wholeBrain/wholeBrain_main.md

Author: James B. Ackman
Date: 2013-09-04 10:54:02
Tags: paper, draft, manuscript, literature, research, #results, retinal waves, spontaneous activity, development, calcium domains

Structured population activity across developing neocortex

Abstract

The cerebral cortex exhibits spontaneous and sensory evoked patterns of activity during fetal and postnatal development that are crucial for the activity-dependent formation and refinement of circuits [#Katz:1996]. Knowing the source and flow of these activity patterns locally and globally is crucial to understanding self-organization in the developing brain. Here we show that neural population activity within newborn mice in vivo is characterized by spatially discrete domains that are coordinated in a state dependent and areal dependent fashion throughout developing isocortex. Whole brain optical recordings from neonatal mice expressing a genetic calcium reporter showed that ongoing activity in the cerebral cortex was characterized by distinct and repetitively active domains measuring hundreds of microns in diameter. Domain activity exhibited mirror-symmetric patterns between the hemispheres, with strong correlations between specific portions of frontal and parietal cortex. Ongoing activity across the cortical hemispheres showed characteristic network architectures with a frontal-motor regions functionally connected to a parietal-sensory areas through secondary motor cortex, retrosplenial cortex, and posterior parietal cortex. Furthermore, ongoing cortical activity was regulated by physiological state with frontal cortex activity shifting from negative to positive correlations with motor behavior during the course of development. This study provides the first comprehensive description of population activity in the developing isocortex at a scope and scale that bridges the microscopic or macroscopic spatiotemporal resolutions provided by traditional neurophysiological or neuroimaging techniques. Mesoscale maps of cortical population dynamics within animal models will be vital to engineering future repair strategies and brain-machine interfaces for neurodevelopmental disorders.

Introduction

Brain development requires neural activity and calcium dynamics for establishing proper circuit structure and function. The importance of neural activity in the prenatal and neonatal period can be easily recognized in children exposed to chemical agents affecting neurotransmission during the fetal period that result in severe brain malformations, epilepsy, and mental retardation. Indeed, embryonic limb movements in species ranging from chick to human are thought to be initiated by spontaneous motor neuron activity in the spinal cord and thought to be crucial for activity-dependent development of motor synapses [Schoenberg:2003] [Marder,Lichtmann]. However it is only recently that we have begun to appreciate the underlying patterns of persistent neural activity that in fact exist in the developing brain in vivo. For example, sensori-motor feedback associated with spontaneous movement generated by spinal motor neurons triggers synchronized 'spindle-burst' potentials among cells in somatosensory cortex [Yang:2009][Khazipov:2004a] before the start of locomotion and tactile behavior. Correlated bursts of activity occur in the developing rat hippocampus in vivo [#Leinekugel:2002] [Mohns&Blumberg]. Spontaneous retinal waves drive patterned activation of circuits throughout the immature visual system before the onset of vision [#Ackman:2012] [Hanganu,Colonnese?]. Furthermore, prenatal EEG recordings have demonstrated spindle burst oscillations and slow activity transients in the human infant somatosensory and occipital cortices before birth [#Vanhatalo:2005][#Tolonen:2007]. Nonetheless, a comprehensive account of the structural dynamics of persistent activity throughout the developing isocortex in vivo has not been undertaken.

Results

Ongoing activity in developing neocortex is characterized by discrete domains

Neocortical organization consists of cortical modules tiled across the cortical surface in a topographic fashion such that vertical arrays of cells concerned with specific sensory features are grouped together as columns [#Mountcastle:1997]. Most evidence to date suggests that columns/hyper/macro columns are 300-500µm diameter across species.

The patterns of activity that exist in the developing brain are unknown. We performed recordings from mice expressing the genetic calcium indicator GCaMP (gcamp3 or gcamp6) throughout cortical neurons. We performed our recordings in three age groups: P2-P5, P8-P9, and P12-13. We found that cortical activity was characterized by discrete domains of activation during the first two postnatal weeks. These activity domains ranged from 200-800 µm in diameter (Ns, fig), with larger sized domains of activation in the visual cortex and motor cortex (Ns, fig). In the second postnatal week the size of activations in the hindlimb/trunk representation was larger, The average duration of these domain activations was about 600 ms – 1 s (Ns, fig) with longer activations on the order of seconds to tens of seconds in visual cortex driven by retinal waves [#Ackman:2012].

We parcellated the brain into distinct anatomical boundaries by using reference coordinates from a mouse line that expressed the tdtomato reporter in thalamocortical afferents. The expression can be used to parcellate out areal boundearies of primary sensory cortical areas (wong riley 1979). We matched these parcellations to a Allen brain atlas adult mouse reference image and than linearly scaled the remaining parcellations in our FOV on to the images of our recordings that contain fucntional boundaries (like in the domain centroid activation plot and in the normalized domain frequency plots).

