User:Tphelpsdu/Drosophila Development/sandbox

= Introduction = Drosophila which are also known as fruit flies are one of the model organism systems that we use to understand genes and other organisms. Drosophila are very complex organisms. They have neural development similar to mammals which make them a great model system for learning more about development.

Lifecycle

Drosophila is a fruit fly seen on bananas, and its life cycle happens really quickly. This helps scientist to easily study them, it is highly preferred, and it helps answer the question of the link between genetics and developmental biology. Drosophila get to their adult stage by nine days. An organism that has larval and pupal stage without a nymph stage before being an adult is called holometabolous, and drosophila is one of them. Drosophila mates in the ten weeks of their life span, and the sperm is stored in the female's body in a seminal receptacle for internal fertilization. Even before an egg is fertilized in a female's body, females still lay eggs from 50 to 70 in a day. The ovum of drosophila had layers in the outer and inner. The outer layer is tough, and it is called the chorion, while the inner layer is a thin envelope. There are two small filaments at the anterior end of the egg called respiratory filaments that helps in gas exchange. The egg needs these filaments because the females usually lay the eggs almost half-way into a rotten fruit. Within 22-24 hours the eggs hatch at room temperature.

The larva then comes out as a little worm, and this first larva appearance is called the first instar larva. The food the instar larva feeds on is the substrate that the eggs were laid in. After about an additional   25 hours the larva, molts into a big worm which is the second instar larva. After enough feeding, it molts into the third instar larva which happens after 24 hours. The third instar larva is the largest of the three. As it feeds it also climbs out of the substrate to be clean and dry awaiting pupation. After about 30 hours the third instar larva molts into the pupa. At the early stages, the pupa is very immobile and yellowish- white in color. It darkens as it continues to develop. The pupal stage is where the development into an adult fly happens. The adult fly is also known as the imago. As it is metamorphosing, some of the larval organs are lysed but some are also kept. An example of an organ that is not lysed is the nervous system. Some and maybe most of the adult organs form fresh from two cells. These cells are what is referred to as the imaginal disc and the histoblasts. These cells lay dormant through the instar stages. Imaginal   discs, which are formed from epithelial cells, are what will later form wings, legs, eyes, etc. The histoblasts form the abdominal epidermis and internal organs. It takes about 3-4 days for the pupal stage and then the imago breaks out of the pupal case known as the eclosion. When they emerge, the female eggs are not ripe for reproduction until two days after eclosion for the cycle to begin again even though the male is very sexually active.

= Fertilization = Fertilization within Drosophila occurs a bit differently compared to other organisms. In Drosophila fertilization is internal and females store sperm Many post-mating barriers occur within fertilization that can exist at a variety of levels. These allow the process of unification with the gametes to  occur. Sperm must successfully enter the female and be transported to the storage organs, the spermathecae or ventral receptacle. The sperm must stay alive until they are utilized by the female. The sperm later will be retrieved from the storage organs, activated, and then will enter an oocyte. It must pass through the reproductive tract to complete this process. Entrance of sperm to the egg must travel through the micropyle to trigger the formation of a normal zygote. A failure at any of these steps prevents fertilization. This is one of the reasons that many sperm are withheld in case the fertilization are not successful. In order to help assortative fertilization, there must be some degree of heritable specificity in the male and female components in the process. Fertilization barriers help to remove abnormal, non-viable sperm, or ejaculates to ensure successful fertilization. The male must also signal the female to keep his sperm alive thus allowing her to utilize them in fertilization for many more eggs. Since the female can hold onto sperm from one or many males, then the female must be able to detect and respond to the sperm differences. This will also lead to differential fertilization within the eggs. Having sperm from different males will cause different potential signals to be sent out. These can signal different receptors and will further complicate the fertilization process.

Both the sperm and non-sperm components of the ejaculate are highly different in Drosophila. Sperm in Drosophila species have a high levels of sperm length variability when compared to other animal taxa. They range from 0.32 mm in Drosophila persimilis to 58.29 mm in Drosophila bifurca. In the bifurca, the sperm are approximately 12 times longer than the male itself. There is little to no variation when analyzing individuals of the same Drosophila species. Species also differ in how much of the sperm tail enters the egg. These differences are important when analyzing post-      fertilization isolation. Female sperm storage organs show interspecific variability as well; species   also differ in which of those two organs, the spermathecae or the ventral receptacle, sperm are stored. These differences lead to whether or not assortative fertilization may be mediated by a mismatch between sperm morphology or storage organs within the females. In four different species of Drosophila, sperm differ considerably in length. The sizes of the storage sites within the       females also differ in length. Females of Drosophila pachea and Drosophila wassermani store sperm only in the spermathecae. Drosophila nannoptera females use only the ventral receptacle.

