Activity Of Specific Cell Types Research Articles

A proximal enhancer regulates RORA expression during early human Th17 cell differentiation

Gene regulatory elements, such as enhancers, greatly influence cell identity by tuning the transcriptional activity of specific cell types. Dynamics of enhancer landscape during early human Th17 cell differentiation remains incompletely understood. Leveraging ATAC-seq-based profiling of chromatin accessibility and comprehensive analysis of key histone marks, we identified a repertoire of enhancers that potentially exert control over the fate specification of Th17 cells. We found 23 SNPs associated with autoimmune diseases within Th17-enhancers that precisely overlapped with the binding sites of transcription factors actively engaged in T-cell functions. Among the Th17-specific enhancers, we identified an enhancer in the intron of RORA and demonstrated that this enhancer positively regulates RORA transcription. Moreover, CRISPR-Cas9-mediated deletion of a transcription factor binding site-rich region within the identified RORA enhancer confirmed its role in regulating RORA transcription. These findings provide insights into the potential mechanism by which the RORA enhancer orchestrates Th17 differentiation.

SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes.

Small extracellular vesicles (sEVs) are emerging as pivotal players in a wide range of physiological and pathological processes. However, a pressing challenge has been the lack of high-throughput techniques capable of unraveling the intricate heterogeneity of sEVs and decoding the underlying cellular behaviors governing sEV secretion. Here we leverage droplet-based single-cell RNA sequencing (scRNA-seq) and introduce an algorithm, SEVtras, to identify sEV-containing droplets and estimate the sEV secretion activity (ESAI) of individual cells. Through extensive validations on both simulated and real datasets, we demonstrate SEVtras' efficacy in capturing sEV-containing droplets and characterizing the secretion activity of specific cell types. By applying SEVtras to four tumor scRNA-seq datasets, we further illustrate that the ESAI can serve as a potent indicator of tumor progression, particularly in the early stages. With the increasing importance and availability of scRNA-seq datasets, SEVtras holds promise in offering valuable extracellular insights into the cell heterogeneity.

High Fat Diet-Induced Obesity Dysregulates Splenic B Cell Mitochondrial Activity.

Diet-induced obesity impairs mitochondrial respiratory responses in tissues that are highly metabolically active, such as the heart. However, less is known about the impact of obesity on the respiratory activity of specific cell types, such as splenic B cells. B cells are of relevance, as they play functional roles in obesity-induced insulin resistance, inflammation, and responses to infection. Here, we tested the hypothesis that high-fat-diet (HFD)-induced obesity could impair the mitochondrial respiration of intact and permeabilized splenic CD19+ B cells isolated from C57BL/6J mice and activated ex vivo with lipopolysaccharide (LPS). High-resolution respirometry was used with intact and permeabilized cells. To reveal potential mechanistic targets by which HFD-induced obesity dysregulates B cell mitochondria, we conducted proteomic analyses and 3D serial block face scanning electron microscopy (SBFEM). High-resolution respirometry revealed that intact LPS-stimulated B cells of obese mice, relative to controls, displayed lower ATP-linked, as well as maximal uncoupled, respiration. To directly investigate mitochondrial function, we used permeabilized LPS-stimulated B cells, which displayed increased H2O2 emission and production with obesity. We also examined oxidative phosphorylation efficiency simultaneously, which revealed that oxygen consumption and ATP production were decreased in LPS-stimulated B cells with obesity relative to controls. Despite minimal changes in total respiratory complex abundance, in LPS-stimulated B cells of obese mice, three of the top ten most downregulated proteins were all accessory subunits of respiratory complex I. SBFEM showed that B cells of obese mice, compared to controls, underwent no change in mitochondrial cristae integrity but displayed increased mitochondrial volume that was linked to bioenergetic function. Collectively, these results establish a proof of concept that HFD-induced obesity dysregulates the mitochondrial bioenergetic metabolism of activated splenic B cells.

