Final Exam - Developmental Bio

amniotes

A group of vertebrates that lay eggs on land or maintain embryos within the mother, including reptiles, birds, and mammals. Amniotes are characterized by having an amniotic egg, which provides a protective environment for the developing embryo.

amnion

A membrane that surrounds and protects the developing embryo within the amniotic egg, filled with amniotic fluid.

hypoblast

The layer of cells located beneath the epiblast in early embryonic development, contributing to the formation of extraembryonic structures and the definitive endoderm.

epiblast

single layer epithelium in amniote embryos that give rise to all tissues of the embryo proper through gastrulation

Koller’s sickle

crucial organizer in early bird development (gastrulation) where the primitive streak forms

Primitive streak

The structure that forms during gastrulation in embryonic development, marking the beginning of the body plan and establishing the three germ layers.

Hensen’s node

The organizing center at the anterior end of the primitive streak during gastrulation, essential for axial patterning and development of the notochord.

key organizer in early chick embryo

Polar bodies

small, haploid cells formed during oogenesis

zona pellucida

extracellular matrix surrounding eggs and early embryos

crucial role in initial gamete recognition

prevents polyspermy

protects embryo during its journey through the oviduct before implantation

morula

solid ball of cells formed early in embryonic development, typically around 3-4 days after fertilization

blastocyst

a hollow ball of cells formed from the morula, consisting of an inner cell mass that will develop into the embryo and an outer layer called the trophoblast that contributes to the placenta.

trophoblast

layer of tissue on the outside of a mammalian blastula, supplying the embryo with nourishment and forms major part of the placenta

syncytiotrophoblast vs. cytotrophoblast

syncytiotrophoblast is the outer layer of the trophoblast that invades the uterine lining and facilitates implantation, while cytotrophoblast is the inner layer that provides mononucleated cells for growth and development of the placenta.

chorionic villi

finger-like projections forming the outer layer of the developing embryo and grows into the placenta

inner cell mass

embryoblast

cluster of cells within the blastocyst that develops into the embryo and some extra-embryonic tissues

morphogenesis

biological process that causes a cell, tissue, or organism to develop its shape

holeoblastic clevage

an entire zygote undergoes division, resulting in a complete cleavage of the egg cytoplasm into smaller cells (blastomeres)

meroblastic clevage

incomplete or partial division of the egg cell

generally occurs in fertilized eggs that contain a greater quantity of yolk

telolecithal vs. centrolecithal discoidal cleavage

Telolecithal cleavage involves uneven yolk distribution leading to a discoidal pattern of division, while centrolecithal cleavage occurs in eggs with yolk concentrated in the center, resulting in partial cleavage around the yolk.

Describe how the developing embryo is implanted in the endometrium.

sperm → egg = fertilization and blastocyst are formed, goes towards uterus to implant

after 5 days, blastocyst reaches uterus and created inner cell mass (which becomes embryo) and trophoblast (which will become placenta)

blastocyst creates enzymes to break down cells of endometrium to adhere to it

trophoblast invades deeper, creating syncytiotrophoblast and cytotrophoblast, and then eventually creating the placenta

placenta then creates blood vessels and secretes human chorionic gondadotropin hormone

How does a chorionic villi sample work?

prenatal test used to detect genetic abnormalities in developing fetus by taking a small sample of the chorionic villi from the placenta, which contains fetal DNA. The sample is then analyzed for chromosomal abnormalities or genetic disorders.

testing includes karyotyping and genetic testing

Outline how a chicken egg develops in the oviduct of the hen

yolk → formed in ovary

yolk released from ovary into oviduct

enters magnum where albumen begins to form

then enters isthmus, where inner and outer shell membranes form around the egg white

then the egg enters the uterus, where calcium carbonate is deposited to form the hard eggshell

before the egg is laid, a bloom is applied, then the egg is laid

Identify the different extraembryonic membranes

amnion - protective membrane that holds amniotic fluid and cushions the embryo

chorion - outer membrane that assist with gas exchange and contributes to the placenta

allantois - involved in waste storage, gas exchange, and formation of umbilical cord

yolk sac - provides nutrients to the embryo early in development

nest cells

cluster of cells within organs or tissues

primordial germ cell

initial precursors of gametes during embryonic development

germinal vesicle

large, visible nucleus of a primary oocyte before it has completed its first meiotic division

vitelline envelope

protective, acellular layer surrounding the egg

follicle cells

specialized cells primarily found in the thyroid gland and in the ovaries

lampbrush chromosomes

large, looped structures formed by the uncoiling of chromatin in certain oocytes during diplotene stage of meiosis, allowing for active transcription.

