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Article ; Online: Determination of Krogh Coefficient for Oxygen Consumption Measurement from Thin Slices of Rodent Cortical Tissue Using a Fick's Law Model of Diffusion.

Steyn-Ross, D Alistair / Steyn-Ross, Moira L / Sleigh, Jamie W / Voss, Logan J

International journal of molecular sciences

2023 Volume 24, Issue 7

Abstract: To investigate the impact of experimental interventions on living biological tissue, ex vivo rodent brain slices are often used as a more controllable alternative to a live animal model. However, for meaningful results, the biological sample must be ... ...

Abstract	To investigate the impact of experimental interventions on living biological tissue, ex vivo rodent brain slices are often used as a more controllable alternative to a live animal model. However, for meaningful results, the biological sample must be known to be healthy and viable. One of the gold-standard approaches to identifying tissue viability status is to measure the rate of tissue oxygen consumption under specific controlled conditions. Here, we work with thin (400 μm) slices of mouse cortical brain tissue which are sustained by a steady flow of oxygenated artificial cerebralspinal fluid (aCSF) at room temperature. To quantify tissue oxygen consumption (
MeSH term(s)	Animals ; Mice ; Rodentia ; Diffusion ; Oxygen ; Respiratory Function Tests ; Oxygen Consumption
Chemical Substances	Oxygen (S88TT14065)
Language	English
Publishing date	2023-03-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24076450
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Article ; Online: Evidence for a short-lived resonance state in enzyme catalysis via rate-equation convolution.

Steyn-Ross, Moira L / Steyn-Ross, D A / Prentice, Erica J / Walker, Emma J / Arcus, V L

Physical review. E

2023 Volume 107, Issue 6-1, Page(s) 64407

Abstract: At the cellular level, all biological function relies on enzymes to provide catalytic acceleration of essential biochemical processes driving cellular metabolism. The enzyme is presumed to lower the activation energy barrier separating reactants from ... ...

Abstract	At the cellular level, all biological function relies on enzymes to provide catalytic acceleration of essential biochemical processes driving cellular metabolism. The enzyme is presumed to lower the activation energy barrier separating reactants from products, but the precise mechanism remains unresolved. Here we examine the temperature dependence of the enzyme-catalyzed dissociation of p-nitrophenyl-α-D-glucopyranoside (pNPG), a chromogenic analog for maltose, isomaltose, and sucrose disaccharide sugars, into p-nitrophenol (pNP) and glucose (monosaccharide). The enzymes of interest are the wild type and mutant forms of glucosidase MalL produced by the probiotic bacterium Bacillus subtilis. The per-enzyme production rates k(T) for the pNPG→ glucose reaction all show a characteristic temperature profile with an Arrhenius-like (approximately exponential) slow acceleration at low temperatures, rising through a point of inflexion to reach a maximum, then turning over to decline steeply towards zero production at high temperatures. This asymmetric profile is found to be well fitted by convolving an exponential growth function f(T) with a Gaussian temperature distribution g(T) to produce an exponentially modified Gaussian function h(T). To give a physical interpretation of the convolution components, we make the temperature mapping Θ≡T_{ref}-T where T_{ref} marks the temperature at which a given mutant becomes fully denatured (unfolded) and therefore inactive, then convert the convolution components to probability density functions which obey the convolution theorem of statistics. Working in Θ space, we identify f(Θ) as the density function for an Arrhenius-like transition from ground-state A to metastable-state B, and g(Θ) as the Gaussian distribution of offset-temperature fluctuations for the metastable state. By mapping the standard thermodynamic relations for temperature and energy fluctuations to the enzyme frame of reference, we are able to derive an expression for the lifetime for the metastable B state. For the 15 enzyme experiments, we obtain a mean value 〈Δt〉≳(29.0±1.3)×10^{-15}s, in remarkably good agreement with the ∼30-fs estimate for the period of glycosidic bond oscillations extracted from published infrared spectroscopy. We suggest that the metastable B state provides a low-energy target that has the effect of lowering the activation energy barrier by presenting an alternative axis for the reaction coordinate.
MeSH term(s)	Temperature ; Thermodynamics ; Catalysis ; Hot Temperature ; Glucose ; Kinetics
Chemical Substances	Glucose (IY9XDZ35W2)
Language	English
Publishing date	2023-07-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.107.064407
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Article ; Online: The molecular dynamics of possible inhibitors for SARS-CoV-2.