135-OR: Mapping Cis-Regulatory Programs Affecting Diabetes Risk in Pancreatic Islet Cell Types Using Single-Cell Multimodal Profiling

Genetic variants influencing type 1 diabetes (T1D) risk identified by genome-wide association studies (GWAS) are primarily non-coding and affect cis-regulatory element (cRE) activity in specific cell types. A more detailed understanding of cell type-specific cis-regulatory programs in the pancreas is therefore crucial for deciphering the functional impact of T1D risk. Recently developed assays that generate multimodal single nucleus RNA-seq (snRNA-seq) and ATAC-seq (snATAC-seq) profiles from the same cell enable high-resolution mapping of cis-regulatory programs in specific cell types. We generated deeply sequenced data from 28 nondiabetic pancreatic islet samples from the Alberta Diabetes Institute IsletCore using 10x multiome assays. After extensive quality control and filtering, we clustered multimodal profiles from 174,819 cells and identified ten major cell types. For several cell types we identified evidence of heterogeneous sub-populations; for example, in beta cells there were six sub-populations corresponding to cellular states associated with insulin secretion, stress response, and others. We identified 263,223 cREs across all cell types and developed a novel method to predict target genes of cREs based on the correlation of multimodal profiles across single cells. In beta cells, there were 122,352 cRE-target gene links involving 16,907 unique genes. We mapped chromatin accessibility quantitative trait loci (caQTLs) for cREs in each cell type and identified a total of 14,535 caQTLs at FDR<.10. Finally, we annotated T1D risk variants from high-resolution fine-mapping of 136 T1D signals with cRE-target gene links and caQTLs. At 27 T1D signals including at the INS, MAPT, and DLK1 loci, variants affecting chromatin accessibility were linked to putative target genes in beta cells suggesting mechanisms of action at these loci. Experimental follow up of variant activity at these loci using genome editing in beta cell lines is ongoing. Disclosure H. Mummey: None. W. Elison: None. K. Korgaonkar: None. Y.S. Lee: None. J.M. Newsome Ashmus: None. P. Benaglio: Employee; Shoreline Biosciences. M.T. Miller: None. J.E. Manning Fox: None. A.L. Gloyn: Other Relationship; Genentech, Inc., Roche Pharmaceuticals. P. MacDonald: None. S. Preissl: None. K.J. Gaulton: Stock/Shareholder; Neurocrine Biosciences, Inc. Consultant; Genentech, Inc. Stock/Shareholder; Vertex Pharmaceuticals Incorporated. Funding National Institutes of Health (HG012059, DK105554, DK122607, DK114650)

Transforming growth factor β in breast cancer: another new trick for the old dog.

Two recent papers from the laboratory of Professor Ming Li demonstrate that inhibition of transforming growth factor β specifically in CD4+ T cells can suppress tumor growth through an unanticipated mechanism.

A Platform for Brain-wide Volumetric Functional Ultrasound Imaging and Analysis of Circuit Dynamics in Awake Mice

Imaging large-scale circuit dynamics is crucial to understanding brain function, but most techniques have a limited depth of field. Here, we describe volumetric functional ultrasound imaging (vfUSI), a platform for brain-wide vfUSI of hemodynamic activity in awake head-fixed mice. We combined a high-frequency 1,024-channel 2D-array transducer with advanced multiplexing and high-performance computing for real-time 3D power Doppler imaging at a high spatiotemporal resolution (220× 280× 175μm3, up to 6Hz). We developed a standardized software pipeline for registration, segmentation, and temporal analysis in 268 individual brain regions based on the Allen Mouse Common Coordinate Framework. We demonstrated the high sensitivity of vfUSI under multiple experimental conditions, and we successfully imaged stimulus-evoked activity when only a few trials were averaged. We also mapped neural circuits invivo across the whole brain during optogenetic activation of specific cell types. Moreover, we identified the sequential activation of sensory-motor networks during a grasping water-droplet task.

