scholarly journals Stimulus-Induced Intercolumnar Synchronization of Neuronal Activity in Rat Barrel Cortex: A Laminar Analysis

2004 ◽  
Vol 92 (3) ◽  
pp. 1464-1478 ◽  
Author(s):  
Mengliang Zhang ◽  
Kevin D. Alloway
Keyword(s):  
Neuronal Activity ◽  
Cross Correlation ◽  
Barrel Cortex ◽  
Sensory Information ◽  
Stimulus Frequency ◽  
Correlation Coefficients ◽  
Brain Regions ◽  
Neuronal Synchronization ◽  
Cross Correlation Analysis ◽  
Whisker Stimulation

We used cross-correlation analysis to characterize the coordination of stimulus-induced neuronal activity in the primary somatosensory barrel cortex of isoflurane-anesthetized rats. On each trial, multiple whiskers were simultaneously deflected at frequencies that corresponded to 2, 5, 8, or 11 Hz. Among 476 neuron pairs that we examined, 342 (71.8%) displayed significant peaks of synchronized activity that exceeded the 99.9% confidence limits. The incidence and strength of these functional associations varied across different cortical layers. Only 52.9% of neuron pairs in layer IV displayed synchronized responses, whereas 84.1% of the infragranular neuron pairs were synchronized during whisker stimulation. Neuronal synchronization was strongest in the infragranular layers, weakest in layer IV, and varied according to the columnar configuration of the neuron pairs. Thus correlation coefficients were largest for neuron pairs in the same whisker barrel row but were smallest for neurons in different rows and arcs. Spontaneous activity in the infragranular layers was also synchronized to a greater degree than in the other layers. Although infragranular neuron pairs displayed similar amounts of synchronization in response to each stimulus frequency, granular and supragranular neurons were synchronized mainly during stimulation at 2 or 5 Hz. These results are consistent with previous studies indicating that infragranular neurons have intrinsic properties that facilitate synchronized activity, and they suggest that neuronal synchronization plays an important role in transmitting sensory information to other cortical or subcortical brain regions.

Single-Neuron Analysis of Human Thalamus in Patients With Intention Tremor and Other Clinical Signs of Cerebellar Disease

2002 ◽  
Vol 87 (4) ◽  
pp. 2084-2094 ◽  
Author(s):  
F. A. Lenz ◽  
C. J. Jaeger ◽  
M. S. Seike ◽  
Y. C. Lin ◽  
S. G. Reich
Keyword(s):  
Neuronal Activity ◽  
Cross Correlation ◽  
Clinical Signs ◽  
Emg Activity ◽  
Phase Lag ◽  
Cerebellar Disease ◽  
Intention Tremor ◽  
Cross Correlation Analysis ◽  
Relay Nucleus ◽  
Cerebellar Tremor

Tremor that occurs as a result of a cerebellar lesion, cerebellar tremor, is characteristically an intention tremor. Thalamic activity may be related to cerebellar tremor because transmission of some cerebellar efferent signals occurs via the thalamus and cortex to the periphery. We have now studied thalamic neuronal activity in a cerebellar relay nucleus (ventral intermediate—Vim) and a pallidal relay nucleus (ventralis oral posterior—Vop) during thalamotomy in patients with intention tremor and other clinical signs of cerebellar disease (tremor patients). The activity of single neurons and the simultaneous electromyographic (EMG) activity of the contralateral upper extremity in tremor patients performing a pointing task were analyzed by spectral cross-correlation analysis. EMG spectra during intention tremor often showed peaks of activity in the tremor-frequency range (1.9–5.8 Hz). There were significant differences in thalamic neuronal activity between tremor patients and controls. Neurons in Vim and Vop had significantly lower firing rates in tremor patients than in patients undergoing thalamic surgery for pain (pain controls). Other studies have shown that inputs to Vim from the cerebellum are transmitted through excitatory connections. Therefore the present results suggest that tremor in these tremor patients is associated with deafferentation of the thalamus from cerebellar efferent pathways. The thalamic X EMG cross-correlation functions were studied for cells located in Vim and Vop. Neuronal and EMG activity were as likely to be significantly correlated for cells in Vim as for those in Vop. Cells in Vim were more likely to have a phase lag relative to EMG than were cells in Vop. In monkeys, cells in the cerebellar relay nucleus of the thalamus, corresponding to Vim, are reported to lead movement during active oscillations at the wrist. In view of these monkey studies, the present results suggest that cells in Vim are deafferented and have a phase lag relative to tremor that is not found in normal active oscillations. The difference in phase of thalamic spike X EMG activity between Vim and Vop may contribute to tremor because lesions of pallidum or Vop are reported to relieve cerebellar tremor.

