User:Mgriggs3/sandbox

=Chick Development= The chick was the original model organism, dating back to the 1600’s. Due to the extensive history, the chick is an ideal organism to study and is now used to study immunology, genetics, virology, cancer, and cell biology.

The chick takes 21 days to hatch after the egg is laid and becomes an adult three months after hatching. Once an adult, they live 8-10 years.

Fertilization and cleavage both take place in the first 24 hours before the egg is laid. Fertilization occurs after the yolk is released from the ovary and cleavage immediately follows fertilization.

Gastrulation takes place after cleavage. It gives rise to the three germ layers. The ectoderm, which is the outer layer, gives rise to the to the skin, epidermis, and tissue that will eventually turn into the nervous system. The mesoderm, middle layer, gives rise to the circulatory system, the kidneys, skeletal compartments, and somites. The endoderm is the inner layer and gives rise to the respiratory system and gastrointestinal tracts. The primitive streak marks the beginning of gastrulation. Convergent extension promotes the elongation of the primitive streak. The anterior region of the streak is referred to as Hensen’s node. The order that cells enter and pass through Hensen’s node will help determine which germ layer they become. At the end of gastrulation, Hensen’s node regresses and the notochord forms.

Neurulation occurs after gastrulation and will form the central nervous system in the chick. The notochord signals stem cells to orient themselves along the dorsal axis of the embryo, which creates the neural plate. The neural plate then elevates itself and forms neural folds. It also will invaginate to form the neural groove. Chick embryos perform both primary and secondary neurulation.

Axis Formation is the establishment of differentiated portions of the embryo. The basis for axis formation has been broken down into three types of axis formation. First, Anterior and Posterior axis formation where the anterior is the head region and the posterior is defined by the lower half of the embryo. Next, is Dorsal and Ventral axis formation where Dorsal is the back side of the embryo and Ventral is the belly side of the embryo. Finally, Right and Left axis formation which is crucial for determining how organs will form such as the heart and gut folds. All of these are established through gene regulation mechanisms and are crucial in the creation of a healthy functional organism.

Lifecycle
Similar to mammals, oogenesis occurs during fetal life and chicks have a lifetime supply of oocytes upon hatching. The oocyte can only become fertilized if the hen has mated recently and occurs after ovulation when the oocyte is released form the ovary to the oviduct. In the roughly 20 hours the oocyte spends in the oviduct, the uterus, its shell is formed. The egg remains in the vagina of the hen until it is laid. When the egg is laid, gastrulation typically begins. The beginning part of development is described by Eyal-Giladi and Kochav in series and the rest of the developmental life cycle of a chick is best described in 46 stages described by Hamburger and Hamilton. The chick takes roughly 21 days to hatch. The chick becomes an adult after 3 months and they live for 8-10 years, the overall cycle can be best seen here.

Fertilization
Fertilization of the chick embryo requires a sperm and the ovum on the yolk.

Yolk
The yolk is primarily consisted of water, protein, fat, and carbohydrates. It provides nutrients to the developing embryo and takes approximently ten days to become 55 g and ready to be releasled from the ovary, into the oviduct, and become fertilized. The ovum is located at the top part of the yolk and is what ultimately becomes fertilized to create the embryo. It is covered by the vitelline membrane.

Ovulation
When the yolk is mature in the ovary, the luteinising hormone creates signals that allows the yolk to be released from the ovary into the oviduct.

Egg formation
The release of the yolk from the ovary begins fertilization and egg formation in the oviduct. The sperm cell travels from the cloaca to the infundibulum of the oviduct to penetrate the egg membrane to create the embryo, beginning as the blastoderm, or germ disc. The albumen layer, which is the egg white containing protein, of the egg is created in the magnum of the oviduct. Once the egg gets to the isthmus, the shell membrane is added to the egg and the final part of the oviduct, the uterus, creates the shell of the egg to give it protection and calcium.