Irani, Amir H / Steyn-Ross, D A / Steyn-Ross, Moira L / Voss, Logan / Sleigh, Jamie

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 20, Page(s) 10023–10032

Abstract: The novel coronavirus SARS-CoV-2, responsible for the present COVID-19 global pandemic, is known to bind to the angiotensin converting enzyme-2 (ACE2) receptor in human cells. A possible treatment of COVID-19 could involve blocking ACE2 and/or disabling ... ...

Abstract	The novel coronavirus SARS-CoV-2, responsible for the present COVID-19 global pandemic, is known to bind to the angiotensin converting enzyme-2 (ACE2) receptor in human cells. A possible treatment of COVID-19 could involve blocking ACE2 and/or disabling the spike protein on the virus. Here, molecular dynamics simulations were performed to test the binding affinities of nine candidate compounds. Of these, three drugs showed significant therapeutic potential that warrant further investigation: SN35563, a ketamine ester analogue, was found to bind strongly to the ACE2 receptor but weakly within the spike receptor-binding domain (RBD); in contrast, arbidol and hydroxychloroquine bound preferentially with the spike RBD rather than ACE2. A fourth drug, remdesivir, bound approximately equally to both the ACE2 and viral spike RBD, thus potentially increasing risk of viral infection by bringing the spike protein into closer proximity to the ACE2 receptor. We suggest more experimental investigations to test that SN35563-in combination with arbidol or hydroxychloroquine-might act synergistically to block viral cell entry by providing therapeutic blockade of the host ACE2 simultaneous with reduction of viral spike receptor-binding; and that this combination therapy would allow the use of smaller doses of each drug.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Angiotensin-Converting Enzyme 2/antagonists & inhibitors ; Angiotensin-Converting Enzyme 2/chemistry ; Binding Sites ; COVID-19 ; Hydroxychloroquine/pharmacology ; Molecular Dynamics Simulation ; Protein Binding ; Receptors, Virus/antagonists & inhibitors ; Receptors, Virus/chemistry ; SARS-CoV-2/drug effects ; Spike Glycoprotein, Coronavirus/antagonists & inhibitors ; Spike Glycoprotein, Coronavirus/chemistry ; Antiviral Agents/pharmacology
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Hydroxychloroquine (4QWG6N8QKH) ; Receptors, Virus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; umifenovir (93M09WW4RU) ; Antiviral Agents
Language	English
Publishing date	2021-07-06
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1942215
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Article ; Online: Analysis of the Hindriks and van Putten model for propofol anesthesia: Limitations and extensions.

Noroozbabaee, Leyla / Steyn-Ross, D A / Steyn-Ross, Moira L / Sleigh, J W

NeuroImage

2020 Volume 227, Page(s) 117633

Abstract: We present a detailed analysis of the Hindriks and van Putten thalamocortical mean-field model for propofol anesthesia [NeuroImage 60(23), 2012]. The Hindriks and van Putten (HvP) model predicts increases in delta and alpha power for moderate (up to 130%) ...

Abstract	We present a detailed analysis of the Hindriks and van Putten thalamocortical mean-field model for propofol anesthesia [NeuroImage 60(23), 2012]. The Hindriks and van Putten (HvP) model predicts increases in delta and alpha power for moderate (up to 130%) prolongation of GABA
MeSH term(s)	Anesthetics, Intravenous/pharmacology ; Cerebral Cortex/drug effects ; Cerebral Cortex/physiology ; Humans ; Models, Neurological ; Nerve Net/drug effects ; Nerve Net/physiology ; Neural Inhibition/drug effects ; Neural Inhibition/physiology ; Neurons/drug effects ; Neurons/physiology ; Propofol/pharmacology
Chemical Substances	Anesthetics, Intravenous ; Propofol (YI7VU623SF)
Language	English
Publishing date	2020-12-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1147767-2
ISSN	1095-9572 ; 1053-8119
ISSN (online)	1095-9572
ISSN	1053-8119
DOI	10.1016/j.neuroimage.2020.117633
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Article ; Online: From individual spiking neurons to population behavior: Systematic elimination of short-wavelength spatial modes.

