Compartmentalization of a bistable switch enables memory to cross a feedback-driven transition.

Cells make accurate decisions in the face of molecular noise and environmental fluctuations by relying not only on present pathway activity, but also on their memory of past signaling dynamics. Once a decision is made, cellular transitions are often rapid and switch-like due to positive feedback loops in the regulatory network. While positive feedback loops are good at promoting switch-like transitions, they are not expected to retain information to inform subsequent decisions. However, this expectation is based on our current understanding of network motifs that accounts for temporal, but not spatial, dynamics. Here, we show how spatial organization of the feedback-driven yeast G1/S switch enables the transmission of memory of past pheromone exposure across this transition. We expect this to be one of many examples where the exquisite spatial organization of the eukaryotic cell enables previously well-characterized network motifs to perform new and unexpected signal processing functions.

CDK and MAPK Synergistically Regulate Signaling Dynamics via a Shared Multi-site Phosphorylation Region on the Scaffold Protein Ste5.

We report an unanticipated system of joint regulation by cyclin-dependent kinase (CDK) and mitogen-activated protein kinase (MAPK), involving collaborative multi-site phosphorylation of a single substrate. In budding yeast, the protein Ste5 controls signaling through a G1 arrest pathway. Upon cell-cycle entry, CDK inhibits Ste5 via multiple phosphorylation sites, disrupting its membrane association. Using quantitative time-lapse microscopy, we examined Ste5 membrane recruitment dynamics at different cell-cycle stages. Surprisingly, in S phase, where Ste5 recruitment should be blocked, we observed an initial recruitment followed by a steep drop-off. This delayed inhibition revealed a requirement for both CDK activity and negative feedback from the pathway MAPK Fus3. Mutagenesis, mass spectrometry, and electrophoretic analyses suggest that the CDK and MAPK modify shared sites, which are most extensively phosphorylated when both kinases are active and able to bind their docking sites on Ste5. Such collaborative phosphorylation can broaden regulatory inputs and diversify output dynamics of signaling pathways.

Aperiodic components of local field potentials reflect inherent differences between cortical and subcortical activity.

Information flow in brain networks is reflected in local field potentials that have both periodic and aperiodic components. The 1/fχ aperiodic component of the power spectra tracks arousal and correlates with other physiological and pathophysiological states. Here we explored the aperiodic activity in the human thalamus and basal ganglia in relation to simultaneously recorded cortical activity. We elaborated on the parameterization of the aperiodic component implemented by specparam (formerly known as FOOOF) to avoid parameter unidentifiability and to obtain independent and more easily interpretable parameters. This allowed us to seamlessly fit spectra with and without an aperiodic knee, a parameter that captures a change in the slope of the aperiodic component. We found that the cortical aperiodic exponent χ, which reflects the decay of the aperiodic component with frequency, is correlated with Parkinson's disease symptom severity. Interestingly, no aperiodic knee was detected from the thalamus, the pallidum, or the subthalamic nucleus, which exhibited an aperiodic exponent significantly lower than in cortex. These differences were replicated in epilepsy patients undergoing intracranial monitoring that included thalamic recordings. The consistently lower aperiodic exponent and lack of an aperiodic knee from all subcortical recordings may reflect cytoarchitectonic and/or functional differences. SIGNIFICANCE STATEMENT: The aperiodic component of local field potentials can be modeled to produce useful and reproducible indices of neural activity. Here we refined a widely used phenomenological model for extracting aperiodic parameters (namely the exponent, offset and knee), with which we fit cortical, basal ganglia, and thalamic intracranial local field potentials, recorded from unique cohorts of movement disorders and epilepsy patients. We found that the aperiodic exponent in motor cortex is higher in Parkinson's disease patients with more severe motor symptoms, suggesting that aperiodic features may have potential as electrophysiological biomarkers for movement disorders symptoms. Remarkably, we found conspicuous differences in the aperiodic parameters of basal ganglia and thalamic signals compared to those from neocortex.

