<?xml version='1.0' encoding='UTF-8'?><?xml-stylesheet href="http://www.blogger.com/styles/atom.css" type="text/css"?><feed xmlns='http://www.w3.org/2005/Atom' xmlns:openSearch='http://a9.com/-/spec/opensearchrss/1.0/' xmlns:georss='http://www.georss.org/georss' xmlns:gd='http://schemas.google.com/g/2005' xmlns:thr='http://purl.org/syndication/thread/1.0'><id>tag:blogger.com,1999:blog-8752779924787100904</id><updated>2012-02-16T12:46:38.885-08:00</updated><title type='text'>development from a naiad</title><subtitle type='html'></subtitle><link rel='http://schemas.google.com/g/2005#feed' type='application/atom+xml' href='http://developmentfromanaiad.blogspot.com/feeds/posts/default'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default?max-results=100'/><link rel='alternate' type='text/html' href='http://developmentfromanaiad.blogspot.com/'/><link rel='hub' href='http://pubsubhubbub.appspot.com/'/><author><name>Logan</name><uri>http://www.blogger.com/profile/04166352677595317480</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='16' height='16' src='http://img2.blogblog.com/img/b16-rounded.gif'/></author><generator version='7.00' uri='http://www.blogger.com'>Blogger</generator><openSearch:totalResults>6</openSearch:totalResults><openSearch:startIndex>1</openSearch:startIndex><openSearch:itemsPerPage>100</openSearch:itemsPerPage><entry><id>tag:blogger.com,1999:blog-8752779924787100904.post-3935031752269756620</id><published>2010-12-15T09:20:00.000-08:00</published><updated>2010-12-15T09:20:43.758-08:00</updated><title type='text'>BATS!!</title><content type='html'>This is the second essay test that I have written for P.Z.'s developmental class. The style is supposed to be similar to what you would see in Scientific American or The New York Times science section. I hope you guys enjoy it:&lt;br /&gt;&lt;br /&gt;&lt;div style="text-align: center;"&gt;&lt;u&gt;Lab rats with wings: The development, genetics and evolution of bat wings &lt;/u&gt;&lt;/div&gt;&lt;br /&gt;&lt;br /&gt;&lt;a name='more'&gt;&lt;/a&gt;&lt;br /&gt;Life on earth is dazzling in its diversity. There are millions of species, each one having its own biological particularities for scientists to discover. Despite the massive array of species that can be studied, some fields, such as developmental and molecular biology, have focused on studying only a small number of species. Many species are too difficult to raise, or mature too slowly to be useful. Since studying the true diversity of biological life is impossible, these scientists attempt to generalize the findings from simple species, such as E-coli bacteria, or lab mice, to more complex species. This effort has been wildly successful, and we have been able to discover many biological concepts that are true throughout all life on earth. The discovery of cells, DNA, and the genetic code all make clear the usefulness of model organisms for discovering traits that unify many organisms, but can they also be useful for researching traits that are unique to a specific, poorly studied group? Recent research seems to show that they are. For instance, we have begun to gain an understanding of how a unique feature, the wing of a bat, develops and evolved. This has been possible because of our understanding of the genetics and development of a model organism, the common lab mouse, Mus musculus.&lt;br /&gt;Bats, the order Chiroptera, are one of the most specious groups of mammals. One out of every five mammal species is a bat. Bats have been able to flourish in a number of ecological roles, with different species feeding on fruit, insects, fish and perhaps most famously, blood. The reason for this spectacular diversity is the bat’s ability to fly. Once early bats had evolved the ability to fly, numerous ecological niches opened up to them, and many species were able to diverge in a relatively short period of geological time. This is an evolutionary phenomenon called “adaptive radiation”. However, due to the speed of these adaptive radiation events, they leave few traces in the paleontological record. In the case of bats, all recognizable fossils already have the hallmark elongated flingers, which would have supported wings capable of flight. Since we cannot discover clues to bat evolution from fossils, we have to look in other places. Development and genetics have been able to shed considerable light on evolutionary change, but the genetics of bats has not been thoroughly examined. Thankfully, discoveries in model organisms, such as mice, have made clear the developmental and genetic changes that have occurred during bat evolution to allow the formation of wings. Two of the most important and best studied of these changes are the elongation of the finger bones and the appearance of webbing between those fingers.