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Biology subjects

Selvaggio, G.

Publications and source records attributed to Selvaggio, G..

7 recordsLinked to original sources

Exploring alternative quorum sensing model structures and quorum quenching strategies

Bacterial quorum sensing (QS) is a cell-to-cell communication mechanism through which bacteria share information about cell density, and tune gene expression accordingly. Pathogens exploit QS to orchestrate virulence and regulate the expression of genes related to antimicrobial resistance. Despite the vast literature on QS, the properties of the underlying molecular network are not entirely clear. We compare two synthetic QS circuit architectures: in the first, a single positive feedback loop autoinduces the synthesis of the signal molecule; the second includes an additional positive feedback loop enhancing the synthesis of the signal molecule receptor. Our comprehensive analysis of the two systems and their equilibria highlights the differences in the bistable and hysteretic behaviors of the alternative QS structures. Finally, we investigate three different QS inhibition approaches; numerical analysis predicts their effect on the steady-state behavior of the two different QS models, revealing critical parameter thresholds that guarantee an effective QS suppression.

synthetic biology↗

In silico logical modelling to uncover cooperative interactions in cancer

The multistep development of cancer involves the cooperation between multiple molecular lesions, as well as complex interactions between cancer cells and the surrounding tumour microenvironment. The search for these synergistic interactions using experimental models made tremendous contributions to our understanding of oncogenesis. Yet, these approaches remain labour intensive and challenging. To tackle such a hurdle, an integrative, multidisciplinary effort is required. In this article, we highlight the use of logical computational models combined to experimental validations as an effective approach to identify cooperative mechanisms and therapeutic strategies in the context of cancer biology. In silico models overcome limitations of reductionist approaches by capturing tumour complexity, and by generating powerful testable hypotheses. We review representative examples of logical models reported in the literature and their validation. We then provide further analyses of our logical model of Epithelium to Mesenchymal Transition (EMT), searching for additional cooperative interactions involving inputs from the tumour microenvironment and gain of function mutations in NOTCH.

cancer biology↗

Probing cellular arrhythmogenesis using the O'Hara-Rudy model of the undiseased human ventricular cardiomyocyte

The ventricular action potential (AP) is subserved by an interdependent system of voltage-gated ion channels and pumps that both alter and respond (directly or indirectly) to the dynamic transmembrane potential ({Delta}{psi}m(t)) via voltage-dependent state transitions governing inward and outward ion currents. The native dynamic inward-outward current balance is subject to disruption caused by acquired or inherited loss or gain of function in one or more ion channels or pumps. Building on our previous work, we used a modified version of the OHara-Rudy (ORd) model of the undiseased human ventricular cardiomyocyte to study the pro-arrhythmic effects of three types of arrhythmia-inducing perturbations in midmyocytes (M cells): O_LIBlockade of the human ether-a-go-go related gene (hERG) K+ channel introduced via a Markov state binding model. C_LIO_LIMutation-induced voltage shifts in hERG channel gating, resulting in faster inactivation or slowed recovery of both phosphorylated and non-phosphorylated forms of the channel (known as LQT2 syndrome). C_LIO_LIMutation-induced voltage shifts in Nav1.5 gating, resulting in slowed late inactivation of the phosphorylated and non-phosphorylated forms of the channel (known as LQT3 syndrome). C_LI We studied the relationships between ion current anomalies and AP morphology as a function of cycle length (CL) and perturbation type/level. The results are summarized as follows: O_LIAP duration (APD) is governed directly by Kir2.1 activation (IK1), which is delayed when repolarization is slowed by abnormal net inward tipping of the dynamic inward-outward current balance (reflected in decreased d({Delta}{psi}m(t))/dt during the late AP repolarization phase). In the case of hERG blockade by non-trappable compounds, the perturbation level consists of the dynamic fractional occupancy of the channel, which is governed by blocker kon relative to the rate of channel opening, pharmacokinetic exposure, and koff (in that order). C_LIO_LIArrhythmia progresses from prolonged paced APs [->] atypical APs (spontaneous and paced) [->] self-sustaining oscillations. Abrupt transitions between these regimes occur at CL- and perturbation-specific thresholds (denoted as T1, T2, and T3, respectively), whereas intra-regime progression proceeds in a graded fashion toward the subsequent threshold. APD and d({Delta}{psi}m(t))/dt during the late repolarization phase varied significantly across the 200 APs of our simulations near the T1 threshold at CL = 1/35 min, reflecting increasing instability of the AP generation system. C_LIO_LIArrhythmic APs exhibit highly variable cycle-to-cycle morphologies, depending on the perturbation level, type, and phasing between the underlying ion channel states and pacing cycle. C_LIO_LIAtypical APs may be triggered by typical or atypical depolarizations prior to the T3 threshold, depending on perturbation type/level and phasing relative to CL: O_LIAPD/CL resides outside of the Goldilocks zone: O_LIAPD/CL [->] 1 at shorter CL and/or longer APD, resulting in pro-arrhythmic "collisions" between successive paced APs (APi and APj) within a given cardiomyocyte. We studied this scenario at 60 and 80 beats per minute (BPM), equating to CL = 1/60 and 1/80 min. C_LIO_LIAPD/CL < 1 at longer CL results in spontaneous atypical depolarizations within prolonged paced APs at elevated takeoff {Delta}{psi}m(t) and increased channel phosphorylation levels. We studied this scenario at CL = 1/35 min. C_LI C_LIO_LIAPD and d({Delta}{psi}m(t))/dt during the late repolarization phase become increasingly variable over successive APs on approach to the T1 threshold, which is the possible source of short-long-short sequences observed in the ECG preceding torsades de pointes arrhythmia (TdP). C_LI C_LIO_LIAll atypical depolarizations are solely Cav1.2 (ICa,L)-driven ({Delta}{psi}m(t) falls within the Nav1.5 inactivation window), whereas typical depolarizations are Nav1.5 (INa) + ICa,L-driven. Atypical depolarization versus typical repolarization occurrences are determined by the faster of Cav1.2 and Kir2.1 (IK1) activation (where IK1 becomes increasingly dampened as the minimum {Delta}{psi}m(t) drifts above the Kir2.1 activation window). C_LIO_LICav1.2 inactivation gates reset to the open position (accompanied by recovery) synchronously with channel closing under control conditions, generating a small ICa,L window current in the process. This current grows toward a depolarizing spike when the lag time between recovery and closing grows above a threshold level. C_LIO_LIAPs undergo damped oscillatory Cav1.2 recovery/re-inactivation cycles above the T3 threshold, which are refreshed by subsequent pacing signals (nodal or reentrant in origin). C_LI