Biophysical Principles and Computational Modeling of Deep Brain Stimulation.

BACKGROUND: Deep brain stimulation (DBS) has revolutionized the treatment of neurological disorders, yet the mechanisms of DBS are still under investigation. Computational models are important in silico tools for elucidating these underlying principles and potentially for personalizing DBS therapy to individual patients. The basic principles underlying neurostimulation computational models, however, are not well known in the clinical neuromodulation community. OBJECTIVE: In this study, we present a tutorial on the derivation of computational models of DBS and outline the biophysical contributions of electrodes, stimulation parameters, and tissue substrates to the effects of DBS. RESULTS: Given that many aspects of DBS are difficult to characterize experimentally, computational models have played an important role in understanding how material, size, shape, and contact segmentation influence device biocompatibility, energy efficiency, the spatial spread of the electric field, and the specificity of neural activation. Neural activation is dictated by stimulation parameters including frequency, current vs voltage control, amplitude, pulse width, polarity configurations, and waveform. These parameters also affect the potential for tissue damage, energy efficiency, the spatial spread of the electric field, and the specificity of neural activation. Activation of the neural substrate also is influenced by the encapsulation layer surrounding the electrode, the conductivity of the surrounding tissue, and the size and orientation of white matter fibers. These properties modulate the effects of the electric field and determine the ultimate therapeutic response. CONCLUSION: This article describes biophysical principles that are useful for understanding the mechanisms of neurostimulation.

Lateralized and Region-Specific Thalamic Processing of Lexical Status during Reading Aloud.

To explore whether the thalamus participates in lexical status (word vs nonword) processing during spoken word production, we recorded local field potentials from the ventral lateral thalamus in 11 essential tremor patients (three females) undergoing thalamic deep-brain stimulation lead implantation during a visually cued word and nonword reading-aloud task. We observed task-related beta (12-30 Hz) activity decreases that were preferentially time locked to stimulus presentation, and broadband gamma (70-150 Hz) activity increases, which are thought to index increased multiunit spiking activity, occurring shortly before and predominantly time locked to speech onset. We further found that thalamic beta activity decreases bilaterally were greater when nonwords were read, demonstrating bilateral sensitivity to lexical status that likely reflects the tracking of task effort; in contrast, greater nonword-related increases in broadband gamma activity were observed only on the left, demonstrating lateralization of thalamic broadband gamma selectivity for lexical status. In addition, this lateralized lexicality effect on broadband gamma activity was strongest in more anterior thalamic locations, regions which are more likely to receive basal ganglia than cerebellar afferents and have extensive connections with prefrontal cortex including Brodmann's areas 44 and 45, regions consistently associated with grapheme-to-phoneme conversions. These results demonstrate active thalamic participation in reading aloud and provide direct evidence from intracranial thalamic recordings for the lateralization and topography of subcortical lexical status processing.SIGNIFICANCE STATEMENT Despite the corticocentric focus of most experimental work and accompanying models, there is increasing recognition of the role of subcortical structures in speech and language. Using local field potential recordings in neurosurgical patients, we demonstrated that the thalamus participates in lexical status (word vs nonword) processing during spoken word production, in a lateralized and region-specific manner. These results provide direct evidence from intracranial thalamic recordings for the lateralization and topography of subcortical lexical status processing.

Differentiation of speech-induced artifacts from physiological high gamma activity in intracranial recordings.