&lt;br /&gt;Embryological studies of model organisms, such as mice, have revealed that the limbs of most vertebrates have webbed digits in early development. Later on, molecular signals in the embryo instruct the cells that make up the webbing to undergo programmed cell death. The molecule that creates this signal, called bone morphogenetic protein (BPM), has been identified in mice and other model organisms. How do bats evade the action of BMP to maintain their primordial webbing? Again the first clues were found in animals that are far easier to study than bats: ducks. Ducks are domesticated and lay eggs that can easily examined for developmental research, but they also produce membranous webbing between their toes. Research showed that they produced BMP just like mice did, but were suppressing its action. That suppression was due to the production&lt;br /&gt;of a molecule called GREMLIN, that interacts antagonistically with BMP. By producing GREMLIN, ducks were blocking BMP from communicating with any cells, allowing the webbing between the toes to evade destruction and appear in the adult. Could bats be using a similar method to maintain the webbing in their wings? This seems to be the case. Once developmental research was conducted, it was found that although bats produce BMP, they also produce GREMLIN, blocking its action. However, the story is more complex than that. Experimentally raising the dosage of BMP, so that it could not be completely blocked by GREMLIN, did not degrade the bat’s wing membranes. Some other factor was helping GREMLIN maintain the initial webbed state of the digits. Thankfully, due to careful work in model organisms, there have been numerous molecules identified that reduce the likelihood that cells will undergo the planned self destruction that BMP causes. One group of these molecules, fibroblast growth factors (FGFs) are abundant in the developing tissues that will become a bat’s wing membrane. When scientists reduced the amount of FGFs, and increased the amount of BMP, the affected bat wings were significantly reduced. It now seems as though those two molecules, GREMLIN and FGFs, are responsible for the membranes that have allowed bats to evolve the ability to fly. Work conducted in model organisms was able to shed light on an evolutionary novelty and identify the changes that might have taken place genetically during bat evolution.&lt;br /&gt;But bat evolution is characterized by more than webbed fingers. For that webbing to become a wing, the fingers themselves must grow significantly. Once again, research conducted in model organisms can help illuminate how these changes take place. The development of limbs has been very closely studied in mice and other model&lt;br /&gt;vertebrates. Each limb begins as a bulge of cells protruding from the body. These cells then divide, with some cells forming central cartilage based struts, which lay out the framework for future bones. When the development of bat embryos is observed, the pattern is initially similar. The limb bud and early wings of bat embryos look similar to the corresponding stages of mouse arm development. But before the cartilage struts give way to bone, differences begin to appear. The cartilage struts spend a much longer time dividing and growing before they finally turn into bone, and the fingers therefore become much longer. How do these differences in development arise? The answer once again was found due to our understanding of mouse development. In mice, the growth of the cartilage struts is controlled by a molecule that we have already become familiarized with, BMP. The role that this molecule plays in limb development was worked out by experimentally modifying the levels of BMP in the limbs of developing mice. The mice that were exposed to high levels of BMP grew particularly long fingers, and the cartilage struts that they formed during development grew for a longer period of time before becoming bone. To put it another way, mice limbs that are grown in high BMP environments develop in a way that is similar to normal bat limb development. These findings seem to suggest that the elongated fingers of bats could be due to higher levels of BMP. This idea is supported by research that shows that bats do in fact produce high levels of BMP in their developing limbs.