Nieuwkoop center

organized gastrulation

a lot of vegetation region that had inducing factors to develop mesoderm

Explain how sperm entry sets up the anterior and posterior axis’s

sperm entry → cortical rotation, which re-localizes maternal determinants, and marks the posterior end of the embryo

cortical rotation → relocation of maternal determinants

• proteins and RNA molecules that were initially distributed asymmetrically in the egg’s cytoplasm

• formation of gradient of signaling molecules that defines anterior and posterior ends

once sperm enter eggs, markers and molecular signals initiate stabilization of embryo axes

• posterior markers include Vg1 and beta-catenin

• anterior markers are relatively unmarked

Identify and explain the genes involved in the dorsal/ventral axis formation.

Cortical rotation - triggered by sperm entry, plays crucial role in setting up axis by redistributing maternal determinants within the egg

Wnt/beta-catenin - central pathway involved in determination of the dorsal side of the embryo

TGF-beta - plays critical role in establishing the D/V axis

Nodal - secreted factor that is crucial for establishing the dorsal side of the embryo

BMP4 - key factor in formation of ventral region of the embryo

Chordin - antagonist that is highly expressed on the dorsal side of the embryo

Noggin - binds to BMPs and prevents ventralizing effects

Outline how the germinal vesicle becomes an egg.

• Primary oocytes will become follicle cells 

• One of the 16 will become egg 

  • Other eggs surround it 

• Focusing on one cell of nest and becomes an oocyte 

• Starts meiotic prophase 

  • Long prophase (2 weeks) 

  • Multiple nucleoli 

    • Sub structure of nucleus 

    • Ribosomes are assembled here 

      • Make proteins 

• Lampbrush chromosomes 

  • Bigger chromosome 

  • Region of chromosome is amplified and makes a lot of RNA 

• Getting a lot of nutrients becoming the yolk 

• Follicle cells contribute to proteins becoming the yolk 

• Cell will become germinal vesicle 

• Protein being produced called vitellogenin 

  • Made by mom’s live

• Hormones from pituitary gland will produce progesterone 

  • Gonadotropin 

• Signal for egg (diploid) to cause breakdown of the nucleus and go into meiosis 1 

  • Produces polar body 

• Ready for meiosis 2 but it needs to fertilize in order to unfreeze 

• Now the frog can put the egg in the water 

• In order to release eggs, the male must “massage” the female frog 

  • Amplexus 

• Male frog can release sperm right away 

• Laying eggs in the water = spawning 

• Cytostatic-factor 

  • Can’t move the egg 

  • X- Emi2

    • Rest the oocyte in meiosis 1 

  • Mos 

    • Allows entry of meiosis 2

    • Quick release of calcium 

• 30 degree rotation once it enters meiosis 2 

• Helps set up dorsal and ventral sides 

• If it stayed in meiosis 1, it would be radial symmetry, but if it rotates, then it is bilateral symmetry (different types of cleavage)

• Sets up anterior and posterior

hemimetabolous

having no pupal stage in the transition from larva to adult

holometabolous

insects that undergo complete metamorphosis

imago

adult fly

hypocotyl

part of the stem of an embryo plant beneath the stalks of the seed leaves and directly above the root

apomictic development

a form of asexual reproduction in plants where seeds are produced without fertilization.

molting

exoskeleton removed

corpora allata

endocrine glands near or attached to the brain

releases juvenile hormone

juvenile hormone (PTTH)

secreted from the brain

stimulates the prothoracic glands to produce ecdysone

ecdysone

hormone that triggers molting

imaginal disc

what takes larvae to imago

A tadpole is given Thyroxine. What will happen to the tadpole?

