Bio


I am a postdoctoral researcher in the lab of Prof. Priscilla Yang since September 2021. I am interested in virus-induced changes in membrane lipid composition of infected cells and my research focuses on developing experimental systems to interrogate the impact of lipid composition on membrane-associated RNA virus replication, using hepatitis C virus and brome mosaic virus as model systems.
During my doctoral studies, under the supervision of Prof. ALN Rao at the University of California-Riverside, I investigated capsid dynamics in multipartite bromoviruses, a group of icosahedral, plant-pathogenic RNA viruses belonging to the alphavirus-like super-family.

Honors & Awards


  • Calavan Award in Recognition of Excellence and Creative, Forward Thinking in Research, University of California, Riverside (2021)
  • Charles W. Coggins Jr. Endowed Scholarship Award, University of California, Riverside (2021)
  • CEPCEB Graduate Student Award for Outstanding Research, Center for Plant Cell Biology, University of California, Riverside (2020)
  • Dissertation Year Program Award, University of California, Riverside (2019)
  • Graduate Student Travel Award, American Society for Virology (2019)
  • Klotz Memorial Fund Travel Award, University of California, Riverside (2019)
  • NSF Innovation-Corps Fellowship, National Science Foundation (NSF) Innovat’R Program (2019)
  • APS Foundation Mathre Education Endowment Award, American Phytopathological Society (2018)

Professional Education


  • Doctor of Philosophy, University of California, Riverside (2021)
  • Master of Science, University of Hyderabad (2013)
  • Bachelor of Science, Presidency College, University of Calcutta (2011)

Stanford Advisors


All Publications


  • Genome organization and interaction with capsid protein in a multipartite RNA virus PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Beren, C., Cui, Y., Chakravarty, A., Yang, X., Rao, A. N., Knobler, C. M., Zhou, Z., Gelbart, W. M. 2020; 117 (20): 10673-10680

    Abstract

    We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a sample consisting exclusively of particles with the same RNA content-specifically, RNAs 3 and 4-assembled in planta by agrobacterium-mediated transient expression. We find that the interior of the particle is nearly empty, with most of the RNA genome situated at the capsid shell. However, this density is disordered in the sense that the RNA is not associated with any particular structure but rather, with an ensemble of secondary/tertiary structures that interact with the capsid protein. Our results illustrate a fundamental difference between the ssRNA organization in the multipartite BMV viral capsid and the monopartite bacteriophages MS2 and Qβ for which a dominant RNA conformation is found inside the assembled viral capsids, with RNA density conserved even at the center of the particle. This can be understood in the context of the differing demands on their respective lifecycles: BMV must package separately each of several different RNA molecules and has been shown to replicate and package them in isolated, membrane-bound, cytoplasmic complexes, whereas the bacteriophages exploit sequence-specific "packaging signals" throughout the viral RNA to package their monopartite genomes.

    View details for DOI 10.1073/pnas.1915078117

    View details for Web of Science ID 000535585100016

    View details for PubMedID 32358197

    View details for PubMedCentralID PMC7245085

  • Unravelling the Stability and Capsid Dynamics of the Three Virions of Brome Mosaic Virus Assembled Autonomously In Vivo JOURNAL OF VIROLOGY Chakravarty, A., Reddy, V. S., Rao, A. N. 2020; 94 (8)

