A transcriptional rheostat couples past activity to future sensory responses.

Animals traversing different environments encounter both stable background stimuli and novel cues, which are thought to be detected by primary sensory neurons and then distinguished by downstream brain circuits. Here, we show that each of the ∼1,000 olfactory sensory neuron (OSN) subtypes in the mouse harbors a distinct transcriptome whose content is precisely determined by interactions between its odorant receptor and the environment. This transcriptional variation is systematically organized to support sensory adaptation: expression levels of more than 70 genes relevant to transforming odors into spikes continuously vary across OSN subtypes, dynamically adjust to new environments over hours, and accurately predict acute OSN-specific odor responses. The sensory periphery therefore separates salient signals from predictable background via a transcriptional rheostat whose moment-to-moment state reflects the past and constrains the future; these findings suggest a general model in which structured transcriptional variation within a cell type reflects individual experience.

Encoding of 3D Head Orienting Movements in the Primary Visual Cortex.

Animals actively sample the sensory world by generating complex patterns of movement that evolve in three dimensions. Whether or how such movements affect neuronal activity in sensory cortical areas remains largely unknown, because most experiments exploring movement-related modulation have been performed in head-fixed animals. Here, we show that 3D head-orienting movements (HOMs) modulate primary visual cortex (V1) activity in a direction-specific manner that also depends on light. We identify two overlapping populations of movement-direction-tuned neurons that support this modulation, one of which is direction tuned in the dark and the other in the light. Although overall movement enhanced V1 responses to visual stimulation, HOMs suppressed responses. We demonstrate that V1 receives a motor efference copy related to orientation from secondary motor cortex, which is involved in controlling HOMs. These results support predictive coding theories of brain function and reveal a pervasive role of 3D movement in shaping sensory cortical dynamics.

64-Channel Carbon Fiber Electrode Arrays for Chronic Electrophysiology.

A chief goal in neuroscience is to understand how neuronal activity relates to behavior, perception, and cognition. However, monitoring neuronal activity over long periods of time is technically challenging, and limited, in part, by the invasive nature of recording tools. While electrodes allow for recording in freely-behaving animals, they tend to be bulky and stiff, causing damage to the tissue they are implanted in. One solution to this invasiveness problem may be probes that are small enough to fly under the immune system's radar. Carbon fiber (CF) electrodes are thinner and more flexible than typical metal or silicon electrodes, but the arrays described in previous reports had low channel counts and required time-consuming manual assembly. Here we report the design of an expanded-channel-count carbon fiber electrode array (CFEA) as well as a method for fast preparation of the recording sites using acid etching and electroplating with PEDOT-TFB, and demonstrate the ability of the 64-channel CFEA to record from rat visual cortex. We include designs for interfacing the system with micro-drives or flex-PCB cables for recording from multiple brain regions, as well as a facilitated method for coating CFs with the insulator Parylene-C. High-channel-count CFEAs may thus be an alternative to traditional microwire-based electrodes and a practical tool for exploring the neural code.

A Micro-CT-based Method for Characterizing Lesions and Locating Electrodes in Small Animal Brains.

Lesion and electrode location verification are traditionally done via histological examination of stained brain slices, a time-consuming procedure that requires manual estimation. Here, we describe a simple, straightforward method for quantifying lesions and locating electrodes in the brain that is less laborious and yields more detailed results. Whole brains are stained with osmium tetroxide, embedded in resin, and imaged with a micro-CT scanner. The scans result in 3D digital volumes of the brains with resolutions and virtual section thicknesses dependent on the sample size (12-15 and 5-6 µm per voxel for rat and zebra finch brains, respectively). Surface and deep lesions can be characterized, and single tetrodes, tetrode arrays, electrolytic lesions, and silicon probes can also be localized. Free and proprietary software allows experimenters to examine the sample volume from any plane and segment the volume manually or automatically. Because this method generates whole brain volume, lesions and electrodes can be quantified to a much higher degree than in current methods, which will help standardize comparisons within and across studies.

A micro-CT-based method for quantitative brain lesion characterization and electrode localization.

Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12-15 and 5-6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.

Unstable neurons underlie a stable learned behavior.

Motor skills can be maintained for decades, but the biological basis of this memory persistence remains largely unknown. The zebra finch, for example, sings a highly stereotyped song that is stable for years, but it is not known whether the precise neural patterns underlying song are stable or shift from day to day. Here we demonstrate that the population of projection neurons coding for song in the premotor nucleus, HVC, change from day to day. The most dramatic shifts occur over intervals of sleep. In contrast to the transient participation of excitatory neurons, ensemble measurements dominated by inhibition persist unchanged even after damage to downstream motor nerves. These observations offer a principle of motor stability: spatiotemporal patterns of inhibition can maintain a stable scaffold for motor dynamics while the population of principal neurons that directly drive behavior shift from one day to the next.

