Biology subjects

Sheremet, A.

Publications and source records attributed to Sheremet, A..

8 recordsLinked to original sources

bioRxiv2020

Spectrum Degradation of Hippocampal LFP during Euthanasia

AO_SCPLOWBSTRACTC_SCPLOWThe hippocampal local field potential (LFP) exhibits a strong correlation with behavior. During rest, the theta rhythm is not prominent, but during active behavior, there are strong rhythms in the theta, theta harmonics, and gamma ranges. With increasing running velocity, theta, theta harmonics and gamma increase in power and in cross-frequency coupling, suggesting that neural entrainment is a direct consequence of the total excitatory input. While it is common to study the parametric range between the LFP and its complementing power spectra between deep rest and epochs of high running velocity, it is also possible to explore how the spectra degrades as the energy is completely quenched from the system. Specifically, it is unknown whether the 1/f slope is preserved as synaptic activity becomes diminished, as low frequencies are generated by large pools of neurons while higher frequencies comprise the activity of more local neuronal populations. To test this hypothesis, we examined rat LFPs recorded from the hippocampus and entorhinal cortex during barbiturate overdose euthanasia. Within the hippocampus, the initial stage entailed a quasi-stationary stage when the LFP spectrum exhibited power-law feature while the frequency components over 20 Hz exhibited a power decay with a similar decay rate. This stage was followed by a rapid collapse of power spectrum towards the absolute electrothermal noise background. As the collapse of activity occurred later in hippocampus compared with medial entorhinal cortex or visual cortex, it suggests that the ability of a neural network to maintain the 1/f slope with decreasing energy is a function of general connectivity. Broadly, these data support the energy cascade theory where there is a cascade of energy from large cortical populations into smaller loops, such as those that supports the higher frequency gamma rhythm. As energy is pulled from the system, neural entrainment at gamma frequency (and higher) decline first. The larger loops, comprising a larger population, are fault-tolerant to a point capable of maintaining their activity before a final collapse.

neuroscience↗

bioRxiv2020

Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota

The recent leveraging of genome-resolved metagenomics has opened a treasure trove of genomes from novel uncultured microbial lineages, yet left many clades undescribed. We here present a global analysis of genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in the Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, chloromethanes, and potentially methane as substrates. Methylotrophy in the Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e. the utilization of diverse sets of genes, pathways and combinations to achieve a specific metabolic goal. The genomes also encoded an arsenal of alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, {beta} and {gamma} carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified; although absence of key genes and failure to identify a photosynthetic reaction center precludes proposing phototrophic capacities. Analysis of 16S rRNA databases showed Binatotas preferences to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges supporting their suggested potential role in mitigating methanol and methane emissions, alkanes degradation, and nutritional symbiosis with sponges. Our results expand the lists of methylotrophic, aerobic alkane degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways and gene shrapnel in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.

microbiology↗

bioRxiv2020

THERMODYNAMIC MODEL OF MESOSCALE NEURAL FIELD DYNAMICS: DERIVATION AND LINEAR ANALYSIS

Motivated by previous research suggesting that mesoscopic collective activity has the defining characteristics of a turbulent system, we postulate a thermodynamic model based on the fundamental assumption that the activity of a neuron is characterized by two distinct stages: a sub-threshold stage, described by the value of mean membrane potential, and a transitional stage, corresponding to the firing event. We therefore distinguish between two types of energy: the potential energy released during a spike, and the internal kinetic energy that triggers a spike. Formalizing these assumptions produces a system of integro-differential equations that generalizes existing models [Wilson and Cowan, 1973, Amari, 1977], with the advantage of providing explicit equations for the evolution of state variables. The linear analysis of the system shows that it supports single- or triple-point equilibria, with the refractoriness property playing a crucial role in the generation of oscillatory behavior. In single-type (excitatory) systems this derives from the natural refractory state of a neuron, producing "refractory oscillations" with periods on the order of the neuron refractory period. In dual-type systems, the inhibitory component can provide this functionality even if neuron refractory period is ignored, supporting mesoscopic-scale oscillations at much lower activity levels. Assuming that the model has any relevance for the interpretation of LFP measurements, it provides insight into mesocale dynamics. As an external forcing, theta may play a major role in modulating key parameters of the system: internal energy and excitability (refractoriness) levels, and thus in maintaining equilibrium states, and providing the increased activity necessary to sustain mesoscopic collective action. Linear analysis suggest that gamma oscillations are associated with the theta trough because it corresponds to higher levels of forced activity that decreases the stability of the equilibrium state, facilitating mesoscopic oscillations.