Stimulate pituitary gland 

Stimulates TSH 

Produce T4 and T3 

Increase in thyroxine as they proceed to develop 

We have thyroid T4 and T3 being released from the thyroid hormone 

Stimulates hypothalamus

Once it reaches climax, then it is blocked and is no longer self regulating

Explain the hormonal control for metamorphosis in insects. Include the organ(s) responsible for the synthesis of the hormone(s).

Ecdysone - primary hormone responsible for triggering molting and initiation of metamorphosis by binding to ecdysone receptors in insect’s epidermis; they rise as insect approaches time to molt; also regulates pupation

• Prothoracic gland and corpora allata are primary organs secreting this to the brain and other regulatory factors

Juvenile hormone - regulates larval stage and prevents insect from prematurely undergoing metamorphosis into its adult form; controls timing of when an insect will complete its final molt and transition from larval stage into pupal or adult stage

Explain the hormonal control for metamorphosis in frogs. Include the organ(s) responsible for the synthesis of the hormone(s).

Thyroid hormones, primarily thyroxine (T4), control metamorphosis in frogs by stimulating growth and transformation from tadpole to adult form. The thyroid gland is responsible for synthesizing these hormones, which trigger developmental changes.

ecdysone activates transcription of genes. List three of these genes.

BR-C - encodes for a family of zinc finger transcription factors

E74 - encodes for an ETS-domain transcription factor

E75 - encodes for a novel site-specific DNA binding protein

Be able to identify the imaginal disc and the body parts Drosophila become during pupation.

Describe how frog leg segmentation is formed, include genes/proteins

During frog development, leg segmentation is regulated by the expression of specific genes such as Hox genes, which provide positional information along the body axis. Proteins like FGF and Wnt are involved in the patterning and formation of the limb mesoderm, guiding the development of distinct leg segments.

Explain how the different organ systems change in the frog during metamorphosis.

Gills to lungs 

Movement changes

Herbivore to carnivore 

Gut is very lengthy, becomes more compact

Movement of the eyes changes

Vision gets developed 

• More terrestrial eye 

Nitrogen excretion 

• Ammonia (gas) to urea (liquid) 

Skin needs to go from thin to thick and have mucous glands 

instar

developmental stage in arthropods that occurs between 2 successive molts

larva

active immature form of an insect

pupa

insect undergoes complete metamorphosis

ovariole

basic unit of an insect ovary

tubular structure where eggs develop

Drosophila has 2 ovaries

germarium

anterior or front portion of an ovariole where germ cells are produced

vitellarium

modified part of the ovary that flatworms and rotifers produce yolk-filled cells serving to nourish eggs

nurse cells

specialized cells that support the development of other cells, especially in the reproductive process

follicle cells

specialized cells found in the thyroid gland

pole cells

specialized cells in early insect and vertebrae embryos giving rise to germ cells

maternal vs. zygotic genes (examples and definitions)

maternal genes are genes whose produces are produced/deposited in the oocyte and are present in the fertilized egg/embryo before the embryo’s own genes start expressing. examples include mitochondrial DNA

zygotic genes are genes expressed in the early embryo, marking as transition from relying on maternal genetic information to the embryo’s own genome. examples include nanos and Bicoid.

gap genes (examples and definition)

gap genes are a group of segmented genes in early embryonic development that, when mutated, cause the loss of multiple contagious segments, creating gaps in the embryo’s body plan

examples include hunchback, knirps, and Krüppel

pair rule genes (examples and definitions)

the first genes to be expressed in periodic patterns in Drosophila embryo

examples include hairy, even-skipped, runt, and fushi-tarazu

segment polarity genes (examples and definition)

segment polarity genes are in Drosophila, and are crucial for defining/maintaining the internal structure of each segment in the developing embryo

examples include engrailed, wingless, hedgehog, and gooseberry

selector genes

class of genes (Hox usually) that regulate the expression of other genes, which ultimately determine the identity and development of body parts, tissues and cell types

they act as master regulators

Explain the progressional stages of Drosophila egg development starting in the germarium

starts in the germarium at the anterior end of the ovarian follicle → germline stem cells give rise to cystoblasts → oocyte selected and cyst is formed → axis specification (bicoid and nanos) → egg chamber forms → chorion formation and maturation of the egg → egg laid by the female

Identify what determines patterning in Drosophila-include all genes/proteins.

