Biology subjects

Johnston, K.

Publications and source records attributed to Johnston, K..

15 recordsLinked to original sources

bioRxiv2025

Marmoset Anterior Cingulate Area 32 Neurons Exhibit Responses to Presented and Produced Calls During Naturalistic Vocal Communication

Vocal communication is a complex social behavior that entails the integration of auditory perception and vocal production. Both anatomical and functional evidence have implicated the anterior cingulate cortex (ACC), including area 32, in these processes, but the dynamics of neural responses in area 32 during naturalistic vocal interactions remain poorly understood. Here, we addressed this by recording the activity of single area 32 neurons using chronically implanted ultra high density Neuropixels probes in freely moving common marmosets (Callithrix jacchus) engaged in an antiphonal calling paradigm in which they exchanged long-distance "phee" calls with a virtual conspecific. We found that many neurons exhibited complex modulations in discharge rates in response to presented calls, prior to and following self-generated calls, and during the interval between presented and produced vocalizations. These findings are consistent with the conceptualization of area 32 as an audiovocal interface integrating auditory information, cognitive processes, and motor outputs in the service of vocal communication. Significance StatementVocal communication is indispensable in the daily lives of social animals including primates. This sophisticated ability requires processing and production of vocalizations across fluid social contexts. Vocal behavior is controlled by a large network of brain areas. Area 32 within the anterior cingulate cortex may be a linchpin of this network, as it is interconnected with both auditory cortical areas and subcortical structures engaging vocal control. This position is ideal for integrating auditory, motor, and cognitive signals serving vocal behaviour. We show for the first time that neural correlates of these three signal types are present in area 32 neurons recorded in freely moving marmosets during naturalistic vocal exchanges. We conclude that area 32 exhibits the properties of an audiovocal interface.

neuroscience↗

bioRxiv2024

Evaluation of Machine Learning-Assisted Directed Evolution Across Diverse Combinatorial Landscapes

Various machine learning-assisted directed evolution (MLDE) strategies have been shown to identify high-fitness protein variants more efficiently than typical wet-lab directed evolution approaches. However, limited understanding of the factors influencing MLDE performance across diverse proteins has hindered optimal strategy selection for wet-lab campaigns. To address this, we systematically analyzed multiple MLDE strategies, including active learning and focused training using six distinct zero-shot predictors, across 16 diverse protein fitness landscapes. By quantifying landscape navigability with six attributes, we found that MLDE offers a greater advantage on landscapes which are more challenging for directed evolution, especially when focused training is combined with active learning. Despite varying levels of advantage across landscapes, focused training with zero-shot predictors leveraging distinct evolutionary, structural, and stability knowledge sources consistently outperforms random sampling for both binding interactions and enzyme activities. Our findings provide practical guidelines for selecting MLDE strategies for protein engineering.

bioengineering↗

bioRxiv2024

Neural activity for complex sounds in the marmoset medial prefrontal cortex

Vocalizations play an important role in the daily life of nonhuman primates and are likely precursors of human language. Recent functional imaging studies in the highly vocal common marmoset (Callithrix jacchus) have suggested that medial prefrontal cortex area 32 may be a part of a vocalization-processing network but the response properties of area 32 neurons to auditory stimuli remain unknown. Here, we performed electrophysiological recordings in area 32 with high-density Neuropixels probes and characterized neuronal responses to a variety of sounds including conspecific vocalizations. More than half of the neurons in area 32 responded to conspecific vocalizations and other complex auditory stimuli. These responses exhibited dynamics consisting of an initially non-selective reduction in neural activity, followed by an increase in activity that immediately conveyed sound selectivity. Our findings demonstrate that primate mPFC area 32 plays a critical role in processing species-specific and biologically relevant sounds.

neuroscience↗

bioRxiv2023

The marmoset default-mode network identified by deactivation in task-based fMRI studies

Understanding the default-mode network (DMN) in the common marmoset (Callithrix jacchus) has been challenging due to inconsistencies with human and marmoset DMNs. By analyzing task-negative activation in fMRI studies, we identified medial prefrontal cortical areas, rostral auditory areas, entorhinal cortex, posterior cingulate cortex area 31, hippocampus, hypothalamus, and basomedial amygdala as marmoset DMN components. Notable, medial and posterior parietal areas that were previously hypothesized to be part of the DMN were activated during visual task blocks. Seed analysis using resting-state fMRI showed strong connectivity between task-negative areas, and tracer data supported a structural network aligning with this functional DMN. These findings challenge previous definition of the marmoset DMN and reconcile many inconsistencies with the DMNs observed in humans, macaque monkeys, and even rodents. Overall, these results highlight the marmoset as a powerful model for DMN research, with potential implications for studying neuropsychiatric disorders where DMN activity and connectivity are altered.