Cleavage
Chick embryos undergo cleavage, in the oviduct, that is discoidal meroblastic, meaning the cell divisions occurring in cytoplasm at the top of the yolk are partial, only occur in the animal pole, and form a disc of cells. The divisions are random between embryos. Tight junctions link five to six cell layers created from equatorial and vertical cleavages together. A space is eventually created between the yolk and blastoderm as blastoderm cells engulf the surrounding albumin to secrete it in the newly formed space, called the subgerminal cavity. Cells that fall into the cavity die and leave the blastoderm to be epithelium that is one to two cells thick and is known as the area pellucida. The outer part of the blastoderm is translucent and is called the area opaca. The space between the two areas is referred to as the marginal zone.

Gastrulation
Gastrulation is critical to all organism’s survival. It turns a multicellular organism into fully functioning organs. It occurs about seven hours after fertilization and begins as soon as cleavage is complete. The blastula, a single layer of cells, doubles over to form two layers. Each of these layers will play a different role in the formation of the embryo. The formation of the primitive streak marks the start of gastrulation by the rearrangement of cells in the epiblast. Mesodermal precursor cells are the origin of the primitive streak. The primitive streak appears when the epiblast begins to thicken. The cells in the posterior 2/3 region of the embryo move in a counter-clockwise motion and converge at the posterior end of the primitive streak. As cells are migrate throughout the embryo, an indention forms called the primitive groove or the blastopore. Convergent extension allows for the elongation of the primitive streak. Once the primitive streak is formed, the embryo then has true anterior-posterior axis. The anterior region of the primitive streak is referred to as Hensen’s node, which functions as the organizer for the cells.

The order that cells enter the blastocoel and migrate through Hensen’s node will determine which of the three germ layers they will become. Cells differentiate and migrate to form the ectoderm, which is the outer layer, the mesoderm, the middle layer, and the endoderm, the inner layer. Ectoderm cells give rise to skin, epidermis, the neural crest and tissue that will eventually form the nervous system. Mesoderm cells will turn into the circulatory system, the kidneys, and skeletal compartments. It will also give rise to somites, which will form muscle, cartilage for the ribs and vertebrae, the dermis, the notochord, blood vessels, and bone for the chick. The endoderm cells give rise to the respiratory and gastrointestinal tracts, such as the liver and pancreas. As the primitive streak begins to descend, Hensen’s node migrates to the posterior region. This will eventually form the anus of the chick. As a result of the anterior-posterior division, cells progress through the stages at different rates. Typically, the anterior region is more advanced than the posterior. The mesoderm and endoderm cells migrate inward and surround the yolk by epiboly. No true archenteron is formed during chick gastrulation. As gastrulation comes to an end, Hensen’s node begins to regress and leaves behind the notochord and the ectoderm cells finally migrate and surround the yolk.

Neurulation
Neurulation is the formation of the central nervous system and the development of the neural tube in the ectoderm. Once the notochord has been formed during late gastrulation, signals are sent to stimulate stem cells in the embryo of the chick. This causes the stem cells to orient themselves along the dorsal axis of the chick, which creates the neural plate. The neural plate elevates itself, which forms neural folds. Then invagination of the neural plate creates the neural groove. Before the neural groove completely closes, a group of cells called the neural crest form above the tube. The neural crest contributes to the formation of cranial nerve ganglia and skeleton in the skull. There are two types of neurulation, primary and secondary. Primary neurulation is when neuro-plate cells are directed to be proliferated, invaginated, and pinched off to form a hollow tube. This occurs when the neural groove, which is located in the ectoderm, closes to form the neural tube in the anterior region. The dorsal region of the neural tube is formed by bends in the neural plate and fusion of neural folds. As the neural tube closes, it creates the midbrain, forebrain, and hindbrain vesicles. The forebrain will give rise to cerebral hemispheres and optic vesicles. The midbrain will later form the optic receptors for optic nerves and the hindbrain will form the cerebellum and the medulla. Secondary neurulation is when the neural tube is produced by a solid cord of cells that sink into the embryo to form a hollow tube. Like most organisms, chicks perform both primary and secondary neurulation. The anterior portion of the neural tube is formed by primary neurulation. Everything that is posterior to the hind-limbs are made by secondary neurulation. The remainder of the neural tube will form the spinal cord.

Axis formation
Axis formation is the determining of the different portions of the embryo that is detrimental in the developmental process because without this axis formation the embryo would not be successful. Genes are the establishers and determinants of axis formation. There are multiple different mechanisms utilized to control these gene gradients. From gap junction communication, movement of cytoplasm to move a gene to one side of the embryo, activating and inhibiting proteins, and Henson’s node in the case of the chicken. For the simplest explanation of how these are created and maintained is that specific genes are expressed in certain parts of the embryo and usually inhibit the opposite sides expression to maintain these genetic gradients.

