CBNS 121 Midterm Review Notes PDF

-​ Early neural development: a)​ A subset of ectodermal cells of the developing embryo are instructed to form neural tissue. b)​ Cell identity is specified further along the anterior-posterior and dorsal-ventral axes. c)​ Specific neural cell types defined....

-​ Early neural development: a)​ A subset of ectodermal cells of the developing embryo are instructed to form neural tissue. b)​ Cell identity is specified further along the anterior-posterior and dorsal-ventral axes. c)​ Specific neural cell types defined. -​ Embryonic germ layers: a)​ During a process called gastrulation, which is a rearrangement of the cells of the early embryo, three distinct germinal layers arise. b)​ The ectoderm is told to become neural tissue and skin. -​ The entire nervous system comes from the ectoderm. -​ Outermost layer (ecto). c)​ The mesoderm becomes the skeleton, muscle, kidney, heart, and blood. -​ Middle layer (meso). d)​ The endoderm becomes the gut, liver, and lungs. -​ Innermost layer (endo). -​ Neural lineages arise during gastrulation: a)​ The dorsal or axial mesoderm goes inward, and will start releasing factors to tell the ectoderm above it to become neural tissue. b)​ We know this happens during gastrulation because if we take the animal cap (future ectoderm) from the frog embryo, and culture it by itself before gastrulation (pregastrula), it will give rise to skin. The animal cap a little while later after the mesoderm has already gone in will primarily give rise to neural tissue. -​ Suggesting the timing of this induction of neural fates happens during gastrulation. -​ What is telling part of the ectoderm to become neural tissue? a)​ The organizer -​ Region of the dorsal mesoderm that will give rise to the axial mesoderm in the future animal will release factors that will tell the surrounding ectoderm to become neural tissue. b)​ We know this from experiments by Spemann and Mangold (hence, Spemann-Mangold organizer). -​ Transplanted the dorsal lip of the blastopore to another embryo, which led to two distinct blastopore lips, resulting in two axes in the host embryo (two brains and two spinal cords).  -​ The blastopore is the first opening that appears in an embryo, connecting the embryo's internal cavity to the outside world. -​ Gastrulation in chickens: a)​ The role of the dorsal lip of the blastopore is taken by what is called the Hensen’s Node. b)​ Cells going in through Hensen’s Node form the head mesoderm, foregut, and notochord. c)​ Cells going in through streak form other endoderm and mesoderm. d)​ Hensen’s Node is the organizer in chickens (birds and mammals), whereas the dorsal lip of the blastopore is the organizer in frogs. -​ Role is the same. -​ They are analogous structures. -​ The search for neural inducing molecules: a)​ Through expression cloning, certain factors were able to rescue embryos that were treated with UV light and would otherwise not have a neural tube. -​ Using an assay where they inject different gene products into a ventralized embryo (no dorsal parts, including the nervous system). -​ Show that some combinations of gene products (mRNAs), are able to induce neural tissue in an embryo that otherwise would not have one. -​ Rescue assay. -​ Noggin can rescue ventralized embryos: a)​ Purify one gene product, one mRNA, called Noggin b)​ Noggin is able to rescue ventralized embryos. -​ Noggin has inducing power. c)​ Different concentrations injected have different effects. -​ Induction of neural fates is mediated by blocking BMP signaling and activation of FGF signaling: a)​ After a series of experiments, two other factors had very similar activity to Noggin -​ Chordin -​ Follistatin b)​ All three (Noggin, Chordin, and Follistatin) actually block BMP signaling. c)​ BMP signaling, early in development, is actually pushing these ectodermal cells to become the epidermis (skin). -​ You want to block that activity so that part of the ectoderm can turn on neural genes that will turn that part of the ectoderm into neural tissue. d)​ In higher vertebrates, in addition to blocking BMP signaling, you also have to activate FGF signaling.  -​ FGF signaling + blocking BMP signaling via Noggin, Chordin, and Follistatin = promote induction of neural genes that will result in the formation of future neural tissue. -​ Quick summary: a)​ Neural tissue is induced during gastrulation. b)​ The nervous system is derived from the ectoderm. c)​ In vertebrates, signals from the mesoderm are important for neural induction. -​ Noggin, Chordin, Follistating → block BMP signaling. d)​ In higher vertebrates (birds and mammals), you also need activation of a different signaling pathway. e)​ Together, blocking BMP signaling and activation of FGF signaling will induce neural tissue on the ectoderm. -​ Not everything that is in the neurogenic region is going to be a neural progenitor: a)​ Neural progenitors are neural stem cells. b)​ Lateral inhibition -​ A stochastic (random variable over time) process where a few cells within that neurogenic region will be selected to become the neuroblast (neural stem cell in drosophila). c)​ In the future neural ventral cord, the neurogenic region, there are these proneural clusters that express a transcription factor called Asc. -​ Only one cell per cluster will keep the expression and raise the expression of ASC while the others will lose it. d)​ Asc expressing cells will turn into the neural progenitors. e)​ The cell that randomly has slightly more Asc is able to inhibit the other cells within the cluster. -​ Lateral inhibition restricts the number of neural progenitors: a)​ This inhibition is done via the Notch signaling pathway. -​ The expression of Asc, a transcription factor, will drive the expression of a molecule called delta (a transmembrane protein) that will activate on the surrounding cells, the Notch receptor. -​ Notch is a receptor protein. b)​ The cells that have more Asc will have more delta, and more delta will lead the cells to inhibit their neighbors more than the neighbors inhibit the cells, and that is the cell that will eventually win out.  -​ Delta is a membrane-bound inhibitory signal protein. -​ This winning cell keeps the expression of Asc. c)​ Delta up-regulation in the prospective neuroblast activates Notch receptors on the surrounding cells and inhibits them. -​ Once this whole process of induction and lateral inhibition happens, then the cell identity will be further specified along the anterior-posterior and dorsal-ventral axes. -​ Vertebrate brain vesicles: a)​ Forebrain (most anterior) can be divided into two regions, the telencephalon and diencephalon. b)​ Midbrain can be visualized as a single vesicle within the neural tube. -​ More formally called the mesencephalon. c)​ Hindbrain (most posterior) is divided into two regions, the metencephalon and the myelencephalon. -​ Hindbrain is also called rhombencephalon because the entire hindbrain is divided into 8 smaller segments, called rhombomeres. d)​ Posterior to the hindbrain is the spinal cord. -​ Anterior-posterior specification: a)​ AP identity and polarity in invertebrates is already decided in the egg. b)​ Through a cascade of events, proteins that control the expression of genes (transcription factors) and translational regulators will subdivide the embryos into smaller and smaller regions, eventually triggering the expression of what are called segment polarity genes and homeotic genes. c)​ The segment polarity genes will subdivide the insect embryo into different segments, defining where segments start and where they end. d)​ The homeotic genes, or hox genes, will tell each segment what identity each segment will have. -​ Hox gene clusters in fly and mouse: a)​ Hox genes are very important because if they are removed, those structures go missing. b)​ In vertebrates, they are very important for the identity of neurons within the neural tube. -​ In particular, in the hindbrain and part of the spinal cord. -​ Rhombencephalon is segmented: a)​ Divided into eight segments (rhombomeres) b)​ r1-r8, anterior-posterior c)​ Each rhombomere has distinct characteristics. -​ Hox loss of function mutations: a)​ Hox genes are important to specify the identity of each of these rhombomeres. b)​ Different combinations of hox genes will be present in each of these rhombomeres. c)​ Hoxa1 -​ When Hoxa1 is removed, specification of r4 and r5 will go missing -​ Activator-transformer hypothesis (in vertebrates): 1)​ Activators (BMP inhibitors, FGF signaling) induce neural tissue with anterior characteristics. -​ Most neural tissue will become forebrain and midbrain. 