Morphological differences may end up deciding storage site, sperm viability or its reduction. This can also result from biochemical interactions that occur while the ejaculate passes through the female reproductive tract.

Extensive variation has been found within research in the chemistry and function of the non-sperm component of the ejaculate. More specifically, the accessory gland proteins or Acps of the ejaculate. Approximately 80 of these proteins are transferred to females at the time of mating. Only 9               of these proteins have been described based on function and chemistry. It is clear from these studies that this group of substances are used to alter female behavior. This alters female behavior by stimulating oviposition and delaying the time that the female will mate to another male and facilitate the storage of sperm in the female.

It is clear that within species there is considerable sequence polymorphism at the loci encoding these proteins and that the proteins show considerable sequence divergence between species as well as species specificity of their functions. In D. melanogaster, variation in four accessory gland proteins examined appears to be associated with displacement abilities in ejaculate competition experiments, although these experiments were not designed to detect any interaction with female genotype. Once the sperm is inside the female, there are a variety of reactions that must occur for successful fertilization. Some of these reactions occur within the female reproductive tract itself, but others involve the action of male-derived substances in other sites in the female. Evidence of the reactions inside the female reproductive tract is both direct and indirect. Acp36DE has been shown to localize at the entrance to the sperm storage organs. This will help to put all of the sperm into storage without any diversion.

Some reactions occur outside of the female tract come from three different protein: esterase 6, sex peptide and Acp26Aa. These small proteins are transferred quickly to the female hemolymph, even before copulation has terminated. They produce the same response in females. This is: increased oviposition and decreased receptivity to mating with another male. The 2 effects from sex peptides on female behavior are from the same unknown molecular target. The increase in oogenesis is mediated by the resultant increase in juvenile hormone synthesis in response to the sex peptide. An important direction for future research is the identification of the female targets of these proteins and the detection of variation in the targets that could provide mechanisms for differential fertilization. Species-specific morphological and biochemical features of the female tract are easily inferred from the larger size and longer duration of the insemination reaction mass. In house flies, female accessory gland secretions have been demonstrated to activate the sperm acrosome, enabling it to penetrate the micropyle. The actual substance involved has not been identified, nor is there any evidence as to species specificity in the activation process.

Cleavage

Most insect eggs undergo superficial cleavage, wherein a large mass of centrally located yolk confines cleavage to the cytoplasmic rim of the egg. One of the fascinating features of this cleavage type is that cells do not form until after the nuclei have divided. Cleavage in a Drosophila egg in the image below. The zygote nucleus undergoes several mitotic divisions within the central portion of the egg. In Drosophila, 256 nuclei are produced by a series of eight nuclear divisions averaging 8 minutes each. The nuclei then migrate to the periphery of the egg, where the mitoses continue, at a progressively slower rate. During the ninth division cycle, about five nuclei reach the surface of the posterior pole of the embryo. These nuclei become enclosed by cell membranes and generate the pole cells that give rise to the gametes of the adult. Most of the other nuclei arrive at the periphery of the embryo at cycle 10 and then undergo four more divisions at progressively slower rates. During these stages of nuclear division, the embryo is called a syncytial blastoderm, meaning that all the cleavage nuclei are contained within a common cytoplasm. No cell membranes exist other than that of the egg itself.

Although the nuclei divide within a common cytoplasm, this does not mean that the cytoplasm is itself. When the nuclei reach the periphery of the egg during the tenth cleavage cycle, each nucleus becomes surrounded by microtubules and microfilaments. The nuclei and their associated cytoplasmic islands are called energids. Following cycle 13, the oocyte plasma membrane folds inward between the nuclei, eventually partitioning off each somatic nucleus into a single cell. This process creates the cellular blastoderm, in which all the cells are arranged in a single-layered jacket around the yolky core of the  egg. Like any other cell formation, the formation of the cellular blastoderm involves a delicate interplay between microtubules and microfilaments. The first phase of blastoderm cellularization is characterized by the invagination of cell membranes and their underlying actin microfilament network into the regions between the nuclei to form furrow canals. This process can be inhibited by drugs that block microtubules. After the furrow canals have passed the level of the nuclei, the second phase of cellularization occurs. Here, the rate of invagination increases, and the actin-membrane complex begins to constrict at what will be the basal end of the cell. In Drosophila, the cellular blastoderm consists of approximately 6000 cells and is formed within 4 hours of fertilization.