Maternal proteins: bicoid, nanos/hunchback - caudal 

• Important for setting up axis of developing embryo

• Before egg

• Zygote 

Zygotic (gap): krüppel, hunchback, giant, abdomen, thorax 

Pair rule genes: hairy, even skipped, rant 

• Segmentation of the developing fetus 

• 7 segments 

Segment polarity: engrailed, wingless

• 14 segments 

• Boundaries of segments (anterior and posterior)

Hox genes: antennapedia, bithorax, etc.

Identify the genes for anterior/posterior and dorsal/ventral axis

anterior/posterior:

• bicoid

• nanos

• caudal

• hunchback

• kruppel

• giant

• knirps

• even-skipped

• fushi tarazu

• runt

• engrailed

• wingless

• hedgehog

• antennapedia

dorsal/ventral:

• gurken

• toll receptor pathway

• spätzle

• dorsal protein

• twist

• snail

• rhomboid

Toll receptor is used for dorsal-ventral axis. Outline the interactions of proteins/genes in the ultimate activation of twist and snail.

Fragment binds to TOLL - receptor 

Toll receptors are in cancers and development 

Activate Tube and Pelle to activate Cactus and phosphorylate cactus

Allows dorsal to be removed after phosphorylation 

Cactus goes into nucleus 

Twist and snail gets stimulated and represses Zen 

Involved in expression of the mesoderm 

Helps set up vaso dorsal segment 

• Moves to the side 

Ultimately homeotic genes are expressed to give specific segment identity (head, thorax, abdomen). Discuss how they are regulated/expressed.

Homeotic genes, such as the Hox genes, are regulated by a combination of maternal and zygotic proteins that establish segmental boundaries and identities. They respond to gradients of transcription factors, including the anterior-posterior and dorsal-ventral gradients, influencing the activation or repression of specific genes to determine the fate of each segment in the developing embryo.

In the diagram below, put these genes Biocoid, Dorsal, wingless, kruppel, fushi tarazu, antennapedia , engrailed, nanos, even paired, hunchback (gene expressed) in order of expression for the development of the Drosophila larva. Label the diagram for where you would see pair-rule genes, homeotic genes, gap genes, segment-polarity genes and maternal effect genes (gene types)

a. bicoid

b. gap genes

• hunchback

c. pair rule genes

• even-skipped

• fushi tarazu

d. segmentation genes

• wingless

e. selector genes

• abdominal-A

For the germline tissue below, what final tissue do they develop into…

endoderm

mesoderm

ectoderm

Endoderm develops into gastrointestinal tract and organs, mesoderm into muscles and circulatory system, ectoderm into skin and nervous system.

The eve strip results from a specific region of the even-skipped promoter. The promoter has binding sites for the activators (bicoid and hunchback) and repressors (giant, kruppel). The eve promoter DNA can drive expression in the strip pattern when fused to a reporter gene. Explain How and Why the pattern of the eve-reporter gene would change if the Kruppel binding sites in the promoter were removed.

Removing the Kruppel binding sites would allow the eve promoter to be less inhibited by Kruppel, potentially leading to increased expression of the eve gene in areas where it was previously repressed. This could result in a broader pattern of expression for the eve-reporter gene, as Kruppel acts as a repressor in specific regions, thus defining the spatial pattern of the eve stripe.

sHH, wnt and BMB proteins are involved in many areas of development, and we heard about them in multiple organ developments. What are they and what do they do?

sHH - sHH - Sonic hedgehog protein that regulates cell growth and differentiation during limb and brain development.
wnt - A group of signal proteins that play important roles in regulating embryonic development, cell proliferation, and tissue regeneration.
BMB - Bone morphogenetic proteins crucial for bone development and involved in the regulation of embryonic development.

telomere

protective DNA-protein structures found at the ends of chromosomes in eukaryotic cells

proteostasis

process by which cells maintain a healthy balance of proteins to ensure proper folding, functioning, and degradation of proteins.

proteosome

large, multiprotein complex responsible for degrading proteins within cells, primarily those marked for destruction by ubiquitin.

epigenetic

study of how the environment and other factors can influence gene expression without altering the underlying DNA sequence

mTOR

protein synthesis

inhibit and increased lifespan in mice

ROS

molecules produced during normal cellular metabolism, serving as important signaling molecules that regulate various cellular processes, like cell growth, differentiation, and immune responses

cellular senescence

• stress/accumulation of damage over time causes cells to enter a state called cellular senescence 

