Biology subjects

Srivastava, Y.

Publications and source records attributed to Srivastava, Y..

4 recordsLinked to original sources

bioRxiv2025

Template-based RNA structure prediction advanced through a blind code competition

Automatically predicting RNA 3D structure from sequence remains an unsolved challenge in biology and biotechnology. Here, we describe a Kaggle code competition engaging over 1700 teams and 43 previously unreleased structures to tackle this challenge. The top three submitted algorithms achieved scores within statistical error of the winners of the recent CASP16 competition. Unexpectedly, the top Kaggle strategy involved a pipeline for discovering 3D templates, without the use of deep learning. We integrated this template-modeling pipeline and other Kaggle strategies to develop a single model RNAPro that retrospectively outperformed individual Kaggle models on the same test set. These results suggest a growing importance of template-based modeling in RNA structure prediction.

biophysics↗

bioRxiv2025

ILP4 and InR regulate Paclitaxel-induced hypersensitivity differently in Drosophila larvae

Paclitaxel (PTX), a chemotherapeutic that stabilizes microtubules, induces nociceptive hypersensitivity and sensory neuron damage in humans, mice, and flies. To enhance our basic understanding of PTX-induced effects we undertook a molecular/genetic dissection of PTX-induced nociceptive hypersensitivity. Larvae fed viable doses of PTX exhibited dose-dependent hypersensitivity to sub-noxious thermal stimuli. Hypersensitivity developed rapidly and did not completely resolve at the larval stage. Live imaging of peripheral thermal nociceptors showed that lower doses of PTX (< 10 {micro}M) caused hyper-sprouting of tertiary dendritic branches. At 10 {micro}M and above, dendritic beading was observed. PTX-induced hypersensitivity does not depend on signaling pathways previously implicated in acute injury-induced nociceptive sensitization. However, the insulin-like peptide 4 (ILP4), was required for PTX-induced thermal hypersensitivity at 10 {micro}M PTX. Surprisingly, RNAi targeting the insulin receptor (InR) in nociceptors increased PTX-induced hypersensitivity, suggesting that ILP4 does not activate InR in this context. The salivary gland is likely the primary tissue source of functional ILP4. ILP4 mutant larvae did not exhibit PTX-induced beading (10 {micro}M) but did exhibit hypersprouting at lower PTX concentrations. In summary, our model of PTX-induced hypersensitivity reveals a disconnect between hypersensitivity and neuronal morphology and a genetic separation of ILP4 and InR in PTX-induced hypersensitivity.

genetics↗

bioRxiv2025

Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers

Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular. Here, we report quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs, however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, e.g., the nucleic-acid backbone bends or a base forms a non-standard hydrogen bond. These bends and non-canonical interactions are integral to form functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life-cycle, posing a future challenge for the community.

biophysics↗

bioRxiv2023

Role of a Pdlim5:PalmD complex in directing dendrite morphology

Neuronal connectivity is regulated during normal brain development with the arrangement of spines and synapses being dependent on the morphology of dendrites. Further, in multiple neurodevelopmental and aging disorders, disruptions of dendrite formation or shaping is associated with atypical neuronal connectivity. We showed previously that Pdlim5 binds delta-catenin and promotes dendrite branching (Baumert et al., J Cell Biol 2020). We report here that Pdlim5 interacts with PalmD, a protein previously suggested by others to interact with the cytoskeleton (e.g., via adducin/spectrin) and to regulate membrane shaping. Functionally, the knockdown of PalmD or Pdlim5 in rat primary hippocampal neurons dramatically reduces branching and conversely, PalmD exogenous expression promotes dendrite branching as does Pdlim5. Further, we show that each proteins effects are dependent on the presence of the other. In summary, using primary rat hippocampal neurons we reveal the contributions of a novel Pdlim5:PalmD protein complex, composed of functionally inter-dependent components responsible for shaping neuronal dendrites.

neuroscience↗