After the nuclei reach the periphery, the time required to complete each of the next four divisions becomes progressively longer. While cycles 1–10 are each 8 minutes long, cycle 13, the last cycle in the syncytial blastoderm, takes 25 minutes to complete. Cycle 14, in which the Drosophila embryo forms cells (after 13 divisions), is asynchronous. Some groups of cells complete this cycle in 75 minutes, whereas other groups of cells take 175 minutes. Transcription from the nuclei (which begins around the eleventh cycle) is greatly enhanced at this stage. This slowdown of nuclear division and the concomitant increase in RNA transcription is often referred to as the mid-blastula transition. Such a transition is also seen in the embryos of numerous vertebrate and invertebrate phyla. The control of this mitotic slowdown appears to be affected by the ratio of chromatin to cytoplasm.

= Gastrulation = Gastrulation is after cleavage and its main contribution to embryonic development is by infolding of a band of cells in the midventral region. Before gastrulation happens, the drosophila embryo is divided into seven parts. There is the anterior midgut, posterior midgut, neural and epidermal ectoderm, hindgut ectoderm, stomodeal ectoderm, extraembryonic amnioserosa, mesoderm. The initial step in the process of gastrulation is the formation of a ventral furrow, where two cell groups invaginate to form  the endoderm and mesoderm. This happens in conjunction with the infolding of the mesoderm.

Mesoderm invaginates and the germ band and pole cells move forward. The furrow that is formed as  the cells move forward has an anterior and posterior end, and at these two positions there is an invagination of the endoderm which results in the formation of the anterior and posterior midgut respectively, the ventral endoderm invaginates and creates the anterior midgut, while the dorsal endoderm create the posterior midgut. The anterior stomodeum, also known as the foregut, and posterior proctodeum, also known as hindgut, are later formed by the invagination of the ectoderm and as the endoderm thickens. The stomodeum and the hindgut invaginate and get deeper. The anterior and posterior midgut start to extend and get longer. The cells around the ventral midline then change shape to form the ventral furrow. After everything is formed, the germ band and cells start to move back  down, and this creates the posterior gut or airduct opening. Anterior and posterior midget joins  together, and segmentation becomes obvious. Germ band moves to the head region and make head disappear to the interior. The process is very quick, and it turns epithelium cells that are identical to invaginated tube cells. Another form of infolding process called the cephalic furrow also happens in addition to that of the ventral infolding discussed above. This lateral infolding indicates the exact  position of the future head.

The consequence of gastrulation is the creation of three germ layers that extends around the ventral circumference of the egg. This multilayered germ band formed stretches along the dorsal side of the egg and with this the embryo performs, for the lack of a better term, acrobatic maneuvers to touch its head to the posterior end. Following this the germ band bounces back to its position. As this happens, major parts of the embryo appear. These include the mandibular, maxillary, labial, thoracic and abdominal regions. One important thing to note during gastrulation is the fact that at some point the head that forms disappears causing the thoracic regions to overgrow the head region. Only a little region of the head will appear.

= Neurulation = In Drosophila this is the process where neuroblasts generate the Central Nervous System (CNS). The neuroblasts divide asymmetrically and can eventually become glia cells or neurons. [7] After the division of neuroblasts they produce a daughter neuroblast and a ganglion mother cell or GMC. If the neuroblasts divide at an increasing rate they may very well be the cause of tumors that are malignant.

[9] The GMC produce two new cells during the single division that they have. The cells that are a result of their division can either become glial cells or neuron cells. The neuroectodermal cells are the cells that will end up becoming the central nervous system. The ventral nerve cord comes from the side of the neuroectoderm that is towards the tail and the belly side.

The neuroblasts form into segments. There are three segments for the brain, subesophageal and thoracic. The abdomen has nine segments for a total of 18 segments. After the division of neuroblasts they produce a daughter neuroblast and a ganglion mother cell or GMC. If the neuroblasts divide at an increasing rate they may very well be the cause of tumors that are malignant. Researchers have discovered the information they have about Drosophila from conducting experiments and searching for mutations then identifying them. By doing this they have discovered that sensory axons only grow towards the Central Nervous System. Photoreceptors are different than other parts of the body, they are connected to the brain by interneurons, therefore they don’t form axons.