Molecular and cytological analysis of widely-used Gal4 driver lines for Drosophila neurobiology

BackgroundThe Drosophila central nervous system (CNS) is a convenient model system for the study of the molecular mechanisms of conserved neurobiological processes. The manipulation of gene activity in specific cell types and subtypes of the Drosophila CNS is frequently achieved by employing the binary Gal4/UAS system. However, many Gal4 driver lines available from the Bloomington Drosophila Stock Center (BDSC) and commonly used in Drosophila neurobiology are still not well characterized. Among these are three lines with Gal4 driven by the elav promoter (BDSC #8760, #8765, and #458), one line with Gal4 driven by the repo promoter (BDSC #7415), and the 69B-Gal4 line (BDSC #1774). For most of these lines, the exact insertion sites of the transgenes and the detailed expression patterns of Gal4 are not known. This study is aimed at filling these gaps.ResultsWe have mapped the genomic location of the Gal4-bearing P-elements carried by the BDSC lines #8760, #8765, #458, #7415, and #1774. In addition, for each of these lines, we have analyzed the Gal4-driven GFP expression pattern in the third instar larval CNS and eye-antennal imaginal discs. Localizations of the endogenous Elav and Repo proteins were used as markers of neuronal and glial cells, respectively.ConclusionsWe provide a mini-atlas of the spatial activity of Gal4 drivers that are widely used for the expression of UAS–target genes in the Drosophila CNS. The data will be helpful for planning experiments with these drivers and for the correct interpretation of the results.

Neuronal Activity in the Hibernating Brain.

Hibernation is a natural phenomenon in many species which helps them to survive under extreme ambient conditions, such as cold temperatures and reduced availability of food in the winter months. It is characterized by a dramatic and regulated drop of body temperature, which in some cases can be near 0°C. Additionally, neural control of hibernation is maintained over all phases of a hibernation bout, including entrance into, during and arousal from torpor, despite a marked decrease in overall neural activity in torpor. In the present review, we provide an overview on what we know about neuronal activity in the hibernating brain focusing on cold-induced adaptations. We discuss pioneer and more recent in vitro and in vivo electrophysiological data and molecular analyses of activity markers which strikingly contributed to our understanding of the brain’s sensitivity to dramatic changes in temperature across the hibernation cycle. Neuronal activity is markedly reduced with decreasing body temperature, and many neurons may fire infrequently in torpor at low brain temperatures. Still, there is convincing evidence that specific regions maintain their ability to generate action potentials in deep torpor, at least in response to adequate stimuli. Those regions include the peripheral system and primary central regions. However, further experiments on neuronal activity are needed to more precisely determine temperature effects on neuronal activity in specific cell types and specific brain nuclei.

Sharp-wave ripple features in macaques depend on behavioral state and cell-type specific firing.

Sharp‐wave ripples (SWRs) are spontaneous, synchronized neural population events in the hippocampus widely thought to play a role in memory consolidation and retrieval. They occur predominantly in sleep and quiet immobility, and in primates, they also appear during active visual exploration. Typical measures of SWRs in behaving rats include changes in the rate of occurrence, or in the incidence of specific neural ensemble activity contained within the categorical SWR event. Much less is known about the relevance of spatiotemporal SWR features, though they may index underlying activity of specific cell types including ensemble‐specific internally generated sequences. Furthermore, changes in SWR features during active exploratory states are unknown. In this study, we recorded hippocampal local‐field potentials and single‐units during periods of quiescence and as macaques performed a memory‐guided visual search task. We observed that (a) ripples during quiescence have greater amplitudes and larger postripple waves (PRW) compared to those in task epochs, and (b) during “remembered” trials, ripples have larger amplitudes than during “forgotten” trials, with no change in duration or PRWs. We further found that spiking activity influences SWR features as a function of cell type and ripple timing. As expected, larger ripple amplitudes were associated with putative pyramidal or putative basket interneuron (IN) activity, even when the spikes in question exceed the duration of the ripple. In contrast, the PRW was attenuated with activity from low firing rate cells and enhanced with activity from high firing rate cells, with putative IN spikes during ripples leading to the most prominent PRW peaks. The selective changes in SWR features as a function of time window, cell type, and cognitive/vigilance states suggest that this mesoscopic field event can offer additional information about the local network and animal's state than would be appreciated from SWR event rates alone.