There is great interest in identifying the neurophysiological underpinnings of speech production. Deep brain stimulation (DBS) surgery is unique in that it allows intracranial recordings from both cortical and subcortical regions in patients who are awake and speaking. The quality of these recordings, however, may be affected to various degrees by mechanical forces resulting from speech itself. Here we describe the presence of speech-induced artifacts in local-field potential (LFP) recordings obtained from mapping electrodes, DBS leads, and cortical electrodes. In addition to expected physiological increases in high gamma (60-200 Hz) activity during speech production, time-frequency analysis in many channels revealed a narrowband gamma component that exhibited a pattern similar to that observed in the speech audio spectrogram. This component was present to different degrees in multiple types of neural recordings. We show that this component tracks the fundamental frequency of the participant's voice, correlates with the power spectrum of speech and has coherence with the produced speech audio. A vibration sensor attached to the stereotactic frame recorded speech-induced vibrations with the same pattern observed in the LFPs. No corresponding component was identified in any neural channel during the listening epoch of a syllable repetition task. These observations demonstrate how speech-induced vibrations can create artifacts in the primary frequency band of interest. Identifying and accounting for these artifacts is crucial for establishing the validity and reproducibility of speech-related data obtained from intracranial recordings during DBS surgery.

Different Principles Govern Different Scales of Brain Folding.

The signature folds of the human brain are formed through a complex and developmentally regulated process. In vitro and in silico models of this process demonstrate a random pattern of sulci and gyri, unlike the highly ordered and conserved structure seen in the human cortex. Here, we account for the large-scale pattern of cortical folding by combining advanced fetal magnetic resonance imaging with nonlinear diffeomorphic registration and volumetric analysis. Our analysis demonstrates that in utero brain growth follows a logistic curve, in the absence of an external volume constraint. The Sylvian fissure forms from interlobar folding, where separate lobes overgrow and close an existing subarachnoid space. In contrast, other large sulci, which are the ones represented in existing models, fold through an invagination of a flat surface, a mechanistically different process. Cortical folding is driven by multiple spatially and temporally different mechanisms; therefore regionally distinct biological process may be responsible for the global geometry of the adult brain.

Syringeal EMGs and synthetic stimuli reveal a switch-like activation of the songbird's vocal motor program.

The coordination of complex vocal behaviors like human speech and oscine birdsong requires fine interactions between sensory and motor programs, the details of which are not completely understood. Here, we show that in sleeping male zebra finches (Taeniopygia guttata), the activity of the song system selectively evoked by playbacks of their own song can be detected in the syrinx. Electromyograms (EMGs) of a syringeal muscle show playback-evoked patterns strikingly similar to those recorded during song execution, with preferred activation instants within the song. Using this global and continuous readout, we studied the activation dynamics of the song system elicited by different auditory stimuli. We found that synthetic versions of the bird's song, rendered by a physical model of the avian phonation apparatus, evoked very similar responses, albeit with lower efficiency. Modifications of autogenous or synthetic songs reduce the response probability, but when present, the elicited activity patterns match execution patterns in shape and timing, indicating an all-or-nothing activation of the vocal motor program.

Subthalamic Nucleus and Sensorimotor Cortex Activity During Speech Production.

The sensorimotor cortex is somatotopically organized to represent the vocal tract articulators such as lips, tongue, larynx, and jaw. How speech and articulatory features are encoded at the subcortical level, however, remains largely unknown. We analyzed LFP recordings from the subthalamic nucleus (STN) and simultaneous electrocorticography recordings from the sensorimotor cortex of 11 human subjects (1 female) with Parkinson's disease during implantation of deep-brain stimulation (DBS) electrodes while they read aloud three-phoneme words. The initial phonemes involved either articulation primarily with the tongue (coronal consonants) or the lips (labial consonants). We observed significant increases in high-gamma (60-150 Hz) power in both the STN and the sensorimotor cortex that began before speech onset and persisted for the duration of speech articulation. As expected from previous reports, in the sensorimotor cortex, the primary articulators involved in the production of the initial consonants were topographically represented by high-gamma activity. We found that STN high-gamma activity also demonstrated specificity for the primary articulator, although no clear topography was observed. In general, subthalamic high-gamma activity varied along the ventral-dorsal trajectory of the electrodes, with greater high-gamma power recorded in the dorsal locations of the STN. Interestingly, the majority of significant articulator-discriminative activity in the STN occurred before that in sensorimotor cortex. These results demonstrate that articulator-specific speech information is contained within high-gamma activity of the STN, but with different spatial and temporal organization compared with similar information encoded in the sensorimotor cortex.SIGNIFICANCE STATEMENT Clinical and electrophysiological evidence suggest that the subthalamic nucleus (STN) is involved in speech; however, this important basal ganglia node is ignored in current models of speech production. We previously showed that STN neurons differentially encode early and late aspects of speech production, but no previous studies have examined subthalamic functional organization for speech articulators. Using simultaneous LFP recordings from the sensorimotor cortex and the STN in patients with Parkinson's disease undergoing deep-brain stimulation surgery, we discovered that STN high-gamma activity tracks speech production at the level of vocal tract articulators before the onset of vocalization and often before related cortical encoding.