scholarly journals Voltage-sensitive dye imaging reveals shifting spatiotemporal spread of whisker-induced activity in rat barrel cortex

2013 ◽  
Vol 109 (9) ◽  
pp. 2382-2392 ◽  
Author(s):  
Brian R. Lustig ◽  
Robert M. Friedman ◽  
Jeremy E. Winberry ◽  
Ford F. Ebner ◽  
Anna W. Roe
Keyword(s):  
Barrel Cortex ◽  
Sensory Information ◽  
Population Level ◽  
Spatiotemporal Pattern ◽  
Voltage Sensitive Dye ◽  
Barrel Field ◽  
Spatial Shift ◽  
Response Peak ◽  
Whisker Stimulation ◽  
Spike Firing

In rats, navigating through an environment requires continuous information about objects near the head. Sensory information such as object location and surface texture are encoded by spike firing patterns of single neurons within rat barrel cortex. Although there are many studies using single-unit electrophysiology, much less is known regarding the spatiotemporal pattern of activity of populations of neurons in barrel cortex in response to whisker stimulation. To examine cortical response at the population level, we used voltage-sensitive dye (VSD) imaging to examine ensemble spatiotemporal dynamics of barrel cortex in response to stimulation of single or two adjacent whiskers in urethane-anesthetized rats. Single whisker stimulation produced a poststimulus fluorescence response peak within 12–16 ms in the barrel corresponding to the stimulated whisker (principal whisker). This fluorescence subsequently propagated throughout the barrel field, spreading anisotropically preferentially along a barrel row. After paired whisker stimulation, the VSD signal showed sublinear summation (less than the sum of 2 single whisker stimulations), consistent with previous electrophysiological and imaging studies. Surprisingly, we observed a spatial shift in the center of activation occurring over a 10- to 20-ms period with shift magnitudes of 1–2 barrels. This shift occurred predominantly in the posteromedial direction within the barrel field. Our data thus reveal previously unreported spatiotemporal patterns of barrel cortex activation. We suggest that this nontopographical shift is consistent with known functional and anatomic asymmetries in barrel cortex and that it may provide an important insight for understanding barrel field activation during whisking behavior.

scholarly journals Theoretical characterisation of strand cross-correlation in ChIP-seq

2019 ◽  
Author(s):  
Hayato Anzawa ◽  
Hitoshi Yamagata ◽  
Kengo Kinoshita
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Cross Correlation ◽  
Simulation Analysis ◽  
Signal To Noise Ratio ◽  
Correlation Coefficients ◽  
Peak Calling ◽  
The Public ◽  
Cross Correlation Analysis ◽  
Maximum Coefficient ◽  
High Consistency

Abstract Background: Strand cross-correlation profiles are used for both peak calling pre-analysis and quality control in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis. Despite its potential for robust and accurate assessments of signal-to-noise ratio (S/N) of ChIP-seq samples, it remains unclear what aspects of quality such strand cross-correlation profiles actually measure. Results: We introduced a simple model to simulate the mapped read-density of ChIP-seq and then derived the theoretical maximum and minimum of cross-correlation coefficients between strands. The results suggest that the maximum coefficient of typical ChIP-seq samples is directly proportional to the number of total mapped reads and the square of the ratio of signal reads, and inversely proportional to the number of peaks and the length of read-enriched regions. We also developed PyMaSC to efficiently generate strand cross-correlation profiles. Simulation analysis supported our results and evaluation using 790 ChIP-seq data obtained from the public database demonstrated high consistency between calculated cross-correlation coefficients and estimated coefficients based on the theoretical relations and peak calling results. In addition, we found that the mappability-bias-correction improved sensitivity, enabling differentiation of maximum coefficients from the noise level. Conclusions: We present the first theoretical insights into the strand cross-correlation and the results reveal the potential and the limitations of strand cross-correlation analysis. Our work will help in the establishment of better QC metrics using strand cross-correlation.

