Developmental Genomics and Stem Cell Biology BCH512 Fall 2010
1) Definition: The study of how the spatial and temporal readout of the genome is achieved during
development, and conversely on how forced changes in gene expression patterns can affect developmental
processes. Merger of Developmental Biology and Genomics. How does the Genome get read out to create the
Organism.
Different organism appear to use different strategies due to refinement of systems throughout evolution.
Why use different organisms to study?
A) Knowing how different systems work gives insight into possible mechanisms. Nature is building
continuously, reusing and refining. What can happen? How did system evolve?
B) Some systems are more useful than others to study specific aspects of development.
Bacteria, fungi, protists, insects and nematodes, simple invertebrates, vertebrates, mammals.
2) Principals:
A) Cellular continuity: Every cell comes from another cell.
B) Polarity: Can be established in several ways:
Prexisting in oocyte. develops by how material is transported into the developing oocyte.
Drosophila oocyte development
Page 1
B) Can be established by fertilization.
Worms, point of sperm entry defines the posterior pole of the egg.
Picture of P granules from Strome Lab
a) fertilized egg with distributed P-granules
b)At pronuclear migration P-granules redistribute to posterior, where sperm nucleus was located.
c)After first cell division all P-granules in Posterior cell.
Page 2
P granules are initially distributed throughout the cytoplasm, but then move posteriorly.
C) Can be established in tissues by differential gene expression (Gradients)
From Gilbert. http://www.devbio.com/article.php?ch=3&id=17
Figure 1. A hypothetical model for gradients establishing positional information. The concentration of the
morphogen drops from the source. In this diagram, the receptors for the morphogen are enhancer elements of
two genes that control cell fate, but the receptors could also be cytoplasmic receptors or membrane receptors.
One of the receptors (in this case, the enhancer on gene A) needs a high concentration of morphogen in order to
act. At high concentrations of morphogen, both genes A and B are active. In moderate concentrations, only gene
B is active. Where the morphogen concentration falls below another threshold, neither gene is active. (After
Wolpert, 1978.)
This positional and temporal information is continuously changing in the developing embryo. Figure 3.19 Activin (Or a
Closely Related Protein) Is Thought to Be Responsible for Converting Animal Hemisphere Cells into Mesoderm
Page 3
Page 4
How does one study Developmental Genomics: Controlled Interference (Kaltoff).
1) Generate a hypothesis about how a process occurs. 2) Make a small controlled change that you predict will
have a specific effect and 3) see what happens.
Classical techniques: 1) Isolation
Wilhelm Roux (1888) Destruction of 1/2 2-cell frog embryo
Flaws in experiment
Later studies by Oskar Herwig and others showed that separation of two cell
embryos using constriction of a hair loop allowed the development of 1/2 size but
essentially normal full embryos. Leaving dead cell attached to other cell
apparently inhibited development. Shows both autonomy and induction.
Isolation can also be done in vitro, by removal of a tissue or region and culturing it to determine whether it can
develop autonomously or whether it requires co-culture with adjacent tissues.
Page 5
2) Removal
Hans Spemann (1901) Removed optic vesicle to ask whether lens would develop.
Optic vesicle grows out from brain and lens forms from
epidermal tissue overlying vesicle. To ask whether vesicle
induced epidermal differentiation Spemann removed the
optic vesicle from one side of an embryo. No lens
appeared on the side where the Optic vesicle was removed
therefore it is necessary for lens formation.
Page 6
3) Transplantation: Warren H. Lewis (1904) asked whether the Optic vesicle was sufficient to induce lens
formation by transplanting the vesicle under the flank and/or transplanting flank epidermis over the optic
vesicle. In either case lenses formed over the vesicle, indicating that the vesicle was both necessary and
sufficient to induce lens formation.
Such studies indicated whether certain differentiation functions were cell-autonomous or inductive.
Genetic techniques: Traditional and reverse genetics.
Traditional genetics: Start with Wild-type allele. Induce mutations. Observe phenotype due to presence of
mutant allele. Map and characterize gene. Isolate revertant mutations that correct phenotype (suppressor
mutation) or modifier genes that intensify the phenotype. Construct genetic pathway.
Mutations can be null alleles (complete loss of gene function), partial loss-of-function alleles, or gain-offunction alleles. Early studies also found Dominant-negative alleles which can overcome the effect of one or
more copies of a wild-type allele.
