},

author = {R. M. Ruprecht and T. W. Baba and V. Liska and S. Ayehunie and J. Andersen and D. C. Montefiori and A. Trichel and M. Murphey-Corb and L. Martin and T. A. Rizvi and B. J. Bernacky and S. J. Buchl and M. Keeling},

url = {https://pubmed.ncbi.nlm.nih.gov/9581893/},

issn = {0889-2229 (Print) 0889-2229},

year  = {1998},

date = {1998-01-01},

urldate = {1998-01-01},

journal = {AIDS Res Hum Retroviruses},

volume = {14 Suppl 1},

pages = {S97-103},

abstract = {Several strains of simian immunodeficiency virus (SIV), including uncloned and molecularly cloned SIV strains, can cross intact mucosal surfaces after oral exposure in both adult and neonatal rhesus macaques, resulting in viremia and disease. Cell-free SIV strains as well as infected whole blood have resulted in systemic infection after oral inoculation. Neonatal macaques, exposed orally to the chimeric SHIV-vpu+, a derivative of SIVmac239 that encodes the env gene of the T cell-tropic HIV-IIIB, have also become persistently infected. These data indicate that oral exposure to various virus strains, including T cell-tropic variants, leads to infection. After nontraumatic inoculation, the oral route was more efficient than the rectal route in permitting SIV entry in adult macaques. Infection and AIDS resulting from oral exposure of adult macaques have implications for the transmission of the human immunodeficiency virus type 1 (HIV-1) during oral-genital contact.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN27,

title = {Mason-Pfizer monkey virus (MPMV) constitutive transport element (CTE) functions in a position-dependent manner},

author = {T. A. Rizvi and R. D. Schmidt and K. A. Lew},

doi = {10.1006/viro.1997.8728},

issn = {0042-6822 (Print) 0042-6822},

year  = {1997},

date = {1997-01-01},

urldate = {1997-01-01},

journal = {Virology},

volume = {236},

number = {1},

pages = {118-29},

abstract = {The Mason-Pfizer monkey virus (MPMV) constitutive transport element (CTE) is a cis-acting RNA element located in the 3' untranslated region (UTR) of the viral genome. The HIV-1 and SIV Rev/RRE regulatory system can be replaced with MPMV CTE (Bray et al., 1994; Zolotukhin et al., 1994; Rizvi et al., 1996a); similarly, CTE function can also be replaced by the HIV or SIV Rev/RRE regulatory system (Rizvi et al., 1996b; Ernst et al., 1997). In addition, we have shown that in the context of the SIV genome, position is important for CTE function (Rizvi et al., 1996a). To determine the importance of position for CTE function in the context of the MPMV genome, MPMV molecular clones were generated by deleting CTE or removing it from the 3' UTR and placing it in the approximately 40 bp of intervening sequences between the pol termination codon and env initiation codon. A test of these molecular clones in a single round of replication assay revealed that deletion or displacement of CTE in the intervening sequences between pol and env completely abrogated virus replication. Western blot analysis of cell lysates and pelleted culture supernatants revealed negligible amounts of Pr78 Gag/Pol precursor and the processed p27(gag) when CTE was deleted or displaced. Slot blot analysis of fractionated RNAs revealed entrapment of the viral Gag/Pol mRNA in the nucleus with CTE deletion or displacement. Upon reinsertion of CTE in the original genomic position of clones with the deleted or displaced CTE, virus replication, Gag/Pol protein production, and nucleocytoplasmic transport of viral mRNA were restored to normal levels. Displacement of CTE to the 5' UTR immediately upstream of the Gag initiation codon also resulted in aberrant Gag/Pol protein production and nucleocytoplasmic transport of viral RNA. Reinsertion of CTE at the original genomic position of the clone with CTE displacement at the 5' UTR restored normal Gag/Pol protein production and RNA transport, demonstrating that the 3' terminal position of CTE is important for its function. To explore why the 3' terminal location of CTE is important, heterologous DNA sequences of increasing lengths were inserted between CTE and the polyadenylation (poly(A)) signal of the virus to augment the distance between the two cis-acting elements. Test of these constructs revealed that CTE function was progressively lost with incremental increase in distance between CTE and poly(A). To explore this relationship further, CTE was displaced to the env region approximately 2000 bp upstream of the poly(A) signal which abrogated CTE function. However, cloning of poly(A) signal to approximately 200 bp downstream of CTE in the env region (the natural distance between CTE and poly(A)) restored CTE function. Together, these results demonstrate that the close proximity of CTE to the poly(A) signal is important for CTE function, suggesting a functional interaction between CTE and the polyadenylation machinery.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN142,

