Alan Bush

Massachusetts General Hospital | MGH · Functional Neurosurgery

Speech is a complex behavior that can be used to study unique contributions of the basal ganglia to motor control in the human brain. Computational models suggest that the basal ganglia encodes either the phonetic content or the sequence of speech elements. To explore this question, we investigated the relationship between phoneme and sequence feat...

Neurosurgical procedures that enable direct brain recordings in awake patients offer unique opportunities to explore the neurophysiology of human speech. The scarcity of these opportunities and the altruism of participating patients compel us to apply the highest rigor to signal analysis. Intracranial electroencephalography (iEEG) signals recorded...

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 relatio...

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 protoco...

Speech is a complex behavior that can be used to study unique contributions of the basal ganglia to motor control in the human brain. Computational models suggest that the basal ganglia encodes either the phonetic content or the sequence of speech elements. To explore this question, we investigated the relationship between phoneme and sequence feat...

Speaking evokes modulation of neuronal activity in the subthalamic nucleus (STN), a basal ganglia node that receives both mono- and polysynaptic inputs from cortex and subcortex. Indeed, speech provides a rich context for exploring interactions within human cortical-basal ganglia circuits, but direct intracranial recordings are rare. Here, we synch...

How the human brain maintains information in working memory (WM), a process critical for all our goal-directed function, has been debated for decades. Classic neurophysiological models, which argue that WM is maintained via persistent content-specific delay activity, have been challenged by alternative ideas suggesting a combination of dynamic acti...

Brain computer interfaces (BCI) provide unprecedented spatiotemporal precision that will enable significant expansion in how numerous brain disorders are treated. Decoding dynamic patient states from brain signals with machine learning is required to leverage this precision, but a standardized framework for identifying and advancing novel clinical...

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 under...

Neurosurgical procedures, in which electrodes can be placed in the brain of awake patients, offer remarkable opportunities to discover the neurophysiology underlying human speech. The relative scarcity of these opportunities and the altruism of participating patients obligates us to apply the highest possible rigor to signal interpretation. Intracr...

Information flow in brain networks is reflected in intracerebral local field potential (LFP) measurements that have both periodic and aperiodic components. The 1/f χ 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 patter...

Background: Using electrocorticography for research (R-ECoG) during deep brain stimulation (DBS) surgery has advanced our understanding of human cortical-basal ganglia neurophysiology and mechanisms of therapeutic circuit modulation. The safety of R-ECoG has been established, but potential effects of temporary ECoG strip placement on targeting acc...

Nuclear transport is an essential part of eukaryotic cell function. Here, we present scFRAP, a model assisted- fluorescent recovery after photobleaching (FRAP)- based method to determine nuclear import and export rates independently in individual live cells. To overcome the inherent noise of single-cell measurements, we performed sequential FRAPs o...

Speech requires successful information transfer within cortical-basal ganglia (BG) loop circuits to produce the desired acoustic output. For this reason, up to 90% of Parkinson's disease (PD) patients experience impairments of speech articulation. Deep brain stimulation (DBS) is highly effective in controlling the symptoms of PD, sometimes alongsid...

The first commercially sensing enabled deep brain stimulation (DBS) devices for the treatment of movement disorders have recently become available. In the future, such devices could leverage machine learning based brain signal decoding strategies to individualize and adapt therapy in real-time. As multi-channel recordings become available, spatial...

Nuclear transport is an essential part of eukaryotic cell function. Several assays exist to measure the rate of this process, but not at the single-cell level. Here, we developed a fluorescent recovery after photobleaching (FRAP)- based method to determine nuclear import and export rates independently in individual live cells. To overcome the inher...

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...

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...

Objective To assess whether hippocampal spindles and barques are markers of epileptogenicity. Methods Focal epilepsy patients that underwent stereo-electroencephalography implantation with at least one electrode in their hippocampus were selected (n=75). The occurrence of spindles and barques in the hippocampus was evaluated in each patient. We cr...

Speaking precisely is important for effective verbal communication, and articulatory gain is one component of speech motor control that contributes to achieving this goal. Given that the basal ganglia have been proposed to regulate the speed and size of limb movement, that is, movement gain, we explored the basal ganglia contribution to articulator...