Homeostasis Meets Motivation in the Battle to Control Food Intake.

Signals of energy homeostasis interact closely with neural circuits of motivation to control food intake. An emerging hypothesis is that the transition to maladaptive feeding behavior seen in eating disorders or obesity may arise from dysregulation of these interactions. Focusing on key brain regions involved in the control of food intake (ventral tegmental area, striatum, hypothalamus, and thalamus), we describe how activity of specific cell types embedded within these regions can influence distinct components of motivated feeding behavior. We review how signals of energy homeostasis interact with these regions to influence motivated behavioral output and present evidence that experience-dependent neural adaptations in key feeding circuits may represent cellular correlates of impaired food intake control. Future research into mechanisms that restore the balance of control between signals of homeostasis and motivated feeding behavior may inspire new treatment options for eating disorders and obesity.

AMP-activated protein kinase has diet-dependent and -independent roles in Drosophila oogenesis

Multiple aspects of organismal physiology influence the number and activity of stem cells and their progeny, including nutritional status. Previous studies demonstrated that Drosophila germline stem cells (GSCs), follicle stem cells (FSCs), and their progeny sense and respond to diet via complex mechanisms involving many systemic and local signals. AMP-activated protein kinase, or AMPK, is a highly conserved regulator of energy homeostasis known to be activated under low cellular energy conditions; however, its role in the ovarian response to diet has not been investigated. Here, we describe nutrient-dependent and -independent requirements for AMPK in Drosophila oogenesis. We found that AMPK is cell autonomously required for the slow down in GSC and follicle cell proliferation that occurs on a poor diet. Similarly, AMPK activity is necessary in the germline for the degeneration of vitellogenic stages in response to nutrient deprivation. In contrast, AMPK activity is not required within the germline to modulate its growth. Instead, AMPK acts in follicle cells to negatively regulate their growth and proliferation, thereby indirectly limiting the size of the underlying germline cyst within developing follicles. Paradoxically, AMPK is required for GSC maintenance in well-fed flies (when AMPK activity is presumably at its lowest), suggesting potentially important roles for basal AMPK activity in specific cell types. Finally, we identified a nutrient-independent, developmental role for AMPK in cyst encapsulation by follicle cells. These results uncover specific AMPK requirements in multiple cell types in the ovary and suggest that AMPK can function outside of its canonical nutrient-sensing role in specific developmental contexts.

Detection and manipulation of live antigen-expressing cells using conditionally stable nanobodies.

The ability to detect and/or manipulate specific cell populations based upon the presence of intracellular protein epitopes would enable many types of studies and applications. Protein binders such as nanobodies (Nbs) can target untagged proteins (antigens) in the intracellular environment. However, genetically expressed protein binders are stable regardless of antigen expression, complicating their use for applications that require cell-specificity. Here, we created a conditional system in which the stability of an Nb depends upon an antigen of interest. We identified Nb framework mutations that can be used to rapidly create destabilized Nbs. Fusion of destabilized Nbs to various proteins enabled applications in living cells, such as optogenetic control of neural activity in specific cell types in the mouse brain, and detection of HIV-infected human cells by flow cytometry. These approaches are generalizable to other protein binders, and enable the rapid generation of single-polypeptide sensors and effectors active in cells expressing specific intracellular epitopes.

Ex Vivo Optogenetic Dissection of Fear Circuits in Brain Slices.