animal behavior and cognition↗

bioRxiv2023

Effects of ketamine on frontoparietal interactions during working memory in macaque monkeys

Schizophrenia is known as a syndrome of dysconnection among brain regions. As a model for this syndrome, low doses of N-methyl-D-aspartate (NMDA) receptor antagonists, such as ketamine, produce schizophrenia-like symptoms and cognitive deficits in healthy humans and animals. One of such deficits is impaired working memory, a process that engages an extended network of both frontal and parietal areas. While ketamine is known to disrupt working memory by altering both spiking and oscillatory activities in the lateral prefrontal cortex (lPFC), it remains unknown whether NMDA receptor antagonists also produce frontoparietal dysconnection during working memory processes. Here, we simultaneously recorded both single unit activities and local field potentials from lPFC and posterior parietal cortex (PPC) in macaque monkeys during a rule-based working memory task. Like previous work in the lPFC alone, we found that ketamine compromised delay-period rule coding in single neurons and reduced low-frequency oscillations in the PPC. Furthermore, ketamine reduced task-related connectivity in both fronto-parietal and parieto-frontal directions. Consistent with this, ketamine also weakened interareal coherence between spiking and low-frequency oscillatory activities. Our findings demonstrate the utility of acute NMDA receptor antagonist in simulating a syndrome of dysconnection and support this model in its potential for the exploration of novel treatment strategies for schizophrenia.

neuroscience↗

bioRxiv2023

A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations of genes to a biological outcome, we have developed a multiplex, randomized CRISPR interference sequencing (MuRCiS) approach. At its center is a new method for the randomized self-assembly of CRISPR arrays from synthetic oligonucleotide pairs. When paired with PacBio long-read sequencing, MuRCiS allowed for near-comprehensive interrogation of all pairwise combinations of a group of 44 Legionella pneumophila virulence genes encoding highly conserved transmembrane proteins for their role in pathogenesis. Both amoeba and human macrophages were challenged with L. pneumophila bearing the pooled CRISPR array libraries, leading to the identification of several new virulence-critical combinations of genes. lpg2888 and lpg3000 were particularly fascinating for their apparent redundant functions during L. pneumophila human macrophage infection, while lpg3000 alone was essential for L. pneumophila virulence in the amoeban host Acanthamoeba castellanii. Thus, MuRCiS provides a method for rapid genetic examination of even large groups of redundant genes, setting the stage for application of this technology to a variety of biological contexts and organisms.

genetics↗

bioRxiv2022

Delay-related activity in marmoset prefrontal cortex

Persistent delay-period activity in prefrontal cortex (PFC) has long been regarded as a neural signature of working memory (WM). Electrophysiological investigations in macaque PFC have provided much insight into WM mechanisms, however a barrier to understanding is the fact that a portion of PFC lies buried within the principal sulcus in this species and is inaccessible for laminar electrophysiology or optical imaging. The relatively lissencephalic cortex of the New World common marmoset (Callithrix jacchus) circumvents such limitations. It remains unknown however, whether marmoset PFC neurons exhibit persistent activity. Here, we addressed this gap by conducting wireless electrophysiological recordings in PFC of marmosets performing a delayed-match-to-location task on a home cage-based touchscreen system. As in macaques, marmoset PFC neurons exhibited sample, delay, and response-related activity that was directionally tuned and linked to correct task performance. Models constructed from population activity consistently and accurately predicted stimulus location throughout the delay period, supporting a framework of delay activity in which mnemonic representations are relatively stable in time. Taken together, our findings support the existence of common neural mechanisms underlying WM performance in PFC of macaques and marmosets, and thus validate the marmoset as a suitable model animal for investigating the microcircuitry underlying WM.

neuroscience↗

bioRxiv2021

A second specificity-determining loop in Class A sortases: Biochemical characterization of natural sequence variation in chimeric SrtA enzymes

