Biology subjects

Fadaei, F.

Publications and source records attributed to Fadaei, F..

5 recordsLinked to original sources

bioRxiv2026

Integrating longitudinal hyperspectral phenotyping with AI and GWAS to dissect barley waterlogging responses

Waterlogging is a major constraint on barley productivity, yet its dynamic, multi-phase nature makes it challenging to dissect using traditional phenotyping approaches. High-throughput phenotyping (HTP) platforms address this by enabling temporal, multi-sensor imaging of large populations, but generate complex datasets that demand new analytical frameworks. Here, we imaged 230 barley accessions over 14 days of waterlogging stress and seven days of recovery using visible, chlorophyll fluorescence, and hyperspectral sensors. Explainable AI was applied to classify stress responses into early stress, late stress, and recovery phases, achieving 86% classification accuracy, and to identify the hyperspectral indices most informative for each phase. Water index (WATER1) and structure insensitive pigment index (SIPI) emerged as primary predictors of stress response. Longitudinal genome-wide association studies (GWAS), using a treatment-by-marker interaction model, identified 236 significant loci across 12 linkage disequilibrium blocks, implicating candidate genes involved in oxidative stress regulation, transcriptional control, and auxin transport. MYB transcription factors were consistently identified across all stress phases, underscoring their central role in waterlogging adaptation. To support interpretation of longitudinal GWAS results, we developed 3D-QTLVis, an interactive visualisation tool that extends Manhattan plots across time, enabling clearer identification of dynamic genomic regions underlying stress tolerance.

plant biology↗

bioRxiv2026

DNA Double-decker Ring Scaffolded Nanodisc for Self-assembly of Membrane Protein into Lipid Bilayer

Membrane models of scaffolded discoidal lipid bilayers called nanodiscs have proven to be a valuable tool for the study of membrane proteins in a native environment. DNA-scaffolded membrane model has emerged as an alternative tool for membrane protein studies. Taking advantage of the designability of DNA nanostructure, we created a double-decker double-stranded DNA ring (DDring) to self-assemble DNA-based nanodiscs (DNA-ND). The DDring is 17 nm wide and 4 nm high, and equipped with 28 alkyl chains on the inside that can interact with each hydrophobic leaflet of the lipid bilayer. We further demonstrate the functionality of DNA-ND membrane model with the assembly of membrane proteins. DDrings are suited to neutral or cationic charged phospholipids and detergents. This study provides more insights into the potential use of DNA- assisted nanodiscs for membrane protein characterization.

bioengineering↗

bioRxiv2026

Peptide-DNA Conjugates for Formation of Lipid Nanodiscs

Nanoscale lipid bilayer mimetics are powerful tools for research on lipid bilayer, membrane proteins or for drug delivery. Established nanoscale bilayer systems that are stabilized by short peptides or polymers produce a broad size distribution and are difficult to customize. Here we introduce a DNA nanotechnology-based lipid bilayer mimetic, in which we covalently conjugated established nanodisc-forming amphiphilic peptides to oligonucleotides. These peptide-DNA conjugates were then hybridized with a circular single-stranded scaffold to form stiff, circular PDC minicircles with 14 peptide modifications at the inner rim of the torus. Lipid reconstitution yielded defined nanodisc with a tightly controlled circumference and component stoichiometry. Molecular dynamics simulations further validated the structural stability and reveal an asymmetric migration of the DNA to one rim of the bilayer. To mimic membrane protein insertion, we co-reconstituted a transmembrane peptide coupled to a bulky quantum dot. In future applications, the size and peptide arrangement can easily be modified in these DNA-templated PDC nanodiscs.

biochemistry↗

bioRxiv2025

S-Alkyl-Phosphorothioate Modifications Reduce Thermal and Structural Stability of DNA Duplexes

While phosphorothioate (PS) oligonucleotides are usually used in therapeutic applications, they also offer the cheapest and synthetically most straightforward route to introduce hydrophobic modifications for applications in structural DNA nanotechnology and biophysics. For this, the sulfur atom is S-alkylated with alkyl iodides, enabling a hydrophobically tunable interface of DNA nanostructures with lipid bilayers. While longer and more alkyls per helical turn should lead to stronger interactions with lipid membranes, we found that excessive S-alkylations strongly inhibit hybridization of oligonucleotides to their complementary strands and decrease their melting temperature, despite a reduction in electrostatic repulsion between the two strands. Moreover, both the type and placement of alkyl modifications influence the melting temperature. Atomistic molecular dynamics simulations reveal two complementary mechanisms that explain the experimental findings. First, S-alkylated oligonucleotides are more compact and less dynamic than unmodified ones, likely inhibiting their ability to hybridize to their complementary strands. Second, S-alkyls in double-stranded DNA promote defect formation due to alkyl modifications having hydrophobic interactions with other alkyl groups and nucleobases, therefore reducing the thermal and structural stability of alkylated DNA duplexes. This study serves as a practical guide for tuning hydrophobicity while maintaining structural stability in membrane-interfacing DNA nanostructures.

biochemistry↗

bioRxiv2024

Bending Unwinds DNA

DNA is under high bending and torsional strain in many biological contexts 1,2, but elastic limits of tightly bent DNA under simultaneous torsional strain are not fully understood 3-22. We synthesized DNA circles with all possible radii of curvature between r {approx} 2.7 - 5.7 nm in increments of{Delta} r = 0.05 nm and defined helical repeats ranging from h {approx} 10 - 13 base pairs per helical turn. Nuclease digest reveals that DNA can be bent to r {approx} 3.0 nm without kinking, but only when h < ~10.9 bp/turn, while underwound DNA kinks irrespective of curvature. Histone proteins overwind DNA and thereby mechanically stabilize it. The natural helical repeat h0 increases from 10.45 to >11 bp/turn due to twist-bend coupling, which is not caused by kinking before ligation. These findings require reassessing our models and the energetics of molecular mechanisms involving DNA under mechanical stress.

biophysics↗