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288 results on '"Mustafa, Farah"'

5. A discrete event system specification (DEVS)-based model of consanguinity

Author

Akhtar, Noreen, Niazi, Muaz A., Mustafa, Farah, and Hussain, Amir

Subjects
Computer Science - Social and Information Networks, Computer Science - Computers and Society, Computer Science - Discrete Mathematics, Quantitative Biology - Populations and Evolution, Quantitative Biology - Quantitative Methods, I.2, I.2.0, I.6, J.4, J.3, B.1.2, C.4
Abstract

Consanguinity or inter-cousin marriage is a phenomenon quite prevalent in certain regions around the globe. Consanguineous parents have a higher risk of having offspring with congenital disorders. It is difficult to model large scale consanguineous parental populations because of disparate cultural issues unique to regions and cultures across the globe. Although consanguinity, as a social problem has been studied previously, consanguinity from a biological perspective has yet to be modeled. Discrete Event System Specification (DEVS) formalism is a powerful modeling formalism for the study of intricate details of real-world complex systems. In this article, we develop a DEVS model to get an insight into the role of consanguineous marriages in the evolution of congenital disorders in a population. As proof-of-concept, we develop a consanguinity simulation model in Simio simulation software. Our results show the effectiveness of DEVS in the modeling of consanguinity effects in causing congenital defects., Comment: 41 pages, 10 figures

Published
2017
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9. MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals.

Author

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

Subjects
MOUSE mammary tumor virus, RNA, PACKAGING
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. The role of long-range interactions (LRI) in retroviral RNA packaging is unclear. This study found that a specific packaging signal (Psi) structure, maintained by an extended LRI, is crucial for efficient RNA packaging, with Gag binding to key Psi sites essential for selectivity. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Investigation of DNA Sequences Utilizing Frequency-Selective Nanopore Structures

Author

Hilal-Alnaqbi, Ali, Ahmad, Mahmoud Al, Rizvi, Tahir A., Mustafa, Farah, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Rojas, Ignacio, editor, and Ortuño, Francisco, editor

Published
2017
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18. HLA class I associations with the severity of COVID-19 disease in the United Arab Emirates

Author

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

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.

Published
2023

24. Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging

Author

Krishnan, Anjana, Ali, Lizna M., Prabhu, Suresha G., Pillai, Vineeta N., Chameettachal, Akhil, Vivet-Boudou, Valérie, Bernacchi, Serena, Mustafa, Farah, Marquet, Roland, and Rizvi, Tahir A.

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 U85CUG88stretch 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 U85CUG88stretch, 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 U85CUG88sequence is important during FIV RNA packaging. Filter-binding assays performed using purified FIV Pr50Gagon WT and mutant U85CUG88ψ RNAs led to reduced levels of Pr50Gagbinding to mutant U85CUG88ψ RNAs, indicating that the U85CUG88stretch is crucial for ψ RNA–Pr50Gaginteractions. 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.

Published
2024
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27. Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology

Author

Henschel, Andreas, Feng, Samuel F., Hamoudi, Rifat A., Elbait, Gihan Daw, Damiani, Ernesto, Waasia, Fathimathuz, Tay, Guan K., Mahboub, Bassam H., Uddin, Maimunah Hemayet, Acuna, Juan, Alefishat, Eman, Halwani, Rabih, Jelinek, Herbert F., Mustafa, Farah, Alkaabi, Nawal, Alsafar, Habiba S., Henschel, Andreas, Feng, Samuel F., Hamoudi, Rifat A., Elbait, Gihan Daw, Damiani, Ernesto, Waasia, Fathimathuz, Tay, Guan K., Mahboub, Bassam H., Uddin, Maimunah Hemayet, Acuna, Juan, Alefishat, Eman, Halwani, Rabih, Jelinek, Herbert F., Mustafa, Farah, Alkaabi, Nawal, and Alsafar, Habiba S.