neuroscience↗

bioRxiv2018

TURBULENCE IN THE HIPPOCAMPUS: AN ANSATZ FOR THE ENERGY CASCADEHYPOTHESIS

Mesoscopic neural activity may play an important role in the cross-scale integration of brain activity and in the emergence of cognitive behavior. Mesoscale activity in the cortex can be defined as the organization of activity of large populations of neurons into collective actions, such as traveling waves in the hippocampus. A comprehensive description of collective activity is still lacking, in part because it cannot be built directly with methods and models developed for the microscale (individual neurons): the laws governing mesoscale dynamics are different from those governing a few neurons. To identify the characteristic features of mesoscopic dynamics, and to lay the foundations for a theoretical description of mesoscopic activity in the hippocampus, we conduct a comprehensive examination of observational data of hippocampal local field potential (LFP) recordings. We use the strong correlation between rat running-speed and the LFP power to parameterize the energy input into the hippocampus, and show that both the power, and the nonlinearity of mesoscopic scales of collective action (e.g., theta and gamma rhythms) increase as with energy input. Our results point to a few fundamental characteristics: collective-action dynamics are stochastic (the precise state of a single neuron is irrelevant), weakly nonlinear, and weakly dissipative. These are the principles of the theory of weak turbulence. Therefore, we propose weak turbulence as an ansatz for the development of a theoretical description of mesoscopic activity. The perspective of weak turbulence provides simple and meaningful explanations for the major features observed in the evolution of LFP spectra and bispectra with energy input, such as spectral slopes and their evolution, the increased nonlinear coupling observed between theta and gamma, as well as specific phase lags associated with their interaction. The weak turbulence ansatz is consistent with the theory of self organized criticality, which provides a simple explanation for the existence of the power-law background spectrum, and could provide a unifying approach to modeling the dynamics of mesoscopic activity.

neuroscience↗

bioRxiv2018

LINEAR ANALYSIS OF HIPPOCAMPAL LFP: SLOW GAMMA VS HIGH THETA

AO_SCPCAPBSTRACTC_SCPCAPLocal field potential (LFP) oscillations are the superposition of excitatory/inhibitory postsynaptic potentials. In the hippocampus, the 20-55 Hz range ( slow gamma) is proposed to support cognition independent of other frequencies. However, this band overlaps with theta harmonics. We aimed to dissociate the generators of slow gamma versus theta harmonics with current source density and different LFP decompositions. Hippocampal theta harmonic and slow gamma generators were not dissociable. Moreover, comparison of wavelet, ensemble empirical-mode (EEMD), and Fourier decompositions produced distinct outcomes with wavelet and EEMD failing to resolve high-order theta harmonics well defined by Fourier analysis. The varying sizes of the time-frequency atoms used by wavelet distributed the higher-order harmonics over a broader range giving the impression of a low frequency burst (\"slow gamma\"). The absence of detectable slow gamma refutes a multiplexed model of cognition in favor of the energy cascade hypothesis in which dependency across oscillatory frequencies exists.

neuroscience↗

bioRxiv2018

Theta-Gamma Cascades and Running Speed

The local field potentials (LFPs) of the hippocampus are primarily generated by the spatiotemporal accretion of electrical currents via activated synapses. Oscillations in the hippocampal LFP at theta and gamma frequencies are prominent during awake-behavior and have demonstrated several behavioral correlates. In particular, both oscillations have been observed to increase in amplitude and frequency as a function of running velocity. Previous investigations, however, have examined the relationship between velocity and each of these oscillation bands separately. Based on energy cascade models where \"...perturbations of slow frequencies cause a cascade of energy dissipation at all frequency scales\" (Buzsaki 2006), we hypothesized that the cross-frequency interactions between theta and gamma should increase as a function of velocity. We examined these relationships across multiple layers of the CA1 subregion and found a reliable correlation between the power of theta and the power of gamma, indicative of an amplitude-amplitude relationship. Moreover, there was an increase in the coherence between the power of gamma and the phase of theta, demonstrating increased phase-amplitude coupling with velocity. Finally, at higher velocities, phase entrainment between theta and gamma becomes stronger. These results have important implications and provide new insights regarding how theta and gamma are integrated for neuronal circuit dynamics, with coupling strength determined by the excitatory drive within the hippocampus.

neuroscience↗

bioRxiv2018

Theta-gamma coupling: a nonlinear dynamical model

Cross-frequency coupling in the hippocampus has been hypothesized to support higher-cognition functions. While gamma modulation by theta is widely accepted, evidence of phase-coupling between the two frequency components is so far unconvincing. Our observations show that theta and gamma energy increases with rat speed, while the overall nonlinearity of the LFP trace also increases, suggesting that energy flow is fundamental for hippocampal dynamics. This contradicts current representations based on the Kuramoto phase model. Therefore, we propose a new approach, based on the three-wave equation, a universally-valid nonlinear-physics paradigm that synthesizes the effects of leading order, quadratic nonlinearity. The paradigm identifies bispectral analysis as the natural tool for investigating LFP cross-frequency coupling. Our results confirm the effectiveness of the approach by showing unambiguous coupling between theta and gamma. Bispectra features agree with predictions of the three-wave model, supporting the conclusion that cross-frequency coupling is a manifestation of nonlinear energy transfers.

neuroscience↗

bioRxiv2017

Mesoscale turbulence in the hippocampus

Wave turbulence provides a powerful stochastic description for nonlinear collective neural activity in the hippocampus. Recent studies that show theta waves propagating across the hippocampus suggest that turbulence is a natural description for collective neural activity. We formulate the fundamental principles of a turbulence model and demonstrate turbulent behavior by analyzing rat hippocampal LFP traces. LFP spectra and bispectra exhibit fundamental turbulent properties: weak nonlinear coupling, energy cascade, and stationary spectra of the Kolmogorov-Zakharov type (power-law). Weak turbulence holds the promise of quantitative physical models of hippocampal dynamics, in the service of understanding the mechanisms of multi-scale integration of brain activity to cognition.

neuroscience↗