Article
Biochemistry & Molecular Biology
Fathima Nuzra Nagoor Pitchai, Akhil Chameettachal, Valerie Vivet-Boudou, Lizna Mohamed Ali, Vineeta N. Pillai, Anjana Krishnan, Serena Bernacchi, Farah Mustafa, Roland Marquet, Tahir A. Rizvi
Summary: In this study, retroviral Gag proteins were found to select gRNA against spliced viral RNA by simultaneously binding to two single stranded loops on the MPMV Psi RNA. The second Gag binding site, crucial for MPMV gRNA packaging, is located immediately downstream of the major splice donor.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Akhil Chameettachal, Farah Mustafa, Tahir A. Rizvi
Summary: Members of the Retroviridae family are important pathogens in animals and humans. The replication of retroviruses involves multiple unique steps, such as reverse transcription, integration, and specific packaging of their genomic RNA. Although progress has been made in understanding the molecular mechanisms of these steps, many aspects remain unknown or controversial. This review provides a comprehensive analysis of our current understanding of retrovirus replication and RNA packaging, highlighting the interplay between viral and cellular factors and exploring areas for further research.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biology
Xiao Lei, Daniel Goncalves-Carneiro, Trinity M. Zang, Paul D. Bieniasz
Summary: Encapsidation of HIV-1 gRNA into virions is facilitated by the binding of HIV-1 Gag polyprotein's nucleocapsid (NC) domain to the viral RNA packaging signal (psi). However, the subcellular location and oligomeric status of Gag during initial Gag-psi encounter are still uncertain. To investigate the contribution of Gag domains to psi recognition in cells, protein-protein and protein-RNA crosslinking studies were conducted. The results revealed that NC alone does not specifically bind to psi, while full-length Gag and CANC subdomain do. Furthermore, proper assembly of a nascent immature capsid (CA) lattice is essential for the specific interaction between Gag and psi in cells.
Article
Virology
M. I. Zarudnaya, A. L. Potyahaylo, I. M. Kolomiets, L. G. Gorb
Summary: In this study, the secondary structure of specific regions in HIV-1, HIV-2, and SIV genomes was investigated using computational simulation. Similarities and differences were found, providing important insights into the evolution and transmission of these viruses.
Article
Biochemistry & Molecular Biology
Sayuri Sakuragi, Osamu Kotani, Masaru Yokoyama, Tatsuo Shioda, Hironori Sato, Jun-ichi Sakuragi
Summary: This study reveals that the dinucleotide pair at positions 226 and 227 within the psi segment of HIV-1 plays a critical role in regulating the packaging efficiency. Molecular genetic investigations and simulations suggest that nucleotide variations at these positions alter the structural dynamics of the psi element, affecting the binding interface of viral nucleocapsid protein.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Alice Sosic, Richard Gottlich, Dan Fabris, Barbara Gatto
Summary: This study reveals the potential of B-CePs as probes for RNA structures and confirms their ability to help investigate RNA systems that are not readily amenable to traditional high-resolution techniques.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Liqing Ye, Anne-Sophie Gribling-Burrer, Patrick Bohn, Anuja Kibe, Charlene Boertlein, Uddhav B. Ambi, Shazeb Ahmad, Marco Olguin-Nava, Maureen Smith, Neva Caliskan, Max von Kleist, Redmond P. Smyth
Summary: RNA dimerization plays a crucial role in the HIV-1 life cycle and genome packaging. Using FARS-seq, we identified important nucleotides and distinct structural conformations in the HIV-1 5' UTR that regulate the dimerization process. Our findings provide insights into the late stages of HIV-1 life cycle and unravel the mechanistic link between RNA dimerization, Pr55Gag binding, and genome packaging.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Immunology
Farida Ismail AlHosani, Anderson Eduardo Stanciole, Bashir Aden, Andrey Timoshkin, Omar Najim, Walid Abbas Zaher, Fatima AlSayedsaleh AlDhaheri, Shereena Al Mazrouie, Tahir Aziz Rizvi, Farah Mustafa
Summary: This community-based observational study found that the BBIBP-CorV inactivated vaccine is effective in preventing severe COVID-19 outcomes such as hospital admissions and death. Fully vaccinated individuals showed higher protection compared to partially vaccinated individuals.