scholarly journals Relative Changes in Cerebral Blood Flow and Neuronal Activity in Local Microdomains during Generalized Seizures

2004 ◽  
Vol 24 (9) ◽  
pp. 1057-1068 ◽  
Author(s):  
Hrachya Nersesyan ◽  
Peter Herman ◽  
Ersan Erdogan ◽  
Fahmeed Hyder ◽  
Hal Blumenfeld
Keyword(s):  
Visual Cortex ◽  
Somatosensory Cortex ◽  
Neuronal Activity ◽  
Barrel Cortex ◽  
Similar Distribution ◽  
Somatosensory Stimulation ◽  
Doppler Flowmetry ◽  
Absence Seizures ◽  
Generalized Seizures ◽  
Whisker Stimulation

There is broad agreement that generalized tonic–clonic seizures (GTCS) and normal somatosensory stimulation are associated with increases in regional CBF. However, the data regarding CBF changes during absence seizures are controversial. Electrophysiologic studies in WAG/Rij rats, an established animal model of absence seizures, have shown spike-wave discharges (SWD) that are largest in the perioral somatosensory cortex while sparing the visual cortex. Recent functional magnetic resonance imaging (fMRI) studies in the same model have also shown localized increases in fMRI signals in the perioral somatosensory cortex during SWD. Because fMRI signals are only indirectly related to neuronal activity, the authors directly measured CBF and neuronal activity from specific microdomains of the WAG/Rij cortex using a specially designed probe combining laser-Doppler flowmetry and extracellular microelectrode recordings under fentanyl/haloperidol anesthesia. Using this approach, parallel increases in neuronal activity and CBF were observed during SWD in the whisker somatosensory (barrel) cortex, whereas the visual cortex showed no significant changes. For comparison, these measurements were repeated during somatosensory (whisker) stimulation, and bicuculline-induced GTCS in the same animals. Interestingly, whisker stimulation increased neuronal activity and CBF in the barrel cortex more than during SWD. During GTCS, much larger increases that included both the somatosensory and visual cortex were observed. Thus, SWD in this model produce parallel localized increases in neuronal activity and CBF with similar distribution to somatosensory stimulation, whereas GTCS produce larger and more widespread changes. The normal response to somatosensory stimulation appears to be poised between two abnormal responses produced by two physiologically different types of seizures.

Involvement of the lemniscal and paralemniscal pathways in the perception of direction and neuronal activity in the barrel cortex in rodent single-whisker stimulation

2009 ◽  
Vol 65 ◽  
pp. S212-S213
Author(s):  
Shinya Nakamura ◽  
Takaaki Narumi ◽  
Shin-ichiro Yoshizato ◽  
Ken-Ichiro Tsutsui ◽  
Toshio Iijima
Keyword(s):  
Neuronal Activity ◽  
Barrel Cortex ◽  
Whisker Stimulation

scholarly journals Repeated whisker stimulation evokes invariant neuronal responses in the dorsolateral striatum of anesthetized rats: a potential correlate of sensorimotor habits

2011 ◽  
Vol 105 (5) ◽  
pp. 2225-2238 ◽  
Author(s):  
Todd M. Mowery ◽  
Jon B. Harrold ◽  
Kevin D. Alloway
Keyword(s):  
Barrel Cortex ◽  
Neural Mechanism ◽  
Brain Regions ◽  
Original Position ◽  
Induced Response ◽  
Neuronal Responses ◽  
Dorsolateral Striatum ◽  
Stimulus Response ◽  
Computer Controlled ◽  
Whisker Stimulation

