Barbara Clancy

Web-based method for translating neurodevelopment from laboratory species to humans

Biomedical researchers and medical professionals are regularly required to compare a vast quantity of neurodevelopmental literature obtained from an assortment of mammals whose brains grow at diverse rates, including fast developing experimental rodent species and slower developing humans. In this article, we introduce a database-driven website, which was created to address this problem using statistical-based algorithms to integrate hundreds of empirically derived developing neural events in 10 mammalian species (http://translatingtime.net/). The site, based on a statistical model that has evolved over the past decade, currently incorporates 102 different neurodevelopmental events obtained from 10 species: hamsters, mice, rats, rabbits, spiny mice, guinea pigs, ferrets, cats, rhesus monkeys, and humans. Data are arranged in a Structured Query Language database, which allows comparative brain development measured in postconception days to be converted and accessed in real time, using Hypertext Preprocessor language. Algorithms applied to the database also allow predictions for dates of specific neurodevelopmental events where empirical data are not available, including for the human embryo and fetus. By designing a web-based portal, we seek to make these comparative data readily available to all those who need to efficiently estimate the timing of neurodevelopmental events in the human fetus, laboratory species, or across several different species. In an effort to further refine and expand the applicability of this database, we include a mechanism to submit additional data.

Widespread projections from subgriseal neurons (layer VII) to layer I in adult rat cortex.

Theories of information processing and plasticity in mammalian cortex often rely on knowledge of intracortical networks studied in rodent cortex. Accordingly, the contribution of all cells involved in this circuitry is potentially significant, including connections from a subset of neurons that persist from the developmental subplate, called subgriseal neurons in the present study. Ascending corticocortical connections from subgriseal neurons were identified by using in vivo transport of fluorescent retrograde tracers from discrete applications confined to cortical layer I (approximately 1 mm2) or from injections placed into superficial cortical layers. Applications restricted to cortical layer I can be identified by a subsequent retrograde labeling pattern that includes neurons in layers II/III and V but not those in layer IV. In contrast, when retrograde tracer is deposited in layers II/III, layer IV cells are also labeled. By using this identification technique in juvenile and adult rats, widespread interareal projections to superficial layers, including unequivocal connections to cortical layer I, were found to originate from a tangential band of neurons directly below the conventionally identified gray matter (i.e., subgriseal) and from a smaller number of cells in the white matter (WM) proper. Subgriseal and WM neurons were labeled below application and injection sites in somatosensory, auditory, visual, motor, frontal, and adjacent areas at distances of more than 4 mm. However, the subgriseal‐to‐superficial pathway was not sensitive to nonfluorescent retrograde tracers including horseradish peroxidase. Because neurons in the deeper cortical layers can be strongly influenced through input to their apical dendritic extensions in cortical layer I, the widespread connections described in the present study indicate that the ascending subgriseal projections should be considered in models of mature cortical function. J. Comp. Neurol. 407:275–286, 1999.

The course of human events: predicting the timing of primate neural development

A recent model of the timing in which neural developmental events occur in a variety of mammals has shown high predictability of the order and duration of these events across species when appropriately computed. The model, originally derived to study the developmental mechanisms of evolutionary change in the nervous system, is adapted in this paper to predict the course of those events in the developing human, a sequence that has been difficult to determine using non-invasive neuroanatomical techniques. Using a modified version of our original regression model, we generate predicted times of occurrence for a large number of developmental events in the human embryo and fetus, and include a chart of comparable events for macaque monkeys. We discuss a bidirectional variability in the original model which allowed us to identify limbic and cortical primate neural events that are significantly deviant from the general mammalian norm, but which also proved predictable following modification. We test the modified model against empirically derived values for neural events not included in the original model, as well as through comparisons with human developmental sequences inferred by other methods. In view of the remarkable stability in the course of development across species, knowledge of the timing of human neural events need not be entirely restricted to the limited existent embryonic and infant data. Although the primate neural development sequence is somewhat more complex than that for other mammals, primate data continue to support a theory of developmental conservation across evolution.

Cross-species analyses of the cortical GABAergic and subplate neural populations

Cortical GABAergic (γ-aminobutyric acidergic) neurons include a recently identified subset whose projections extend over relatively long distances in adult rodents and primates. A number of these inhibitory projection neurons are located in and above the conventionally identified white matter, suggesting their persistence from, or a correspondence with, the developmental subplate. GABAergic and subplate neurons share some unique properties unlike those of the more prevalent pyramidal neurons. To better understand the GABAergic and subplate populations, we constructed a database of neural developmental events common to the three species most frequently used in experimental studies: rat, mouse, and macaque, using data from the online database www.translatingtime.net as well as GABAergic and subplate developmental data from the empirical literature. We used a general linear model to test for similarities and differences, a valid approach because the sequence of most neurodevelopmental events is remarkably conserved across mammalian species. Similarities between the two rodent populations are striking, permitting us to identify developmental dates for GABAergic and subplate neural events in rats that were previously identified only in mice, as well as the timing in mouse development for events previously identified in rats. Primate comparative data are also compelling, although slight variability in statistical error measurement indicates differences in primate GABAergic and subplate events when compared to rodents. Although human extrapolations are challenging because fewer empirical data points are available, and because human data display more variability, we also produce estimates of dates for GABAergic and subplate neural events that have not yet been, or cannot be, determined empirically in humans.

