Category Archives: Neurons

Early Experiences and the Developing Brain

The developing brain is continuously absorbing sensory information and transforming this information into “fuel” for fine tuning the wiring and architecture of the brain circuit. The types of sensory information and early experiences the brain perceives during the malleable development period are critical for the evolution and structure of the brain circuit throughout life.

Part 1 from the “Three Core Concepts in Early Development” Series by the Center on the Developing Child at Harvard University.

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March 13, 2014 · 7:09 pm

Brain Tumors and Glucose: New Data on how Brain Tumors Survive Hypoglycemic Environments and Grow

A recent paper in Nature Neuroscience by Flavahan et al. shows that brain tumor initiating cells (BTICs), have special adaptations that not only allow them to survive hypoglycemic conditions, but also to proliferate. The authors in a series of experiments, show that when exposed to hypoglycemic conditions, cells taken from brain tumor samples acquire stem-like features such as expressing higher levels of the stem cell markers Sox2 and Oct4 and also of CD133+.  BTICs survive, otherwise lethal hyperglycemic conditions due to high expression of the glucose transporter, Glut3 , which is highly sensitive to glucose. The BTICs adapt to the hypoglycemic conditions, due to the high glucose sensitivity of Glut3, which allows the cells to detect and take up even very low levels of glucose.  At the next level, meta-analysis of multiple brain tumor data sets,  showed that high Glut3 expression in brain tumors is associated with patients with poor survival. Interestingly, Glut3 is also associated with poor survival in other types of cancers such as breast, ovary and colon. In addition , this study shows that Glut3 expression is associated with pluripotency. This, suggests that it might be a common mechanism which tumors use evolve and expand. Thus, the a in depth study of the role of Glut3 in tumorigenesis could prove valuable in fighting cancer.


Flavahan, W. et al. Nat. Neurosci. 16, 1371–1380 (2013).

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Filed under Biology, Cancer, Neurons, Neuroscience

On p300, enhancers and neurodevelopmental disorders.

The P300 or adenovirus E1A-associated cellular p300 transcriptional co-activator protein, is a transcriptional regulator (1, 2). It harbours an intrinsic acetyltransferase activity. Thus, by definition it affects gene transcription by inducing chromatin remodelling close to promoter sites and by providing chromatin accessibility to transcription factors and the transcriptional machinery (1). Moreover, P300 can interact with all four histone types of the nucleosome core i.e., H2A, H2B, H3 and H4 (2). Depending on the context of interactions with its co-regulators, gene transcription can either be upregulated  or downregulated, like in the case of p53 and ACTR respectively (3). By specifically interacting with the phosphorylated form of CREB, it also affects cAMP-gene regulation. Furthermore, the P300 protein has a critical role in embryonic development and neuraldevelopment. This is evident in humans, in the case of p300 mutations that cause loss of function and/or copy number alteration (reductions in copy number). These mutations cause an embryo to develop a condition called, broad thumb-hallux syndrome. Some of the phenotypic features of this syndrome, is craniofacial and limb formation abnormalities and mental retardation, highlighting the importance of p300 function during morphogenesis and neuraldevelopment in humans. The massive amount of genes under P300 control during these critical stages of embryonic development was revealed when Visel et al. (2009)(4), examined P300 binding sites by chromatin immunoprecipitation coupled to parallel massive sequencing (Chip-seq) in mouse embryos. Specifically the authors examined, P300 binding sites, in mouse embryos of embryonic age 11.5 (E11.5). This is an important stage for especially for neuraldevelopment, since in the mouse embryo, this is the stage were the neocortex epithelium initiates to expand by increasing proliferative divisions of radial glia cells (neural progenitors). Binding sites where examined in the forebrain (includes both the neocortex and the ventral telencephalon), the limbs and the midbrain. The sample size was more than 150 (!!!) embryos per tissue. In this case P300 binding was used to predict enhancer areas, since P300 was shown to associate in vitro with enhancer areas.Enhancers are DNA regions which enhance the transcription of a gene. Just for the forebrain, 2,543 P300 binding sites were identified by Chip-seq. Moreover, to examine the correspondence of binding sites to known genes, the authors performed tissue specific microarrays. In the forebrain’s case, they found that for the 885 genes which are overexpressed in the forebrain, 14 % of the identified P300 binding sites are within 101 kb from the promoter. Moreover, the enrichment for P300 binding sites was observed to increase according to the level of overexpression of forebrain-specific genes. The conclusion by the authors was that mapping P300 binding is a very accurate way to detect enhancers. In a relatively recent review, Williamson et al. (2011), provide information around enhancers and how knowing more about them might be useful to understand human disease. For example, quoting the authors and Noonan and McCallion (2010): “almost half of single nucleotide polymorphisms (SNPs) that show statistical associations with common/complex human disease and quantitative traits in genome-wide association studies (GWAS) are within noncoding regions and gene deserts and thus, potentially involve enhancers“. For the case of neurodevelopmental disorders, such as autism and schizophrenia, gaining more insights on how early imbalances in the brain structure come up though gene expression de-regulation, is critical. Achieving such progress, will help to understand how the disorder evolves and establishes in the brain. Also, this information, can hopefully lead us into finding ways to treat and perhaps prevent the disorder from evolving .

