creating+a+plan+for+the+body

Creating a Body Plan by Matthew Bogen, Rachael Judson, Christine Muise

**There** are genes in the body that control the where certain cells form, and they act as an on and off switch for other cells' genes. Pattern formation is a basic example. These genes are able to use spatial organization to form a body of everything from a fly to a mouse to a human being.

**Fate maps** are a way to track cells as they become more specialized in the body. A German scientist Walther Vogt used this to form the foundation of how germ layers lead to different specialized parts of the body and there use in the embryo. The use of //C. Elegans//, in research has allowed scientists to draw a fate map for a fully formed nematode. Because of the relatively small size and amount of cells - 959 - scientists are able to watch the cells form and track them, allowing a better understanding of specialized tissue formation. It helps show the loss of cells' ability to be totipontent, or specialize into any kind of cell.(11)

Fate Map for C. Elegans, a nematod.

**Cell signaling** and its importance in embryogenesis: **The Extracellular Matrix** (ECM) guides cells in morphogenesis by aiding in their migration through the embryo. Dually, it also inhibits certain movements in order to direct cells where they are supposed to be. The ECM, made up of glycoproteins, allows for cell movement in animals. By contrast, plant embryonic cells do not move around in a comparable manner during development.(11)

By way of an example, the glycoprotein fibronectin is used by frogs to cause cells to involute, or move inwards. There is constant signaling between cells, the ECM, and other cells by way of signaling molecules that cause a cell to change its cytoskeleton to movement. Signal pathways also have a major impact. Local signals and use of proteins and steroids made by the genes that are active or mRNA given to the to the zygote when the mother first made the egg or was in the sperm.(11)


 * Morphogenesis** is the process by which an organism forms all the tissues, organs, and differentiated cells that make up an organism. It not only involves the //shaping// of cells but also the //movement// of them. One particular type of change, convergent extension, is where cells will become longer and thinner. It does this by manipulating its cytoskeleton. (11) Genes, once expressed, effect their embryonic environment in one of two ways. In one case, nearby cells will react simply as a result to an expressed gene's product. in the second case, the product will establish a concentration gradient along a segment of the developing embryo, and cells along the embryo will react differently, based on the concentration in their immediate environment. Substances that do this are called **morphogens**. (11)

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A look at the in depth world of Axis formation in a fly.

**Homeobox Genes** are a group of related genes that determine the basic structure and orientation of an organism. (1) These genes are important to the placement of segments of a developing embryo, such as legs developing in the proper area. (6) All Hox genes contain a homeobox, a sequence of DNA containing 180 nucleotides that code the homeodomain, which is a sixty amino acids long polypeptide. The homeodomain is often found in transcription factors because it binds DNA and/or RNA. Hox genes are mostly found together on the chromosome, and are found in this cluster in the order of the expression pattern on the organism’s head-tail axis. Hox genes produce transcription factors called Hox proteins. These proteins act as transcription factor, what activates or represses a gene or series of genes. These proteins are classified into groups by the section of the body they represent. A simple look at Hox genes in a forming mouse


 * Egg polarity genes,** otherwise known as Maternal Effect genes, are determined by the mother's implantation of mRNA into the egg. This creates creates poles called the animal pole and vegetal pole in most animals. In some species, the force of gravity decides the orientation of these poles. In addition, the pH dec the dorsal and ventral poles. In mammals, however, the axis are not defined until cleavage. It is now believed that the orientation of the oocyte and spermatozoa has an affect on the axes of the zygote.(11)


 * Segmentation genes** direct the formation of of segments after the definition of the major axes.(11) They are the genes involved in the early stages of pattern formation in an embryo. These genes are classified as either gap genes, pair-rule genes, or segment polarity genes. (6) Segment Polarity genes define the anterior and posterior polarities in segments within a developing embryo, and are responsible for these polarities in the embryonic segments. Segment Polarity Genes are expressed after Pair-rule genes.


 * Gap genes** map out the subdivisions along the anterior-posterior axis after the segmentation genes have activated.(11)They are segmentation genes that express the formation of gaps in the normal pattern of embryo structure. (6) These genes are the first of the zygotic genes activated in fertilization.

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 * Pair-rule** genes determine the modular pattern.(11) Pair-rule genes are segmentation genes that subdivide the embryo of an organism and set the boundaries of segments. (6) Pair-rule genes also regulate the expression of segment polarity genes. Pair-rule genes are expressed next to the gap genes and before segment polarity genes. The products of gap genes and maternal genes activate pair-rule genes. ======

. This picture shows the genes effect the body plan of of a Fruit Fly.


