2017 no case should the answer fill more than

2017 Final examination for Gene 505


book test. This test is designed to assess your level of understanding of the
concepts described in the lectures and in the readings and your ability to seek
out and integrate knowledge across the three domains of this course. You may
use Carlson, Epstein, or any other book or published source to research your
answer. You do not have to give citations, but you may not copy and paste text
from any source.

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answer should be as concise as possible, in no case should the answer fill more
than one side of a piece of paper with 1″ margins and a reasonable sized font
(Geneva, Times, or Helvetica 12 point). Your grade for that question will be
reduced ½ grade for each answer that exceeds this limit.


answers should be emailed to me by Saturday Dec 16 at midnight EST. Tests
received between 12:01 am Sunday Oct 28 and midnight Sunday Dec 16 will have a
full grade scoring penalty. Tests received after that will not receive a grade
and considered incomplete. If you have a serious medical or family emergency
that precludes competing the examination by the due date, please discuss this
with me.


Do not
reuse an example from one question in another question. Do not reuse an answer
from your midterm. Suggestion: to avoid frustration, read all of the questions
before you answer the first one so you can decide which examples you wish to
use in which answers. Remember to include all three elements in each answer.


send the answers as an attachment to an email message with the following
filename: FT505_17_XXX.doc (replace “XXX” with your initials). Please also
replace the footer text with your name (you only need to do this once, it
carries through to all pages).


typing your name here, you agree that you have neither received assistance from
another individual on this examination nor provided assistance to another
student and that what you have written here is original.

NAME: Ariel

1. A relatively uncommon, but not extremely rare phenotype is a
partially or completely fused midline eye with a tube-like proboscis above that eye. Explain why in this
defect that the nasal structure is above (cranial or anterior) to the ocular
structure whereas in the normal, the nose is mostly below (caudal or inferior)
to the eye.

Synophthalmia and
proboscis are rare craniofacial features characteristic of severe holoprosencephaly
(HPE), a midline developmental defect that affects 1 in 250 conceptuses. A
hallmark manifestation of HPE is the failure of the forebrain to completely
separate during early development, influencing the surrounding craniofacial
structures and resulting in the various facial malformations. Classic HPE can
be divided into various types depending on clinical severity: alobar (most
severe), semilobar, lobar, and middle interhemispheric variant (less severe). Typical
brain findings include interhemispheric fusion (complete or partial),
monoventricle, and agenesis of the corpus callosum. Common craniofacial
findings in individuals without severe features (such as synophthalmia and a
proboscis) include microcephaly, hypotelorism, depressed nasal bridge, single
maxillary central incisor, and cleft lip and/or palate.

chief events in HPE occur during gastrulation (week 3 of life), as a result of
sonic hedgehog (SHH) signaling defects. One of the key signaling centers
crucial for HPE pathogenesis is at the most anterior portion of the midline
mesoderm, the prechordal plate (PCP). Several signaling molecules, including SHH,
originate in the PCP and trigger a secondary patterning center in the ventral
forebrain. The eye field originates as a continuous structure anterior to and
around the PCP in late gastrulation and its left-right separation is induced by
SHH with the help of two other key factors, SIX3 and RAX. SIX3 and RAX have
anti-BMP and anti-WNT activity and create a zone in the eye field and forebrain
where these signals are neutralized. Mutations in SIX3 cause HPE with

and FGF-8 have an essential role in face development. Structures of the face begin
to form around week 4-5 from various processes around the stomodeal opening: a
single frontonasal prominence at the rostral most part for the face, paired
nasomedial and nasolateral processes, and paired maxillary and mandibular
processes. The frontonasal ectodermal zone in the frontonasal prominence is an
important SHH signaling center in face formation. The nose arises from the bilaterally
symmetrical nasomedial and nasolateral domains, that migrate medially and fuse
in response to FGF signaling as the frontonasal process recedes from the
stomodeum. SHH signaling also allows lateral expansion and later formation of
medial bone structures. This is how the nose forms, with two nostrils separated
by a septum and underneath the eyes. If midline SHH signaling is disrupted, the
frontonasal process fails to recede from the stomodeum and the nasal domains
are no longer separated by intervening medial structures. As a result, the alae
of the nose are juxtaposed to form a tubular appendix without a nasal septum
that localizes above the eyes.