Optogenetic approaches are now widely used to study the function of neural populations and circuits by combining targeted expression of light-activated proteins and subsequent manipulation of neural activity by light. Channelrhodopsins (ChRs) are light-gated cation-channels and when fused to a fluorescent protein their expression allows for visualization and concurrent activation of specific cell types and their axonal projections in defined areas of the brain. Via stereotactic injection of viral vectors, ChR fusion proteins can be constitutively or conditionally expressed in specific cells of a defined brain region, and their axonal projections can subsequently be studied anatomically and functionally via ex vivo optogenetic activation in brain slices. This is of particular importance when aiming to understand synaptic properties of connections that could not be addressed with conventional electrical stimulation approaches, or in identifying novel afferent and efferent connectivity that was previously poorly understood. Here, a few examples illustrate how this technique can be applied to investigate these questions to elucidating fear-related circuits in the amygdala. The amygdala is a key region for acquisition and expression of fear, and storage of fear and emotional memories. Many lines of evidence suggest that the medial prefrontal cortex (mPFC) participates in different aspects of fear acquisition and extinction, but its precise connectivity with the amygdala is just starting to be understood. First, it is shown how ex vivo optogenetic activation can be used to study aspects of synaptic communication between mPFC afferents and target cells in the basolateral amygdala (BLA). Furthermore, it is illustrated how this ex vivo optogenetic approach can be applied to assess novel connectivity patterns using a group of GABAergic neurons in the amygdala, the paracapsular intercalated cell cluster (mpITC), as an example.

A Multichannel Recording System with Optical Stimulation for Closed-Loop Optogenetic Experiments.

Selective perturbation of the activity of specific cell types in the brain tissue is essential in understanding the function of neuronal circuits involved in cognition and behavior and might also provide therapeutic neuromodulation strategies. Such selective neuronal addressing can be achieved through the optical activation of light-sensitive proteins called opsins that are expressed in specific cell populations through genetic methods-hence the name "optogenetics." In optogenetic experiments, the electrical activity of the targeted cell populations is optically triggered and monitored using arrays of microelectrodes. In closed-loop studies, the optical stimulation parameters are adjusted based on the recorded activity, ideally in real time. Here we describe the basic tools and the protocols allowing closed-loop optogenic experiments in vivo.

A Novel Transgenic Mouse Line for Tracing MicroRNA-155-5p Activity In Vivo.

MicroRNA-155 (miR-155) plays significant role in various physiological processes involving both innate and adaptive immunity. miR-155 expression level changes dynamically during various immune responses. However, current approaches for miR-155 detection at the RNA level do not precisely reflect the real-time activity. Herein, we generated a transgenic mouse line (R26-DTR-155T) for determination of miR-155-5p activity in vivo by inserting miR-155-5p target sequence downstream of a reporter transgene comprising Diphtheria Toxin Receptor and TagBlue fluorescence protein. Using this approach, R26-DTR-155T mice were able to measure variation in levels of miR-155-5p activity in specific cell types of interest. The DTR expression levels were inversely correlated with the endogenous miR-155 expression pattern as detected by quantitative RT-PCR. Our data demonstrate a novel transgenic mouse line which could be useful for tracing miR-155-5p activity in specific cell types through measurement of miR-155-5p activity at single cell level.

Global analyses revealed age-related alterations in innate immune responses after stimulation of pathogen recognition receptors.

Aging leads to dysregulation of multiple components of the immune system that results in increased susceptibility to infections and poor response to vaccines in the aging population. The dysfunctions of adaptive B and T cells are well documented, but the effect of aging on innate immunity remains incompletely understood. Using a heterogeneous population of peripheral blood mononuclear cells (PBMCs), we first undertook transcriptional profiling and found that PBMCs isolated from old individuals (≥ 65 years) exhibited a delayed and altered response to stimulation with TLR4, TLR7/8, and RIG-I agonists compared to cells obtained from adults (≤ 40 years). This delayed response to innate immune agonists resulted in the reduced production of pro-inflammatory and antiviral cytokines and chemokines including TNFα, IL-6, IL-1β, IFNα, IFNγ, CCL2, and CCL7. While the major monocyte and dendritic cell subsets did not change numerically with aging, activation of specific cell types was altered. PBMCs from old subjects also had a lower frequency of CD40+ monocytes, impaired up-regulation of PD-L1 on monocytes and T cells, and increased expression of PD-L2 and B7-H4 on B cells. The defective immune response to innate agonists adversely affected adaptive immunity as TLR-stimulated PBMCs (minus CD3 T cells) from old subjects elicited significantly lower levels of adult T-cell proliferation than those from adult subjects in an allogeneic mixed lymphocyte reaction (MLR). Collectively, these age-associated changes in cytokine, chemokine and interferon production, as well as co-stimulatory protein expression could contribute to the blunted memory B- and T-cell immune responses to vaccines and infections.