&lt;br /&gt;But BMP is not the only molecule that might be implicated in the elongation of bat limbs. In fact, there are many genes that are suspected to impact this process, and not all of them are as well understood as BMP. Thankfully, even when the specific functions of these genes are not well understood, model organisms allow us to determine how these&lt;br /&gt;genes might be implicated in bat evolution. For instance, one gene, Prx1, was implicated in limb elongation because mice that were missing the gene had very small, shortened limbs. To assess whether this gene was more active in bats than mice, scientists simply removed part of the mouse genome that controls how active Prx1 is, and replaced it with the corresponding portion of the bat genome. In these transgenic mice, the limbs developed in a way that was slightly similar to bat development, with a resulting limb that was a little bit longer. Because of work in model organisms, biologists can identify the small genetic changes such as these that were likely important during bat evolution.&lt;br /&gt;Despite the lack of fossil evidence, a picture is beginning to emerge of how bats might have evolved. This picture is based on developmental and genetic evidence, despite the fact that very little genetic work has been done in bats. This problem is bypassed because of the utility of model organisms. Animals that are easy to raise and develop quickly, such as mice, have been studied in great detail, and the insights from that research can be used to shed light on novelties in other species, such as bats. For many decades, scientists have been able to use model organisms to discover traits that are universal to all life on earth. Because of this, the biologist Jacques Monod once famously quipped that: “What is true for E. coli is true for the elephant.” But the way in which model organisms have proven useful in studying evolutionary novelties demands a new slogan: “what is unique in the elephant is explained by E. coli.”&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;div style="text-align: center;"&gt;&lt;u&gt;Bibliography&lt;/u&gt;&lt;/div&gt;Cooper K, Tabin C. 2008. Understanding of bat wing evolution takes flight. Genes &amp;amp; development 22: 121.&lt;br /&gt;Cretekos C, Wang Y, Green E, Martin J, Rasweiler J, Behringer R. 2008. Regulatory&lt;br /&gt;divergence modifies limb length between mammals. Genes &amp;amp; development 22: 141.&lt;br /&gt;Sears KE. 2007. Molecular Determinants of Bat Wing Development. Cells Tissues Organs 187: 6-12.&lt;br /&gt;Sears KE, Behringer RR, Iv JJR, Niswander LA. 2006. Development of Bat Flight: Morphologic and Molecular Evolution of Bat Wing Digits. Proceedings of the National Academy of Sciences of the United States of America 103: 6581-6586.&lt;div class="blogger-post-footer"&gt;&lt;img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/8752779924787100904-3935031752269756620?l=developmentfromanaiad.blogspot.com' alt='' /&gt;&lt;/div&gt;</content><link rel='replies' type='application/atom+xml' href='http://developmentfromanaiad.blogspot.com/feeds/3935031752269756620/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/12/bats.html#comment-form' title='1 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/3935031752269756620'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/3935031752269756620'/><link rel='alternate' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/12/bats.html' title='BATS!!'/><author><name>Logan</name><uri>http://www.blogger.com/profile/04166352677595317480</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='16' height='16' src='http://img2.blogblog.com/img/b16-rounded.gif'/></author><thr:total>1</thr:total></entry><entry><id>tag:blogger.com,1999:blog-8752779924787100904.post-3758811632445725925</id><published>2010-11-07T14:25:00.000-08:00</published><updated>2010-11-07T14:25:27.137-08:00</updated><title type='text'>"There were giants in the earth in those days"</title><content type='html'>There is an article from Wired that highlights some &lt;a href="http://www.wired.com/wiredscience/2010/11/huge-dragonflies-oxygen/"&gt;research&lt;/a&gt; that is (sorta) about insect development. From the article:&lt;br /&gt;&lt;blockquote&gt;&lt;br /&gt;To explore the effects of &lt;a href="http://www.wired.com/wiredscience/2010/09/oxygen-and-evolution/"&gt;ancient oxygen levels&lt;/a&gt;,  VandenBrooks’ team raised &lt;i&gt;dragonflies and&lt;/i&gt; 11 other “living fossils,” including beetles  and cockroaches, in three habitats with different oxygen concentrations —  one at the late Paleozoic’s 31 percent oxygen level, another at today’s  21 percent level and the third at 12 percent from 240 million years ago  (Earth’s lowest oxygen level since complex life exploded onto the scene  half a billion years ago).&lt;br /&gt;They found that dragonflies and beetles grew faster, as well as  bigger, in a high-oxygen environment, while cockroaches grew slower and  remained the same size. All but two bug species grew smaller than normal  at low concentrations of oxygen.