title = {Reactivation of HIV type 1 in chronically infected chimpanzees following xenostimulation with human cells or with pulses of corticosteroid},

author = {R. Shibata and C. Siemon and T. A. Rizvi and T. Matano and W. C. Satterfield and H. C. Lane and M. A. Martin},

doi = {10.1089/aid.1997.13.377},

issn = {0889-2229 (Print) 0889-2229},

year  = {1997},

date = {1997-01-01},

urldate = {1997-01-01},

journal = {AIDS Res Hum Retroviruses},

volume = {13},

number = {5},

pages = {377-81},

abstract = {Following resolution of a primary HIV-1 infection initially induced by inoculating a mixture of three different virus strains, a chimpanzee was exposed to both immunostimulatory and immunosuppressive agents in an attempt to assess the contributions of different components of the immune system in suppressing circulating virus. The infusion of human leukocytes as an xenogeneic stimulus induced the replication of one of the input virus strains that had not previously been isolated or detected by PCR. The administration of high-dose, 17-day courses of corticosteroids resulted in coordinate and transient increases of each of the three viruses present in the original inoculum and elevation of HIV-1-specific ELISA antibody levels. Steroids administered to a second chimpanzee, chronically infected with a single HIV-1 isolate, also induced elevations of cell-associated virus. These results highlight the intimate relationship between immune system activation/immunosuppression and HIV replication in an animal model.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN127,

title = {Development of a novel anti-HIV-1 agent from within: effect of chimeric Vpr-containing protease cleavage site residues on virus replication},

author = {D. Serio and T. A. Rizvi and M. Cartas and V. S. Kalyanaraman and I. T. Weber and H. Koprowski and A. Srinivasan},

doi = {10.1073/pnas.94.7.3346},

issn = {0027-8424 (Print) 0027-8424},

year  = {1997},

date = {1997-01-01},

urldate = {1997-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {94},

number = {7},

pages = {3346-51},

abstract = {Effective antiviral agents will be of great value in controlling virus replication and delaying the onset of HIV-1-related disease symptoms. Current therapy involves the use of antiviral agents that target the enzymatic functions of the virus, resulting in the emergence of resistant viruses to these agents, thus lowering their effectiveness. To overcome this problem, we have considered the idea of developing novel agents from within HIV-1 as inhibitors of virus replication. The specificity of the Vpr protein for the HIV-1 virus particle makes it an attractive molecule for the development of antiviral agents targeting the events associated with virus maturation. We have generated chimeric Vpr proteins containing HIV-1-specific sequences added to the C terminus of Vpr. These sequences correspond to nine cleavage sites of the Gag and Gag-Pol precursors of HIV-1. The chimeric Vpr constructs were introduced into HIV-1 proviral DNA to assess their effect on virus infectivity using single- and multiple-round replication assays. The virus particles generated exhibited a variable replication pattern depending on the protease cleavage site used as a fusion partner. Interestingly, the chimeric Vpr containing the cleavage sequences from the junction of p24 and p2, 24/2, completely abolished virus infectivity. These results show that chimeric proteins generated from within HIV-1 have the ability to suppress HIV-1 replication and make ideal agents for gene therapy or intracellular immunization to treat HIV-1 infection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN126,

title = {Spontaneous anaplastic large cell lymphoma in a chimpanzee: a clinicopathological and immunohistochemical study},