Reverse genetics: Start with a gene of interest, affect it's expression, see what happens.
Transgenic and knockout techniques used in mouse development.
Understanding these techniques will be important in future lectures.
1) Standard Transgenic mice: This technique is used to make a mouse
that expresses any gene of interest in any tissue of interest. A
recombinant DNA construct is make where the coding region of a gene is
placed downstream of the control elements (promoter and enhancer
elements) needed to express the gene in a tissue of interest. A poly
adenylation signal is placed after the coding region in the construct. This
DNA is linearized and injected into the male pronucleus of a fertilized
oocyte (see figure). The DNA integrates randomly, sometimes multiple
copies in multiple places in the genome. The embryo develops in vitro
and is introduced into the uterus of foster mice. The progeny mice are
screened to identify those that integrated the DNA and then the organs of
interest are harvested to see whether the transgene is expressed in the
animal. Because integration is random in each embryo, only some
animals of the initial litter will contain the transgene (these are called
founder mice) and different levels of expression are seen with integration
at different sites in the genome. Several founder mice are bred to see that
they transmit the transgene and that stable expression is obtained.
Sometimes, transgenes are expressed in the first generation but then
silenced in future generations due to modification of the chromatin
structure at the site of integration. This is not something that one likes to
see, as it complicates analysis. Most transgenes are stably expressed in
all future generations.
Page 7
2) Tet-On "conditional" transgenic mice: These are more complicated to make than a standard transgenic,
but have the advantage that you can then express the transgene in whatever tissue in which you can express the
rtTA (reverse tetracycline tranasactivator protein) protein by breeding 2 transgenic mouse strains together.
With this system you need to make a minimum of 2 transgenic mouse lines.
1) The first we will call the operator mice. To make this mouse you
place the coding region of any gene that you want to express (in the
diagram a dominant-negative NFIA protein is used) downstream of a special promoter sequence containing
binding sites for the rtTA protein. In the diagram this promoter region is shown as the tetO7-CMV fragment
which has 7 copies of the tetO (tetracycline operator) sequence next to a minimal promoter region from human
cytomegalovirus (CMV). A polyadenylation site is put downstream (BGHpA for example). Once you've done
the cloning, you make a transgenic mouse as above. However, this promoter is normally inactive in mice, so
you can only test for the presence of the transgenic DNA in the progeny mice, not for expression of the
transgene. These mouse will have no phenotype because the transgene is not being expressed. You then put
these mice containing the integrated operator transgene aside and make the second transgenic mouse, the rtTA
expressing activator mice.
2) For the rtTA expressing mice (we'll call these the activator mice) you clone the coding sequence for the
rtTA (reverse tetracycline TransActivator) protein downstream of a promoter/enhancer region that will express
the rtTA protein in the tissue that you want to study. We'll use lung as an example and clone the rtTA coding
sequence downstream of the CCSP promoter that express only in lung. So you now make another standard
transgenic with the rtTA protein being expressed from the CCSP promoter. In this transgenic mouse line, you
can screen for expression of the rtTA protein with antibodies or the mRNA for the rtTA protein using reverse
transcription and PCR. Again, these mice will have no phenotype because they are expressing only the rtTA
protein in a tissue of interest, in this case lung. The rtTA protein is a site-specific DNA-binding protein that
binds to tetO sequences only in the presence of the drug tetracycline. It then activates transcription from
transgene promoters that contain tetO sequences. In this single activator transgenic mouse there are no
promoters to which rtTA can bind.
Now you begin the experiment, you breed mice the
operator mice with the activator mice and screen for mice that
contain BOTH transgenes. These bi-transgenic mice still have no
phenotype because while the rtTA protein is being expressed from
the activator transgene in lung, there is no tetracycline (actually the
related doxycycline is used in animals) to bind to the protein and
therefore rtTA cannot activate transcription from operator
transgene. If you take mice containing both transgenes and feed
them doxycycline (labeled d in lower figure) it binds to the rtTA
protein (shown as a black box/arrow), the rtTA protein binds to the
tetO sequences and activates transcription from the operator
transgene, expressing your protein of interest.