Gram-positive bacteria contain sortase enzymes on their cell surfaces that catalyze transpeptidation reactions critical for proper cellular function. In vitro, sortases are used in sortase-mediated ligation (SML) reactions for a variety of protein engineering applications. Historically, sortase A from Staphylococcus aureus (saSrtA) has been the enzyme of choice for SML reactions. However, the stringent specificity of saSrtA for the sequence motif LPXTG limits its uses. Here, we use principal component analysis to identify a structurally conserved loop with a high degree of variability in all classes of sortases. We investigate the contribution of this {beta}7-{beta}8 loop, located between the catalytic cysteine and arginine residues and immediately adjacent to the target binding cleft, by designing and testing chimeric sortase enzymes. Our chimeras utilize natural sequence variation of Class A sortases from 8 species engineered into the SrtA sequence from Streptococcus pneumoniae (spSrtA). While some of our chimeric enzymes mimic the activity and selectivity of the wild-type protein from which the loop sequence is derived (e.g., that of saSrtA), others result in chimeric spSrtA enzymes able to accommodate a range of residues in the final position of the substrate motif (LPXTX). Using mutagenesis, structural, and sequence analyses, we identify three interactions facilitated by {beta}7-{beta}8 loop residues that appear to be broadly characteristic of Class A sortase enzymes. These studies provide the foundation for a deeper understanding of sortase target selectivity and can expand the sortase toolbox for future SML applications.

biochemistry↗

bioRxiv2021

Ketamine disrupts gaze patterns during face viewing in the common marmoset

Faces are stimuli of critical importance for primates. The common marmoset (Callithrix jacchus) is a promising model for investigations of face processing, as this species possesses oculomotor and face processing networks resembling those of macaques and humans. Face processing is often disrupted in neuropsychiatric conditions such as schizophrenia (SZ) and thus it is important to recapitulate underlying circuitry dysfunction preclinically. The N-Methyl-D-aspartate (NMDA) non-competitive antagonist ketamine has been used extensively to model the cognitive symptoms of SZ. Here, we investigated the effects of a subanesthetic dose of ketamine on oculomotor behaviour in marmosets during face viewing. Four marmosets received systemic ketamine or saline injections while viewing phase-scrambled or intact videos of conspecifics faces. To evaluate effects of ketamine on scan paths during face viewing, we identified regions of interest in each face video, and classified locations of saccade onsets and landing positions within these areas. A preference for the snout over eye regions was observed following ketamine administration. In addition, regions in which saccades landed could be significantly predicted by saccade onset region in the saline but not the ketamine condition. No significant drug effects were observed for phase-scrambled videos. Effects on saccade control were limited to a reduction in saccade amplitudes during viewing of scrambled videos. Thus, ketamine induced a significant disruption of scan paths during viewing of conspecific faces but limited effects on saccade motor control. These findings support the use of ketamine in marmosets for investigating changes in neural circuits underlying social cognition in neuropsychiatric disorders.

neuroscience↗

bioRxiv2020

Structural alterations in the macaque frontoparietal white matter network after recovery from prefrontal cortex lesions

Unilateral damage to the frontoparietal network typically impairs saccade target selection within the contralesional visual hemifield. Severity of deficits and the degree of recovery have been associated with widespread network dysfunction, yet it is not clear how these behavioural and functional changes relate with the underlying structural white matter pathways. Here, we investigated whether recovery after unilateral prefrontal cortex (PFC) lesions was associated with structural white matter remodeling in the distributed frontoparietal network. Diffusion-weighted MRI was acquired in four macaque monkeys before the lesions and at 2-4 months post-lesion, after recovery of deficits in saccade selection of contralesional targets. Probabilistic tractography was used to reconstruct inter- and intra-hemispheric frontoparietal fiber tracts: bilateral superior longitudinal fasciculus (SLF) and transcallosal fibers connecting bilateral PFC or bilateral posterior parietal cortex (PPC). After behavioural recovery, tract-specific fractional anisotropy in contralesional SLF and transcallosal PPC increased after small lesions and decreased after larger lesions compared to pre-lesion. These findings indicate that remote fiber tracts may provide optimal compensation after small PFC lesions. However, larger lesions may have induced widespread structural damage and hindered compensatory remodeling in the structural frontoparietal network.