Steyn-Ross, Moira L / Steyn-Ross, D A

Physical review. E

2016 Volume 93, Issue 2, Page(s) 22402

Abstract: Mean-field models of the brain approximate spiking dynamics by assuming that each neuron responds to its neighbors via a naive spatial average that neglects local fluctuations and correlations in firing activity. In this paper we address this issue by ... ...

Abstract	Mean-field models of the brain approximate spiking dynamics by assuming that each neuron responds to its neighbors via a naive spatial average that neglects local fluctuations and correlations in firing activity. In this paper we address this issue by introducing a rigorous formalism to enable spatial coarse-graining of spiking dynamics, scaling from the microscopic level of a single type 1 (integrator) neuron to a macroscopic assembly of spiking neurons that are interconnected by chemical synapses and nearest-neighbor gap junctions. Spiking behavior at the single-neuron scale ℓ≈10μm is described by Wilson's two-variable conductance-based equations [H. R. Wilson, J. Theor. Biol. 200, 375 (1999)], driven by fields of incoming neural activity from neighboring neurons. We map these equations to a coarser spatial resolution of grid length Bℓ, with B≫1 being the blocking ratio linking micro and macro scales. Our method systematically eliminates high-frequency (short-wavelength) spatial modes q(->) in favor of low-frequency spatial modes Q(->) using an adiabatic elimination procedure that has been shown to be equivalent to the path-integral coarse graining applied to renormalization group theory of critical phenomena. This bottom-up neural regridding allows us to track the percolation of synaptic and ion-channel noise from the single neuron up to the scale of macroscopic population-average variables. Anticipated applications of neural regridding include extraction of the current-to-firing-rate transfer function, investigation of fluctuation criticality near phase-transition tipping points, determination of spatial scaling laws for avalanche events, and prediction of the spatial extent of self-organized macrocolumnar structures. As a first-order exemplar of the method, we recover nonlinear corrections for a coarse-grained Wilson spiking neuron embedded in a network of identical diffusively coupled neurons whose chemical synapses have been disabled. Intriguingly, we find that reblocking transforms the original type 1 Wilson integrator into a type 2 resonator whose spike-rate transfer function exhibits abrupt spiking onset with near-vertical takeoff and chaotic dynamics just above threshold.
MeSH term(s)	Cell Membrane/metabolism ; Diffusion ; Electrophysiological Phenomena ; Gap Junctions/metabolism ; Models, Neurological ; Neurons/cytology
Language	English
Publishing date	2016-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.93.022402
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Article ; Online: Spinodal decomposition in a mean-field model of the cortex: Emergence of hexagonally symmetric activation patterns.

Steyn-Ross, Moira L / Steyn-Ross, D A / Voss, L J / Sleigh, J W

Physical review. E

2019 Volume 99, Issue 1-1, Page(s) 12318

Abstract: Spinodal decomposition is a well-known pattern-forming mechanism in metallurgic alloys, semiconductor crystals, and colloidal gels. In metallurgy, if a heated sample of a homogeneous Zn-Al alloy is suddenly quenched below a critical temperature, then the ...