The application of machine learning to intracranial signal analysis has the potential to revolutionize deep brain stimulation (DBS) by personalizing therapy to dynamic brain states, specific to symptoms and behaviors. Most decoding pipelines for movement decoding in the context of adaptive DBS are based on single channel frequency domain features,...

Many language functions are traditionally assigned to cortical brain areas, leaving the contributions of subcortical structures to language processing largely unspecified. The present study examines a potential role of the subthalamic nucleus (STN) in lexical processing, specifically, reading aloud of words (e.g., 'fate') and pseudowords (e.g., 'fa...

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...

The mechanisms by which the human cerebral cortex folds into its final form remain poorly understood. With most of the current models and evidence addressing secondary folds, we sought to focus on the global geometry of the mature brain by studying its most distinctive feature, the Sylvian fissure. A digital human fetal brain atlas was developed us...

To explore whether the thalamus participates in lexical status encoding, local field potentials were recorded in patients undergoing deep brain stimulation lead implantation while they read aloud single-syllable words and nonwords. Bilateral decreases in thalamic beta (12-30Hz) activity were locked preferentially to stimulus presentation, and these...

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 combi...

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 combi...

Objective: Cortical folding places regions that are separated by a large distance along the cortical surface in close proximity. This process is not homogeneous; regions such as the insular opercula have a much higher cortical surface distance (CSD) to euclidean distance (ED) than others. Here the authors explore the hypothesis that in the folded...

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 local field potential (LFP) recordings from the subthalamic nucleus (STN) and simultaneous ele...

Significance The study of the integration between sensory inputs and motor commands has greatly benefited from the finding that in sleeping oscine birds, playback of their own song evokes highly specific firing patterns in neurons also involved in the production of that song. Nevertheless, the sparse spiking patterns that can be recorded from few s...

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 th...

Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in theSaccharomyces cerevisiaepheromone response system (PRS) that reduced cell-to-cell variability in signal strength and cellular response. Here, we screened 1,141 non-essential genes to id...

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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 phospho...

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 cont...

Acquisition and maintenance of complex vocal behaviors like human speech and oscine birdsong require continuous auditory feedback. The exact way in which this feedback is integrated into the vocal motor programs is not completely understood. Here we show that in sleeping zebra finches ( Taeniopygia guttata ), the activity of the song system selecti...

In a companion paper, we carried out a high-throughput screen to identify genes that suppressed cell-to-cell variability in signaling in yeast. Two genes affected cytoplasmic microtubules that can connect the nucleus to a signaling site on the membrane. Here, we show that microtubule perturbations that affected polymerization and depolymerization,...

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),...

Appendix

Review Process File

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Model EV1

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 feedb...

In order to contribute to the design of crossfeeding systems, we modeled population control in a coculture of two crossfeeding strains of an organism, each of which secretes a metabolite the other strain requires to grow. Differential equations show that the steady-state population ratio can be tuned by varying the ratio of the metabolite secretion...

Significance Many cell decisions depend on precise measurements of external ligands reversibly bound to receptors. Yeast cells orient in gradients of sex pheromone detecting differences in the amount of ligand-receptor complex. However, yeast can orient in gradients with nearly all receptors occupied. We describe a general systems-level mechanism,...

Environmental and internal conditions expose cells to a multiplicity of stimuli whose consequences are difficult to predict. We investigate the response to mating pheromone of yeast cells adapted to high osmolarity. Events downstream of pheromone binding involve two mitogen-activated protein kinase (MAPK) cascades: the pheromone response (PR) and t...

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 Saccharom...

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 os...

Copasi and SBML model file with data used in the Copasi file for fitting and ranking.

Supplementary Tables S1–14, Supplementary Figures S1–10

This unit describes a method for quantifying various cellular features (e.g., volume, total and subcellular fluorescence localization) from sets of microscope images of individual cells. It includes procedures for tracking cells over time. One purposely defocused transmission image (sometimes referred to as bright-field or BF) is acquired to segmen...

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 metho...

This unit describes a method for quantifying various cellular parameters (e.g., volume, total and subcellular fluorescence localization) from sets of microscope images of individual cells. It includes procedures for tracking cells over time. One purposefully defocused transmission image (sometimes referred to as bright-field or BF) is acquired to l...