Biology subjects

Naik, T.

Publications and source records attributed to Naik, T..

3 recordsLinked to original sources

bioRxiv2026

Decoupled phenology and PSII thermal plasticity in seasonally dry tropical forest trees

We tested whether seasonal plasticity in photosystem II (PSII) heat tolerance aligns with leaf phenology in tropical trees, comparing evergreen and deciduous species across the wettopostwet transition in a seasonally dry tropical forest of the central Western Ghats, India. This transition, preceding droughtinduced senescence, represents the key window to assess true unstressed thermal plasticity. PSII thermal traits: damage onset (T5), damage midpoint (T50), and temperature between damage onset to full loss (T95-T5), decline width (DW) were quantified in 27 cooccurring species during the wet (27.5{square}{degrees}C) and postwet (31.6{square}{degrees}C) periods. Contrary to phenologybased predictions, PSII plasticity was not structured by leaf habit or successional status. Both T5 (+1.7{square}{degrees}C) and T50 (+0.9{square}{degrees}C) increased significantly across seasons, but responses were speciesspecific, with evergreen and deciduous trees acclimating similarly. The preventionversusforbearance tradeoff (T5 - DW relationship) remained conserved, though leaf habits diverged under postwet conditions. Thermal safety margins based on T50 were large, but T5 revealed vulnerable latesuccessional evergreens (Saraca asoca, Ficus spp.) and Careya arborea. These results show that PSII thermotolerance regulation operates largely independently of droughtavoidance phenology, indicating species identity and not leaf habit drives plasticity in PSII thermal response in seasonally dry tropical forests.

physiology↗

bioRxiv2023

Intermediate antiparallel fibrils in Aβ40 Dutch mutant aggregation: nanoscale insights from AFM-IR

Cerebral Amyloid Angiopathy (CAA), which involves amyloid deposition in blood vessels leading to fatal cerebral hemorrhage and recurring strokes, is present in the majority Alzheimers disease cases. Familial mutations in the amyloid {beta} peptide is correlated to higher risks of CAA, and are mostly comprised of mutations at residues 22 and 23. While the structure of the wild type A{beta} peptide has been investigated in great detail, less is known about the structure of mutants involved in CAA and evolutions thereof. This is particularly true for mutations at residue 22, for which detailed molecular structures, as typically determined from Nuclear Magnetic Resonance (NMR) spectroscopy or electron microscopy, do not exist. In this report, we have used nanoscale infrared (IR) spectroscopy augmented with Atomic Force Microscopy (AFM-IR) to investigate structural evolution of the A{beta} Dutch mutant (E22Q) at the single aggregate level. We show that that in the oligomeric stage, the structural ensemble is distinctly bimodal, with the two subtypes differing with respect to population of parallel {beta}-sheets. Fibrils on the other hand are structurally homogeneous, with early-stage fibrils distinctly anti parallel in character, which develop parallel {beta}-sheets upon maturation. Furthermore, the antiparallel structure is found to be a persistent feature across different stages of aggregation.

biophysics↗

bioRxiv2020

High quality single amplicon sequencing method for illumina platforms using N (0-10) spacer primer pool without PhiX spik-in

Illumina sequencing platform requires base diversity in initial 11 cycles for efficient cluster identification and color matrix estimation. This limitation yields low quality data for amplicon libraries having homogeneous base composition. Spike-in of PhiX library ensures base diversity but overall reduces the number of sequencing reads for data analysis. To overcome such low diversity issues during amplicon sequencing on illumina platforms we developed high throughput single amplicon sequencing method by introducing N spacers in target gene amplification primers that are pooled for simple handling. We evaluated the efficiency of N spacer primers by targeting bacterial 16S V3-V4 region, demonstrating heterogonous base library construction. Addition of N spacer causes sequencing frame shift at every base that leads to base diversity and produces heterogenous high quality reads within single amplicon library. We have written a python script "MetReTrim" to trim the heterogenous N spacers from the pre-processed reads. This method terminates the need for PhiX spike-in and allows for multiplexing of multiple samples, greatly reducing the overall cost and yields improved sequence quality.

genomics↗