P300 Binding Sites in the mouse heart and (on the left ) conservation in rat, human, dog and elephant, by Hardison R.C., Nature Genetics (2010)

We are still a long way from home. Nevertheless, the rapid advancement of next generation sequencing technology (NGS), coupled with the parallel advancement in the computational methods created to explain sequencing and gene expression data, provide significant insights towards steps of progress.

1. Wikipedia>p300-CBP
2. GeneCards>p300
3. Li,Q. et al.(2002), Mol.Endo., 16(12),1819-2827.
4. Visel, A., et al.(2009), Nature 457(12), 854-858.
5. Williamson et al. (2011), Dev.Cell., 21(1), 17-19.
6. Noonan, J.P., and McCallion, A.S. (2010), Annu.Rev. Genomics Hum. Genet., 11, 1–23.
7. Hardison, R.C. (2010), Nature Genetics, 42, 734–735.

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Filed under Biology, Cell Cycle, Gene Expression, Microarray, Neurons, Neuroscience, Science, The Development Series

On Networks, Neurons and the Brain

When we think of our brain what comes in mind? Well, typically, words as memory and neurons are some keywords associated with the word brain. Moreover, other keywords can be schizophrenia, depression, Alzheimer’s, Parkinson’s. All these characterize different functional aspects of the brain. But, lets take a more spherical look at this structure which holds the most valuable process in humans: cognition. The brain can be considered as the world, consisting of many countries and smaller communities. Countries will be brain regions, such as the prefrontal cortex, the parietal cortex or the hippocampus. Communities would then be smaller neuronal networks within the individual brain areas. All these functional units work together to produce an output, may it be a single thought or better an array of thoughts, or, a complex grasping movement. At the heart of this output, lie neuronal units.  This post provides some introduction on the examination of the functional and architectural hierarchy of the brain, under the scope of Graph Theory.  The information is taken by the excellent review of Bullmore and Sporns [2009]. I urge you to read this review for more details and references on the topic.

Graph Theory, which is the study of graphs, has been steadily gaining interest in brain research. Regardless of time and scale and species [Bullmore and Sporns, 2009], the brain has been shown to have the characteristics of a small-world network. Before going into the specifics of brain networks, lets go over some definitions.

What is a network? A network is characterized by a set of nodes (may it be anatomical brain areas, functional brain areas as measured by electroencephalography or neurons) and a set of edges that connect these nodes. The connection is determined on the basis of the actual experimental question e.g. an edge can represent anatomical connections between brain areas e.g. the corpus callosum between the two cerebral hemispheres (a very simple 2 node graph/network with one edge) or the individual 200–250 million (!!!) contralateral axonal projections of the corpus callosum ( more complex graph; the nodes in this case may be the individual neurons receiving these connections and their topology). Key attributes of a network are: Node Degree, the number of connections of the specific node; the Clustering Coefficient, which is the ratio of the number of connections of a node to the maximum possible number connections a node may have. Moreover other important network attributes are: Hubs, which are nodes with high degree or else, high centrality, which is simply the number of shortest paths of other nodes, that cross the node under question. Short path, denotes the minimum number of edges, one may cross between a specific pair of nodes.