Single-cell profiling screen identifies microtubule-dependent reduction of variability in signaling.

Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell-to-cell variability in signal strength and cellular response. Here, we screened 1,141 non-essential genes to identify 50 "variability genes". Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct "axes" of system behavior. Three genes affected cytoplasmic microtubule function: BIM1, GIM2, and GIM4 We used genetic and chemical perturbations to show that, without microtubules, PRS output is reduced but variability is unaffected, while, when microtubules are present but their function is perturbed, output is sometimes lowered, but its variability is always high. The increased variability caused by microtubule perturbations required the PRS MAP kinase Fus3 and a process at or upstream of Ste5, the membrane-localized scaffold to which Fus3 must bind to be activated. Visualization of Ste5 localization dynamics demonstrated that perturbing microtubules destabilized Ste5 at the membrane signaling site. The fact that such microtubule perturbations cause aberrant fate and polarity decisions in mammals suggests that microtubule-dependent signal stabilization might also operate throughout metazoans.

From electromyographic activity to frequency modulation in zebra finch song.

Behavior emerges from the interaction between the nervous system and peripheral devices. In the case of birdsong production, a delicate and fast control of several muscles is required to control the configuration of the syrinx (the avian vocal organ) and the respiratory system. In particular, the syringealis ventralis muscle is involved in the control of the tension of the vibrating labia and thus affects the frequency modulation of the sound. Nevertheless, the translation of the instructions (which are electrical in nature) into acoustical features is complex and involves nonlinear, dynamical processes. In this work, we present a model of the dynamics of the syringealis ventralis muscle and the labia, which allows calculating the frequency of the generated sound, using as input the electrical activity recorded in the muscle. In addition, the model provides a framework to interpret inter-syllabic activity and hints at the importance of the biomechanical dynamics in determining behavior.

Gating related activity in a syringeal muscle allows the reconstruction of zebra finches songs.

Birdsong production involves the simultaneous and precise control of a set of muscles that change the configuration and dynamics of the vocal organ. Although it has been reported that each one of the different muscles is primarily involved in the control of one acoustic feature, recent advances have shown that they act synergistically to achieve the dynamical state necessary for phonation. In this work, we present a set of criteria that allow the extraction of gating-related information from the electromyographic activity of the syringealis ventralis muscle, a muscle that has been shown to be involved in frequency modulation. Using dynamical models of the muscle and syringeal dynamics, we obtain a full reconstruction of the zebra finch song using only the activity of this muscle.

Yeast GPCR signaling reflects the fraction of occupied receptors, not the number.