While this seems very complicated, there are currently many
laboratories producing their own strains of activator mice that express
rtTA in different tissues. Therefore, if you decide to study the role of
a given gene (such as the NFI-A engrailed dominant negative gene
shown) in another tissue, you just have to breed your operator mouse
with different activator mice that express rtTA if different tissues
and you can ask what effect your gene has in that tissue, and you can control when the gene is expressed by
Page 8
giving doxycycline. This technique has revolutionized the ability to express a gene in a temporally controlled
(by dox) and spacially controlled (by transgene promoter) manner. It's easier to breed 2 mouse strains together
than to create a new transgene that expresses in a specific tissue.
Similarly, you could use your activator mouse and it's transgene to drive the expression of different operator
transgenes in lung, thus eliminating the need to make multiple transgenes that express in lung. This mixing of
different activator and operator mice is very flexible and allows one to express a transgene in multiple tissues
just by interbreeding different pairs of mice.
3) Traditional mouse knockouts: A traditional knockout deletes the function of
a gene in every cell of the organism. Loss of genes that are required for early
development cause the embryos to die early, preventing analysis of the role of the
gene at later stages of development. To make a traditional knockout (figure at
right):
1) Create DNA construct with neo-resistance gene flanked by genomic sequences
(attach negative selectable marker to one or both ends, see diagram next page).
2) Electroporate into Embryonal stem cells, select for neo gene and loss of
flanking negative selection marker.
3) Screen for homologous recombination (targeted integration) as opposed to
random insertion. See figure on next page for pictoral description of this process.
4) Inject correctly targeted ES cells into Blastocysts of mouse strain with different
coat color (C57 Black). Check chimeric animals (usually males are used) with
altered coat color for ability to transmit the targeted gene. If coat color is
transmitted to progeny then sperm have been derived from ES cells.
5) Screen appropriately colored progeny of chimera for disrupted gene and breed
heterozygous animals to achieve homozygosity. Correctly colored progeny from
the male chimera will carry one copy either the normal gene or the disrupted gene
from the ES cells, with the other copy coming from the normal female parent.
6) Observe phenotype in mice carrying one or two copies of the mutant gene compared to mice with 2 copies of
the normal gene.
Homologous recombination in step 3 will result
in correctly targeted genes in only a fraction of
the neo-resistant colonies. This diagram shows
the structure of a targeting construct, a wild-type
gene, and a correctly targeted allele from a
recent paper of ours. The large Xs mark the
regions in which homologous recombination
occured. Correct targeting was screened for by
Southern blot looking for a 23kb Sac1
restriction fragment from the normal gene but
an 8kb fragment from the correctly targeted gene.
Page 9
Modification of Knockout: Conditional Knockout (also considered a Knockin)
In this technique, instead of deleting part of a gene one
specifically integrates a region that contains an essential
part of the gene that is flanked on either side by a sitespecific recombination site (Cre or Flp). This is usually
an essential exon with the recombination sites within
intronic sequences. Specifically integrate this region
replacing the normal region of the gene and make a
mouse that contains this altered gene. The goal is to have
a "normal" animals where the gene can be deleted at will
from specific locations. The Cre and Flp recombinases mediate highly efficient recombination reactions
between specific short DNA sites know as loxP sites (for Cre) or FRT sites (for Flp). The figure on the right
shows a targeted allele (TA) with FRT sites as small open rectangles and loxP sites as open triangles. The
targeting vector would look like the targeted allele but contain a negative selection marker at one end. The
"conditional allele" (CA) has removed the neo resistance gene by treatment with Flp recombinase leaving one
FRT site and 2 loxP sites surrounding the essential exon. The deleted allele (TSNA) has been treated with Cre
recombinase and has lost the essential 2nd exon leaving only a single loxP site in the gene.
Two ways to conditionally "knockout" the gene.
1) Treat organs or tissues with an adenovirus that expresses the appropriate recombination protein.
2) Breed this mouse with a mouse in which the Cre or FLP protein is expressed in a cell or region of interest
from a specific transgene (developmental specific knockout). Generally this transgenic mouse also need to
carry a disruption in the gene being studied so that when it breeds with the Conditional knockout the offspring
will have one KO allele and one conditional KO allele. Versions of Cre recombinase are now available that are
conditionally active, only activate with steroid hormone analogs. This allows turning on the recombinase at
specific times, while spatial expression of the recombinase is regulated with a specific promoter. The FLP
(yeast) recombinase is also being used for conditional deletions. The diagram below shows the Cre
recombinase transgene being driven by a liver-specific albumin enhancer/promoter region so that in most cells
the gene will remain intact, but in liver cells that express albumin and the albumin promoter-Cre transgene the
essential exon is deleted.