author = {A. A. Binhazim and D. R. Lee and B. J. Bernacky and T. A. Rizvi},

doi = {10.1111/j.1600-0684.1997.tb00221.x},

issn = {0047-2565 (Print) 0047-2565},

year  = {1997},

date = {1997-01-01},

urldate = {1997-01-01},

journal = {J Med Primatol},

volume = {26},

number = {5},

pages = {260-6},

abstract = {An anaplastic large cell lymphoma with disseminated abdominal metastases was diagnosed in a 35-year-old male chimpanzee. Clinically, the animal displayed lethargy, weight loss, ascites, and abdominal distention. Imaging studies showed several large abdominal masses. At necropsy, variably sized masses of neoplastic mesenteric lymph nodes that encompassed several intestinal loops were present throughout the abdomen. The largest mass measured 9 x 5 cm and had cauliflower-like protrusions into the jejunal lumen. The entire abdominal cavity was covered by a sheet of neoplastic tissue. Histopathologically, the tumor consisted of solid sheets of proliferating lymphoid cells forming a cohesive growth that filled the lymph node sinuses. The tumor had invaded the intestinal wall. Anaplastic large cell lymphoma was diagnosed from immunohistochemistry findings on the basis of positive reaction to the CD3 and CD30 markers and negative reaction to the CD20 marker. Serologic analysis revealed positive titers for Epstein-Barr, cytomegalo-, and varicella-zoster viruses. Both serologic and virologic studies showed no evidence of detectable retroviral infection. This type of tumor has not been reported before in the chimpanzee.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN93,

title = {Role of Mason-Pfizer monkey virus (MPMV) constitutive transport element (CTE) in the propagation of MPMV vectors by genetic complementation using homologous/heterologous env genes},

author = {T. A. Rizvi and K. A. Lew and Jr. E. C. Murphy and R. D. Schmidt},

doi = {10.1006/viro.1996.0558},

issn = {0042-6822 (Print) 0042-6822},

year  = {1996},

date = {1996-01-01},

urldate = {1996-01-01},

journal = {Virology},

volume = {224},

number = {2},

pages = {517-32},

abstract = {To study Mason-Pfizer monkey virus (MPMV) replication over a single round, virus particles were generated that contain a replication-defective vector encoding a dominant selectable marker, the hygromycin B phosphotransferase (hyg) gene. Genetic complementation with a homologous MPMV envelope glycoprotein (Env-gp) or pseudotyping by several heterologous Env-gps from a variety of viruses resulted in infectious MPMV particles containing the replication-defective RNA. Recently, it has been shown that human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) Rev and Rev-responsive element (RRE) functions can be substituted in vitro by a cis-acting sequence, the constitutive transport element (CTE), from simian type D retroviruses like MPMV and simian retrovirus type 1 (SRV-1). To determine whether CTE of MPMV is necessary for MPMV nucleic acid propagation, an MPMV vector that lacked the terminally located CTE was generated. Propagation of this vector was completely abrogated in the absence of CTE, showing the importance of CTE in MPMV replication. Insertion of CTE back into the MPMV genome in the sense orientation rescued replication to wild-type levels. Slot-blot analysis of nuclear versus cytoplasmic RNA fractions revealed that most of the messages were sequestered in the nucleus of cells transfected with the CTE(-) vectors and very little was transported to the cytoplasm. To test whether HIV-1 or SIV RREs could complement CTE function, the HIV-1 or SIV RREs were inserted in the CTE(-) vectors, trans complementation of CTE(-)RRE(+) vectors with Env-and Rev-expression plasmids rescued propagation of the CTE(-) vectors. Computer analysis predicted an RNA secondary structure in MPMV CTE analogous to the HIV-1 and SIV RREs that could form three stable stem loops, the first of which contains a site similar to the Rev-binding domain in the HIV-1 RRE. The presence of a higher-order CTE structure was analyzed by mutational analysis. We conclude that CTE is important in the replication of MPMV and affects the nucleocytoplasmic transport and/or stability of viral messages similar to the Rev/RRE regulatory system of HIV-1 and SIV.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN86,