&lt;/blockquote&gt;&amp;nbsp;*Italics added*&lt;br /&gt;This is super neat! A single environmental factor seems to be having substantial effects on the development of these insects.&amp;nbsp; Oxygen levels seem to be having most of their effect on the &lt;a href="http://en.wikipedia.org/wiki/Invertebrate_trachea"&gt;tracheal &lt;/a&gt;system of these insects, which is what you would expect, since the trachea are the organs that bring oxygen to insect tissues. They also seem to think that they could use tracheal&amp;nbsp; measurements from insects trapped in amber to determine ancient oxygen levels.&lt;br /&gt;It would be interesting to see if there are developmental reasons why cockroaches don't respond as quickly to increased oxygen. Could the dragonflies' aquatic larvae impact the process? Or might there be genetic factors that create other growth constraints in cockroaches? Would there be similar effects on arthropods that do not have trachea, but have &lt;a href="http://en.wikipedia.org/wiki/Book_lungs"&gt;book lungs&lt;/a&gt;? It's neat stuff, but the &lt;a href="http://gsa.confex.com/gsa/2010AM/finalprogram/abstract_181665.htm"&gt;research&lt;/a&gt; was presented at a geological meeting, so the developmental questions were not the ones that were most addressed. Also, they said things like this:&lt;br /&gt;&lt;blockquote&gt;dragonflies and other insect groups do develop and evolve larger body sizes in hyperoxia... &lt;/blockquote&gt;They &lt;i&gt;evolve&lt;/i&gt; larger body sizes!? Were the changes in body size heritable?&amp;nbsp; Has the author never heard of Lamarck? This seems wrong, but I don't know any of the details of the research, so frankly I can't make any better of a judgment than that. I hope to see an article about this at some point, because I really want to know more.&lt;br /&gt;&lt;br /&gt;The quote in the title is from Genesis 6:4.&lt;div class="blogger-post-footer"&gt;&lt;img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/8752779924787100904-3758811632445725925?l=developmentfromanaiad.blogspot.com' alt='' /&gt;&lt;/div&gt;</content><link rel='replies' type='application/atom+xml' href='http://developmentfromanaiad.blogspot.com/feeds/3758811632445725925/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/11/there-were-giants-in-earth-in-those.html#comment-form' title='6 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/3758811632445725925'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/3758811632445725925'/><link rel='alternate' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/11/there-were-giants-in-earth-in-those.html' title='&quot;There were giants in the earth in those days&quot;'/><author><name>Logan</name><uri>http://www.blogger.com/profile/04166352677595317480</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='16' height='16' src='http://img2.blogblog.com/img/b16-rounded.gif'/></author><thr:total>6</thr:total></entry><entry><id>tag:blogger.com,1999:blog-8752779924787100904.post-1623761487693823043</id><published>2010-10-31T19:03:00.000-07:00</published><updated>2010-11-04T21:54:12.330-07:00</updated><title type='text'>Test 1 (bicoid)</title><content type='html'>This is the text of the first test that I wrote for P.Z.'s class. The test is supposed to be free-standing essay written for a popular audience, so it seemed perfect for the blog. It's long, but the topic is pretty cool, so you should read it. The title is Bicoid: Evolution of novelties.&lt;br /&gt;&lt;br /&gt;&lt;a name='more'&gt;&lt;/a&gt;&lt;br /&gt;&lt;br /&gt;Now and again, when the compost bin in my kitchen has not been taken out recently enough, or some fruit has gotten a little too ripe, we get some unexpected visitors. Fruit flies, those persistent, minute and irritating insects, are all too common in university housing, are also common in university research labs. Fruit flies are a model organism, something that biologists use as a proxy, an animal that can be studied easily with results that can hopefully be generalized to other animals. It is not surprising, then, that the development of these flies, and the molecular basis of that development, has been studied in exacting detail. One of the best studied genes that affects fly development is called Bicoid. Although this gene is very specialized and is not found in many other organisms, it can still inform us about the evolutionary acquisition of novel traits.