What then is a Small-World Network? A small-world network is a type of graph/network which is characterized by high node degree, hence, most nodes are neighbors between them. Also, a small-world network is characterized by small short path lengths, thus each node can be reached from another within a small number of lengths. This type of graph has received a lot of attention, when studying social networks. A famous example is the Six-Degrees of Separation which refers to the theory that a person is approximately 6 steps (edges of connection) away from another person on Earth. The brain satisfies the criteria of a small-world network, and this holds true on various scales in time and space and along the evolutionary ladder.

Caenorhabdidis elegans is the first organism to have its  nervous system described at a cellular level and shown to be a small-world network in terms of connectivity [Watts and Strogatz, 1998]. The organism has merely 302 neurons, a fact that made mapping of its connectome very easy in comparison to higher organisms such as human. In the human case, data produced by many methods of brain imaging have been used to build structural brain networks. For example, application of graph theory on data from Diffusion Tensor Imaging, revealed that a few areas such as the superior frontal cortex, superior parietal cortex, the precuneus and the insula have high correlation between them, in terms of centrality [Sporns and Kötter, 2004]. Moreover, functional brain networks have been constructed with the use of fMRI, MEG, EEG. Combination of data from the BOLD signal of fMRI which provides better spatial resolution and data from electrophysiological methods such as EEG, which provide better temporal resolution, and application of interpolation methods made it possible to generate more accurate networks of brain activation. Moreover, science has gone further down the line, and scientists are able to record neuronal network activity in a dish (in vitro) by MEA (multielectrode array). From these in vitro studies and animal studies, graph theory has shown that neuronal nodes with  similar connection patterns, tend to have similar functions [White et al., 1986]. Graph theory has and is proving very useful in understanding the changes that take place in various neurological and neuropsychiatric syndromes. For example, network analysis of MEG and fMRI data from Alzheimer’s and schizophrenic patients showed that small-world organization is lost and this held true both on the functional and on the structural scale. Moreover network analysis, offers the ability to ”visualize” changes that happen in the molecular level, and allows better understanding of processes such as synaptic plasticity, which is a process fine-tuned on the scale of milliseconds, and it is considered (LTP), to be the molecular underpinning of memory formation.  Comparison of the functional networks on the molecular scale, to functional networks collected from humans while performing a memory task , may help us understand the functional and even the structural changes taking place in the brain during memory formation and shed light in the pathophysiology of memory-related conditions.

This post only provides a brief introduction on the subject of Graph Analysis and brain function and structure. Nevertheless, it is clear from the little described here, that Graph Analysis along with other mathematical and statistical methods, may provide the key to understand better this eloquently-build structure called brain.


Bullmore, E. & Sporns, O. Complex brain networks: graph theoretical analysis of structural and functional systems.         Nat.Rev.Neurosc.10, 186-198 (2009)

Watts, D. J. & Strogatz, S. H. Collective dynamics of “small-world” networks. Nature 393, 440–442 (1998).

Sporns, O. & Kötter, R. Motifs in brain networks. PLoSBiol. 2, 1910–1918 (2004)

White, J. G., Southgate, E., Thomson, J. N. & Brenner, S. The structure of the nervous system of the nematode Caenorhabditis elegans. Philos. Trans. R. Soc. Lond. B Biol. Sci. 314, 1–340 (1986).

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Filed under Biology, Graph Theory, Neurons, Neuroscience

Catchy Scientific Phrase For the Day “Oxytocin – The cuddle hormone”

Baby Cuddle


I stumbled onto this blog while searching the effects of stress on the brain and fertility. From a first sight it looks interesting and has a variety of topics related to the brain and physiology-related brain matters, described in a way that even non-scientist persons can understand. Go on then, explore your amazing brain! 🙂

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Filed under Biology, Links, Neurons, Neuroscience, PhraseOfDay, Science

Hippocampal Interneurons (PtI)

The information below is taken from Danglot et al. review on hippocampal interneurons, and it can serve as short introduction on the subject.


Interneuron hereby signifies a local circuit neuron (unless specified differently), which synthesizes and releases γ-aminobutyric acid (GABA). This type of cell is critical for hippocampal function since it keeps the excitatory glutamatergic component under a yin-yan balance. Accordingly, if the GABA-ergic component is reduced, epileptiform activity develops in the hippocampus, whereas enhancing the GABA-ergic tone impairs hippocampal function. Various types of interneurons are characterized from their axonal projection pattern/target, for example oriens-lacunosum-moleculare cells target the distal apical dendrites of principal cells in the stratum lacunosum-moleculare.