Anatomical characterization of Cre driver mice for neural circuit mapping and manipulation.

Significant advances in circuit-level analyses of the brain require tools that allow for labeling, modulation of gene expression, and monitoring and manipulation of cellular activity in specific cell types and/or anatomical regions. Large-scale projects and individual laboratories have produced hundreds of gene-specific promoter-driven Cre mouse lines invaluable for enabling genetic access to subpopulations of cells in the brain. However, the potential utility of each line may not be fully realized without systematic whole brain characterization of transgene expression patterns. We established a high-throughput in situ hybridization (ISH), imaging and data processing pipeline to describe whole brain gene expression patterns in Cre driver mice. Currently, anatomical data from over 100 Cre driver lines are publicly available via the Allen Institute's Transgenic Characterization database, which can be used to assist researchers in choosing the appropriate Cre drivers for functional, molecular, or connectional studies of different regions and/or cell types in the brain.

Cell type-specific and time-dependent light exposure contribute to silencing in neurons expressing Channelrhodopsin-2.

Channelrhodopsin-2 (ChR2) has quickly gained popularity as a powerful tool for eliciting genetically targeted neuronal activation. However, little has been reported on the response kinetics of optogenetic stimulation across different neuronal subtypes. With excess stimulation, neurons can be driven into depolarization block, a state where they cease to fire action potentials. Herein, we demonstrate that light-induced depolarization block in neurons expressing ChR2 poses experimental challenges for stable activation of specific cell types and may confound interpretation of experiments when 'activated' neurons are in fact being functionally silenced. We show both ex vivo and in vivo that certain neuronal subtypes targeted for ChR2 expression become increasingly susceptible to depolarization block as the duration of light pulses are increased. We find that interneuron populations have a greater susceptibility to this effect than principal excitatory neurons, which are more resistant to light-induced depolarization block. Our results highlight the need to empirically determine the photo-response properties of targeted neurons when using ChR2, particularly in studies designed to elicit complex circuit responses in vivo where neuronal activity will not be recorded simultaneous to light stimulation. DOI: http://dx.doi.org/10.7554/eLife.01481.001.

Influence of Polycomb Proteins and Epigenetic Transcriptional Modifiers on the Development and Activation of T Lymphocytes

Transcriptional regulation of a gene is not always correlated with genetic information in- herited from parents because the transcription of specific genes is often governed by the modification of chromatin structure. The study of transcriptional regulation by modifying chromatin structure is well-known as epigenetics. Several methods involved in the modi- fication of chromatin structure have been developed in the mammalian species during evolution. Among those methods, methylations of specific DNA region or histone are of - ten used to control specific gene transcription. Therefore, understanding the activity of proteins involved in DNA or histone methylation is an initial step to control the transcrip- tional activity of a specific gene. Polycomb group (PcG) proteins were known to be repres - sors of transcription of a specific gene by creating and maintaining methylation or ubiqui - tination of the specific region of histone. Dependent on the target histone, the activity of PcG proteins effects on the development of specific lineage cells or the activity of specific cell types. In this review, the function, expression and activity of PcG proteins related with the development or activation of T cells are discussed.