 * Primitive Knot**: Known as Spemann’s Organizer in Amphibians and Hensen’s Node in Birds, the primitive knot induces other cells to respond to its signals. It's located at the dorsal lip in amphibians. The knot directs the formation of the notochord. (11 and 7)

It was first recognized in 1924 when Hans Spemann and Hilde Mangold transplanted a tissue, called the gray crescent, from one newt embryo onto another. They found that not only did the transplanted tissue lead to a second notochord and related structures around it, but it caused the //recipient// embryo’s cells to form them. (11)

Spemann's Experiment. The dorsal lip was transplanted onto the ventral side of another embryo, and a second notochord and neural tube developed from the site, built by //recipient// cells.

The **Apical Ectodermal Ridge** (AER) is a region at the tip of developing limb buds. It producers **fibroblast growth factors** (FGF), proteins that signal for limb bud outgrowth. The FGF proteins are what cause the bud to continue growing outwards during development.(11 and 10)

Although the subject still requires further research, numerous genes and proteins have been shown to direct identity and placement within the body. Along the **Anterior-Posterior** (AP) axis, **Sonic Hedgehog homolog** (Shh), **Bone Morphogenetic Protein** (BMP), **T-Box transcription factors** (Tbx), and **Noggin** transcription have significant roles in determining the identity of each digit. This is true from the beginning of a developing limb bud, all the way through final determination.(10)

Shh is expressed in **Zones of Polarizing Activity** (ZPA), which is on the posterior side of limb buds. (In pictures, posterior is on the bottom, while anterior is on the top) Scientists have transplanted ZPAs from other limb buds onto anterior sides, and the result is typically a mirror image: The two “hands” will be joined together at the animal equivalent to thumbs. Meanwhile, fingers will develop on //both sides// of the limb buds. In experiments where the ZPA was removed but Shh was added, the limb bud developed normally, showing that Shh is a positional cue for the cells around it.(11 and 10)




 * Sonic the Hedgehog (Shh)** gene is an segmentation gene that produces a protein growth factor. The Shh protein creates a gradient, with a high concentration in the posterior and no concentration in the anterior. In addition to its role in developing limbs, Shh helps direct the formation of the neural tube in a process known as **neurulation**.(7)

Shh, although primarily in the mesoderm, also has significant effects in the ectoderm. When Shh signaling is disrupted in the ectoderm of mouse paws, an additional digit begins to form. There are two processes of neurulation, called //primary neurulation// and //secondary neurulation//. The method a species uses depends on the class of vertebrate. Many species use both methods in different areas of the embryo. Primary Neurulation begins when cells in the neural plate (ectoderm) evaginates, or protudes outward, and undergoe//s// convergent extension. The plate forms a hinge region, called the medial hinge point (MHP in image), where the plate folds inwards and connects to the notochord (mesoderm). After, the plate on either side of the MHP elevates and closes together. Secondary Neurulation involves the formation of a medullary cord, before then getting hollowed out.(12)

These pictures show the formation of the neural tube and the movement of the cells to bring about the neural tube from just cells in the ectoderm. It also shows differentiation in the rest of the embryo.
 * Morphogens & Gene Expression in Developing Limbs**

Morphogens have a significant role in identifying distinct digits in a developing limb bud. In 2004, scientists in Japan experimented with chick embryonic development by manipulating BMP, Tbx2, and Tbx3 expression, all of two which are active in limb buds and have complex interactions with each other. They found that the //interdigit space// determines how the digit immediately anterior to it will develop. (For instance, interdigit 1 determines digit I, ID2 for digit 2, and so on.) Each digit is distinguishable by how many bones are present in it. Digits I, II, III, and IV have 2, 3, 4, and 5 bones respectively. When the ID space is altered, different digits will develop in place of what //should// be there for normal development. For instance, by placing a bead of //noggin//, an inhibitor of BMP, in ID 3, scientists found that digit III would develop into a digit II. When they repeated this experiment but caused Tbx2 to be misexpressed, digit III developed normally, suggesting that Tbx2 can counteract noggin. It’s known that BMP and Tbx2 have an amplifying effect on each other, and the Tbx2 misexpresion may have led to abnormal Bmp-4 expression such that it overcame the inhibitions posed by noggin.(10)



In addition, when Retinoic acid (RA) was added, Tbx3 was found to be expressed in the anterior end of the limb bud, and a digit III developed. RA causes genes that are normally active to turn off, and activates genes that typically stay dormant. In fact, the higher concentration of RA added, the more abnormally the limb developed. At 100 micrograms/ml of RA, both Tbx2 and Tbx3 were expressed in the anterior of the limb, and a digit IV resulted. (Figure 1) (10)

The experiments also made clear that a concentration gradient is present along the entire limb bud for T-box genes. When a noggin bead was placed in ID 2, the digit developed into a digit I. When Tbx3 was misexpressed in that region, however, digit II developed normally. Although the T-box transcription factors are primarily expressed in the posterior interdigit spaces, they //are// morphogens, and are slightly expressed in the anterior. It should be noted that although Tbx2 and Tbx3 are distinct, sharing only 54% total homology, their T-boxes and regulatory regions share over 90% similarity.(10)