2)​ Transformers (RA, Wnt, FGF) are required to transform a portion of neural tissue to more posterior structures i.e. spinal cord and hindbrain -​ Transformers promote posterior fates at the expense of anterior fates: a)​ RA (retinoic acid) is powerful and can cause embryological defects. b)​ More importantly it can promote posterior fates at the expense of anterior fates. c)​ Example is adding RA to developing frog embryos, forebrain and eyes disappear, and we get bigger and thicker spinal cords. -​ Anterior sacrifice for posterior structures. d)​ Blocking the RA receptor will lead to bigger eyes, bigger forebrain, etc. and smaller spinal cords. e)​ Transformers do this by promoting the TFs that convey posterior identity and inhibit the TFs that convey the anterior identity. -​ Transformers regulate the expression of TFs that cross repress each other: a)​ Antagonistic relationship. b)​ Example is Otx2 (anterior) and Gbx2 (posterior) cross inhibit each other. c)​ Forms a sharp boundary between A and P regions. -​ Midbrain-hindbrain boundary. -​ A signaling center at the midbrain-hindbrain boundary (MHB or isthmus): a)​ Secondary organizer since it has an inducing power. b)​ Can induce midbrain structures on the more anterior side and the cerebellum on the more posterior side. c)​ Taking a piece of the MHB and transferring it to the telencephalon can create an ectopic midbrain and cerebellum. -​ Tiny piece of tissue can secrete factors to organize tissue around it. d)​ The MHB has organizer activity. -​ Formation and maintenance of the isthmic organizer (MHB): a)​ Otx2 and Gbx2 cross inhibit each other. b)​ Gbx2 promotes the expression of Fgf8, while Otx2 inhibits the expression of Fgf8. c)​ Fgf8 can lead to expressions of En1 and Wnt1. -​ These three factors will regulate the formation of the midbrain and cerebellum and will define where the boundary will form. -​ Shh specifies ventral, whereas BMP specifies dorsal fates, in a concentration dependent manner: a)​ Just like how transformers are signals that promote posterior fates, there are also signals that will regulate the polarity along the dorsal-ventral axis. b)​ Shh is a released factor that will act as a morphogen to promote ventral fates. -​ Morphogens are secreted by specialized cells and diffuse through the surrounding environment, creating concentration gradients. c)​ Shh is released by the notochord and floor plate (ventral). d)​ BMP is released by the future epidermis and roof plate (dorsal). e)​ Shh and BMP act antagonistically. -​ Shh induces ventral neural markers in a concentration-dependent manner (same as BMP). -​ Shh is sufficient to induce ectopic floorplate (ventral) markers in vivo (inside a living organism). a)​ Overexpression of Shh leads to more floor plates, more ventral interneurons, etc. -​ More importantly, Shh is required for ventral fate specification: a)​ If Shh is removed, those ventral fates disappear. b)​ At the expense of the ventral fates, you get an expansion of the dorsal fates. c)​ Shh acts at a distance to pattern different tissues. -​ Limbs, lungs, other organs -​ Control of neuronal number: expansion vs neurogenic phase: a)​ While these progenitors are starting to acquire identity along the AP and DV axis, they will start generating neurons. b)​ These progenitors line the cavity of the neural tube. c)​ Initially, they will expand to create more progenitor cells. -​ Since you start with a very limited amount of progenitors. d)​ Eventually, they will switch to divide asymmetrically to generate one progenitor cell and one neuron. e)​ A lot of these progenitor cells will end up quitting by generating two glial cells or two neurons. -​ Expansion phase has a low Q (quitting fraction)  -​ Neurogenic phase has a high Q -​ The choice between becoming a neuron or glia is affected by multiple signaling pathways: a)​ When these progenitors decide to quit and how long their cell cycle is will define how many neurons you will have in the end. -​ Another contributing factor is when the progenitors decide to start generating glia and stop generating neurons. b)​ Gliogenic switch that happens during the end of embryonic development. -​ Involve lateral inhibition -​ Notch-delta signaling -​ Organization of the mammalian cortex: a)​ Neurons born at the ventricle will have to migrate to their final location. b)​ Some structures in