These conditional knockouts are being used routinely to ask what function a given gene has in a specific celltype or tissue.
Page 10
RNAi and microRNAs
RNAi: Short dsRNAs oligos homologous to endogenous mRNAs that induce degradation of mRNA and loss of
gene expression. Generated by dicer enzymes from exogenous dsRNA. Discovered in C. elegans by
attempting to use antisense RNA to inhibit gene expression.
MicroRNAs (miRNAs): Short duplex RNAs homologous to endogenous mRNAs that affect message
translation or stablilty. Required for stable cell differentiation and epigenetic regulation.
Mechanisms of RNAi and miRNAs
Tang, TIBS, vol. 30 (2005) siRNA and miRNA: an insight into RISCs
Page 11
Tang, TIBS, vol. 30 (2005) siRNA and miRNA: an insight into RISCs
Page 12
Definitions to know in Developmental Genomics.
Many biochemical and molecular biological assays are performed in homogenous solutions. In contrast, within
cells, tissues and organs there is often restriction of diffusion and organization of materials in defined spatial
patterns. Many of the terms below are used to describe such patterns and will help you understand papers in
developmental biology.
Polarity: The finding of differences between different regions of a single cell or a group of cells. For example,
polarity can be induced in an oocyte by fertililization. Polarity can be established in embryos by
gradients of gene expression in specific groups of cells.
Gradients: Distributions of molecules that are higher in one region than another. Gradients can be established
by Organizers.
Organizers: A cell or group of cells that express diffusible signalling molecules that can form gradients and
can induce polarity in a tissue. Such Organizers can also induce changes in nearby cells. Organizers
are compnonents of “morphogenic fields”.
Partitioning: A change in the distribution of a molecule or cell from being homogenous to being localized to a
specific area of a single cell or tissue. For example, specific RNAs and proteins are partitioned into
different cells during early cell divisions in mammalian embryos and other RNAs and proteins are
partitioned differentially in mother cells or daughter cells during yeast cell division.
Cell autonomous vs. inductive phenotypes: A cell-autonomous defect or phenotype is one due to an intrinsic
defect within the cell that is affected. For example, in many human thallasemias there is a mutation
in a globin gene that causes a failure of globin synthesis in reticulocytes. The failure of globin
synthesis in these cases would be cell-autonomous defects in the reticulocyte since the defective
genes are expressed only within the reticulocyte. However it is also possible to generate anemias
(loss of red blood cells) by the deletion or loss of hormones produced elsewhere such as
erythropoeitin. In this case the cells themselves are not defective but the phenotype is caused by
failure to induce proper growth and differentiation of reticulocytes. Giving back the hormone would
"cure" the defect.
Epithelial-mesenchymal inductions: In many organ systems the development of the organ or tissue is
dependent upon the different layers of the tissue sending signals to each other that regulate specific
differentiation events. In specific cases it has been shown by transplantation studies (also called
tissue recombination studies) that the specific underlying mesenchyme of an organ is essential to
induce differention events in overlying epithelial cells. Conversely, specific regions of epithelium
have also been shown to induce underlying mesenchyme. In many tissues these are referred to as
"reciprocal epithelial-mesenchymal interactions or inductions".
Reverse genetics and "traditional" genetics: Traditional genetics involves the generation of random
mutations and selection or screening for a specific phenotype (the observed property of an
organism). Thus one alters the genotype at random and observes a phenotype. In reverse genetics,
one selects a specific gene of interest, deletes or modifies it, and then observes the phenotype
obtained. Thus in traditional genetics one obtains a number of previously unknown genes involved in
a specific phenotype and can put together genetic pathways involved in a phenotype. In reverse
Page 13
genetics, one addresses the specific role of a given gene in all developmental processes in an
organism. Each technique has it's strengths and weaknesses and each is suitable to ask specific
questions about the role of genes in development.
Knockouts, knockins and transgenes: It is important to distinguish between these three types of genetic
modification in the mouse. Transgenes are randomly integrated genes usually containing a promoter
and a coding sequence to be expressed. Sometimes coding sequences lacking elements essential for
expression are randomly integrated in order to "trap" elements required for expression of a gene.