systems biology↗

Toward in vivo-relevant hERG safety assessment and mitigation strategies based on relationships between non-equilibrium blocker binding, three-dimensional channel-blocker interactions, dynamic occupancy, dynamic exposure, and cellular arrhythmia

The human ether-a-go-go-related voltage-gated cardiac ion channel (commonly known as hERG) conducts the rapid outward repolarizing potassium current in cardiomyocytes (IKr). Inadvertent blockade of this channel by drug-like molecules represents a key challenge in pharmaceutical R&D due to frequent overlap between the structure-activity relationships of hERG and many primary targets. Building on our previous work, together with recent cryo-EM structures of hERG, we set about to better understand the energetic and structural basis of promiscuous blocker-hERG binding in the context of Biodynamics theory. We propose a two-step blocker binding process consisting of: Diffusion of a single fully solvated blocker copy into a large cavity lined by the intracellular cyclic nucleotide binding homology domain (the initial capture step). Occupation of this cavity is a necessary but insufficient condition for ion current disruption.Translocation of the captured blocker along the channel axis (the IKr disruption step), such that: The head group, consisting of a quasi-linear moiety, projects into the open pore, accompanied by partial de-solvation of the binding interface.One tail moiety packs along a kink between the S6 helix and proximal C-linker helix adjacent to the intra-cellular entrance of the pore, likewise accompanied by mutual de-solvation of the binding interface (noting that the association barrier is comprised largely of the total head + tail group de-solvation cost).Blockers containing a highly planar moiety that projects into a putative constriction zone within the closed channel become trapped upon closing, as do blockers terminating prior to this region.A single captured blocker molecule may associate and dissociate from the pore many times before exiting the CNBHD cavity.Lastly, we highlight possible flaws in the current hERG safety index (SI) and propose an alternate in vivo-relevant strategy factoring in: Benefit/risk.The predicted arrhythmogenic fractional hERG occupancy (based on action potential simulations of the undiseased human ventricular cardiomyocyte).Alteration of the safety threshold due to underlying disease.Risk of exposure escalation toward the predicted arrhythmic limit due to patient-to-patient pharmacokinetic variability, drug-drug interactions, overdose, and use for off-label indications in which the hERG safety parameters may differ from their on-label counterparts.View Full Text

pharmacology and toxicology↗

Exfoliated near infrared fluorescent CaCuSi4O10 nanosheets with ultra-high photostability and brightness for biological imaging