Anterior/Posterior formation:
In chicken axis formation Dorsal and Ventral formation is closely related to Anterior and Posterior due to the disc embryo design that causes much overlap in these two cycles. The original step in these two axis formations is the centrifugation of the egg as it travels down the reproductive tract. This causes the proteins to be moved to appropriate locations in the embryo. The Posterior end of the embryo is highly expressed with bone morphogenetic protein (BMP) and B-Catenin coming from the posterior marginal zone (PMZ) in the vegetal pole of the embryo establishing the organizer. The next steps in anterior and posterior axis formation can be broken down into three steps.

First, in chicken embryos, there is the use of Hensen’s node, which is their organizer.[3] Hensen’s node is in high concentration of anterior expression gene noggin.[3]  Hensen’s node begins at the most anterior part of the embryo and then moves down the notochord of the embryo to the posterior end of the embryo while, establishing the head and somites as it moves down as well as leaving behind a trail of gene expression.[2][3] These gene gradients that are established are detrimental in creation of axis formation.

The next step in anterior/posterior formation is when Smad1 comes in by upregulation through BMP binding bone morphogenetic protein receptor, type IA (BMPR1A) and bone morphogenetic protein receptor type II (BMPR2) and then creates Smad1.[3]  While this is happening, BMP is being repressed by Noggin while Noggin is repressing BMP, with Noggin being highly expressed in the anterior and BMP being highly expressed in the posterior.[3]  While they both inhibit each other from being expressed on the wrong side.[3]

In the final step of anterior and posterior axis formation, a signaling pathway is creating concentration gradients that have retinoic acid (RA) and fibroblast growth factor 4 (FGF4) both expressing posterior strongly.[1][3]  While cytochrome P450 family 26 (cyp26) is the prominent anterior gene.[1][3]

Left/Right axis formation:
In left and right axis formation of chick embryos there is a movement of proteins by cell gap junctions that signal for an intercellular current.[1]  This moves pituitary homeobox 2 (PitX2) to the left as well as Cerberus and Nodal that establish the heart and gut folds.[3] While, fibroblast growth factor 8 (FGF8) is found to be the determinate of the right side because it suppresses all three of the left side proteins.[1] [3]

Advantages
The chick was the first organism used to study development. The long history of studying the chick is an advantage because it was the only focus for so long so a lot of time and research was spent on understanding it. Other advantages include:
 * Cheap
 * Easy to make room for
 * Availability
 * Resembles human embryo at anatomical, molecular and cellular levels
 * External development allows for accessibility at all stages
 * Cutting a small hole in the shells allows for manipulation in ovo
 * Advanced embryos can be used to transfer small pieces of tissue onto the chorioallantoic membrane
 * Culture of some undeveloped or immature parts of organs is possible in vitro
 * Useful in medicine, agriculture, and biology
 * Technological advancements in the last twenty years has brought back the use of the chick as a model organism to study in vivo electroporation, embryonic stem cells and create a draft of their genome sequence

Disadvantages
Despite all of the advantages, chicks also have disadvantages as a model system that include:
 * Poor use for genetic work


 * Long life cycle


 * Take up a lot of space once they hatch[2]


 * Unable to successfully establish genetic modified chicken lines


 * Different compositions of amniotic fluid and blood compared to humans and that can alter things in development and make them hard to use as research for humans


 * Transgenesis and targeted mutagenesis do not have a routine protocol

Life cycle
A chick takes 21 days to hatch and roughly three months to become an adult and the overall cycle can be best seen here. Similar to mammals, oogenesis occurs during fetal life and chicks have a lifetime supply of oocytes upon hatching. The oocyte becomes fertilized if the hen has mated recently, after ovulation when the oocyte is released form the ovary to the oviduct. In the roughly 20 hours the oocyte spends in the oviduct, uterus, its shell is formed. The egg remains in the vagina of the hen until it is laid. When the egg is laid, gastrulation typically begins. The beginning part of development is described by Eyal-Giladi and Kochav in series and the rest of the developmental life cycle of a chick is best described in 46 stages described by Hamburger and Hamilton. The chick takes roughly 21 days to hatch.The chick becomes an adult after 3 months and they live for 8-10 years, the overall cycle can be best seen here.

