Biology subjects

Nayak, A. R.

Publications and source records attributed to Nayak, A. R..

4 recordsLinked to original sources

bioRxiv2026

Characterization of the vertical distribution of plankton and the formation of thin layers in the northern Gulf of Mexico using digital holography

The Mississippi River (MR) is the largest source of freshwater and nutrients to the Gulf of Mexico (GoM), strongly influencing stratification, primary production, and plankton organization. The interaction between buoyant plume waters and denser shelf waters in the northern Gulf of Mexico (nGoM) generates sharp density gradients that can promote fine-scale biological aggregation. We investigated how hydrographic structure associated with the MR plume controls the vertical distribution of plankton during May 2017 using an integrated instrumentation suite that included an in situ digital holographic imaging system (HOLOCAM) coupled with CTD and optical sensors. Phytoplankton thin layers were repeatedly detected at plume-edge stations within or immediately above a compressed pycnocline formed by bottom-trapped saline wedges. These layers were 1.2-3.5 m thick and exhibited chlorophyll-a concentrations up to threefold higher than background levels. The assemblage was dominated by chain-forming diatoms, particularly Chaetoceros debilis and C. socialis, whose local abundance maxima coincided with chlorophyll peaks. In contrast, copepods, appendicularians, and other zooplankton were broadly distributed throughout the upper water column and rarely aggregated within the layers. Redundancy analysis indicated that chlorophyll concentration and stratification intensity were primary drivers of community structure across stations. Satellite imagery revealed rapid short-term variability in plume extent, helping explain differences in stratification and thin layer development among sampling days. Our results demonstrate that salt-wedge dynamics at the plume-shelf interface constitute a key physical mechanism governing transient phytoplankton thin layer formation in the nGoM, while zooplankton responses remain weakly coupled at the temporal scales resolved here.

ecology↗

bioRxiv2025

Structural Basis for Promoter Recognition and Transcription Factor Binding and Release in Human Mitochondria

Transcription in human mitochondria is driven by a core apparatus consisting of a Pol A family RNA polymerase (mtRNAP), the initiation factors TFAM and TFB2M, and the elongation factor TEFM. While earlier structures of initiation and elongation complexes provided valuable snapshots, they represent isolated stages of a highly dynamic and multistep process. Critical aspects of mitochondrial transcription--such as DNA recognition and melting, promoter escape, and the release of initiation factors--remain poorly understood. Here, we present a series of cryo-EM structures that capture the transcription complex as it transitions from the initial open promoter complex to the processive elongation complex through intermediate stages. Our data reveal new determinants of promoter specificity, the sequential disengagement of mtRNAP from TFAM and the promoter, the release of TFB2M, and the recruitment of TEFM. Together, these findings provide a detailed molecular mechanism underlying transcription in human mitochondria.

molecular biology↗

bioRxiv2024

Interplay between Mg2+ and Ca2+ at multiple sites of the ryanodine receptor

RyR1 is an intracellular Ca2+ channel important in excitable cells. Ca2+ activates it at low concentrations and inhibits it at high concentrations. Mg2+ is the main physiological RyR1 inhibitor, an effect that is overridden upon activation. Despite the significance of Mg2+-mediated inhibition, the molecular-level mechanisms remain unclear. We determined two cryo-EM structures of RyR1 with Mg2+ up to 2.8 [A] resolution, identifying multiple Mg2+ binding sites. Mg2+ inhibits at the known Ca2+ activating site and we propose that the EF hand domain is an inhibitory divalent cation sensor. Both divalent cations bind to ATP within a crevice, contributing to the precise transmission of allosteric changes within the enormous channel protein. Notably, Mg2+ inhibits RyR1 by interacting with the gating helices as validated by molecular dynamics. This structural insight enhances our understanding of how Mg2+ inhibition is overcome during excitation.

biophysics↗

bioRxiv2022

Cryo-EM structure of the Type IV pilus extension ATPase from enteropathogenic Escherichia coli

Type 4 pili (T4P) are retractable surface appendages found on numerous bacteria and archaea that play essential roles in various microbial functions, including host colonization by pathogens. An ATPase is required for T4P extension, but the mechanism by which chemical energy is transduced to mechanical energy for pilus extension has not been elucidated. Here we report the cryo-electron microscopy (cryo-EM) structure of the BfpD ATPase from enteropathogenic Escherichia coli (EPEC) in the presence of either ADP or a mixture of ADP and AMP-PNP. Both structures, solved at 3 [A] resolution, reveal the typical toroid shape of AAA+ ATPases and unambiguous six-fold symmetry. This six-fold symmetry contrasts with the two-fold symmetry previously reported for other T4P extension ATPase structures, all of which were from thermophiles and solved by crystallography. In the presence of the nucleotide mixture, BfpD bound exclusively AMP-PNP and this binding resulted in a modest outward expansion in comparison to the structure in the presence of ADP, suggesting a concerted model for hydrolysis. De novo molecular models reveal a partially open configuration of all subunits where the nucleotide binding site may not be optimally positioned for catalysis. ATPase functional studies reveal modest activity similar to that of other extension ATPases, while calculations indicate that this activity is insufficient to power pilus extension. Our results reveal that, despite similarities in primary sequence and tertiary structure, T4P extension ATPases exhibit divergent quaternary configurations. Our data raise new possibilities regarding the mechanism by which T4P extension ATPases power pilus formation.

microbiology↗