&lt;br /&gt;&lt;i&gt;Bicoid &lt;/i&gt;(&lt;i&gt;bcd&lt;/i&gt;) is not a normal gene. We typically think of genes being used by cells to be translated into a protein that can then perform various tasks throughout the cell. &lt;i&gt;Bcd&lt;/i&gt; does not follow these rules. In fact, during the normal life of a fruit fly &lt;i&gt;bcd&lt;/i&gt; is never produced. The DNA that encodes this gene is almost always silent. The exception to this rule is in the ovary of a pregnant female fly. Here there are cells that produce all of the important proteins and other chemicals that the egg will need to develop. These “nurse cells” are the only ones that transcribe the&lt;i&gt; bcd&lt;/i&gt; gene into mRNA, but the nurse cells never translate those mRNAs into proteins. Instead the &lt;i&gt;bcd&lt;/i&gt; mRNA is shuttled out of the nurse cells and into the cytoplasm of the ovum. Once it is there &lt;i&gt;bcd&lt;/i&gt; will perform its single immense task, to inform the developing embryo of its orientation, telling certain cells to&lt;br /&gt;Logan Luce October 14, 2010&lt;br /&gt;build a head and cells on the other end to build an abdomen. To understand how &lt;i&gt;bcd&lt;/i&gt; imparts this knowledge onto other cells, we must first examine some basic fly embryology.&lt;br /&gt;The very early fly embryo does not consist of a multitude of differentiated cells. Instead there are a plethora of nuclei all floating near the outer membrane of a large sac of cytoplasm. This is the environment where &lt;i&gt;bcd&lt;/i&gt; takes effect. Because there are no membranes dividing cells, signaling molecules like the &lt;i&gt;bicoid&lt;/i&gt; protein (BCD) can flow freely throughout the organism, reaching all of the nuclei of the embryo without having to cross any membrane barriers. This particular embryonic organization allows for BCD to form a concentration gradient. The mRNAs that were produced by the nurse cells are localized in the anterior portion of the embryo, but the protein that is then translated can flow freely around the embryo until it is broken down into its component pieces. This means that there is a high concentration of BCD in the anterior of the embryo, where new protein is constantly being produced, but much lower concentrations near the posterior of the embryo, because BCD is being broken down without being replaced. This is the key to anterior-posterior patterning in fruit flies. By reading the concentration gradient of BCD, a nucleus can determine its location within the embryo. If BCD is high, that nucleus must be close to the front of the embryo and should therefore start making a head. If BCD is low, then the nucleus must be close to the rear, and should begin making an abdomen. It is important to remember, however, that cells are not intelligent, and “reading a concentration gradient” is not as easy as it may sound. To understand how BCD concentrations actually transfer information about what body parts to build, we will need to delve into some elementary molecular biology.&lt;br /&gt;Multicellular organisms such as fruit flies and humans have to have to create differentiated tissues from the same genome. This is accomplished through the use of proteins called transcription factors. Transcription factors are proteins that attach to DNA within the nucleus and encourage (or discourage) the transcription of nearby genes. They are the notes written in the margin of each cell’s copy of the giant genetic cookbook, the markers that show cells the proteins they need to make.&lt;br /&gt;As you may have guessed by now, the protein BCD is a transcription factor. It is, however, a particularly complex one, which affects the transcription of dozens of genes by attaching to DNA in hundreds of places. There are some genes (ones that lead towards head development for instance) that are stimulated by BCD, while there are others that BCD represses. In some instances the situation is even more involved. For instance there are genes where BCD can either stimulate or repress transcription, depending on the concentration. By combining the BCD concentration gradient with the varied reactions and sensitivities to BCD as a transcription factor, a single molecule can create varied effects across the length of a developing fly. This complex and Byzantine system allows for fruit flies to get a patterned body that stars with a head and ends with an abdomen. But how did this system come to be? How did evolution create the many interconnected processes that are required for fruit flies to develop normally?