Biology subjects

Miranda, P.

Publications and source records attributed to Miranda, P..

4 recordsLinked to original sources

bioRxiv2026

Direct detection of electrogenic polyamine transport

Polyamines are cationic metabolites that support critical cellular processes including transcription, translation, and cell proliferation. Although polyamine synthesis and transport are emerging therapeutic targets in human disease, the polyamine transport system remains poorly understood. ATP13A2-4 were recently identified as endolysosomal polyamine exporters, transporting putrescine (PUT), spermidine (SPD), and spermine (SPM) from the vesicular lumen to the cytosol. Despite interest in pharmacologically targeting these transporters, existing assays of transporter function rely on indirect or endpoint measures that cannot resolve transport as it occurs. Here, we report the first voltage-clamp recordings of polyamine transporter activity, directly detecting ATP13A2- and ATP13A3-mediated charge movement across cell membranes. When expressed in Xenopus oocytes, these transporters localized to the plasma membrane, enabling electrophysiological measurements. Polyamines induced inward currents dependent on transporter catalytic activity, and their dose-dependence correlated with ATPase assays. ATP13A2 currents were largest in response to SPM, whereas ATP13A3 currents were largest with PUT, consistent with their established substrate preferences. Polyamine-induced currents were blocked by the polyamine transport inhibitor AMXT-1501. These findings establish ATP13A2 and ATP13A3 as electrogenic polyamine pumps and demonstrate the utility of two-electrode voltage clamp as a label-free, transporter-resolved assay to complement other approaches in polyamine transporter-targeted drug discovery.

biophysics↗

bioRxiv2023

In silico thermodynamic evaluation of the effectiveness of RT-LAMP primers to SARS-CoV-2 variants detection

Viral mutations are the primary cause of mismatches in primer-target hybridisation, affecting the sensibility of molecular techniques, potentially leading to detection dropouts. Despite its importance, little is known about the quantitative effect of mismatches in primer-target hybridisation. We use up-to-date and highly detailed thermodynamic model parameters of DNA mismatches to evaluate the sensibility to variants of SARS-CoV-2 RT-LAMP primers. We aligned 18 RT-LAMP primer sets, which were underwent clinical validation, to the genomes of Wuhan strain (ws), 7 variants and 4 subvariants, and calculated hybridisation temperatures allowing up to three consecutive mismatches. We calculate the coverage when the mismatched melting temperature falls by more than 5{degrees}C in comparison to the matched alignments. If no mismatches are considered, the average coverage found would be 94% for ws, falling the lowest value for Omicron: 84%. However, considering mismatches the coverage is much higher: 97% (ws) to 88% (Omicron). Stabilizing mismatches (higher melting temperatures), account for roughly 1/3 of this increase. The number of primer dropouts increases for new each variant, however the effect is much less severe if mismatches are considered. We suggest using melting temperature calculations to continuously assess the trend of primer dropouts.

molecular biology↗

bioRxiv2020

Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes

BackgroundDNA mismatches can affect the efficiency of PCR techniques if the intended target has mismatches in primers or probes regions. The accepted rule is that mismatches are detrimental as they reduce the hybridization temperatures, yet a more quantitative assessment is rarely performed. MethodsWe calculate the hybridization temperatures of primer/probe sets after aligning to SARS-COV-2, SARS-COV-1 and non-SARS genomes, considering all possible combinations of single, double and triple consecutive mismatches. We consider the mismatched hybridization temperature within a range of 5 {degrees}C to the fully matched reference temperature. ResultsWe obtained the alignments of 19 PCR primers sets that were recently reported for the detection of SARS-CoV-2 and to 21665 SARS-CoV-2 genomes as well as 323 genomes of other viruses of the coronavirus family of which 10 are SARS-CoV-1. We find that many incompletely aligned primers become fully aligned to most of the SARS-CoV-2 when mismatches are considered. However, we also found that many cross-align to SARS-CoV-1 and non-SARS genomes. ConclusionsSome primer/probe sets only align substantially to most SARS-CoV-2 genomes if mismatches are taken into account. Unfortunately, by the same mechanism, almost 75% of these sets also align to some SARS-CoV-1 and non-SARS viruses. It is therefore recommended to consider mismatch hybridization for the design of primers whenever possible, especially to avoid undesired cross-reactivity.

bioinformatics↗

bioRxiv2018

The BK channel gating ring is strongly coupled to the voltage sensor

The open probability of large conductance voltage- and calcium-dependent potassium (BK) channels is regulated allosterically by changes in the transmembrane voltage and intracellular concentration of divalent ions (Ca2+ and Mg2+). The divalent cation sensors reside within the gating ring formed by eight Regulator of Conductance of Potassium (RCK) domains, two from each of the four channel subunits. Overall, the gating ring contains 12 sites that can bind Ca2+ with different affinities. Using patch-clamp fluorometry, we have shown robust changes in FRET signals within the gating ring in response to divalent ions and voltage, which do not directly track open probability. Only the conformational changes triggered through the RCK1 binding site are voltage-dependent in presence of Ca2+. Because the gating ring is outside the electric field, it must gain voltage sensitivity from coupling to the voltage-dependent channel opening, the voltage sensor or both. Here we demonstrate that alterations of voltage sensor dynamics known to shift gating currents produce a cognate shift in the gating ring voltage dependence, whereas changing BK channels relative probability of opening had little effect. These results strongly suggest that the conformational changes of the RCK1 domain of the gating ring are tightly coupled to the voltage sensor function, and this interaction is central to the allosteric modulation of BK channels.

biophysics↗