The dorsolateral striatum (DLS) receives extensive projections from primary somatosensory cortex (SI), but very few studies have used somesthetic stimulation to characterize the sensory coding properties of DLS neurons. In this study, we used computer-controlled whisker deflections to characterize the extracellular responses of DLS neurons in rats lightly anesthetized with isoflurane. When multiple whiskers were synchronously deflected by rapid back-and-forth movements, whisker-sensitive neurons in the DLS responded to both directions of movement. The latency and magnitude of these neuronal responses displayed very little variation with changes in the rate (2, 5, or 8 Hz) of whisker stimulation. Simultaneous recordings in SI barrel cortex and the DLS revealed important distinctions in the neuronal responses of these serially connected brain regions. In contrast to DLS neurons, SI neurons were activated by the initial deflection of the whiskers but did not respond when the whiskers moved back to their original position. As the rate of whisker stimulation increased, SI responsiveness declined, and the latencies of the responses increased. In fact, when whiskers were deflected at 5 or 8 Hz, many neurons in the DLS responded before the SI neurons. These results and earlier anatomic findings suggest that a component of the sensory-induced response in the DLS is mediated by inputs from the thalamus. Furthermore, the lack of sensory adaptation in the DLS may represent a critical part of the neural mechanism by which the DLS encodes stimulus-response associations that trigger motor habits and other stimulus-evoked behaviors that are not contingent on rewarded outcomes.

scholarly journals Theoretical characterisation of strand cross-correlation in ChIP-seq

2020 ◽  
Author(s):  
Hayato Anzawa ◽  
Hitoshi Yamagata ◽  
Kengo Kinoshita
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Cross Correlation ◽  
Simulation Analysis ◽  
Signal To Noise Ratio ◽  
Correlation Coefficients ◽  
Peak Calling ◽  
The Public ◽  
Cross Correlation Analysis ◽  
Maximum Coefficient ◽  
High Consistency

Abstract Background: Strand cross-correlation profiles are used for both peak calling pre-analysis and quality control (QC) in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis. Despite its potential for robust and accurate assessments of signal-to-noise ratio (S/N) because of its peak calling independence, it remains unclear what aspects of quality such strand cross-correlation profiles actually measure. Results: We introduced a simple model to simulate the mapped read-density of ChIP-seq and then derived the theoretical maximum and minimum of cross-correlation coefficients between strands. The results suggest that the maximum coefficient of typical ChIP-seq samples is directly proportional to the number of total mapped reads and the square of the ratio of signal reads, and inversely proportional to the number of peaks and the length of read-enriched regions. Simulation analysis supported our results and evaluation using 790 ChIP-seq data obtained from the public database demonstrated high consistency between calculated cross-correlation coefficients and estimated coefficients based on the theoretical relations and peak calling results. In addition, we found that the mappability-bias-correction improved sensitivity, enabling differentiation of maximum coefficients from the noise level. Based on these insights, we proposed virtual S/N (VSN), a novel peak call-free metric for S/N assessment. We also developed PyMaSC, a tool to calculate strand cross-correlation and VSN efficiently. VSN achieved most consistent S/N estimation for various ChIP targets and sequencing read depths. Furthermore, we demonstrated that a combination of VSN and pre-existing peak calling results enable the estimation of the numbers of detectable peaks for posterior experiments and assess peak calling results. Conclusions: We present the first theoretical insights into the strand cross-correlation, and the results reveal the potential and the limitations of strand cross-correlation analysis. Our quality assessment framework using VSN provides peak call-independent QC and will help in the evaluation of peak call analysis in ChIP-seq experiments.

scholarly journals Theoretical characterisation of strand cross-correlation in ChIP-seq

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Hayato Anzawa ◽  
Hitoshi Yamagata ◽  
Kengo Kinoshita
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Cross Correlation ◽  
Simulation Analysis ◽  
Signal To Noise Ratio ◽  
Correlation Coefficients ◽  
Peak Calling ◽  
The Public ◽  
Cross Correlation Analysis ◽  
Maximum Coefficient ◽  
High Consistency