    Abstract

    Viral capsids are dynamic assemblies that undergo controlled conformational transitions to perform various biological functions. The replication-derived four-molecule RNA progeny of Brome mosaic virus (BMV) is packaged by a single capsid protein (CP) into three types of morphologically indistinguishable icosahedral virions with T=3 quasisymmetry. Type 1 (B1V) and type 2 (B2V) virions package genomic RNA1 and RNA2, respectively, while type 3 (B3+4V) virions copackage genomic RNA3 (B3) and its subgenomic RNA4 (sgB4). In this study, the application of a robust Agrobacterium-mediated transient expression system allowed us to assemble each virion type separately in planta Experimental approaches analyzing the morphology, size, and electrophoretic mobility failed to distinguish between the virion types. Thermal denaturation analysis and protease-based peptide mass mapping experiments were used to analyze stability and the conformational dynamics of the individual virions, respectively. The crystallographic structure of the BMV capsid shows four trypsin cleavage sites (K65, R103, K111, and K165 on the CP subunits) exposed on the exterior of the capsid. Irrespective of the digestion time, while retaining their capsid structural integrity, B1V and B2V released a single peptide encompassing amino acids 2 to 8 of the N-proximal arginine-rich RNA binding motif. In contrast, B3+4V capsids were unstable with trypsin, releasing several peptides in addition to the peptides encompassing four predicted sites exposed on the capsid exterior. These results, demonstrating qualitatively different dynamics for the three types of BMV virions, suggest that the different RNA genes they contain may have different translational timing and efficiency and may even impart different structures to their capsids.IMPORTANCE The majority of viruses contain RNA genomes protected by a shell of capsid proteins. Although crystallographic studies show that viral capsids are static structures, accumulating evidence suggests that, in solution, virions are highly dynamic assemblies. The three genomic RNAs (RNA1, -2, and -3) and a single subgenomic RNA (RNA4) of Brome mosaic virus (BMV), an RNA virus pathogenic to plants, are distributed among three physically homogeneous virions. This study examines the thermal stability by differential scanning fluorimetry (DSF) and capsid dynamics by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analyses following trypsin digestion of the three virions assembled separately in vivo using the Agrobacterium-mediated transient expression approach. The results provide compelling evidence that virions packaging genomic RNA1 and -2 are distinct from those copackaging RNA3 and -4 in their stability and dynamics, suggesting that RNA-dependent capsid dynamics play an important biological role in the viral life cycle.

    View details for DOI 10.1128/JVI.01794-19

    View details for Web of Science ID 000522728700005

    View details for PubMedID 31996436

    View details for PubMedCentralID PMC7108849

  • Zebrafish twist2/dermo1 regulates scale shape and scale organization during skin development and regeneration CELLS & DEVELOPMENT Jacob, T., Chakravarty, A., Panchal, A., Patil, M., Ghodadra, G., Sudhakaran, J., Nuesslein-Volhard, C. 2021; 166: 203684

    Abstract

    Scales are skin appendages in fishes that evolutionarily predate feathers in birds and hair in mammals. Zebrafish scales are dermal in origin and develop during metamorphosis. Understanding regulation of scale development in zebrafish offers an exciting possibility of unraveling how the mechanisms of skin appendage formation evolved in lower vertebrates and whether these mechanisms remained conserved in birds and mammals. Here we have investigated the expression and function of twist 2/dermo1 gene - known for its function in feather and hair formation - in scale development and regeneration. We show that of the four zebrafish twist paralogues, twist2/dermo1 and twist3 are expressed in the scale forming cells during scale development. Their expression is also upregulated during scale regeneration. Our knockout analysis reveals that twist2/dermo1 gene functions in the maintenance of the scale shape and organization during development as well as regeneration. We further show that the expression of twist2/dermo1 and twist3 is regulated by Wnt signaling. Our results demonstrate that the function of twist2/dermo1 in skin appendage formation, presumably under regulation of Wnt signaling, originated during evolution of basal vertebrates.

    View details for DOI 10.1016/j.cdev.2021.203684

    View details for Web of Science ID 000687603400009

    View details for PubMedID 33994357

  • The interplay between capsid dynamics and pathogenesis in tripartite bromoviruses CURRENT OPINION IN VIROLOGY Chakravarty, A., Rao, A. N. 2021; 47: 45-51

    Abstract

    Infectious virus capsids or virions are considered static structures and undergo various conformational transitions to replicate and infect a wide range of eukaryotic cells. Therefore, virus capsids must be stable enough to overcome the physicochemical environment and flexible enough to reorganize their biologically relevant surface peptides for optimal interaction with the host machinery. Although viral capsid fluctuations, referred to as dynamics or breathing, have been well studied in RNA viruses pathogenic to animals, such information is limited among plant viruses. However, more recent attempts have been made in characterizing the capsid dynamics in the plant virus genus bromovirus characterized by having a tripartite, positive-sense RNA genome. Using the available research data on the genus bromovirus members, this review is focused on updating the readers on the interrelationships between the viral capsid dynamics and host-pathogen interactions.

    View details for DOI 10.1016/j.coviro.2020.12.005

    View details for Web of Science ID 000642042600007

    View details for PubMedID 33517133