There are groups of cells that Drosophila have called neural equivalence groups. These groups are the first to divide which is what starts neurogenesis. This occurs when one neuroblast splits or migrates into two. Proneural genes are expressed by certain cells within this zone. These will become neural cells  while the ones that don’t express proneural genes will end up becoming epidermal cells. Certain transcription factors allow Delta, a ligand, to bind to Notch. This then interacts with other genes which in turn cause transcriptional repressors that then act on the proneural genes. This is a process called  lateral inhibition, which means that a gene or neuron is reducing the activity and decreasing the amount of possible movement that its neighboring genes or neurons have.

The process of neurulation in Drosophila is a cascade of transcription factors. Hox genes have an important role in determining the formation of segmentation and specification of the identities for some motoneurons. They also seem to have a hand in segment-specific cell determination. This is something that they do with the help of their cofactors. At least that is what is believed to be the case there hasn’t been a lot of research completed on this.

= Axis Signaling = Localizing mRNA during oogenesis is important producing axes and maintain polarity in Drosophila. The mRNA gets localized due to the proteins within the organism. This process is done using microtubules. Localizing RNA also helps produce germline and somatic cells in the embryos future. Microtubules use localization to create the body axes by using three major genes. The first two genes are Bicoid (bcd) and Oskar (osk) which help create the anterior- posterior axis by localizing mRNA. The third gene is Gurken (Grk) and it produces the dorsal- ventral axis.

ANTERIOR-POSTERIOR

In the development of the A-P axis, Bicoid is localized to the anterior side while Oskar is on the posterior. Bicoid creates a protein gradient that determines the head and thoracic regions. Oskar helps produce the poles and the abdominal region with the help of Nanos RNA.

Oskar produces a long and short form which comes from start codons. The long form is just used for anchoring while the short form nucleates pole plasm. Bicoid is localized using Exu protein and involves several different proteins to keep it on the anterior side.

DORSAL-VENTRAL

There are two main genes that produces the dorsal-ventral axes and those are Gurken (Grk) and torpedo (Top). The two genes are used for signaling to distinguish dorsal cells. The Toll receptor is used for the asymmetry in the embryo. The Toll receptor is constrained to the ventral region and inhibited on the dorsal due to Grk-Top signaling. Wingless (Wg) and Decapentaplegic (Dpp) are also genes that control the D-V and A-P axes of the wings and legs. Wg is expressed in ventral cells while Dpp is inhibited the same cells, but it is opposite in the dorsal region. Dpp is expressed while Wg is inhibited.

PROXIMAL-DISTAL

While Wg and Dpp plays an important role in D-V and A-P axes, they also are genes that determine the proximal-distal axes of the legs of drosophila. The expression of the two genes are met in the middle of the leg. These two genes encode of three different genes that define the different domains within the legs. Distal-less codes for a protein (DII) that is used for early leg formation, but as the organism matures, DII is only expressed in the distal portions of the leg. Dachshund also codes for another protein that is partially shown in the same domain as DII but helps with the portion that contains the parts of the upper leg like the femur. Extradenticle (Exd) and homothorax (Hth) are expressed in the proximal regions around the hip and connective parts to the body.

Advantages/Disadvantages

Drosophila is an important model organism for many reasons. They have short generation times, inexpensive and they also have balancer chromosomes. One of those is that drosophila has been important for cancer studies. Researches have picked these organisms due to their variations within their genome, and they can also do large screenings. Drosophila has helped scientists understand many tumors forming genes like Hippo, Notch, Dpp and JAK-STAT. They have also been used to understand genes that cause heart failure. The genes of drosophila are similar to the genes of mammals. A large percentage of human diseases has been found with the drosophila genome. A disadvantage of using the fruit fly is that they are really small, only 3mm in length.

'''These references need to be added to the paper. (comment by PD)'''

12.) Leptin, M. (1999). Gastrulation in Drosophila: the logic and the cellular mechanisms. The EMBO Journal, 18(12), 3187-3192. doi:10.1093/emboj/18.12.3187

13.) Kam, Z., Minden, J. S., Agard, D. A., Sedat, J. W., & Leptin, M. (1991). Drosophila gastrulation: analysis of cell shape changes in living embryos by three-dimensional fluorescence microscopy. Retrieved from, http://dev.biologists.org/content/develop/112/2/365.full.pdf

14.) Development of the Fruit Fly Drosophila melanogaster. Bainbridge and Bownes, (1981).

Retrieved from,   http://web.as.uky.edu/Biology/faculty/cooper/Population%20dynamics%20examples%20with

%20fruit%20flies/08Drosophila.pdf