Biology subjects

Hastings, R.

Publications and source records attributed to Hastings, R..

3 recordsLinked to original sources

bioRxiv2024

Arabidopsis thaliana RHAMNOSE 1 condensate formation drives UDP-rhamnose synthesis

Rhamnose is an essential component of the plant cell wall and is synthesized from uridine diphosphate (UDP)-glucose by the RHAMNOSE1 (RHM1) enzyme. RHM1 localizes to biomolecular condensates in plants, but their identity, formation, and function remain elusive. Combining live imaging, genetics, and biochemical approaches in Arabidopsis and heterologous systems, we show that RHM1 alone is sufficient to form enzymatically active condensates, which we name rhamnosomes. Rhamnosome formation is required for UDP-rhamnose synthesis and organ development. Overall, our study demonstrates a novel role for biomolecular condensation in metabolism and organismal development, and provides further support for how organisms have harnessed this biophysical process to regulate small molecule metabolism. One-Sentence SummaryCondensation of RHM1 drives UDP-rhamnose synthesis during plant development.

plant biology↗

bioRxiv2023

High-throughput thermodynamic and kinetic measurements of transcription factor/DNA mutations reveal how conformational heterogeneity can shape motif selectivity

Transcription factors (TFs) bind DNA sequences with a range of affinities, yet the mechanisms determining energetic differences between high- and low-affinity sequences ( selectivity) remain poorly understood. Here, we investigated two basic helix-loop-helix TFs, MAX (H. sapiens) and Pho4 (S. cerevisiae), that bind the same high-affinity sequence with highly similar nucleotide-contacting residues and bound structures but are differentially selective for non-cognate sequences. By measuring >1700 Kds and >500 rate constants for Pho4 and MAX mutant libraries binding multiple DNA sequences and comparing these measurements with thermodynamic and kinetic models, we identify the biophysical mechanisms by which changes to TF sequence alter both bound and unbound conformational ensembles to shape specificity landscapes. These results highlight the importance of conformational heterogeneity in determining sequence specificity and selectivity and can guide future efforts to engineer nucleic acid-binding proteins with enhanced selectivity.

biophysics↗

bioRxiv2020

Causal Understanding of the Stone Dropping Task in Two Species of Macaw

Causal understanding in animal cognition can be divided into two broad categories (Woodward, 2011): learned associations between cause and effect (Le Pelley et al., 2017) and understanding based on underlying mechanisms (Johnson and Ahn, 2017). One experiment that gives insight to animals use of causal mechanisms is the stone-dropping task. In this, subjects are given an opportunity to push a platform to make it collapse and are then required to innovate dropping a stone tool to recreate the platform collapsing (von Bayern et al., 2009). We describe how 16/18 subjects of two species of macaw (n=18; Ara ambiguus (n=9) & Ara glaucogularis (n=9)) were able to innovate the solution in this task. Many of the subjects were able to innovate the behaviour through exploratory object combination, but it is also possible that a mechanistic understanding of the necessity for contact with the platform influenced some subjects behaviour. All the successful subjects were able to recreate their novel stone-dropping behaviour in the first or second trial after innovation (and all trials thereafter) and they were also able to do the behaviour increasingly faster. This suggests they also rely on learned associations of cause and effect. However, in a transfer task in which subjects had to guide a stick tool to make it touch a differently positioned platform, all but one of the subjects failed. This would suggest that the majority of the subjects were not using an understanding of platform contact to solve the task, although the subjects difficulty with using stick tools may have also affected their performance in this transfer.

animal behavior and cognition↗