Hippocampal Neurogenesis

Pyramids and other cells

Pioneer work by Bayer and Altman in the rat and of Soriano et al in mice, back in the late 70s and 80s, gave insight in the neurogenetic events taking place in the putative hippocampus. It was recognized that the hippocampal neuroepithelium consists of three distinct components, each  giving birth to different neuronal types. Accordingly, the Ammonic neuroepithelium, gives rise to the pyramidal cells and large neurons in the stratum oriens and radiatum, the Dentate neuroepithelium generates granule cells and stratum moleculare large neurons. Lastly, the Fimbrial glioepithelium generates the fimbria glial cells. There is a specific timeline in the generation of each cell type , which differs among the hippocampal areas, as also within the same area pending on the cell type. Therefore, pyramidal cells of CA3 show a peak in neurogenesis on embryonic day 17 (E17) in the rat, whereas for CA1 pyramids peak neurogenesis is seen on E19.  In mice, CA3 pyramids are generated between E14-E15 and CA1 between  E15-E16 (Soriano et al., 1986, 1989a,b). Generally there is a succession of steps before the pyramids are established in the pyramidal layer: one day folowing their genesis, they migrate in the intermediate plate , a temporary lamina, and the next day they migrate towards the hippocampal plate, taking around four days for CA1 pyramids to reach their lamina and even longer for CA3.Hence, in rat, the CA1 pyramidal layer is obvious around E20 and CA3 on E22. The Dentate Gyrus can be distinguished around E21 since around 85% of the granules are generated postnatally.


Both in rats and mice GABA-ergic interneurons are generated prenatally, around E13-E18 in rat and E11-E17 for mice. Again there are regional differences in the birth time of the interneurons even within one hippocampal area. Hence, like cortical neurons there is a inside-out gradient of interneuron settling in the pyramidal layer, early generated neurons populate the deep positions whereas younger  interneurons pass by them to occupy higher positions.  Moreover, interneurons of the stratum oriens and stratum radiatum (plexiform layers or dendritic layers) are formed before the ones of the stratum pyramidale. In contrast to most CA1 and CA3 interneurons generated between E12-E13, DG interneurons arise later, between E13-E14.

Hippocampal Interneuron Matrix  (or matrices? )

Early tracing studies by Altman and Bayer suggested that interneurons may originate from the roof of the telencephalon. There is still dichotomy as to where the GABA-ergic interneurons originate, but according to Danglot et al., a considerable number of interneurons arise from the subpallial telencephalon (ventral telencephalon) , migrate tangenially ( in contrast to cortical neurons that migrate radially) and populate the hippocampus, striatum and neocortex. The Medial  and  Caudal Ganglionic Eminences  supply the hippocampus with interneurons (MGE: supplies only CA areas and CGE: supplies both CA and DG). These GABA-ergic interneurons are positive for Dlx2 (Dlx1/2 are homeobox genes expressed in the subpallium and have a role in the induction of GABA-ergic interneuron fate). Dlx2 positive cells can be seen on E15.5 in stratum radiatum and on E16.5 in stratum oriens (Pleasure et al. 2000). Due to this early placement in the hippocampus, its has been postulated that interneurons serve as “lighthouses” for incoming pyramidal cells and hippocampal afferents.


Danglot, L., Triller, A. & Marty, S. The development of hippocampal interneurons in rodents. Hippocampus 16, 1032-1060 (2006).

Soriano, E., Cobas, A. & Fairen, A. Asynchronism in the neurogenesis of GABAergic and non-GABAergic neurons in the mouse hippocampus. Brain Res 395, 88-92 (1986).

Soriano, E., Cobas, A. & Fairen, A. Neurogenesis of glutamic acid decarboxylase immunoreactive cells in the hippocampus of the mouse. II: Area dentata. J Comp Neurol 281, 603-611 (1989).

Soriano, E., Cobas, A. & Fairen, A. Neurogenesis of glutamic acid decarboxylase immunoreactive cells in the hippocampus of the mouse. I: Regio superior and regio inferior. J Comp Neurol 281, 586-602 (1989).

Pleasure, S.J., et al. Cell migration from the ganglionic eminences is required for the development of hippocampal GABAergic interneurons. Neuron 28, 727-740 (2000).

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Filed under Biology, Cell Cycle, Hippocampus, Neurons, Neuroscience, The Development Series