neuroscience↗

bioRxiv2019

Single unit activity in marmoset posterior parietal cortex in a gap saccade task

Abnormal saccadic eye movements can serve as biomarkers for patients with several neuropsychiatric disorders. To investigate cortical control mechanisms of saccadic responses, the common marmoset (Callithrix jacchus) is a promising non-human primate model. Their lissencephalic brain allows for accurate targeting of homologues of sulcal areas in the macaque brain. Here we recorded single unit activity in the posterior parietal cortex of two marmosets using chronic microelectrode arrays, while the monkeys performed a saccadic task with Gap trials (stimulus onset lagged fixation point offset by 200ms) interleaved with Step trials (fixation point disappeared when the peripheral stimulus appeared). Both marmosets showed a gap effect--shorter saccadic reaction times (SRTs) in Gap vs. Step trials. On average, stronger gap-period response across the entire neuronal population preceded shorter SRTs on trials with contralateral targets, although this correlation was stronger among the 15% gap neurons, which responded significantly during the gap. We also found 39% target neurons with significant visual target-related responses, which were stronger in Gap trials and correlated with the SRTs better than the remaining cells. Compared with slow saccades, fast saccades were preceded by both stronger gap-related and target-related response in all PPC neurons, regardless of whether such response reached significance. Our findings suggest that the PPC in the marmoset contains an area that is involved in the modulation of saccadic preparation and plays roles comparable to those of area LIP in macaque monkeys in eye movements.\n\nSIGNIFICANCE STATEMENTAbnormal saccadic eye movements can serve as biomarkers for different neuropsychiatric disorders. So far, processes of cerebral cortical control of saccades are not fully understood. Non-human primates are ideal models for studying such processes, and the marmoset is especially advantageous since their smooth cortex permits laminar analyses of cortical microcircuits. Using electrode arrays implanted in the posterior parietal cortex of marmosets, we found neurons responsive to key periods of a saccadic task in a manner that contribute to cortical modulation of saccadic preparation. Notably, this signal was correlated with subsequent saccadic reaction times and was present in the entire neuronal population. We suggest that the marmoset model will shed new light on the cortical mechanisms of saccadic control.

neuroscience↗

bioRxiv2019

Functional localization of the frontal eye fields in the common marmoset using microstimulation

The frontal eye field (FEF) is a critical region for the deployment of overt and covert spatial attention. While investigations in the macaque continue to provide insight into the neural underpinnings of the FEF, due to its location within a sulcus the macaque FEF is virtually inaccessible to electrophysiological techniques such as high-density and laminar recordings. With a largely lissencephalic cortex, the common marmoset (Callithrix jacchus) is a promising alternative primate model for studying FEF microcircuitry. Putative homologies have been established with the macaque FEF on the basis of cytoarchitecture and connectivity, however physiological investigation in awake, behaving marmosets is necessary to physiologically locate this area. Here we addressed this gap using intracortical microstimulation in a broad range of frontal cortical areas in marmosets. We implanted marmosets with 96-channel Utah arrays and applied microstimulation trains while they freely viewed video clips. We evoked short-latency fixed vector saccades at low currents (<50 A) in areas 45, 8aV, 8C and 6DR. We observed a topography of saccade direction and amplitude consistent with findings in macaques and humans; we observed small saccades in ventrolateral FEF and large saccades combined with contralateral neck and shoulder movements encoded in dorsomedial FEF. Our data provide compelling evidence supporting homology between marmoset and macaque FEF and suggest the marmoset is a useful primate model for investigating FEF microcircuitry and its contributions to oculomotor and cognitive functions.\n\nSignificance StatementThe frontal eye field (FEF) is a critical cortical region for overt and covert spatial attention. The microcircuitry of this area remains poorly understood, as in the macaque, the most commonly used model, it is embedded within a sulcus and is inaccessible to modern electrophysiological and optical imaging techniques. The common marmoset is a promising alternative primate model due to its lissencephalic cortex and potential for genetic manipulation. However, evidence for homologous cortical areas in this model remains limited and unclear. Here we applied microstimulation in frontal cortical areas in marmosets to physiologically identify the FEF. Our results provide compelling evidence for a frontal eye field in the marmoset, and suggest that the marmoset is a useful model for FEF microcircuitry.

neuroscience↗

bioRxiv2019

Electrical microstimulation evokes saccades in posterior parietal cortex of common marmosets