This is called promoter (or sometimes enhancer or polyA site) trapping. A knockout is a site-specific
integration that usually deletes an essential part of a gene of interest. A knockin is jargon for
replacement of a specific part of a known gene with a new element, either a new gene or a mutation
in the gene of interest.
Germ layers of vertebrate embryos: Ectoderm (ectos "outside"), the outermost layer which forms the
nervous system and skin; Endoderm (endon "within") the innermost layer that forms the lining of the
digestive tract and associated organs; Mesoderm (mesos "middle"), the middle layer gives rise to the
skeleton, muscle, heart, vasculature, kidneys and reproductive organs. Many organs are made up of
contributions by more than one germ layer.
Page 14
Some general cell types: epithelial, endothelial, mesenchymal, blood cells, secretory, others. There are many
specific cell types, both circulating and tissue-associated. Epithelial and mesenchymal cells make up
much of the solid structure in vertebrates but are specialized in function in different tissues and
organs. Epithelial-mesenchymal interactions are important in the formation of many tissues.
Morphogenesis and Organogenesis: Frequently groups of cells will undergo morphological rearrangement or
restructuring to make things like limbs or organs like the lung, liver, heart, brain, etc. When the final
tissue is an organ such transformations are called organogenesis and when they're not organs it's
referred to as simply morphogenesis. When organs are formed from preexisting groups of cells or
tissue the "preorgan" is frequently referred to as an organ primordium or primordial organs.
Anlagen: Of German origin the term anlagen refers to any group of relatively undifferentiated cells that is
destined to become a particular group of differentiated cells at a later time in development. It is used
to identify distinct cell groups in fly development and also in vertebrate development for example the
"optic anlagen" is the group of cells that will become the eye in many vertebrates. The term is related
to fatemaps, defined cell lineages, and differentiation.
Lineages: In some organisms (C. elegans (referred to hereafter as worms) is a good example) individual cells
are destined from their time of creation to become specific regions or cells of the final organism. In
worms the entire map of cell divisions from the fertilized ovum to the complete adult animals is
known. This map is referred to as the Lineage map. In worm jargon, to observe and record the entire
cell division pattern of a worm is called "lineaging" the worm. Such lineage maps are useful to
determine where in development a specific mutation affects the organism and generates the final
phenotype. In vertebrates the cell lineages are somewhat less defined but there are still regions of the
early embryo which become destined to differentiate into specific tissues or organs. Later in
development the term lineage in used to define the continuous line of distinct cell types that make up
the immune system, the hematopoietic system, the skin and other continuously differentiating cells
and tissues.
Germ cells vs. somatic cells: Germ cells are those that are used in reproduction such as mature sperm and
oocytes but also their progenitors. Taken together these cells are known as the germline of the
organism and represent a specific cell lineage. Somatic cells are all other cells not functioning in
reproduction such as general epithelial cells, mesenchymal cells and blood cells.
Stem cells: Stem cells are cells that are capable of both self-renewal and the generation of other differentiated
cell types. The term is derived from the stem of a plant, which gives rise by branching events to the
more differentiated parts of the plant (leaves). Stem cells come in a number of forms, the best known
being pluripotent embryonal stem cells (ES cells) which can differentiate into many different cell
types. It appears that stem cells or "stem-like" cells exist in many tissues as part of normal growth
and repair processes. It is important to remember that not all "stem cells" are alike and some appear
to have restricted lineages into which they can develop. Some labs are referring to some stem cells as
"multipotent progenitor cells" to avoid the recent stigma associated with the name stem cells.
Differentiating/Differentiation: Changing from one form to another. New properties are expressed and old
properties are extinguished. While the term morphogenesis is usually reserved for gross remodeling
of multicellular structures, differentiation of the individual cells frequently coincides with
morphogenic events. Both individual cells and groups of cells can be said to differentiate into
something else.
Page 15
Endocrine, Paracrine and Autocrine effects: Hormones or growth factors can be expressed and have their
effects in at least three distinct manners. Endocrine secretion of hormones is secretion into the blood
stream so that effects can be had at distal locations. Paracrine effects are one cell secreting a
hormone or growth factor locally so that neighboring cells are affected. Autocrine effects are where a
cell secretes a substance that then binds back to the same cell, a type of autostimulation. A fourth
"crine" effect is Exocrine where a substance is secreted outside of the body of the organism either
through the skin or into the intestinal tract.