Article
Biochemistry & Molecular Biology
Camille Libre, Tanja Seissler, Santiago Guerrero, Julien Batisse, Cedric Verriez, Benjamin Stupfler, Orian Gilmer, Romina Cabrera-Rodriguez, Melanie M. Weber, Agustin Valenzuela-Fernandez, Andrea Cimarelli, Lucie Etienne, Roland Marquet, Jean-Christophe Paillart
Summary: The HIV-1 Vif protein decreases the expression of cellular restriction factors APOBEC3G, A3F, A3D, and A3H, which inhibit viral replication. The translation of A3G is regulated by a conserved uORF in the 5' untranslated region of its mRNA. This uORF is also important for Vif-mediated translation inhibition and redirection of A3G mRNA into stress granules.
Article
Engineering, Electrical & Electronic
Mahmoud Al Ahmad, Lillian J. A. Olule, Mohammed Meetani, Farrukh Amin Sheikh, Rahima Al Blooshi, Neena G. Panicker, Farah Mustafa, Tahir A. Rizvi
Summary: This work presents an opto-electrical method to differentiate between SARS-CoV-2 negative and positive nasal swab samples by measuring the interactions between the viral nucleocapsid protein and anti-N antibody. The study found that if the extracted feature value is greater than 1, SARS-CoV-2 can be detected in patient nasal swab samples within two minutes; otherwise, the sample is considered negative.
IEEE JOURNAL OF SELECTED TOPICS IN SIGNAL PROCESSING
(2022)
Article
Infectious Diseases
Agnes Sonnevend, Walid Q. Alali, Sara A. Mahmoud, Akela Ghazawi, Greeshma Bharathan, Szilvia Melegh, Tahir A. Rizvi, Tibor Pal
Summary: Data on the prevalence of MCR-producing Enterobacterales of animal origin are scarce from the Arabian Peninsula. We investigated these strains from poultry fecal specimens in the United Arab Emirates and found mcr-1.1 positive strains in 36 out of 40 samples. Whole genome sequencing revealed the resistance and virulence genes, MLST and cgMLST of 39 selected isolates. Transferability and incompatibility types of the MCR-plasmids were also determined. The diversity of mcr-1 positive strains indicates the need for coordinated surveillance including animals, retail meat and clinical cases.
Article
Infectious Diseases
Agnes Sonnevend, Najiba Abdulrazzaq, Akela Ghazawi, Jens Thomsen, Greeshma Bharathan, Lilla Makszin, Tahir A. Rizvi, Tibor Pal
Summary: This study assessed the prevalence, distribution, and main clonal types of carbapenem-resistant Enterobacterales (CRE) in the United Arab Emirates. The results showed that nearly half of the CRE infections in the country were caused by a limited number of clones. Specific Klebsiella pneumoniae clones were identified as major contributors to CRE. The study also revealed an association between the most resistant clone (CC14) and Emirati patients, highlighting the need for further investigation.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Waleed Ahmed, Ali H. Al-Marzouqi, Muhammad Hamza Nazir, Tahir A. Rizvi, Essam Zaneldin, Mushtaq Khan
Summary: Due to COVID-19 pandemic, novel strategies to combat pathogens are on the rise worldwide. This research investigates an antimicrobial polymeric PLA-based composite material enhanced with different microparticles. Results showed that the sample prepared with 90% copper and 10% PLA exhibited the best antibacterial activity, making it a sustainable solution for various applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Celia Jakob, Rithu Paul-Stansilaus, Martin Schwemmle, Roland Marquet, Hardin Bolte
Summary: The genome of influenza A virus consists of eight unique viral RNA segments, and reassortment events can create new IAVs. Recent research suggests that a viral genome packaging mechanism promotes reassortment by delivering the genome segments into the virus particle. However, there is a current shortage of functionally validated intersegmental RNA-RNA interactions in understanding this mechanism.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Infectious Diseases
Tibor Pal, Aqdas B. Butt, Akela Ghazawi, Jens Thomsen, Tahir A. Rizvi, Agnes Sonnevend
Summary: Recent studies have found that highly resistant clones of Klebsiella pneumoniae, including ST14, ST231, and CC147, dominate the current endemic of carbapenem-resistant Enterobacterales (CRE) in the Emirate of Abu Dhabi. These clones were already present in the early years of the CRE outbreak and have had a significant impact on antibiotic resistance patterns.