Network Structure Implied by Initial Axon Outgrowth in Rodent Cortex: Empirical Measurement and Models

The developmental mechanisms by which the network organization of the adult cortex is established are incompletely understood. Here we report on empirical data on the development of connections in hamster isocortex and use these data to parameterize a network model of early cortical connectivity. Using anterograde tracers at a series of postnatal ages, we investigate the growth of connections in the early cortical sheet and systematically map initial axon extension from sites in anterior (motor), middle (somatosensory) and posterior (visual) cortex. As a general rule, developing axons extend from all sites to cover relatively large portions of the cortical field that include multiple cortical areas. From all sites, outgrowth is anisotropic, covering a greater distance along the medial/lateral axis than along the anterior/posterior axis. These observations are summarized as 2-dimensional probability distributions of axon terminal sites over the cortical sheet. Our network model consists of nodes, representing parcels of cortex, embedded in 2-dimensional space. Network nodes are connected via directed edges, representing axons, drawn according to the empirically derived anisotropic probability distribution. The networks generated are described by a number of graph theoretic measurements including graph efficiency, node betweenness centrality and average shortest path length. To determine if connectional anisotropy helps reduce the total volume occupied by axons, we define and measure a simple metric for the extra volume required by axons crossing. We investigate the impact of different levels of anisotropy on network structure and volume. The empirically observed level of anisotropy suggests a good trade-off between volume reduction and maintenance of both network efficiency and robustness. Future work will test the models predictions for connectivity in larger cortices to gain insight into how the regulation of axonal outgrowth may have evolved to achieve efficient and economical connectivity in larger brains.

Cortical GABAergic Neurons: Stretching it Remarks, Main Conclusions and Discussion.

The articles in this Special Topic cover a range of issues concerning long-distance projecting cortical GABAergic neurons, in the context of interneuron diversity. As several authors report, these neurons are attracting renewed attention spurred by new techniques and markers which show great potential for deciphering their role in cortical organization and microcircuitry. Other authors have emphasized developmental origins of particular subpopulations and their roles in early cortical circuitry. Notable recurring themes are species-specifi c features and probable implications for normal and pathological cortical functioning. A corollary theme, evident in many of these articles, concerns nomenclature. Several terms are almost interchangeably used, but nevertheless distinct; that is: subplate, layer 7, layer VIB, pioneer and interstitial neuron (see comments to follow Clancy et al., below, among others). In this article the main conclusions, and some of what the host editors (Kathleen Rockland and Javier DeFelipe) consider the most inter-esting remarks, have been extracted from each of the individual articles. These commentaries are not necessarily directly derived from the original work of the authors, and may be the result of the collective work of several different laboratories. This is followed by a section dedicated to more general comments and a discussion of the issues raised. The authors who have participated in this article are listed in alphabetical order.

Late Still Equals Large

ly large by rule, independent of specific niches and behaviors – we struggled to account for it in terms of ‘developmental constraints’ and ‘spandrels’. Now, we attempt to understand the conserved pattern of allometric scaling as a substrate for ‘evolvability’. That is, we investigate what features such a conserved plan might afford for graceful scaling and facilitated variability (that is, genetic variation translated through conserved genetic and epigenetic contexts which coordinate and stabilize functionality), working this out in some detail for the nocturnal and diurnal primate eye. Of course, understanding behavioral variability remains the goal, but because relative volumes of specific neural structures rarely correlate well with specific capacities, most researchers have sensibly turned their attention elsewhere.

ttime: an R Package for Translating the Timing of Brain Development Across Mammalian Species

Understanding relationships between the sequence and timing of brain developmental events across a given set of mammalian species can provide information about both neural development and evolution. Yet neurodevelopmental event timing data available from the published literature are incomplete, particularly for humans. Experimental documentation of unknown event timings requires considerable effort that can be expensive, time consuming, and for humans, often impossible. Application of suitable statistical models for translating neurodevelopmental event timings across mammalian species is essential. The present study implements an established statistical model and related functions as an open-source R package (ttime, translating time). The model incorporated into ttime allows predictions of unknown neurodevelopmental timings and explorations of phylogenetic relationships. The open-source package will enable transparency and reproducibility while minimizing redundancy. Sustainability and widespread dissemination will be guaranteed by the active CRAN (Comprehensive R Archive Network) community. The package updates the web-service (Clancy et al. 2007b) www.translatingtime.net by permitting predictions based on curated event timing databases which may include species not yet incorporated in the current model. The R package can be integrated into complex workflows that use the event predictions in their analyses. The package ttime is publicly available and can be downloaded from http://cran.r-project.org/web/packages/ttime/index.html.

Phylogenetic proximity revealed by neurodevelopmental event timings

Statistical properties such as distribution and correlation signatures were investigated using a temporal database of common neurodevelopmental events in the three species most frequently used in experimental studies, rat, mouse, and macaque. There was a fine nexus between phylogenetic proximity and empirically derived dates of the occurrences of 40 common events including the neurogenesis of cortical layers and outgrowth milestones of developing axonal projections. Exponential and power-law approximations to the distribution of the events reveal strikingly similar decay patterns in rats and mice when compared to macaques. Subsequent hierarchical clustering of the common event timings also captures phylogenetic proximity, an association further supported by multivariate linear regression data. These preliminary results suggest that statistical analyses of the timing of developmental milestones may offer a novel measure of phylogenetic classifications. This may have added pragmatic value in the specific support it offers for the reliability of rat/mouse comparative modeling, as well as in the broader implications for the potential of meta-analyses using databases assembled from the extensive empirical literature.