Programmed cell death: The first genetic evidence for programmed cell death (apotosis) was found in the
nematode C. elegans with the ced (C. elegans death) mutations. These mutations decreased the
normal cell death that occurs during C. elegans development. C. elegans adult hemaphrodites contain
959 somatic cells (together with hundreds of germ cells) and during development to the adult stage
131 cells die and are degraded. Thus almost 1/8 of all cells that are made during development are
deliberately lost. Many of the genes defined in the ced pathway have been shown to function during
apotosis in mammalian cells.
Tissue recombination or transplant studies: To demonstrate inductive interactions between epithelial and
mesenchymal tissues or between any groups of cells tissue recombination (aka transplant) studies
have been performed. Such studies involve either grafting of one piece of tissue to another in vivo or
the placement of two tissues abutting each other in vitro. Recently beads soaked in specific growth
factors/hormones have been useful to study the inductive signals generated by tissues.
Parts of an an embryo: One of the most frustrating things about learning developmental genomics is the huge
number of defined parts of embryos that are generated and lost during development. All of the
instructors will try to minimize the number of terms that you need to learn, but the fact is that to
understand what is going on you need to understand the players involved and that requires
remembering a large number of specific embryo parts and a large number of genes. For your own
research the number of parts you will need to learn will likely be fewer because you'll be studying a
specific subset of developmental processes. A very abbreviated list is below.
Germ layers: see above.
Neural fold: a region of early vertebrate embryos that is formed from the neural plate and
eventually folds together and fuses to become the neural tube, which eventually forms the brain and
spinal cord.
Page 16
MHP= medial neural hinge point
DLHP= dorsolateral hinge point
Page 17
Neural crest cells: These are found only in vertebrates and arise from the tops of the neural folds
and then migrate to and seed various regions of the embryo to form large numbers of tissues
including cartilage elements of the head, portions of the teeth, pigment cells of the epidermis, several
types of neurons, hormone-producing gland cells and smooth muscle cells. They are very versatile!
Pharyngeal arches: These are groups of cells that form on the developing "neck" region of
vertebrate embryos and are formed from the pharyngeal pouches that bulge from the pharyngeal
endoderm and generate pharyngeal clefts. Each arch (I-VI) forms distinct regions of the jaw, ear,
larynx and trachea of the term embryo. Neural crest cells migrate into the pharyngeal arches.
Below are pharyngeal arches (branchial arches and gill arches) in Salamander. Ectoderm has been removed.
Rhombomers: These groups of cells are formed within the neural tube from the segmentation of the
hindbrain (Rhombencephalon). Each rhombomere goes on to become a nerve ganglion. Neural crest
cells migrate into the rhombomers.
Ectodermal Placodes: Regions of tissue that form in the Ectodermal layer of the head region and
form the inner ear (Otic Placode), the lens (Lens Placode), the olfactory epithelium (Nasal Placode)
and the sensory ganglia of cranial nerves.
Somites: These are groups of cells that form just outside of and along the neural tube (from paraxial
mesoderm) and go on to generate the cells of connective tissue and muscle. The somites are
Page 18
numbered 1-28 in the chicken from head to tail and each somite forms distinct regions of the term
embryo. The mouse has ~60 somites.
Positions within an embryo: Sometimes it's hard to know what all the various terms are that describe the 3
dimensional position within an embryo. Here are a few examples:
Dorsal: the back of an embryo, sometimes easier to think of as the top of an embryo thats lying on
it's "stomach". Think dorsal fin of a fish.
Ventral: the "front" of an embryo, where the stomach would be if it had one yet.
Anterior (top, cranial, rostral): the "tip of the nose", in front of.
Posterior (caudal): the "end of the tail", think posterior, behind.
Proximal: the region closest in to the body (referring to limbs) or site or origin.
Distal: the region farthest out from the body (referring to limbs) or site of origin.
Sectioning of embryos: Some of these mean different things whether you're talking about a whole embryo or
just a portion of the embyo (like the brain).
Sigittal or parasagittal: sections parallel to the long anterior-posterior axis of an embryo from top
to bottom (dorsal to ventral) dividing the left and right halves of the embryo. I think of these as
"longways" sections.
Transverse or cross section: any sections cut perpendicular to the anterior-posterior axis.
Coronal: sections perpendicular to the dorsal-ventral axis. In brain anatomy, coronal sections go
from the front to the back of the brain. Also known as frontal sections.
Page 19