Abstract	Spinodal decomposition is a well-known pattern-forming mechanism in metallurgic alloys, semiconductor crystals, and colloidal gels. In metallurgy, if a heated sample of a homogeneous Zn-Al alloy is suddenly quenched below a critical temperature, then the sample can spontaneously precipitate into inhomogenous textures of Zn- and Al-rich regions with significantly altered material properties such as ductility and hardness. Here we report on our recent discovery that a two-dimensional model of the human cortex with inhibitory diffusion can, under particular homogeneous initial conditions, exhibit a form of nonconserved spinodal decomposition in which regions of the cortex self-organize into hexagonally distributed binary patches of activity and inactivity. Fine-scale patterns precipitate rapidly, and then the dynamics slows to render coarser-scale shapes which can ripen into a range of slowly evolving patterns including mazelike labyrinths, hexagonal islands and continents, nucleating "mitotic cells" which grow to a critical size then subdivide, and inverse nucleations in which quiescent islands are surrounded by a sea of activity. One interesting class of activity coalesces into a soliton-like narrow ribbon of depolarization that traverses the cortex at ∼4cm/s. We speculate that this may correspond to the thus far unexplained interictal waves of cortical activation that precede grand-mal seizure in an epileptic event. We note that spinodal decomposition is quite distinct from the Turing mechanism for symmetry breaking in cortex investigated in earlier work by the authors [Steyn-Ross et al., Phys. Rev. E 76, 011916 (2007)PLEEE81539-375510.1103/PhysRevE.76.011916].
Language	English
Publishing date	2019-02-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.99.012318
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Article ; Online: Anesthesia modifies subthreshold critical slowing down in a stochastic Hodgkin-Huxley-like model with inhibitory synaptic input.

Bukoski, Alex / Steyn-Ross, D A / Pickett, Ashley F / Steyn-Ross, Moira L

Physical review. E

2018 Volume 97, Issue 6-1, Page(s) 62403

Abstract: The dynamics of a stochastic type-I Hodgkin-Huxley-like point neuron model exposed to inhibitory synaptic noise are investigated as a function of distance from spiking threshold and the inhibitory influence of the general anesthetic agent propofol. The ... ...

Abstract	The dynamics of a stochastic type-I Hodgkin-Huxley-like point neuron model exposed to inhibitory synaptic noise are investigated as a function of distance from spiking threshold and the inhibitory influence of the general anesthetic agent propofol. The model is biologically motivated and includes the effects of intrinsic ion-channel noise via a stochastic differential equation description as well as inhibitory synaptic noise modeled as multiple Poisson-distributed impulse trains with saturating response functions. The effect of propofol on these synapses is incorporated through this drug's principal influence on fast inhibitory neurotransmission mediated by γ-aminobutyric acid (GABA) type-A receptors via reduction of the synaptic response decay rate. As the neuron model approaches spiking threshold from below, we track membrane voltage fluctuation statistics of numerically simulated stochastic trajectories. We find that for a given distance from spiking threshold, increasing the magnitude of anesthetic-induced inhibition is associated with augmented signatures of critical slowing: fluctuation amplitudes and correlation times grow as spectral power is increasingly focused at 0 Hz. Furthermore, as a function of distance from threshold, anesthesia significantly modifies the power-law exponents for variance and correlation time divergences observable in stochastic trajectories. Compared to the inverse square root power-law scaling of these quantities anticipated for the saddle-node bifurcation of type-I neurons in the absence of anesthesia, increasing anesthetic-induced inhibition results in an observable exponent <-0.5 for variance and >-0.5 for correlation time divergences. However, these behaviors eventually break down as distance from threshold goes to zero with both the variance and correlation time converging to common values independent of anesthesia. Compared to the case of no synaptic input, linearization of an approximating multivariate Ornstein-Uhlenbeck model reveals these effects to be the consequence of an additional slow eigenvalue associated with synaptic activity that competes with those of the underlying point neuron in a manner that depends on distance from spiking threshold.
Language	English
Publishing date	2018-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.97.062403
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Article ; Online: Channel-noise-induced critical slowing in the subthreshold Hodgkin-Huxley neuron.

Bukoski, Alex / Steyn-Ross, D A / Steyn-Ross, Moira L

Physical review. E, Statistical, nonlinear, and soft matter physics

2015 Volume 91, Issue 3, Page(s) 32708

Abstract: The dynamics of a spiking neuron approaching threshold is investigated in the framework of Markov-chain models describing the random state-transitions of the underlying ion-channel proteins. We characterize subthreshold channel-noise-induced ... ...