The common marmoset (Callithrix jacchus) is a small-bodied New World primate, increasing in prominence as a model animal for neuroscience research. The lissencephalic cortex of this primate species provides substantial advantages for the application of electrophysiological techniques such as high-density and laminar recordings, which have the capacity to advance our understanding of local and laminar cortical circuits and their roles in cognitive and motor functions. This is particularly the case with respect to the oculomotor system, as critical cortical areas of this network such as the frontal eye fields (FEF) and lateral intraparietal area (LIP) lie deep within sulci in macaques. Studies of cytoarchitecture and connectivity have established putative homologies between cortical oculomotor fields in marmoset and macaque, but physiological investigations of these areas, particularly in awake marmosets, have yet to be carried out. Here, we addressed this gap by probing the function of posterior parietal cortex (PPC) of the common marmoset using electrical microstimulation. We implanted two animals with 32-channel Utah arrays at the location of the putative area LIP and applied microstimulation while they viewed a video display and made untrained eye movements. Similar to previous studies in macaques, stimulation evoked fixed-vector and goal-directed saccades, staircase saccades, and eye blinks. These data demonstrate that area LIP of the marmoset plays a role in the regulation of eye movements, provide additional evidence that this area is homologous with that of the macaque, and further establish the marmoset as valuable model for neurophysiological investigations of oculomotor and cognitive control.\n\nNew & NoteworthyThe macaque monkey has been the preeminent model for investigations of oculomotor control, but studies of cortical areas are limited as many of these areas are buried within sulci in this species. Here we applied electrical microstimulation to the putative area LIP of the lissencephalic cortex of awake marmosets. Similar to the macaque, microstimulation evoked contralateral saccades from this area, supporting the marmoset as a valuable model for studies of oculomotor control.

neuroscience↗

bioRxiv2019

Stimulus-Locked Responses on Human Upper Limb Muscles and Corrective Reaches are Preferentially Evoked by Low Spatial Frequencies

In situations requiring immediate action, humans can generate visually-guided responses at remarkably short latencies. Here, to better understand the visual attributes that best evoke such rapid responses, we recorded upper limb muscle activity while participants performed visually-guided reaches towards Gabor patches composed of differing spatial frequencies. We studied reaches initiated from a stable posture (experiment 1, a static condition), or during on-line reach corrections to an abruptly displaced target (experiment 2, a dynamic condition). In both experiments, we detail the latency and prevalence of stimulus-locked responses (SLRs), which are brief bursts of EMG activity that are time-locked to target presentation rather than movement onset. SLRs represent the first wave of EMG recruitment influenced by target presentation, and enable quantification of rapid visuomotor transformations. In both experiments, reach targets composed of low spatial frequencies elicited the shortest latency and most prevalent SLRs, with SLR latency increasing and SLR prevalence decreasing for reach targets composed of progressively higher spatial frequencies. SLRs could be evoked in either the static or dynamic condition, and when present in experiment 2, were associated with shorter latency and larger magnitude corrections. Furthermore, SLRs evolved at shorter latencies (~20 ms) when the arm was already in motion. These results demonstrate that stimuli composed of low spatial frequencies preferentially evoke the most rapid visuomotor responses which, in the context of rapidly correcting an on-going reaching movement, are associated with earlier and larger on-line reach corrections.\n\nSignificance StatementHumans have a remarkable capacity to respond quickly to changes in our visual environment. Although our visual world is composed of a range of spatial frequencies, surprisingly little is known about which frequencies preferentially evoke rapid reaching responses. Here, we systematically varied the spatial frequency of peripheral reach targets while measuring EMG activity on an upper limb muscle. We found that visual stimuli composed of low-spatial frequencies elicit the most rapid and robust EMG responses and corrective reaches. Thus, when time is of the essence, low spatial frequencies preferentially drive fast visuomotor responses.

neuroscience↗

bioRxiv2018

Macaque anterior cingulate cortex deactivation impairs performance and alters lateral prefrontal oscillatory activities in a rule-switching task

In primates, both the dorsal anterior cingulate cortex (dACC) and the dorsolateral prefrontal cortex (dlPFC) are key regions of the frontoparietal cognitive control network. To study the role of the dACC and its communication with the dlPFC in cognitive control, we recorded the local field potentials from the dlPFC before and during the reversible deactivation of the dACC, in macaque monkeys engaging in uncued switches between two stimulus-response rules. Cryogenic dACC deactivation impaired response accuracy during rule-maintenance, but not rule-switching, which coincided with a reduction in the correct-error difference in dlPFC beta activities specifically during maintenance of the more challenging rule. During both rule switching and maintenance, dACC deactivation prolonged the animals reaction time and reduced task-related theta/alpha activities in the dlPFC; it also weakened dlPFC theta-gamma phase-amplitude modulation. Thus, the dACC and its interaction with the dlPFC plays a critical role in the maintenance of a new, challenging rule.

neuroscience↗