• Cortical column (mini/hyper columns) history (20th century anatomists-- Lorente de No, Mountcastle, Hubel & Wiesel, rakic, etc).
• Column physiology-- Hubel and Wiesel. Rodent V1?
• Developmental studies-- fetal monkey ODCs.
• Rodent barrels (early anatomical emergence from TC input, functional/physiological emergence?).
  • What is known about columns/domains in secondary/association/non-primary sensory representations? Rest of rodent S1 (non-barrel cortex?).
• Calcium domains of Yuste, Science 1992 paper. [#Yuste:1992]
• Other slice calcium recordings, patch/gap junctions. In vivo physiology? (Not too many multisite electrode recordings in cortex, spatial resolution issue).
• Calcium imaging-- Konnerth 'waves' in Ent cortex [#Adelsberger:2005]. For visual cortex, domains activity in extrastriate cortex (Ackman Nature 2012). But S1-- [#Golshani:2009] work in later postnatal-- but activity not obeying domains in barrel cortex-- problem with spatial sampling in the xy and the z for this study?

metric	mean	min	max	unit
diameter	396.0	22.7	2383.5	µm
duration	0.6	0.2	14.6	s
frequency	2.9			domains/sec/hemisphere
[Table 1: Domain statistics]

Cortical activity is mirrored between the hemispheres

• Inter hemispheric functional connectivity, importance for autism, schizophrenia. Maybe an activity-dependent mechanism for commisural connectivity.
• olavarria work, evidence for inter hemispheric activity dependence
• [#Hanganu:2006], 30% of spindle bursts correlated across hemispheres
• Activity correlated in anterior-posterior and medial-lateral directions
• Mirror symmetric and non-mirror symmetric patterns
• Regional effects, more corr anticorr in certain regions?
• State dependent corr?

To understand the patterns and how they interact we first looked at correlation between the hemispheres. Cortical activity exhibited high temporal cortelation between the hemispheres () . In additon this activity was highly correlated in the spatial dimension. For example epochs of time would exhibit high correlation in the medial-lateral dimension or in the rostral-caudal dimension. This strength of correlation temporally and spatially increased between the hemsipheres with a function of age.

Conclusions: The two hemispheres seem to be mostly synchronized, though it’s possible the R hemispshere (which is also the slightly more ‘active’ hemisphere, see stats table below) leads the left by a bit. The asymmetric peak at –150–175frames is interesting. That would be about 30–35 sec.

The big secondary peaks around ±30 sec is present in both autocorrs and xcorrs and is far above the random normal xcorr baseline (blue trace). In fact there is a periodicity seen in the autocorrs and the xcorrs where there is a dampening oscillation about on this interval! (See ideal dampening frequency in random sine wave example above). This corresponds to a 1/30sec == 0.033 Hz ultra-slow oscillation.

{==Looking at the above plot showing lags from [–1000, 1000] frames which is ± 200 s, we can see about 5.5 cycles of this underlying dampening oscillation in both autocorr plots. This corresponds to (1000fr*0.2sec/fr)/5.5 => 36.36 sec/cycle => 0.0275 cycles/sec or ~0.03 Hz==}{>>Crazy!<<}

Conclusions: So the activity in both hemispheres at postnatal day 3 (P3) clearly exhibits significant spatial correlations in both in the medial-lateral and anterior-extent. This is consistent with and complementary to the fact that the active pixel fraction in each hemisphere exhibits a strong temporal correlation as I found earlier in this report [Temporal correlation of activity][]. The medial-lateral positional correlation is stronger than the anterior-posterior (higher R and lower p value). The total number of coactive frames is numel(y1(~isnan(y1)&~isnan(y2))) == 1114 frames. This is accounts to 37.13% of the movie or 222.8 s. Cortex.L had 1635 actvFrames and cortex.R had 1677 actvFrames which means that each hemisphere was coactive with the other hemisphere 1114/1635 == 68.13% and 1114/1677 == 66.43% of the active time respectively.

Percentage of cortical activity which exhibits corr with motor signal?

lenActvFraction>0	fracCorr	timeCorr_s	fracCorrPos	timeCorrPos_s	fracCorrNeg	timeCorrNeg_s
2161	0.30032	129.8	0.27441	118.6	0.025914	11.2

Cortical domain activity is state dependent

• EEG slow oscillations not detectable until P10 in rodent.
• Previously demonstrated that general anesthesia abolishes spontaneous activity in visual system [#Ackman:2012].
• What about ongoing activity in other cortical areas during early brain development? Surgical procedure relevance.
• No population calcium activity found during gen'l anesthesia, only slow traveling waves.
• During anesthesia induction, there is rapid (<30 s) knock down of discrete domain activity (P3 mouse <120518_09.tif>). Cingulate, retrosplenial activations the last to go-- default mode/resting state network areas last. <120518_09_mjpeg.mov>

Variation in the strength of correlation between cortical areas and the motor movement signal depended on brain region (p < 2.2e-16, anova) and age (p = 1.627e-05, anova) The first age group in which motor cortex exhibited signficant positive correlation with motor movements was at P12-13 (r=0.06±0.02, p-value = 0.001449, t-test).

Low pass filtered Moving averages of cortical and motor activity at 10 s and >70 s windows.

Developing cortical activity consists of distinct subnetworks

We then calculated a matrix of pearsons correlation coefficients based on the pixel active fraction timecourses for each pair of parcellations. The resulting assocaition matrix was run through a hierarchal clustering alogtithm to reveal functional modules of of activation. These functional modules typically consisted of 3 distinct subnetworks-- a frontal motor network, a posterior parietal network, a S1-body/limb network, and an auditory A1 network at P12.

We found many similarities but some striking differences as a function of age.

Conclusions

• Neural population activity constitutes discrete spatial and temporal activations among developing cortical areas

• Cortical activity exhibits symmetrical spatial and temporal activations across the hemispheres

• Developing cerebral networks comprise distinct functional modules among cortical areas

• Cortical activity is coordinated with motor behavioral state in an areal dependent fashion

• Population activity in developing cortex is not random-- it exhibits distinct structure in space and time.

• Ongoing activity in developing cortex is not random-- specifically coordinated in space and time within and among cortical areas between the hemispheres

• BRAIN initiative (for cover letter to the editor)

  • this work aids at least a couple of the 9 preliminary aims of the Brain project

• template for assessing altered functional dynamics in models for neurological disorders

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