2. A number of organ systems undergo early regionalization
patterning by one set of genes, then later reorganization and differentiation
by another set of genes. Give an example of this.

Gastrulation starts in the third week of
life to give rise to three germinal layers: the ectoderm, mesoderm and
endoderm. Through a series of embryonic induction processes mediated by
discreet groups of genes primordial structures of the embryo develop. Gastrulation
begins with the formation of the primitive streak. At the tip of the streak,
the primitive node (organizer) forms to serve as an important signaling center
in early embryo patterning. Cell of the node express three key markers: Chordin,
Goosecoid and FOXA-2. These factors will determine the establishment of various
embryonic structures including the prechordal plate and the notochord. Influenced
by Goosecoid and FOXA-2, the notochord also produces Noggin and SHH, which are
potent morphogenic factors.

The notochord will
be crucial in determining the axial patterning of the body and defining different
tissues and organ systems. For example, signals originating from the notochord
stimulate the transformation of the overlying surface ectoderm into neural
tissue; transform specific groups of mesodermal cells of the somites into
vertebral bodies; and inhibit cardiac mesoderm specification thereby limiting
the size of the cardiogenic fields.

In early
development of the heart, starting approximately at day 15 of gestation in humans,
cells anterior to the primitive streak are fated to become heart muscle. Agonists
and antagonists of the BMPs, FGF and WNT families of growth factors are
produced by the ectoderm and the endoderm resulting in a unique signal
cross-talk microenvironment that drives cardiac differentiation. Bilateral cardiac
precursor pools unite at the midline, cranial to the oropharyngeal membrane to
form the primary heart field (PHF), which gives rise to the left ventricle and
the atria. A retinoic acid gradient originating in the posterior mesoderm fates
these cells to an atrial identity, whereas the more anterior cells not influenced
by retinoic acid will become the left ventricle. The secondary heart field (SHF),
arising from the pharyngeal mesoderm, localizes adjacent and posterior to the
PHF. The SHF will form the right ventricle, outflow tract and inflow myocardium.

The identity of the PHF is determined by upstream activators NKX2.5 and GATA4,
and that of the SHF is determined by ISL-1 and FOXH-1. In particular, ISL-1 expression
distinguishes the PHF from SHF. These upstream activators regulate a core regulatory
network of transcription factors (MEF2, NKX2, GATA, TBX and Hand) that will coordinate
the differentiation and patterning of the cardiac tissue. Development of the
heart is completed by week 8 to 9.

Heart defects
have an incidence of about 1 in 100 live births, representing the most common
class of congenital malformations. Interfering with the signaling networks
involved in heart specification will result in a number of malformations that
depend on the specific gestational time. For example, mutations in NKX2.5, GATA4,
TBX5 result in atrioventricular septal defects. These defects are expected to originate
late in gestational week 4, which is when the early septum I between the left
and the right atria and the muscular interventricular septum appear. A
condition associated with atrial and ventricular septal defects, as well as
upper limb malformations, is Holt-Oram syndrome, caused by TBX-5 mutations.

3. Induction is a
key process in development.  Describe an
inductive event in development.

Embryonic induction describes the interaction
between inducing and responding tissues that results in molecular and
morphological changes in the responding tissue. Induction drives the
development of various tissues and organs in most animal embryos; for example,
the eye lens, the nervous system and the heart.

The eye is a
complex structure that starts to develop at day 22 of gestation and involves
ectoderm, neural crest cells, and mesenchyme. The major events of eye
development occur between week 3 and week 10. The neural ectoderm gives rise to
the optic nerve, the neural retina, the iris and ciliary body epithelia, the
smooth muscles of the iris, and some of the vitreous humor. The surface
ectoderm gives rise to the lens, the choroid coat and sclera, the conjunctival
and corneal epithelia, the eyelids, and the lacrimal glands. The remaining
ocular structures originate from mesenchyme. Formation of these structures are mediated
by induction processes.