&lt;br /&gt;To answer these questions, scientists began to search the genomes of other animals for something similar to &lt;i&gt;bicoid&lt;/i&gt;. If they could discover how the gene is different in other animals they could perhaps determine what the gene looked like in the last common ancestor, and therefore how it has changed over time. When scientists began to look for &lt;i&gt;bcd&lt;/i&gt; in the genomes of other insects they were faced with a surprise: it wasn’t&lt;br /&gt;there. In fact, the entire process of development outlined above is only present in certain flies. Most insects, such as beetles, have cell membranes separating their nuclei. They do not pattern their entire anterior-posterior axis all at once with a concentration gradient. And most importantly, they do not have &lt;i&gt;bicoid&lt;/i&gt;. It almost appears as though the entire system was created at once. A closer look, however, reveals the true evolutionary ancestry of &lt;i&gt;bcd&lt;/i&gt;. Although the &lt;i&gt;bicoid&lt;/i&gt; gene is unique, the process by which it evolved is not, and the story of its evolution sheds light on the common mechanisms by which evolution creates novelty.&lt;br /&gt;Although there is no gene in beetles that functions in the same way that &lt;i&gt;bcd&lt;/i&gt; does in flies, there could still be genes with similar structure but different functions. Such a gene was found by a group of German scientists in 1999. This gene, Hox3, was known to function in a completely different way than &lt;i&gt;bcd&lt;/i&gt;. Moreover, there was already a fruit fly gene that was similar to Hox3, called zen. How could this be? The researchers determined that there must have been a genetic duplication in the evolutionary lineage leading to fruit flies. This duplication left the flies with two copies of the Hox3 gene. One copy, zen, maintained something close to its original role, while the other copy became more and more derived. Hox3 is sometimes shared from maternal cells into the developing embryo, and &lt;i&gt;bcd&lt;/i&gt; is now only expressed this way, while zen no longer has any maternal expression. By duplication and specialization, &lt;i&gt;bcd&lt;/i&gt; has gained new roles while the functions of the ancestral gene are still present through zen.&lt;br /&gt;This idea of duplication and specialization is a motif in biology. Again and again scientists have discovered that many new genes are specialized duplications of older genes. For instance, the hemoglobin that moves oxygen through our blood stream is&lt;br /&gt;composed of two subunits that are duplicates of ancestral hemoglobin. After the duplication, they specialized until now both are dependent upon the other to function normally.&lt;br /&gt;Other pieces of fruit fly development that seem novel at first glance also have precursors. Hox3 is a transcription factor, so when &lt;i&gt;bcd&lt;/i&gt; diverged from its precursors, it could already affect the transcription of many other genes. As it continued to diverge, the ways in which it affected those genes changed slowly until it assumed a role similar to the one it now plays in fruit flies. Similarly, the process by which &lt;i&gt;bcd&lt;/i&gt; mRNAs are localized in the anterior of the embryo is not a new innovation, but instead a process found in numerous other organisms that has simply been used again for a new purpose in fruit flies. By reusing old mechanisms for a different goal, bcd has managed to create an entirely new mode of development without having to invent anything out of whole cloth.&lt;br /&gt;This repurposing of old genetic equipment is a process that is seen again and again in evolution. Some structures have been repurposed so many times in so many different ways that they no longer seem related. Who would guess that the bacterial flagellum and the syringe that makes some bacterium dangerous would use the same genetics? Although it is hard to fathom, such recycling of genetic elements is quite common. Again, the uniqueness of &lt;i&gt;bicoid&lt;/i&gt; in development illuminated general evolutionary patterns for creating unique structures.&lt;br /&gt;Model organisms such as fruit flies are used in the hopes that they may prove analogous to other species- that they will provide a model of shared patterns within a larger group. The developmental properties of the &lt;i&gt;bicoid&lt;/i&gt; gene fail in this respect. They are novel in nearly every possible aspect. However the evolutionary history of this novel&lt;br /&gt;gene does illuminate the ways that evolution typically produces genetic novelties. Even though fruit flies appear to be unique developmentally, they have at least shown us how uniqueness can evolve. Not bad for a cloud of bugs above a compost bin.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Bibliography&lt;br /&gt;Bonneton F. 2003. Extreme divergence of a homeotic gene: the bicoid case. M S- Medecine Sciences 19: 1265-1270. McGregor AP. 2005. How to get ahead: the origin, evolution and function of bicoid. Bioessays 27: 904-913.&lt;br /&gt;Peel A, Chipman A, Akam M. 2005. Arthropod segmentation: beyond the Drosophila paradigm. Nature Reviews Genetics 6: 905-916. Stauber M, Jockle H, Schmidt-Ott U. 1999. The anterior determinant bicoid of Drosophila is a derived Hox class 3 gene. Proceedings of the National Academy of Sciences of the United States of America 96: 3786.