the neural tube are laminated (layered), while some are not. c)​ One layered structure is the mammalian cortex. d)​ There are six layers in the mammalian cortex. -​ They are formed by layers of glutamatergic pyramidal neurons. -​ Excitatory neurons e)​ Inhibitory (gabaergic) neurons that come from a different source will then mix with these excitatory neurons to keep the balance between excitation and inhibition. -​ Very important balance for healthy brain function. -​ Glutamatergic pyramidal neurons migrate on radial glia: a)​ The excitatory neurons migrate from the ventricle. b)​ Migration happens radially along radial glial cells. -​ Radial glial cells will serve as tracks for these neurons and also are the stem cells that generate neurons (mothers for these future neurons) c)​ Radial glia are the progenitors. -​ The cortical layers form in an inside first/outside last manner: a)​ Radial glial cells in the ventricular zone → produce neurons → neurons crawl on top of radial glial cells after birth → migrate radially (hemisphere cortex) → migrate to the surface of the cortex. b)​ Glutamatergic neurons undergo radial migration. -​ Inhibitory neurons arise from the ventral forebrain: a)​ MGE = medial ganglionic entrance -​ On the ventral part of the forebrain.  b)​ Inhibitory cells migrate tangentially following the surface of the cortex to get to their final destination in the neocortex. -​ Tangential migration follows the surface of the sphere. c)​ Eventually they do some radial migration to get to the appropriate layer, but the majority of their migration is through tangential migration. -​ Summary: a)​ Progenitor cells undergo symmetric and asymmetric cell divisions. b)​ The number of neurons and glia that a progenitor will generate is regulated by length of the cell cycle and when they quit. c)​ Lateral inhibition in vertebrates prevents premature differentiation early on. Later, it is important for switching to glial fates. -​ In invertebrates, it defines how many neural progenitors you have. d)​ Neural progenitors originate in the ventricular zone (close to the cavities of the neural tube). e)​ The cortex develops in an inside first to outside last fashion. -​ Layer 6 born first (deepest). -​ Last layers to be born are layers 2 and 3 (most superficial). f)​ Radial glia are the neural progenitors of cortical excitatory neurons and also serve as tracks for migrating neurons. g)​ Neural cells migrate in two different ways: -​ Radial migration (excitatory) -​ Tangential migration (inhibitory) -​ Granule cell precursors migrate over the Purkinje Cells and form a secondary zone of neurogenesis, the EGL: a)​ Granule cells of the cerebellum. -​ Granule cells are the smallest and most numerous types of neurons in the brain. b)​ The progenitors that will generate these Granule cells are born in the rhombic lip (the structure that surrounds the fourth ventricle in the embryo). c)​ They will initially migrate tangentially towards a more anterior region. d)​ Then they will start generating neurons. e)​ After these neurons are formed, they will initially migrate tangentially again, followed by radial migration on the Bergmann glial cells. -​ Bergmann glia function as guides for migrating granule cells.  -​ Specialized radial glia types that serve structural features that these GCs will use to migrate radially towards the center of the cerebellum. -​ The Reeler mutant: a)​ A signal that contributes to the regulation of these migration events. b)​ Identified through spontaneous mutation that happened in a mouse colony. c)​ Motor phenotype (ataxia, tremor). d)​ Widespread disorganization of the brain patterning in particular layered structures like the cerebellum and the cortex. e)​ The mutation results in clustering of Purkinje cells of the cerebellum. f)​ The layers of the cortex are inverted in these mice. -​ Inverted cortical plate in reeler mutant (outside in): a)​ The neurons that are normally deep layer (5 and 6) neurons will be on the surface of the reeler mutant mouse. b)​ Reeler tells these migrating neurons to detach from the radial glial cells and allow the neurons that are coming behind to migrate past them. c)​ If reeler is not there, it cannot tell the first cells to detach and will cause a pile-up, which inverts the cortex. -​ Specific neural cell types defined: a)​ Cell fates are determined by intrinsic and extrinsic factors. b)​ In C. elegans, there is a cascade of transcription factors (starting with unc-86) that regulates the specification of touch neurons. c)​ In Drosophila, sequential expression of transcription factors (starting with hunchback) regulates the specification of different types of ventral cord neurons. d)​ The neuroblast, the progenitor cell, switches its genetic program that is defined by one of these TFs. -​ Starting with HB, then KR, PDM, and CAS. -​ Mother cell that is born from the neuroblast will keep the program that was present at the time of cell division. -​ The NB itself will switch to the next program. -​ Generate different types of neurons born from the same neuroblast. -​ Neuroblasts are precursors of neurons + glia (Drosophila): a)​ NBs divide asymmetrically to give rise to neuroblasts and GMCs (ganglion mother cells). b)​ GMCs divide just once more to give rise to either two neurons or a neuron and a glial cell.  c)​ The average NB will divide five times, however the minimum is two divisions and some go up to thirteen divisions. d)​ TFs expressed by the NB at the time of birth of each of the GMC will define the identity of the GMC. -​ Asymmetric divisions and cytoplasmic targeting: a)​ Important factor in deciding which cells will stay as a NB that will continue to give rise to more GMCs and NBs and which will become the GMC is called Numb. b)​ The side of the cell that keeps Numb after cytokinesis will be the one that becomes the GMC. c)​ The other side that lost Numb will stay as a NB. -​ Drosophila neuroblasts - spatial and temporal determination: a)​ In Drosophila, the identity of the neuroblast is defined by latitude, longitude, and timing of birth. b)​ Anterior-posterior and hox gene expression. -​ Each segment has different hox genes being expressed that will tell NBs to have different identities. c)​ Dorsal-ventral -​ DPP and different TFs in different ways in these different dorsal-ventral coordinates. -​ MSH expressed in the dorsal most. -​ IND in the intermediate ones. -​ VND in the ventral ones. d)​ Combinatorial program. e)​ Superimpose the temporal axis that give rise to different GMCs, each give rise to different characteristics. f)​ Each of these neurons born from the NB will have three dimensions that are different from each other - time, AP, and DV identities -​ Vertebrate retinogenesis: a)​ Different types of neurons are born at different times in the retina b)​ First neurons to be born are ganglion cells (RGCs) and the last to be born are Muller glia cells. -​ Vertebrate retinal cell fate commitment is flexible: a)​ Early progenitors are very flexible.  b)​ Culture of early progenitors with late progenitors, you will see the early progenitors behave like late progenitors (generate later fates of the retina). -​ Summary: a)​ Specification of different photoreceptor types in Drosophila requires extrinsic (hh, sevenless, notch) and intrinsic (ato) factors. -​ Ato is similar to Asc. b)​ In vertebrates, neural type determination is highly dependent on the timing of cell birth, and regulated by extrinsic signals (RA, CNTF) and TFs (Brn3, Ikaris/hunchback, Casz1). -​ Heterochronic Transplants in neocortex: young → old: a)​ Cortical progenitors also lose competence over time. -​ Loss of potential. b)​ Move progenitors that give rise to the first layers of the cortex (ex. Layer 6) from an early embryo, and move them to an older animal that is already generating the latest layers (2 and 3), these early progenitors will be converted and will be generating the later phase. c)​ However, old progenitors moved to a younger animal embryo are set in their ways. d)​ Older progenitors have lost competence. Newer progenitors have a higher potential. -​ Gradients of BMP and Shh specify different cell fates along the DV axis. -​ Shh promotes the expression of Class II TFs, and represses (inhibits) expression of Class I in progenitors: a)​ Dorsal = Class I TFs b)​ Ventral = Class II TFs c)​ Some of these Class I and II TFs form pairs that cross inhibit each other. -​ Pax6 and Nkx2.2 inhibit each other. -​ Dbx2 and Nkx6.1 inhibit each other. -​ Allows these progenitor cells to define sharp boundaries. -​ Progenitor TFs cross-repress each other and control the expression of other TFs essential for