Review
Biochemistry & Molecular Biology
Akhil Chameettachal, Farah Mustafa, Tahir A. Rizvi
Summary: Members of the Retroviridae family are important pathogens in animals and humans. The replication of retroviruses involves multiple unique steps, such as reverse transcription, integration, and specific packaging of their genomic RNA. Although progress has been made in understanding the molecular mechanisms of these steps, many aspects remain unknown or controversial. This review provides a comprehensive analysis of our current understanding of retrovirus replication and RNA packaging, highlighting the interplay between viral and cellular factors and exploring areas for further research.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Vineeta N. Pillai, Lizna Mohamed Ali, Suresha G. Prabhu, Anjana Krishnan, Saeed Tariq, Farah Mustafa, Tahir A. Rizvi
Summary: This study successfully expressed soluble and full-length SIV Pr55Gag and purified it using affinity and gel filtration chromatography. The purified Pr55Gag could assemble into virus-like particles in vitro and efficiently package SIV genomic RNA. This research provides an important method for future studies on protein structure and RNA-protein interactions during SIV gRNA packaging.
Article
Biochemistry & Molecular Biology
Waleed Ahmed, Ali H. Al-Marzouqi, Muhammad Hamza Nazir, Tahir A. Rizvi, Essam Zaneldin, Mushtaq Khan, Muthanna Aziz
Summary: Novel strategies and materials have gained attention due to the current pandemic, high global market competition, and pathogen resistance. There is a need to develop cost-effective, eco-friendly, and biodegradable materials to combat bacteria. Fused filament fabrication (FFF), also known as fused deposition modeling (FDM), is the most effective method to develop these composites.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Balaji Venkataraman, Saeeda Almarzooqi, Vishnu Raj, Bhoomendra A. Bhongade, Rajesh B. Patil, Veedamali S. Subramanian, Samir Attoub, Tahir A. Rizvi, Thomas E. Adrian, Sandeep B. Subramanya
Summary: Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a debilitating condition with a multifactorial etiology. Current drug therapies for IBD have adverse effects with long-term use, thus the need for new drug candidates. 1,8-cineole, a monoterpene oxide, has potent anti-inflammatory effects through binding to PPAR?. Studies have shown that 1,8-cineole can decrease inflammation, induce antioxidant effects, and increase PPAR? expression. Due to its strong anti-inflammatory effects, 1,8-cineole may be valuable in treating IBD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Celia Jakob, Gabriel L. Lovate, Daniel Desiro, Lara Giessler, Redmond P. Smyth, Roland Marquet, Kevin Lamkiewicz, Manja Marz, Martin Schwemmle, Hardin Bolte
Summary: A study shows that the vRNA-vRNA interactions detected in influenza virus particles using the SPLASH method may not be critical for genome packaging.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Virology
Waqar Ahmad, Bushra Gull, Jasmin Baby, Neena G. Panicker, Thanumol A. Khader, Shaima Akhlaq, Tahir A. Rizvi, Farah Mustafa
Summary: SARS-CoV-2 infection alters host miRNA expression, which could serve as potential biomarkers for COVID-19 prognosis and the development of anti-virals and therapeutics.
REVIEWS IN MEDICAL VIROLOGY
(2023)
Article
Virology
Waqar Ahmad, Neena G. Panicker, Shaima Akhlaq, Bushra Gull, Jasmin Baby, Thanumol A. Khader, Tahir A. Rizvi, Farah Mustafa
Summary: This study aimed to identify genes and pathways dysregulated by MMTV expression in mouse mammary epithelial cells. mRNAseq analysis revealed differentially expressed genes and pathway dysregulation upon MMTV expression. Bioinformatics analysis identified hub genes and dysregulated molecular pathways, including the down-regulation of the PI3-AKT-mTOR pathway. Comparison with other mouse models provided insights into the molecular mechanisms and potential of MMTV to cause cell transformation. These findings have important implications for the understanding of MMTV replication and its involvement in breast cancer.