Abstract

Global and local whole genome sequencing of SARS-CoV-2 enables the tracing of domestic and international transmissions. We sequenced Viral RNA from 37 sampled Covid-19 patients with RT-PCR-confirmed infections across the UAE and developed time-resolved phylogenies with 69 local and 3,894 global genome sequences. Furthermore, we investigated specific clades associated with the UAE cohort and, their global diversity, introduction events and inferred domestic and international virus transmissions between January and June 2020. The study comprehensively characterized the genomic aspects of the virus and its spread within the UAE and identified that the prevalence shift of the D614G mutation was due to the later introductions of the G-variant associated with international travel, rather than higher local transmissibility. For clades spanning different emirates, the most recent common ancestors pre-date domestic travel bans. In conclusion, we observe a steep and sustained decline of international transmissions immediately following the introduction of international travel restrictions.

Published
2022

31. 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

Ismail AlHosani, Farida, primary, Eduardo Stanciole, Anderson, additional, Aden, Bashir, additional, Timoshkin, Andrey, additional, Najim, Omar, additional, Abbas Zaher, Walid, additional, AlSayedsaleh AlDhaheri, Fatima, additional, Al Mazrouie, Shereena, additional, Rizvi, Tahir Aziz, additional, and Mustafa, Farah, additional

Published
2022
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36. Role of Purine-Rich Regions in Mason-Pfizer Monkey Virus (MPMV) Genomic RNA Packaging and Propagation

Author

Ali, Lizna Mohamed, Pitchai, Fathima Nuzra Nagoor, Ali, Lizna, Pitchai, Fathima, Vivet-Boudou, Valérie, Chameettachal, Akhil, Jabeen, Ayesha, Pillai, Vineeta, Mustafa, Farah, Marquet, Roland, Rizvi, Tahir, Architecture et Réactivité de l'ARN (ARN), Institut de biologie moléculaire et cellulaire (IBMC), and Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), RNA packaging, base paired purines, single-stranded purines, retroviruses, [SDV]Life Sciences [q-bio], Mutant, lcsh:QR1-502, RNA-Gag interaction, Biology, Microbiology, Primer extension, Virus, lcsh:Microbiology, Nucleic acid secondary structure, 03 medical and health sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Guide RNA, Binding site, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Original Research, Genetics, 0303 health sciences, 030306 microbiology, RNA, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Stem-loop, RNA secondary structure, SHAPE, Mason-Pfizer monkey virus
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.

Published
2020
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38. A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag

Author

Chameettachal, Akhil, primary, Vivet-Boudou, Valérie, additional, Pitchai, Fathima Nuzra Nagoor, additional, Pillai, Vineeta N, additional, Ali, Lizna Mohamed, additional, Krishnan, Anjana, additional, Bernacchi, Serena, additional, Mustafa, Farah, additional, Marquet, Roland, additional, and Rizvi, Tahir A, additional

Published
2021
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42. Sinopharm's BBIBP-CorV Vaccine Effectiveness on Preventing Hospital Admission and Deaths: Results From a Retrospective Study in the Emirate of Abu Dhabi, United Arab Emirates (UAE)

Author

Hosani, Farida Ismail Al, primary, Stanciole, Anderson Eduardo, additional, Aden, Bashir, additional, Timoshkin, Andrey, additional, Najim, Omar, additional, Zaher, Walid Abbas, additional, AlDhaheri, Fatima AlSayedsaleh, additional, Al Mazrouei, Shereena, additional, Rizvi, Tahir A., additional, and Mustafa, Farah, additional

Published
2021
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48. SARS-CoV-2/COVID-19: Viral Genomics, Epidemiology, Vaccines, and Therapeutic Interventions

Author

Uddin, Mohammed, primary, Mustafa, Farah, additional, Rizvi, Tahir A., additional, Loney, Tom, additional, Al Suwaidi, Hanan, additional, Al-Marzouqi, Ahmed H. Hassan, additional, Kamal Eldin, Afaf, additional, Alsabeeha, Nabeel, additional, Adrian, Thomas E., additional, Stefanini, Cesare, additional, Nowotny, Norbert, additional, Alsheikh-Ali, Alawi, additional, and Senok, Abiola C., additional

Published
2020
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