Imaging of complex (biological) samples in the near infrared (nIR) range of the spectrum is beneficial due to reduced light scattering, absorption, phototoxicity and autofluorescence. However, there are only few near infrared fluorescent materials known and suitable for biomedical applications. Here, we exfoliate the layered pigment CaCuSi4O10 (known as Egyptian Blue, EB) via facile tip sonication into nanosheets (EB-NS) with ultra-high nIR fluorescence stability and brightness. The size of EB-NS can be tailored by tip sonication to diameters < 20 nm and heights down to 1 nm. EB-NS fluoresce at 910 nm and the total fluorescence intensity scales with the number of Cu2+ ions that serve as luminescent centers. Furthermore, EB-NS display no bleaching and ultra-high brightness compared to other nIR fluorophores. The versatility of EB-NS is demonstrated by in vivo single-particle tracking and microrheology measurements in developing Drosophila embryos. Additionally, we show that EB-NS can be uptaken by plants and remotely detected in a low cost stand-off detection setup despite strong plant background fluorescence. In summary, EB-NS are a highly versatile, bright, photostable and biocompatible nIR fluorescent material that has the potential for a wide range of bioimaging applications both in animal and plant systems.

biophysics↗

Biodynamics: A novel quasi-first principles theory on the fundamental mechanisms of cellular function/dysfunction and the pharmacological modulation thereof

Cellular function depends on heterogeneous dynamic intra-, inter-, and supramolecular structure-function relationships. However, the specific mechanisms by which cellular function is transduced from molecular systems, and by which cellular dysfunction arises from molecular dysfunction are poorly understood. We proposed previously that cellular function manifests as a molecular form of analog computing, in which specific time-dependent state transition fluxes within sets of molecular species (\"molecular differential equations\" (MDEs)) are sped and slowed in response to specific perturbations (inputs). In this work, we offer a theoretical treatment of the molecular mechanisms underlying cellular analog computing (which we refer to as \"biodynamics\"), focusing primarily on non-equilibrium (dynamic) intermolecular state transitions that serve as the principal means by which MDE systems are solved (the molecular equivalent of mathematical \"integration\"). Under these conditions, bound state occupancy is governed by kon and koff, together with the rates of binding partner buildup and decay. Achieving constant fractional occupancy over time depends on: 1) equivalence between kon and the rate of binding site buildup); 2) equivalence between koff and the rate of binding site decay; and 3) free ligand concentration relative to koff/k0n (n {middle dot} Kd, where n is the fold increase in binding partner concentration needed to achieve a given fractional occupancy). Failure to satisfy these conditions results in fractional occupancy well below that corresponding to n {middle dot} Kd. The implications of biodynamics for cellular function/dysfunction and drug discovery are discussed.

systems biology↗

Mapping the phenotypic repertoire of the cytoplasmic 2-Cys peroxiredoxin - thioredoxin system. 1. Understanding commonalities and differences among cell types.

The system (PTTRS) formed by typical 2-Cys peroxiredoxins (Prx), thioredoxin (Trx), Trx reductase (TrxR), and sulfiredoxin (Srx) is central in antioxidant protection and redox signaling in the cytoplasm of eukaryotic cells. Understanding how the PTTRS integrates these functions requires tracing phenotypes to molecular properties, which is non-trivial. Here we analyze this problem based on a model that captures the PTTRS conserved features. We have mapped the conditions that generate each distinct response to H2O2 supply rates ({nu}sup), and estimated the parameters for thirteen human cell types and for Saccharomyces cerevisiae. The resulting composition-to-phenotype map yielded the following experimentally testable predictions. The PTTRS permits many distinct responses including ultra-sensitivity and hysteresis. However, nearly all tumor cell lines showed a similar response characterized by limited Trx-S- depletion and a substantial but self-limited gradual accumulation of hyperoxidized Prx at high{nu} sup. This similarity ensues from strong correlations between the TrxR, Srx and Prx activities over cell lines, which contribute to maintain the Prx-SS reduction capacity in slight excess over the maximal steady state Prx-SS production. In turn, in erythrocytes, hepatocytes and HepG2 cells high{nu} sup depletes Trx-S- and oxidizes Prx mainly to Prx-SS. In all nucleated human cells the Prx-SS reduction capacity defined a threshold separating two different regimes. At sub-threshold{nu} sup cytoplasmic H2O2 is determined by Prx, nM-range and spatially localized, whereas at supra-threshold{nu} sup it is determined by much less active alternative sinks and M-range throughout the cytoplasm. The yeast shows a distinct response where the Prx Tsa1 accumulates in sulfenate form at high{nu} sup. This is mainly due to an exceptional stability of Tsa1s sulfenate.\n\nThe implications of these findings for thiol redox regulation and cell physiology are discussed. All estimates were thoroughly documented and provided, together with analytical approximations for system properties, as a resource for quantitative redox biology.\n\nAbbreviationsASK1, apoptosis signal-regulating kinase 1; Cat, catalase; GSH, glutathione; GPx1, glutathione peroxidase 1; Grx, glutaredoxin; KEAP1, Kelch-like ECH-associated protein 1; NRF2, nuclear factor erythroid 2-related factor 2; Prx, typical 2-Cys peroxiredoxin; PTTRS, peroxiredoxin / thioredoxin / thioredoxin reductase system; Srx, sulfiredoxin; Trx, thioredoxin; TrxR, thioredoxin reductase.

systems biology↗