&lt;div class="blogger-post-footer"&gt;&lt;img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/8752779924787100904-1623761487693823043?l=developmentfromanaiad.blogspot.com' alt='' /&gt;&lt;/div&gt;</content><link rel='replies' type='application/atom+xml' href='http://developmentfromanaiad.blogspot.com/feeds/1623761487693823043/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/10/test-1-bicoid.html#comment-form' title='1 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/1623761487693823043'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/1623761487693823043'/><link rel='alternate' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/10/test-1-bicoid.html' title='Test 1 (bicoid)'/><author><name>Logan</name><uri>http://www.blogger.com/profile/04166352677595317480</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='16' height='16' src='http://img2.blogblog.com/img/b16-rounded.gif'/></author><thr:total>1</thr:total></entry><entry><id>tag:blogger.com,1999:blog-8752779924787100904.post-487920030440017161</id><published>2010-10-25T15:06:00.000-07:00</published><updated>2010-11-04T21:54:49.886-07:00</updated><title type='text'>"Since I cannot prove a lover, To entertain these fair well-spoken days, — I am determined to prove a villain"</title><content type='html'>One of the first things that we have learned in our developmental biology class is that development is hierarchical. Which is to say that a cell that becomes a liver cell will not change back to anything else. Moreover, the cells that derive from that cell will also be liver cells, and they too cannot reverse their fate. This is a story about hierarchical determination in a quite extreme form.&lt;br /&gt;&lt;br /&gt;&lt;i&gt;Copidosoma floridanum&lt;/i&gt; is one of the strangest animals around. It is a parasitoid wasp, animals that are normally compared to the Hollywood monster “Alien”, but frankly, this is far stranger. The adult is free living, and flies around laying eggs in moth caterpillars. One of those eggs will then divide rapidly inside the moth, forming not one but many, many larvae. Most of those larvae will begin the mundane parasitoid task of devouring the moth from the inside out while it is still alive. But some larvae will develop early and gain bodies developed for swimming and fighting. These larvae move through their host’s body, seeking out and killing any other parasitoids that they find. They ensure the survival of their sisters by wiping out everyone else. This “soldier caste” of larvae will never make it out of the moth; they die before adulthood, sacrificing themselves for the benefit of their clone siblings (fig. 1).&lt;br /&gt;&lt;table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"&gt;&lt;tbody&gt;&lt;tr&gt;&lt;td style="text-align: center;"&gt;&lt;img border="0" height="115" src="http://1.bp.blogspot.com/_oWpV5UMX-r4/TMX6kelcSXI/AAAAAAAAABU/kR6x211JhPg/s320/Donnell3.gif" style="margin-left: auto; margin-right: auto;" width="320" /&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td class="tr-caption" style="text-align: center;"&gt;&lt;b&gt;Fig 1: &lt;/b&gt;These pictures show the two types of larvae. Soldier caste on the left, reproductive caste on the right. From Donnell et al. 2004.&lt;/td&gt;&lt;/tr&gt;&lt;/tbody&gt;&lt;/table&gt;&lt;div class="separator" style="clear: both; text-align: center;"&gt;&lt;a href="http://1.bp.blogspot.com/_oWpV5UMX-r4/TMX6kelcSXI/AAAAAAAAABU/kR6x211JhPg/s1600/Donnell3.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"&gt;&lt;/a&gt;&lt;/div&gt;&lt;br /&gt;&lt;a name='more'&gt;&lt;/a&gt;Researchers have done substantial research on this species and other so-called “polyembryonic parasitoids” on account of their unmitigated badassery, as well as smaller matters such as the interesting biological questions that they pose. Questions such as: “How do the two castes (reproductive and soldier) develop from a single genetically identical cell in a environment that is completely uniform, i.e. a single host body?”&lt;br /&gt;&lt;br /&gt;Donnell et al. determined the answer to that question by following the inheritance of germ cells (cells that would form eggs and sperm) throughout the development of this wasp. First they identified a gene that is only active in germ cells, called &lt;i&gt;vasa&lt;/i&gt;, and then created a florescent antibody to the gene product of &lt;i&gt;vasa&lt;/i&gt;. They could then follow the cells in &lt;i&gt;Copidosoma floridanum&lt;/i&gt; that will become eggs and sperm. As it turns out, germ cells are all derived from only one of the cells in the four-cell embryo (fig. 2). This asymmetry continues throughout development. When the embryo splits into a bunch of smaller blobs, each of which will develop into a larva, only some of those blobs will have germ cells. The ones that do will be in the reproductive caste, and the ones that do not will be soldiers (fig. 3).