Biology subjects

Eshra, A.

Publications and source records attributed to Eshra, A..

6 recordsLinked to original sources

bioRxiv2025

A Thermodynamically Favoured Molecular Computer: Robust, Fast, Renewable, Scalable

Like life, computers are out-of-equilibrium.1,2 Thermodynamically favoured error states are thwarted by energetically-costly processes such as kinetic proofreading of biological polymers, error-correcting codes in computer data storage, and redundancy in molecular programming. Decades of theoretical work shows that unlike life thermodynamic computers can operate by drifting naturally to equilibrium.3,4 Similar ideas underlie machine learning models5 and search algorithms such as simulated annealing,6 although executed on non-equilibrium architectures at enormous energy cost.7 Physically implementing thermodynamically favoured computation is a decades-long challenge that could reduce dependence on fuel-consuming error-correction and precise kinetic control. Here, we demonstrate a thermodynamically favoured Scaffolded DNA Computer (SDC) on ten programs including MULTIPLICATION-by-3, DO_SCPLOWIVISIONC_SCPLOW-by-2, 8-bit PO_SCPLOWARITYC_SCPLOW-detection, and AO_SCPLOWDDITIONC_SCPLOW of up to 25-bit numbers. SDC algorithms have simple experimental protocols, can be reused dozens of times and small instances run in under a minute. The SDC is grounded in mathematical, physical and computer science principles that explain why the output is thermodynamically favoured, why no error-correction nor precise step-by-step kinetic control are required and how it is programmable and scalable. This work creates a new way to think about equilibrium computation in all manner of synthetic systems.

bioengineering↗

bioRxiv2024

The intracellular Ca2+ sensitivity of transmitter release from neocortical boutons

Synaptotagmin 1 (Syt1) and Syt2 are the main Ca2+ sensors triggering synchronous release in the brain. The Ca2+-sensitivity of Syt2-triggered release has been studied in detail. However, for Syt1, the dominating isoform in the neocortex, quantitative detail is lacking. We measured the Ca2+-dependency of Syt1-triggered release at layer 5 pyramidal neuron synapses by laser photolysis of caged Ca2+. Syt1-triggered release had high Ca2+ affinity and positive cooperativity (EC50, 20 M; Hill coefficient, 3.57). It was steep in a dynamic range between [~]10 and [~]30 M that was covered by action potential-evoked release. A kinetic model reveals significant differences to models of Syt2-triggered release. Our results suggest that Syt1 optimizes neocortical synapses for high reliability at moderate local Ca2+ elevations and for high plastic controllability.

neuroscience↗

bioRxiv2023

Ketamine potentiates a glutamatergic presynapse

Ketamine produces rapid and sustained antidepressant effects after brief exposure to a single dose. Counterintuitively, while ketamine acts primarily as a blocker of postsynaptic N-methyl-D-aspartate receptors (NMDARs), increased signalling at glutamatergic synapses has been reported. Due to technical limitations, however, it remains unclear whether ketamine directly increases presynaptic glutamate release or acts via postsynaptic or network-level mechanisms. To address this knowledge gap, we used presynaptic capacitance measurements to directly monitor glutamate release in a cerebellar synapse. Ketamine increased glutamate release within minutes and this effect persisted >30 minutes after washout. MK-801, another NMDAR blocker, had no effect on glutamate release. Mechanistically, we show that the ketamine-mediated enhancement of presynaptic release results from an increase in both calcium influx and the number of release-ready vesicles. Our data uncover a rapid effect of ketamine on key presynaptic properties of central glutamatergic synapses, which has important implications for the development of antidepressant drugs.

neuroscience↗

bioRxiv2021

Calcium dependence of neurotransmitter release at a high fidelity synapse

The Ca2+-dependence of the recruitment, priming, and fusion of synaptic vesicles are fundamental parameters controlling neurotransmitter release and synaptic plasticity. Despite intense efforts, these important steps in the synaptic vesicles cycle remain poorly understood because disentangling recruitment, priming, and fusion of vesicles is technically challenging. Here, we investigated the Ca2+-sensitivity of these steps at cerebellar mossy fiber synapses, which are characterized by fast vesicle recruitment mediating high-frequency signaling. We found that the basal free Ca2+ concentration (<200 nM) critically controls action potential-evoked release, indicating a high-affinity Ca2+ sensor for vesicle priming. Ca2+ uncaging experiments revealed a surprisingly shallow and non-saturating relationship between release rate and intracellular Ca2+ concentration up to 50 M. Sustained vesicle recruitment was Ca2+-independent. Finally, quantitative mechanistic release schemes with five Ca2+ binding steps incorporating rapid vesicle recruitment via parallel or sequential vesicle pools could explain our data. We thus show that co-existing high and low-affinity Ca2+ sensors mediate recruitment, priming, and fusion of synaptic vesicles at a high-fidelity synapse.

neuroscience↗

bioRxiv2019

Gradients in the cerebellar cortex enable Fourier-like transformation and improve storing capacity

Cerebellar granule cells (GCs) making up majority of all the neurons in the vertebrate brain, but heterogeneities among GCs and potential functional consequences are poorly understood. Here, we identified unexpected gradients in the biophysical properties of GCs. GCs closer to the white matter (inner-zone GCs) had higher firing thresholds and could sustain firing with larger current inputs. Dynamic clamp experiments showed that inner- and outer-zone GCs preferentially respond to high- and low-frequency mossy fiber inputs, respectively, enabling to disperse the mossy fiber input into its frequency components as performed by a Fourier transformation. Furthermore, inner-zone GCs have faster axonal conduction velocity and elicit faster synaptic potentials in Purkinje cells. Neuronal network modeling revealed that these gradients improve spike-timing precision of Purkinje cells and decrease the number of GCs required to learn spike-sequences. Thus, our study uncovers biophysical gradients in the cerebellar cortex enabling a Fourier-like transformation of mossy fiber inputs.

neuroscience↗

bioRxiv2019

HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons

Hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels control electrical rhythmicity and excitability in the heart and brain, but the function of HCN channels at subcellular level in axons remains poorly understood. Here, we show that the action potential conduction velocity in both myelinated and unmyelinated central axons can bidirectionally be modulated by HCN channel blockers, cyclic adenosine monophosphate (cAMP), and neuromodulators. Recordings from mice cerebellar mossy fiber boutons show that HCN channels ensure reliable high-frequency firing and are strongly modulated by cAMP (EC50 40 {micro}M; estimated endogenous cAMP concentration 13 {micro}M). In accord, immunogold-electron microscopy revealed HCN2 as the dominating subunit in cerebellar mossy fibers. Computational modeling indicated that HCN2 channels control conduction velocity primarily via altering the resting membrane potential and was associated with significant metabolic costs. These results suggest that the cAMP-HCN pathway provides neuromodulators an opportunity to finely tune energy consumption and temporal delays across axons in the brain.

neuroscience↗