Abstract	The dynamics of a spiking neuron approaching threshold is investigated in the framework of Markov-chain models describing the random state-transitions of the underlying ion-channel proteins. We characterize subthreshold channel-noise-induced transmembrane potential fluctuations in both type-I (integrator) and type-II (resonator) parametrizations of the classic conductance-based Hodgkin-Huxley equations. As each neuron approaches spiking threshold from below, numerical simulations of stochastic trajectories demonstrate pronounced growth in amplitude simultaneous with decay in frequency of membrane voltage fluctuations induced by ion-channel state transitions. To explore this progression of fluctuation statistics, we approximate the exact Markov treatment with a 12-variable channel-based stochastic differential equation (SDE) and its Ornstein-Uhlenbeck (OU) linearization and show excellent agreement between Markov and SDE numerical simulations. Predictions of the OU theory with respect to membrane potential fluctuation variance, autocorrelation, correlation time, and spectral density are also in agreement and illustrate the close connection between the eigenvalue structure of the associated deterministic bifurcations and the observed behavior of the noisy Markov traces on close approach to threshold for both integrator and resonator point-neuron varieties.
MeSH term(s)	Ion Channels/metabolism ; Markov Chains ; Models, Neurological ; Neurons/cytology ; Neurons/metabolism ; Stochastic Processes
Chemical Substances	Ion Channels
Language	English
Publishing date	2015-03
Publishing country	United States
Document type	Journal Article
ISSN	1550-2376
ISSN (online)	1550-2376
DOI	10.1103/PhysRevE.91.032708
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Article ; Online: Which System Variables Carry Robust Early Signs of Upcoming Phase Transition? An Ecological Example.

Negahbani, Ehsan / Steyn-Ross, D Alistair / Steyn-Ross, Moira L / Aguirre, Luis A

PloS one

2016 Volume 11, Issue 9, Page(s) e0163003

Abstract: Growth of critical fluctuations prior to catastrophic state transition is generally regarded as a universal phenomenon, providing a valuable early warning signal in dynamical systems. Using an ecological fisheries model of three populations (juvenile ... ...

Abstract	Growth of critical fluctuations prior to catastrophic state transition is generally regarded as a universal phenomenon, providing a valuable early warning signal in dynamical systems. Using an ecological fisheries model of three populations (juvenile prey J, adult prey A and predator P), a recent study has reported silent early warning signals obtained from P and A populations prior to saddle-node (SN) bifurcation, and thus concluded that early warning signals are not universal. By performing a full eigenvalue analysis of the same system we demonstrate that while J and P populations undergo SN bifurcation, A does not jump to a new state, so it is not expected to carry early warning signs. In contrast with the previous study, we capture a significant increase in the noise-induced fluctuations in the P population, but only on close approach to the bifurcation point; it is not clear why the P variance initially shows a decaying trend. Here we resolve this puzzle using observability measures from control theory. By computing the observability coefficient for the system from the recordings of each population considered one at a time, we are able to quantify their ability to describe changing internal dynamics. We demonstrate that precursor fluctuations are best observed using only the J variable, and also P variable if close to transition. Using observability analysis we are able to describe why a poorly observable variable (P) has poor forecasting capabilities although a full eigenvalue analysis shows that this variable undergoes a bifurcation. We conclude that observability analysis provides complementary information to identify the variables carrying early-warning signs about impending state transition.
MeSH term(s)	Animals ; Ecology ; Fishes ; Models, Theoretical
Language	English
Publishing date	2016-09-15
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0163003
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Article ; Online: Critical slowing in a Hodgkin-Huxley neuron near spiking threshold

Bukoski Alex / Steyn-Ross D / Steyn-Ross Moira L

BMC Neuroscience, Vol 13, Iss Suppl 1, p P

2012 Volume 34

Keywords	Neurosciences. Biological psychiatry. Neuropsychiatry ; RC321-571 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Neurology ; DOAJ:Medicine (General) ; DOAJ:Health Sciences ; Neurophysiology and neuropsychology ; QP351-495
Language	English
Publishing date	2012-07-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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