title = {Rev/RRE-independent Mason-Pfizer monkey virus constitutive transport element-dependent propagation of SIVmac239 vectors using a single round of replication assay},

author = {T. A. Rizvi and R. D. Schmidt and K. A. Lew and M. E. Keeling},

doi = {10.1006/viro.1996.0444},

issn = {0042-6822 (Print) 0042-6822},

year  = {1996},

date = {1996-01-01},

urldate = {1996-01-01},

journal = {Virology},

volume = {222},

number = {2},

pages = {457-63},

abstract = {In a step toward creating live-attenuated or DNA subunit vaccines for AIDS, the replication of simian immunodeficiency virus (SIV) was studied independently of the Rev and RRE (Rev-responsive element) regulatory system, over a single round. To accomplish this, the env gene of an SIV vector was made defective by the insertion of a SV40 promoter/enhancer hygromycin B phosphotransferase gene cassette. Using this vector as the backbone, molecular clones of SIV were generated that contained a mutated Rev, Rev(-), a deleted RRE, RRE(-), or both, Rev(-)RRE(-). It has been shown recently that human immunodeficiency virus type 1 (HIV-1) Rev and RRE functions can be replaced in vitro by a cis-acting sequence, constitutive transport element (CTE), from simian type D retroviruses. To determine whether such a cis-acting element from Mason-Pfizer monkey virus (MPMV) would substitute for SIV Rev and RRE functions, the MPMV CTE was inserted either into the Nef ORF or at the junction of vpx and vpr of our Rev(-), RRE(-), and Rev(-)RRE(-) SIV molecular clones. Cell-free viral stocks harvested from Cos cells following transfections of these molecular clones revealed that these stocks were infectious over a single round of replication; however, their replication was attenuated 16-fold compared to that of wild-type virus. In addition, our experiments revealed that CTE functions in a position-dependent manner such that its insertion at the junction of vpx and vpr attenuated SIV replication 8- to 12-fold compared to the attenuation observed when it was inserted in the nef region. Our results demonstrate that MPMV CTE is capable of substituting for SIV Rev and RRE functions, resulting in an attenuated ability to produce infectious virus.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN146,

title = {Rhesus thymic/liver xenografts in severe combined immunodeficient mice: immunologic reconstitution and intrathymic infection with simian immunodeficiency virus},

author = {A. A. Binhazim and T. A. Rizvi and L. G. Coghlan and K. Lew and R. Schmidt and P. K. Wong},

url = {https://pubmed.ncbi.nlm.nih.gov/8804357/},

issn = {0023-6837 (Print) 0023-6837},

year  = {1996},

date = {1996-01-01},

urldate = {1996-01-01},

journal = {Lab Invest},

volume = {75},

number = {3},

pages = {339-48},

abstract = {By serving as host recipients of xenografts from both humans and animals, severe combined immunodeficient (SCID) mice have become valuable to many laboratories interested in examining the pathophysiology of different diseases. To gain insight into the usefulness of the SCID mutation in retrovirus research, rhesus monkey fetal hematolymphoid tissues (liver and thymus) were used to construct a SCID-rhesus chimeric mouse (SCID-rh) and were engrafted in the renal capsule. The size and maturation of the thymic engrafts were monitored grossly, histologically, and immunologically. SCID mice were tolerant to rhesus tissues, and thymic engrafts contained thymocytes at different stages of maturation and differentiation that had morphologic features similar to age-matched rhesus thymus. Mature single positive CD2+, CD4+, and CD8+ T lymphocytes that were phenotypically similar to rhesus T lymphocytes were present at low levels (2% to 5%) in the peripheral blood and at moderately higher levels (7% to 15%) in the spleens of SCID-rh mice obtained between 12 and 15 weeks after thymus/liver engraftment. Within 3 weeks after engraftment, > 85% of the thymocytes in the thymic engrafts were immature double positive CD4+CD8+ T cells. The highest number of positive cells were seen in thymic engrafts obtained at 12 to 18 weeks. During these weeks, > 90% of the cells were double positive (CD2+CD4+, CD2+CD8+, and CD4+CD8+). After infection of the engrafted thymus tissue with simian immonodeficiency virus (SIVmac239), PCR analysis revealed successful viral infection of engrafts at 2 and 4 weeks after infection. No significant histopathologic and flow cytometric changes were observed in the thymic engrafts at 2 and 4 weeks after infection. An unrelated lesion of thymic lymphomas involving the SCID host thymus was seen in 12% of the mice. The data presented herein suggest that the SCID-rh is a valuable model for specific studies related to thymus-retrovirus interaction and that it could be used for further studies. The results are discussed in relation to current knowledge of thymus involvement during simian and human immunodeficiency virus infection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN106,