Formation of the
eye lens is a classic example of induction. The eye lens derives from cells in
the prechordal plate and starts forming during late gastrulation in week 3.

Cells in the eye field express RAX and PAX6 as primary factors inducing the
optic vesicle. PAX6 expression in the surface ectoderm allows the underlying
optic vesicle to respond to inductive signals (FGF and BMP) via SOX2, another important
factor. This signals the surface ectoderm to thicken and form the lens placode.

Through VSX2, the optic vesicles are patterned into the future neural retina,
and through MITF and OTX2, into the retinal pigment epithelium. Inductive
interactions between the optic vesicle and the lens placode results in
invagination and formation of the lens vesicle by day 28 and the optic cup by
day 34. Then, the lens vesicle detaches from the surface epithelium and under
the influence of PAX6 and SOX2 primarily, cells in the posterior part of the
lens elongate and differentiate into long, transparent cells called lens fibers.

Here, PAX6-induced FOXE3 plays an essential role in the activation of lens
fiber genes to give rise to the lens crystalline proteins. In future events,
the lens nucleus will form and through successive mitotic divisions and
influences from the retina, of which FGF is a major component, eye lens
development will complete.

            In mammals, disruption of the
apposition of optic vesicles and surface ectoderm interferes with lens
induction, resulting in malformations such as microphthalmia (small eye) or
anophthalmia (absent eye). Mutations in several human genes, including SOX2 and
OTX2 can result in microphthalmia, presumably because the surface ectoderm is
unable to respond to the inductive signals originated in the optic vesicle. Mutations
in the human RAX gene cause anophthalmia
and are usually ascribed to a failure of formation of the optic vesicle.


4. Pleiotropy is
the concept that a mutation in a single gene can cause malformations in multiple
organ systems because those systems use that gene product for their
development.  Describe a malformation
syndrome that illustrates this principle and how the pathway functions in more
than one tissue or organ.

Mutations in the human homologue of the Drosophila eyes absent gene, EYA1, cause
branchio-oto-renal (BOR) syndrome, an autosomal dominant condition mainly characterized
by renal abnormalities, various degrees of hearing loss, structural ear defects,
and branchial fistulas or cysts. To exemplify the concept of pleiotropy in BOR,
the role of EYA1 in kidney and ear
development will be described.

In higher animals,
a network composed of genes belonging to the Pax, Six, Eya and Dach families plays a crucial regulatory role in the development of
multiple structures including the ears, the kidneys, the heart, the placodes
and the pharyngeal pouches, among others. This network is often referred to as
the Pax-Six-Eya-Dach network (PSEDN) and is highly conserved throughout animal
evolution. Eya1 is a key component in this network.

EYA1 is expressed
in different embryonic structures, including the metanephric mesenchyme of the developing
kidney, where it is required for the expression of GDNF, which in turn is
required to orchestrate ureteric bud outgrowth. Eya1 knockout mice show loss of Gdnf
expression. However, EYA1 cannot stimulate Gdnf
transcription by its own, but requires a member of the Six protein family for
nuclear translocation; thus, it is likely that the effect of EYA1 on Gdnf is indirect. Eya1 null mice also show loss of Six1 and Six2 gene expression,
suggesting an EYA–>SIX–>GDNF functional cascade in kidney organogenesis.

In humans, disorders
of the auditory system are usually associated with renal abnormalities when
mutations in EYA genes occur. In
vertebrates, the otic vesicle develops from the otic placode and is marked by high
expression of SIX1 and EYA1, both of which are involved in the pathogenesis of
BOR. Eya1-deficient mice lack ears,
which highlights the importance of this gene in ear formation. Hypomorphic
mutations of the Eya1 gene result in
inner ear abnormalities and hearing problems in both mice and humans. In
addition, EYA1 and SIX1 can induce the putative neurosensory stem cells in the
cochlea (GER cells) to differentiate into hair cells, while EYA1, SIX1 and SOX2
can simultaneously induce GER cells to differentiate into neurons. Therefore, EYA1
(along with SIX1) initiates neuronal precursor differentiation in the inner