Mesoscopic patterns of neural activity support songbird cortical sequences.

Time-locked sequences of neural activity can be found throughout the vertebrate forebrain in various species and behavioral contexts. From "time cells" in the hippocampus of rodents to cortical activity controlling movement, temporal sequence generation is integral to many forms of learned behavior. However, the mechanisms underlying sequence generation are not well known. Here, we describe a spatial and temporal organization of the songbird premotor cortical microcircuit that supports sparse sequences of neural activity. Multi-channel electrophysiology and calcium imaging reveal that neural activity in premotor cortex is correlated with a length scale of 100 µm. Within this length scale, basal-ganglia-projecting excitatory neurons, on average, fire at a specific phase of a local 30 Hz network rhythm. These results show that premotor cortical activity is inhomogeneous in time and space, and that a mesoscopic dynamical pattern underlies the generation of the neural sequences controlling song.

A carbon-fiber electrode array for long-term neural recording.

OBJECTIVE: Chronic neural recording in behaving animals is an essential method for studies of neural circuit function. However, stable recordings from small, densely packed neurons remains challenging, particularly over time-scales relevant for learning. APPROACH: We describe an assembly method for a 16-channel electrode array consisting of carbon fibers (<5 µm diameter) individually insulated with Parylene-C and fire-sharpened. The diameter of the array is approximately 26 µm along the full extent of the implant. MAIN RESULTS: Carbon fiber arrays were tested in HVC (used as a proper name), a song motor nucleus, of singing zebra finches where individual neurons discharge with temporally precise patterns. Previous reports of activity in this population of neurons have required the use of high impedance electrodes on movable microdrives. Here, the carbon fiber electrodes provided stable multi-unit recordings over time-scales of months. Spike-sorting indicated that the multi-unit signals were dominated by one, or a small number of cells. Stable firing patterns during singing confirmed the stability of these clusters over time-scales of months. In addition, from a total of 10 surgeries, 16 projection neurons were found. This cell type is characterized by sparse stereotyped firing patterns, providing unambiguous confirmation of single cell recordings. SIGNIFICANCE: Carbon fiber electrode bundles may provide a scalable solution for long-term neural recordings of densely packed neurons.

Two etomidate sites in α1ß2γ2 γ-aminobutyric acid type A receptors contribute equally and noncooperatively to modulation of channel gating.

BACKGROUND: Etomidate is a potent hypnotic agent that acts via γ-aminobutyric acid receptor type A (GABA(A)) receptors. Evidence supports the presence of two etomidate sites per GABA(A) receptor, and current models assume that each site contributes equally and noncooperatively to drug effects. These assumptions remain untested. METHODS: We used concatenated dimer (ß2-α1) and trimer (γ2-ß2-α1) GABA(A) subunit assemblies that form functional α1ß2γ2 channels, and inserted α1M236W etomidate site mutations into both dimers (ß2-α1M236W) and trimers (γ2-ß2-α1M236W). Wild-type or mutant dimers (D(wt) or D(αM236W)) and trimers (T(wt) or T(αM236W)) were coexpressed in Xenopus oocytes to produce four types of channels: D(wt)T(wt), D(αM236W)T(wt), D(wt)T(αM236W), and D(αM236W)T(αM236W). For each channel type, two-electrode voltage clamp was performed to quantitatively assess GABA EC(50), etomidate modulation (left shift), etomidate direct activation, and other functional parameters affected by αM236W mutations. RESULTS: Concatenated wild-type D(wt)T(wt) channels displayed etomidate modulation and direct activation similar to α1ß2γ2 receptors formed with free subunits. D(αM236W)T(αM236W) receptors also displayed altered GABA sensitivity and etomidate modulation similar to mutated channels formed with free subunits. Both single-site mutant receptors (D(αM236W)T(wt) and D(wt)T(αM236W)) displayed indistinguishable functional properties and equal gating energy changes for GABA activation (-4.9 ± 0.48 vs. -4.7 ± 0.48 kJ/mol, respectively) and etomidate modulation (-3.4 ± 0.49 vs. -3.7 ± 0.38 kJ/mol, respectively), which together accounted for the differences between D(wt)T(wt) and D(αM236W)T(αM236W) channels. CONCLUSIONS: These results support the hypothesis that the two etomidate sites on α1ß2γ2 GABA(A) receptors contribute equally and noncooperatively to drug interactions and gating effects.