title = {Simian immunodeficiency virus RNA is efficiently encapsidated by human immunodeficiency virus type 1 particles},

author = {T. A. Rizvi and A. T. Panganiban},

doi = {10.1128/jvi.67.5.2681-2688.1993},

issn = {0022-538X (Print) 0022-538x},

year  = {1993},

date = {1993-01-01},

urldate = {1993-01-01},

journal = {J Virol},

volume = {67},

number = {5},

pages = {2681-8},

abstract = {Packaging of retroviral RNA is attained through the specific recognition of a cis-acting encapsidation site (located near the 5' end of the viral RNA) by components of the Gag precursor protein. Human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) are two lentiviruses that lack apparent sequence similarity in their putative encapsidation regions. We used SIV vectors to determine whether HIV-1 particles can recognize the SIV encapsidation site and functionally propagate SIV nucleic acid. SIV nucleic acid was replicated by HIV-1 proteins. Thus, efficient lentivirus pseudotyping can take place at the RNA level. Direct examination of the RNA contents of virus particles indicated that encapsidation of this heterologous RNA is efficient. Characterization of deletion mutants in the untranslated leader region of SIV RNA indicates that only a very short region at the 5' end of the SIV RNA is needed for packaging. Comparison of this region with the corresponding region of HIV-1 reveals that both are marked by secondary structures that are likely to be similar. Thus, it is likely that a similar higher-order RNA structure is required for encapsidation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN95,

title = {Propagation of SIV vectors by genetic complementation with a heterologous env gene},

author = {T. A. Rizvi and A. T. Panganiban},

doi = {10.1089/aid.1992.8.89},

issn = {0889-2229 (Print) 0889-2229},

year  = {1992},

date = {1992-01-01},

urldate = {1992-01-01},

journal = {AIDS Res Hum Retroviruses},

volume = {8},

number = {1},

pages = {89-95},

abstract = {In order to study SIV replication over a single round of replication virus particles were generated that contain a replication-defective vector containing a selectable marker. Genetic complementation between an env-deficient SIV variant and plasmid that expresses the env gene of an amphotropic murine retrovirus resulted in infectious SIV particles containing the vector. These pseudotyped particles exhibited an expanded host range through the use of an alternative receptor. This system should be useful in the genetic analysis of SIV nucleic acid replication. To determine whether the terminal cis acting components of the SIV genome might be sufficient for viral nucleic acid propagation a vector was generated which lack the internally located rev-responsive element. Propagation of this vector was reduced by at least 100-fold.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN144,

title = {Simian immunodeficiency virus vectors: replication and pseudotyping},

author = {T. A. Rizvi and A. T. Panganiban},

url = {https://pubmed.ncbi.nlm.nih.gov/1433269/},

issn = {0047-2565 (Print) 0047-2565},

year  = {1992},

date = {1992-01-01},

urldate = {1992-01-01},

journal = {J Med Primatol},

volume = {21},

number = {2-3},

pages = {69-73},

abstract = {We studied a single round of replication of Simian immunodeficiency virus (SIV) through the use of a replication defective vector that expresses the hygromycin resistance gene. It was possible to pseudotype SIV particles by complementation with the env gene from a murine amphotropic retrovirus. Moreover, SIV RNA was packaged and propagated by core particles of the heterologous lentivirus, HIV-1. These results indicate that coinfection of cells with SIV and other retroviruses could lead to infection of new cell types in nature.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}