determination: a)​ Defines the characteristics and also defines what types of neurons are going to be born from these progenitors. b)​ Pairs that cross-repress. Sharp boundaries. -​ Some of the signaling molecules (environmental cues) that specify distinct NC fates: a)​ Extrinsic factors are very important to specify different fates of neural crest cells. -​ Neural crest cells are migratory cells that are derived from the dorsal neural tube that will migrate very long distances to form a variety of different cell types  (sensory neurons, autonomic neurons, Schwann cells, pigment cells, and smooth muscle). b)​ Extrinsic factors the cells will encounter along their migratory path define what these neural crest progenitors will become. -​ BMPs specify noradrenergic fates: a)​ BMPs are factors that tell neural crest progenitor cells to become sympathetic adrenergic cells. b)​ BMP released by the dorsal aorta will act on the progenitors that come close to the aorta and become sympathetic ganglion neurons. -​ Shown both in vivo and in vitro. c)​ Dorsal aorta/BMP → sympathetic-adrenal cells -​ Summary: a)​ Lineage, specific extrinsic and intrinsic factors participate in cell fate determination. b)​ In the neocortex, timing of birth and a combination of transcription factors specify different fates. c)​ Counter-gradients of Shh and BMP regulate TFs in progenitors, which then set up the expression of other TFs that determine spinal cord neural fates. -​ Class I and Class II TFs d)​ Shh activates the expression of Class II TFs, while repressing Class I TFs. e)​ Class I and Class II TFs cross-repress each other, setting up sharp boundaries of gene expression along the DV axis. f)​ Neural crest cell fate is highly dependent upon environment and influence of extrinsic factors. -​ BMPs are one of those cues/extrinsic factors. -​ Summary: a)​ Only one axon develops per neuron. A signal tells other neurons to become dendrites. b)​ If the axon is ablated during development, one dendrite becomes the axon. -​ Axon cut, one dendrite becomes the axon. -​ Inhibits the other dendrites from becoming an axon. -​ One at a time. c)​ Axons grow on adhesive substrates. d)​ Repulsive and attractive cues guide axons to their targets. e)​ Guidance cues or signals act on receptors on the growth cone. f)​ Guidance receptors triggers changes in the actin cytoskeleton to steer the axon.  -​ Promoting the assembly and stabilization of actin or the destabilization of actin. -​ Promoting stabilization = attractive cues. -​ Promoting destabilization = repulsive cues. g)​ Secreted Class 3 semaphorins in general repel axons at a long range. -​ In particular Sema 3A is a guidance cue that repels sensory axons. -​ Act at a long range because they are secreted and can travel and form a gradient to repel these axons. h)​ Topographic maps in the retina are initially established by contact-mediated repulsion (Ephrin signaling). i)​ Netrin is a chemo-attractant for early spinal cord commissural axons. -​ Netrin can also act as a repellent for trochlear axons. -​ Netrin acting as an attractant or repellent depends on the receptor expressed by those axons. j)​ For any signal to act on neurons in any particular way that they normally act, the neurons have to have the receptor. -​ If they don't have the receptor, there won't be any response to that signal because the neuron or the axon cannot see that signal. k)​ In the case of Netrin, there are two types of receptors. -​ DCC is a receptor that for the neuron makes Netrin feel like an attractant. -​ UNC5, expressed by other populations of neurons, will make Netrin feel like a repulsive cue. l)​ Slits are long range repellents that push commissural axons out of the midline. -​ Slits are secreted proteins. -​ The receptors for Slits are Robo (Roundabout). -​ Commissural axons are initially attracted to the midline via Netrin. The midline also expresses Slit, so Robo (Slit receptor) has to be turned off to allow the axons to grow towards the midline. Once the axons hit the midline, Robo is allowed to be turned on again after crossing the midline and won't be allowed to come back. m)​ There are proteins that regulate the sorting and duration of Robo, initially promoting the degradation of Robo, so that the growth cones are insensitive to Slit, to enter and grow towards the midline.