Abstract Background Strand cross-correlation profiles are used for both peak calling pre-analysis and quality control (QC) in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis. Despite its potential for robust and accurate assessments of signal-to-noise ratio (S/N) because of its peak calling independence, it remains unclear what aspects of quality such strand cross-correlation profiles actually measure. Results We introduced a simple model to simulate the mapped read-density of ChIP-seq and then derived the theoretical maximum and minimum of cross-correlation coefficients between strands. The results suggest that the maximum coefficient of typical ChIP-seq samples is directly proportional to the number of total mapped reads and the square of the ratio of signal reads, and inversely proportional to the number of peaks and the length of read-enriched regions. Simulation analysis supported our results and evaluation using 790 ChIP-seq data obtained from the public database demonstrated high consistency between calculated cross-correlation coefficients and estimated coefficients based on the theoretical relations and peak calling results. In addition, we found that the mappability-bias-correction improved sensitivity, enabling differentiation of maximum coefficients from the noise level. Based on these insights, we proposed virtual S/N (VSN), a novel peak call-free metric for S/N assessment. We also developed PyMaSC, a tool to calculate strand cross-correlation and VSN efficiently. VSN achieved most consistent S/N estimation for various ChIP targets and sequencing read depths. Furthermore, we demonstrated that a combination of VSN and pre-existing peak calling results enable the estimation of the numbers of detectable peaks for posterior experiments and assess peak calling results. Conclusions We present the first theoretical insights into the strand cross-correlation, and the results reveal the potential and the limitations of strand cross-correlation analysis. Our quality assessment framework using VSN provides peak call-independent QC and will help in the evaluation of peak call analysis in ChIP-seq experiments.

Cross-correlation analysis of a recurrent inhibitory circuit in the rat thalamus

1986 ◽  
Vol 55 (5) ◽  
pp. 1030-1043 ◽  
Author(s):  
A. Shosaku
Keyword(s):  
Correlation Analysis ◽  
Cross Correlation ◽  
Functional Organization ◽  
Receptive Fields ◽  
Sensory Information ◽  
Thalamic Reticular Nucleus ◽  
Reticular Nucleus ◽  
Cross Correlation Analysis ◽  
Monosynaptic Inhibition ◽  
Inhibitory Circuit

Spontaneous activities of vibrissa-responding neurons in the rat ventrobasal complex (VB) and somatosensory part of the thalamic reticular nucleus (S-TR) were simultaneously recorded and subjected to cross-correlation analysis to investigate the functional organization of recurrent inhibitory action of the S-TR on VB neurons. Excitatory and/or inhibitory interactions were found between approximately 75% (25/34) of the pairs of S-TR and VB neurons with receptive fields (RFs) on the same vibrissa. In contrast, there was no significant interaction between 54 pairs of neurons having RFs on different vibrissae. Among the pairs of neurons with RFs on the same vibrissa, there were four types of correlations, which indicate the following connections: monosynaptic excitation from a VB to an S-TR neuron (7 pairs), monosynaptic inhibition from an S-TR to a VB neuron (10 pairs), reciprocal connection combining the above two types (7 pairs), and common excitation in addition to inhibition from an S-TR to a VB neuron (1 pair). Examples of divergence and convergence of connections between S-TR and VB neurons were demonstrated by testing one S-TR (VB) neuron with more than one VB (S-TR) neuron. Vibrissa-suppressed VB cells, which had exclusively inhibitory RFs, were included in eight pairs of the above samples. These VB cells were more likely to receive inhibitory inputs from S-TR neurons than other VB neurons. Cells with RFs on multiple vibrissae were included in the other 10 pairs. These multiple-vibrissa cells had no interaction with single-vibrissa cells but did with multiple-vibrissa cells. From the incidence of four types of correlation between S-TR and VB neurons with RFs on the same vibrissa, the following connection pattern is suggested: One S-TR neuron receives excitatory inputs from approximately 40% of the VB neurons with RFs on the same vibrissa and sends inhibitory outputs to approximately 55%. Since these two groups of VB neurons were overlapping, the S-TR neuron has reciprocal connections with approximately 20% of the VB neurons with RFs on the same vibrissa. The same estimate was applied to connectivity of one VB neuron. These results indicate that both inputs and outputs of S-TR neurons are precisely and topographically organized, although there is convergence to and divergence from a substantial number of VB neurons with RFs on the same vibrissa. It is proposed that the recurrent inhibitory circuit through the S-TR plays a role in improving discrimination of sensory information transmitted through the VB.

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