Advantages/disadvantages as a model system
The chick was the first organism used to study development. The long history of studying the chick is an advantage because it was the only focus for so long so a lot of time and research was spent on understanding it. Other advantages include: Despite all of the advantages, chicks also have disadvantages as a model system that include:
 * Cheap
 * Easy to make room for
 * Availability
 * Resembles human embryo at anatomical, molecular and cellular levels
 * External development allows for accessibility at all stages
 * Cutting a small hole in the shells allows for manipulation in ovo
 * Advanced embryos can be used to transfer small pieces of tissue onto the chorioallantoic membrane
 * Culture of some undeveloped or immature parts of organs is possible in vitro
 * Poor use for genetic work
 * Long life cycle
 * Take up a lot of space once they hatch
 * Unable to successfully establish genetic modified chicken lines
 * Different compositions of amniotic fluid and blood compared to humans and that can alter things in development and make them hard to use as research for humans
 * Transgenesis and targeted mutagenesis do not have a routine protocol

Article evaluation
Article: embryogenesis

Observations and notes:
 * Intro was bare and short- missed opportunity
 * Fertilization is short and lacking
 * Cleavage is more in depth and the picture helps
 * Gastrulation?
 * Formation of blastula- choppy and has a heavy focus on mammals
 * Formation of gastrula- choppy, begins talking about multiple different organism possibilities and then focuses on mammals, need to explain gastrulation
 * Somitogenesis- where does this fit in exactly?
 * Organogenesis- looks like an incomplete draft with unsure content.
 * References- don't work and where are the rest?

Answers to questions:
 * Is everything in the article relevant to the article topic? Is there anything that distracted you?
 * Overall, it all ties back to embryogenesis. However, it is very jumpy and uses many organisms to explain the various topics. The inconsistency and lack of flow distracted me from the overall article and main points.
 * Is the article neutral? Are there any claims, or frames, that appear heavily biased toward a particular position?
 * The article remains neutral and does not swing one way or another. It just lays out the facts.
 * Are there viewpoints that are overrepresented, or underrepresented?
 * Fertilization and gastrulation are both lacking detail and missed opportunities to go further in depth about the processes. Cleavage is very in depth and well written but does not balance out with the other sections and includes a lot more information in comparison.
 * Check a few citations. Do the links work? Does the source support the claims in the article?
 * None of the citations work. Two of them wouldn't load, one went to the Verizons page and the other went to yahoos home screen.
 * Is each fact referenced with an appropriate, reliable reference? Where does the information come from? Are these neutral sources? If biased, is that bias noted?
 * A majority of the information on the page was not referenced at all. There is only a total of four references cited and that does not seem like near enough to back up all the information on that page. Since none of the links work, it is hard to tell based off of the citations if the references are even reliable.
 * Is any information out of date? Is anything missing that could be added?
 * The information appeared to be relevant and up to date, but, again, without properly working citations, it is hard to judge how accurate and relevant the information is. Fertilization and gastrulation are definitely rooms for improvement. They are overall short sections and there is definitely far more detail out there on both subjects that could be incorporated into this page.
 * Check out the Talk page of the article. What kinds of conversations, if any, are going on behind the scenes about how to represent this topic?
 * The most helpful discussion was about renaming it mammalian embryogenesis and focusing the article strictly on that since that seemed to be the most common theme in the article. There was also a discussion about adding an image to a subsection to help the visualization, which was insightful. There was a discussion about a spelling error and a discussion about being GA nominated and the ays it fell short of the nomination.
 * How is the article rated? Is it a part of any WikiProjects?
 * It is part of three wikiprojects: biology (rated start-class, mid-importance), physiology (rated start-class, high-importance), and anatomy (rated C-class, high-importance).
 * How does the way Wikipedia discusses this topic differ from the way we've talked about it in class?
 * For the most part, this article focused on embryogenesis in mammals and we have only really discussed model organisms up to this point. We have also incorporated cell signaling into our discussions in class and how they effect development and this article was missing that.