In vivo Photometry during Movement Changes Our Understanding of the Direct and Indirect Pathways

The role of the direct and indirect pathways in movement and their dysfunction in the pathophysiology of most movement disorders is difficult to grasp for clinicians. The current model whereby the direct pathway has a role akin to the accelerator when driving and the indirect to the brake makes sense at a basic level for many disorders of movement. However, some clinical phenomenology such as hemiballismus are difficult to reconcile with the current model. Cui et al. (1), using an elegant experimental paradigm employing photometric methods in vivo in a mouse model have observed the moving brain at work and have attempted to disentangle the complex network of spiny projection neurons involved in the direct and indirect pathways. The authors reflect on the prevailing model whereby two distinct projection circuits composed of spiny projection neurons in the striatum act in an opposing fashion to either promote movement (direct pathway) or inhibit movement (indirect pathway). The anatomical location of these pathways is the striatum. Surmeier in an accompanying editorial further identifies the striatum as the seat of “past experiences” and when “asked” by cortex what way to proceed, the current model which he identifies as intrinsically binary sends “go” or “no-go” instructions to cortex, via the thalamus (2). Cui et al. reflect on the fact that despite increased understanding of basal ganglia circuitry, we still do not understand the physiological relationship and interactions between these pathways. To do so we need to observe the activity of the direct and indirect pathway spiny projection neurons in “behaving” animal models (1). However, it is difficult to distinguish direct and indirect spiny projection neuron firing using electrophysiological recordings and antidromic stimulation is unreliable and difficult due to “cross talk” between axons of both pathways (1). The authors highlight that optogenetic technology in vivo facilitates the identification of specific cell types and the monitoring of activity of specific cell types (1). Limitations of this technology include the requirement for head restraint, which limits the study of structures involved in movement and the technology does not penetrate to subcortical structures therein limiting the ability to study the basal ganglia (1). Cui et al. developed an experimental paradigm utilizing in vivo photometry to optically record neural activity within the striatum during free movement in a mouse model (1). They implanted a fiber-optic probe to deliver laser pulses and record emitted photons in the dorsal striatum over time. The optical indicator was a genetically encoded calcium indicator (GECI), selectively expressed in the direct pathway spiny projection neurons by injection with a recombinant viral vector to produce D1-Cre mice (2). A similar technique was used to selectively express the indicator in the indirect pathway spiny projection neurons of A2A-Cre mice (1). Focusing specifically on their examination of the relationship between activity in the direct and indirect pathway spiny projection neurons during movement, the authors measured fluorescence whilst mice performed a lever-pressing task. They demonstrated time-locked increases in fluorescence during the initiation of the task with a similar temporal profile in both the direct and indirect pathways in all of the mice (1). They identified transient increases in fluorescence throughout the completion of different tasks and in addition during the monitoring sessions, mice were exposed to a series of active states and periods of inactivity (1). Using the classical direct and indirect pathway model it would be logical to hypothesize that during the active periods there should be relatively more transients identified in the direct pathway spiny projection neurons compared to the indirect and during periods of inactivity there should be more transients identified in the indirect spiny projection neurons compared to the direct (1). Cui et al. identified increased activity in both direct and indirect pathways during movement and silence of both pathways during periods of inactivity. These results question the accelerator-brake metaphor applied to our current understanding of the interaction between the direct and indirect pathways. Further analysis of self-paced movement initiation toward the contralateral side demonstrated co-activation of both the direct and indirect pathways and furthermore activity in both pathways preceded movement initiation. Activity in both pathways predicted the occurrence of specific movements within 500 ms of transient initiation. In the accompanying editorial it is suggested that rather than giving sequential “go” or “no-go” recommendations, the striatum is simultaneously making recommendations about “what to do and what not to do” (2). Through the interrogation of the direct and indirect pathways in vivo and during movement, this study builds upon and changes our current understanding of the function of the basal ganglia. Whilst the results challenge the current concepts used to explain movement, further work is required including lesional studies to translate this theory into the clinical environment in order to explain the clinical phenomenology we see at the bedside.