Reveiw Questions 1. If an inhibitor of Abc gene is placed in a region where the Abc protein, a morphogen, is produced in a high concentration, the inhibitor’s effect will be to A) Reduce the concentration of Abc protein B) Change the cellular response to Abc protein’s concentration C) Cease expression of the Abc gene, eliminating the concentration D) Increase the concentration of Abc protein E) Cause misexpression of the Abc gene, either increasing or decreasing the concentration

2. Maternal effect genes cause a change in the zygote based on chemicals. What do these genes affect? A) the formation of specific segments B) The formation of the Animal and vegetable poles C) The formation of axes along with other factors D) The formation of a blastula E) It causes the cells to form an anterior and posterior axis

3. What caused the end result of the picture's right half (above), as compared to the left? A) Lack of number of cells B) Too many cells C) None of the correct cells D) Uneven cytoplasmic contents E)The twins formed and the one to the far right ate the one next to it

4.The Extra Cellular Matrix not only relays signal molecules, but also... A) Provides nutrients to cells B) Moves and inhibits movements in cells C) Forces changes in the cytoskeleton D) Contains fibers to link cells E) Has enzymes that cause apoptosis

5. Sonic Hedgehog (Shh) has a crucial role in all of the following EXCEPT A: Establishing the neural plate B: Induction of motor neurons C: Induction of interneurons D: Establishing axes within the embryo E: Directing outward growth of the apical ectodermal ridge

6.Homoebox genes are responsible for A) the Body Plan B) Structures and their formation C) Development of the notochord D) A and B E) A, B, and C

7. In neural tube development, what would happen if Sonic Hegdehog's concentration gradient was in the ventral side of the embryo in stead of the dorsal? A)The neural tube would form in the ventral instead of the dorsal part of the body B) The neural tube would be unable to form C) the BMP genes would turn on D) Wnt genes would run interference and the neural tube would form in the dorsal portion of the body E) none of this

8. The transcription factors produced by Hox Genes that suppress or activate a gene are called: A. Homeobox B. Homeodomain C. Hox Genes D. Hox Proteins E. None of the Above

9. Primary and secondary neurulation differ primarily in their A: End product B: Method used to ensure a hollow tube C: Exclusive use by different species D: Use of distinctive morphogens E: B and C

10. The genes that subdivide the embryo of an organism and set the boundaries of segments are called: A. Hox Genes B. Gap Gene C. Pair-Rule Genes D. Egg Polarity Genes E. C & D

AP Essay: Morphogenesis is a crucial part of embryonic development.

Part A) **Define** and give an example of morphogenetic activity. Explain one mechanism that aids in it. Part B) **Name** two morphogens and explain their role in the embryo. State the axis along which the morphogen works. Part C) **Describe** Spemann’s Organizer and give an example of one thing it is responsible for.

Links For A Better Understanding

Homeobox gene Reference: [|Berkeley Hox gene] (1) [|nature hox genes in development] (2) [|scienceblogs. brief overview of hox genes] (3) [|Hox: descent with Modification] (4) [|the Function of the Hox gene] (5) [|Biology Online] (6)
 * this website is simple summary of Hox Genes
 * An explanation of the working factors of Hox and the keys to Animal Development
 * A simple explanation of Hox Genes.
 * Hox Gene Function is further and put into terms of evolution.
 * Important source for Hox Gene function
 * A good website for finding definitions

Sonic Hedgehog References: [|rndsystems Sonic Hedgehog and the axon] (7) [|genecards SHH] (8) [|sciencedaily SHH and Limbs] (9)
 * For more information on the role of Shh in Neural tube and axon formation
 * a deeper look at Shh
 * Sonic Hedgehog in the ectoderm of mice and formation of extra digits

Takayuki Suzuki, Jun Takeuchi, Kazuko Koshiba-Takeuchi, Toshihiko Ogura  [|**//Tbx//**][| **Genes Specify Posterior Digit Identity through Shh and BMP Signaling**] // Developmental Cell //, //Volume 8, Issue 6//, //June 2005//, (10)
 * the main source of our information. It is a lab on the effects of SHh and BMP and TBx and others.
 * the pictures on ZPA other gene

Other Information: Biology by Cambell the sixth and eighth editions (11)
 * basic information and information on Fate maps

Pictures: [|Fate maps and nematods] [|Extracellular Matrix Picutre is the only reason to site] [|Formation of the Neural Tube Pics] (12)
 * this site was used to get the fate map of C. Elegans Nematoda
 * ECM picture and can be used for people to brush up on the ECM
 * neural tube formation pictures

Animation for More Information Links: [|Video: early assymetry in the embryo] [|Video: Pattern Formation in Fruit Fly embryo's]
 * (Chapter 19, Animation 19.2) for a brief introduction to our topic
 * 19.3 similar to the youtube clip