• Also accumulate during the normal aging process in both humans and mice 

• Hayflick

parabiosis

in 2000 at Standford, scientists paired 2 mice, one old and one young. they peeled back their skin and stitched them together. they saw rejuvenation of muscles and livers in the older mice

other studies looked at the brain and mice improved on cognitive tasks and grew new neurons

deteriorated autophagy

• Autophagy is recycling system in human cells

  • Body’s way of breaking down unwanted and diseased cell components and recycling them elsewhere 

• Evidence that stimulating autophagy increases lifespan and longevity in model organisms, highlighting importance of autophagy in the aging process

dysbiosis

• Microbiome of older people is less complex and characterized by the presence of more pathogenic bacteria 

• Transferring gut microbiome from young to middle-aged fish was sufficient to increase their lifespa

Aging is an ongoing process. Summarize each of the twelve phenomena that contribute/causes aging.

• Genomic instability 

  • DNA damage and mutation 

  • environmental factors

    • Radiation 

  • External factors

    • Drugs 

  • Can ionize 

  • Can affect the lipid structure as well

    • Mitochondria 

      • Reactive oxygen species 

  • Errors in DNA replication 

  • Antitumor drugs 

  • UV-light chemicals 

  • Hydrolysis 

  • Replication errors 

• Telomere degradation 

  • Get shorter as we age 

  • Cancer cells have longer telomeres

    • Stem cell like

  • Doesn’t contain any genes 

  • Starts to get damaged as DNA loses telomeric sequences

• Loss of proteostasis 

  • Accumulation of damaged and non-functional proteins

  • Misfolded proteins can clump together to form aggregates

    • Alzheimers and parkinsons 

  • Improved protein turnover through activation of the proteasome or autophagy 

    • Longer lifespan 

• Epigenetic changes

  • Changes in the modification of histones

  • Shown to affect lifespan of yeast, worms, and flies, suggesting that that the epigenome may not serve as a biomarker but also play a causal role in the aging process

  • DNA modification

  • Non-coding RNA 

  • Imprinting 

  • Histone modification 

• Impaired perception of nutrients 

  • Dietary restrictions (DR)

  • Insulin and mTOR pathway form a central nutrient-sensing network within the cell, which has also been linked to the beneficial effects of DR

• Mitochondria dysfunction 

  • Main source of reactive oxygen species 

    • Produced as a byproduct of mitochondrial respiration

  • Increased levels of ROS may even be beneficial, activating cellular defense and repair mechanisms 

• Cellular senescence 

  • stress/accumulation of damage over time causes cells to enter a state called cellular senescence 

  • Also accumulate during the normal aging process in both humans and mice 

  • Hayflick 

• Exhaustion of Stem cells

  • Injecting blood plasma from young mice to old mice improves stem cell function in the old animals 

• Altered intercellular communication 

  • Hormone, cytokines, metabolic products 

• Prabiosis 

  • in 2000 at Standford, scientists paired 2 mice, one old and one young. they peeled back their skin and stitched them together. they saw rejuvenation of muscles and livers in the older mice

• Deteriorated autophagy 

  • Autophagy is recycling system in human cells

    • Body’s way of breaking down unwanted and diseased cell components and recycling them elsewhere 

  • Evidence that stimulating autophagy increases lifespan and longevity in model organisms, highlighting importance of autophagy in the aging process 

• Chronic inflammation 

  • Often occurs in aging tissues in low levels 

  • Causes tissue damage and being implicated in the development of age-related diseases such as obesity and type 2 diabetes

  • Targeting inflammatory pathways in mice has been shown to rejuvenate tissues and improve lifespan 

• Imbalance of intestinal floral

  • Dysbiosis 

  • Microbiome of older people is less complex and characterized by the presence of more pathogenic bacteria 

  • Transferring gut microbiome from young to middle-aged fish was sufficient to increase their lifespan

Some older men take testosterone. What are the benefits of taking testosterone to combat aging?

improvements in sexual function, better mood overall, better muscle contractions, better fat distribution, higher sperm production