According to receptor theory, the effect of a ligand depends on the amount of agonist-receptor complex. Therefore, changes in receptor abundance should have quantitative effects. However, the response to pheromone in Saccharomyces cerevisiae is robust (unaltered) to increases or reductions in the abundance of the G-protein-coupled receptor (GPCR), Ste2, responding instead to the fraction of occupied receptor. We found experimentally that this robustness originates during G-protein activation. We developed a complete mathematical model of this step, which suggested the ability to compute fractional occupancy depends on the physical interaction between the inhibitory regulator of G-protein signaling (RGS), Sst2, and the receptor. Accordingly, replacing Sst2 by the heterologous hsRGS4, incapable of interacting with the receptor, abolished robustness. Conversely, forcing hsRGS4:Ste2 interaction restored robustness. Taken together with other results of our work, we conclude that this GPCR pathway computes fractional occupancy because ligand-bound GPCR-RGS complexes stimulate signaling while unoccupied complexes actively inhibit it. In eukaryotes, many RGSs bind to specific GPCRs, suggesting these complexes with opposing activities also detect fraction occupancy by a ratiometric measurement. Such complexes operate as push-pull devices, which we have recently described.

Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range.

Cell signaling systems sense and respond to ligands that bind cell surface receptors. These systems often respond to changes in the concentration of extracellular ligand more rapidly than the ligand equilibrates with its receptor. We demonstrate, by modeling and experiment, a general "systems level" mechanism cells use to take advantage of the information present in the early signal, before receptor binding reaches a new steady state. This mechanism, pre-equilibrium sensing and signaling (PRESS), operates in signaling systems in which the kinetics of ligand-receptor binding are slower than the downstream signaling steps, and it typically involves transient activation of a downstream step. In the systems where it operates, PRESS expands and shifts the input dynamic range, allowing cells to make different responses to ligand concentrations so high as to be otherwise indistinguishable. Specifically, we show that PRESS applies to the yeast directional polarization in response to pheromone gradients. Consideration of preexisting kinetic data for ligand-receptor interactions suggests that PRESS operates in many cell signaling systems throughout biology. The same mechanism may also operate at other levels in signaling systems in which a slow activation step couples to a faster downstream step.

Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range.

Although the proteins comprising many signaling systems are known, less is known about their numbers per cell. Existing measurements often vary by more than 10-fold. Here, we devised improved quantification methods to measure protein abundances in the Saccharomyces cerevisiae pheromone response pathway, an archetypical signaling system. These methods limited variation between independent measurements of protein abundance to a factor of two. We used these measurements together with quantitative models to identify and investigate behaviors of the pheromone response system sensitive to precise abundances. The difference between the maximum and basal signaling output (dynamic range) of the pheromone response MAPK cascade was strongly sensitive to the abundance of Ste5, the MAPK scaffold protein, and absolute system output depended on the amount of Fus3, the MAPK. Additional analysis and experiment suggest that scaffold abundance sets a tradeoff between maximum system output and system dynamic range, a prediction supported by recent experiments.

Protocol for FRAP-based estimation of nuclear import and export rates in single yeast cells.

Here, we present a protocol for estimating nuclear transport parameters in single cells. We describe steps for performing four consecutive fluorescence recovery after photobleaching experiments, fitting the obtained data to an ordinary differential equations model, and statistical analysis of the fittings using a specialized R package. This protocol permits the estimation of import and export rates, nuclear or cytosolic fixed fractions, and total number of molecules. For complete details on the use and execution of this protocol, please refer to Durrieu et al.1.

Spatiotemporally-specific cortical-subthalamic coupling differentiates aspects of speech performance.

Speech provides a rich context for exploring human cortical-basal ganglia circuit function, but direct intracranial recordings are rare. We recorded electrocorticographic signals in the cortex synchronously with single units in the subthalamic nucleus (STN), a basal ganglia node that receives direct input from widespread cortical regions, while participants performed a syllable repetition task during deep brain stimulation (DBS) surgery. We discovered that STN neurons exhibited spike-phase coupling (SPC) events with distinct combinations of frequency, location, and timing that indexed specific aspects of speech. The strength of SPC to posterior perisylvian cortex predicted phoneme production accuracy, while that of SPC to perirolandic cortex predicted time taken for articulation Thus, STN-cortical interactions are coordinated via transient bursts of behavior-specific synchronization that involves multiple neuronal populations and timescales. These results both suggest mechanisms that support auditory-sensorimotor integration during speech and explain why firing-rate based models are insufficient for explaining basal ganglia circuit behavior.

Quantitative measurement of protein relocalization in live cells.

Microscope cytometry provides a powerful means to study signaling in live cells. Here we present a quantitative method to measure protein relocalization over time, which reports the absolute fraction of a tagged protein in each compartment. Using this method, we studied an essential step in the early propagation of the pheromone signal in Saccharomyces cerevisiae: recruitment to the membrane of the scaffold Ste5 by activated Gßγ dimers. We found that the dose response of Ste5 recruitment is graded (EC50 = 0.44 ± 0.08 nM, Hill coefficient = 0.8 ± 0.1). Then, we determined the effective dissociation constant (K(de)) between Ste5 and membrane sites during the first few minutes when the negative feedback from the MAPK Fus3 is first activated. K(de) changed during the first minutes from a high affinity of < 0.65 nM to a steady-state value of 17 ± 9 nM. During the same period, the total number of binding sites decreased slightly, from 1940 ± 150 to 1400 ± 200. This work shows how careful quantification of a protein relocalization dynamic can give insight into the regulation mechanisms of a biological system.

Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast.

The high osmolarity glycerol (HOG) pathway in yeast serves as a prototype signalling system for eukaryotes. We used an unprecedented amount of data to parameterise 192 models capturing different hypotheses about molecular mechanisms underlying osmo-adaptation and selected a best approximating model. This model implied novel mechanisms regulating osmo-adaptation in yeast. The model suggested that (i) the main mechanism for osmo-adaptation is a fast and transient non-transcriptional Hog1-mediated activation of glycerol production, (ii) the transcriptional response serves to maintain an increased steady-state glycerol production with low steady-state Hog1 activity, and (iii) fast negative feedbacks of activated Hog1 on upstream signalling branches serves to stabilise adaptation response. The best approximating model also indicated that homoeostatic adaptive systems with two parallel redundant signalling branches show a more robust and faster response than single-branch systems. We corroborated this notion to a large extent by dedicated measurements of volume recovery in single cells. Our study also demonstrates that systematically testing a model ensemble against data has the potential to achieve a better and unbiased understanding of molecular mechanisms.

Broadband aperiodic components of local field potentials reflect inherent differences between cortical and subcortical activity.

Information flow in brain networks is reflected in intracerebral local field potential (LFP) measurements that have both periodic and aperiodic components. The 1/fχ broadband aperiodic component of the power spectra has been shown to track arousal level and to correlate with other physiological and pathophysiological states, with consistent patterns across cortical regions. Previous studies have focused almost exclusively on cortical neurophysiology. Here we explored the aperiodic activity of subcortical nuclei from the human thalamus and basal ganglia, in relation to simultaneously recorded cortical activity. We elaborated on the FOOOF (fitting of one over f) method by creating a new parameterization of the aperiodic component with independent and more easily interpretable parameters, which allows seamlessly fitting spectra with and without an aperiodic knee, a component of the signal that reflects the dominant timescale of aperiodic fluctuations. First, we found that the aperiodic exponent from sensorimotor cortex in Parkinson's disease (PD) patients correlated with disease severity. Second, although the aperiodic knee frequency changed across cortical regions as previously reported, no aperiodic knee was detected from subcortical regions across movement disorders patients, including the ventral thalamus (VIM), globus pallidus internus (GPi) and subthalamic nucleus (STN). All subcortical region studied exhibited a relatively low aperiodic exponent (χSTN=1.3±0.2, χVIM=1.4±0.1, χGPi =1.4±0.1) that differed markedly from cortical values (χCortex=3.2±0.4, fkCortex=17±5 Hz). These differences were replicated in a second dataset from epilepsy patients undergoing intracranial monitoring that included thalamic recordings. The consistently lower aperiodic exponent and lack of an aperiodic knee from all subcortical recordings may reflect cytoarchitectonic and/or functional differences between subcortical nuclei and the cortex.