&lt;span id="goog_2143494457"&gt;&lt;/span&gt;&lt;span id="goog_2143494458"&gt;&lt;/span&gt;&lt;span id="goog_2143494459"&gt;&lt;/span&gt;&lt;span id="goog_2143494460"&gt;&lt;/span&gt;&lt;br /&gt;&lt;table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"&gt;&lt;tbody&gt;&lt;tr&gt;&lt;td style="text-align: center;"&gt;&lt;img border="0" src="http://4.bp.blogspot.com/_oWpV5UMX-r4/TMX6ivihJmI/AAAAAAAAABQ/kke9sGn0Mzg/s1600/donnell1.gif" style="margin-left: auto; margin-right: auto;" /&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td class="tr-caption" style="text-align: center;"&gt;In the four-celled stage, only one cell will produce all of the germ cells for all of the reproductive adults. This cell contains a florescent die that makes it appear red and it is pointed out by a white arrow. From Donnell et al. 2004.&lt;/td&gt;&lt;/tr&gt;&lt;/tbody&gt;&lt;/table&gt;&lt;div class="separator" style="clear: both; text-align: center;"&gt;&lt;a href="http://4.bp.blogspot.com/_oWpV5UMX-r4/TMX6ivihJmI/AAAAAAAAABQ/kke9sGn0Mzg/s1600/donnell1.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"&gt;&lt;/a&gt;&lt;/div&gt;&lt;table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"&gt;&lt;tbody&gt;&lt;tr&gt;&lt;td style="text-align: center;"&gt;&lt;img border="0" height="316" src="http://4.bp.blogspot.com/_oWpV5UMX-r4/TMX8QKpSDkI/AAAAAAAAABc/suEbuCwLSIA/s320/donnell2.gif" style="margin-left: auto; margin-right: auto;" width="320" /&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td class="tr-caption" style="text-align: center;"&gt;Once the embryo is being partitioned into clumps of cells that will each develop into a larva, the germ cells are more widely spread out. Most clumps have some germs cells (again they are the glowing red ones) and they will develop into the reproductive caste (labeled SM). The clumps that do not have germ cells are going to grow into soldiers (PS) or are already starting to develop into soldiers (S). From Donnell et al. 2004.&lt;/td&gt;&lt;/tr&gt;&lt;/tbody&gt;&lt;/table&gt;&lt;div class="separator" style="clear: both; text-align: center;"&gt;&lt;a href="http://4.bp.blogspot.com/_oWpV5UMX-r4/TMX8QKpSDkI/AAAAAAAAABc/suEbuCwLSIA/s1600/donnell2.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"&gt;&lt;/a&gt;&lt;/div&gt;This paper seems to provide a lovely example of hierarchy in development. The cells that will develop into germ cells are already partitioned off by the four-cell stage. No other cells will become germ cells and none of the cells derived from the first germ cell will be anything else. The asymmetrical partitioning of those germ cells then allows for the differentiation of different castes when it could not be accomplished with genetic or environmental cues. And again, these divisions are final; if you do not get any germ cells you are doomed to a brief, violent life and an early death. No other options are possible, if none of your cells came are derived from that one special cell in the four-cell embryo, your fate is sealed, and you will never grow your wings, and you will never see the sky.&lt;br /&gt;&lt;br /&gt;The quote in the title is from Shakespeare's &lt;i&gt;Richard III. &lt;/i&gt;&amp;nbsp; &lt;br /&gt;&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;Donnell D, Corley L, Chen G, Strand M. 2004. Caste determination in a polyembryonic wasp involves inheritance of germ cells. Proceedings of the National Academy of Sciences of the United States of America 101: 10095.&lt;div class="blogger-post-footer"&gt;&lt;img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/8752779924787100904-487920030440017161?l=developmentfromanaiad.blogspot.com' alt='' /&gt;&lt;/div&gt;</content><link rel='replies' type='application/atom+xml' href='http://developmentfromanaiad.blogspot.com/feeds/487920030440017161/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/10/since-i-cannot-prove-lover-to-entertain.html#comment-form' title='2 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/487920030440017161'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/487920030440017161'/><link rel='alternate' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/10/since-i-cannot-prove-lover-to-entertain.html' title='&quot;Since I cannot prove a lover, To entertain these fair well-spoken days, — I am determined to prove a villain&quot;'/><author><name>Logan</name><uri>http://www.blogger.com/profile/04166352677595317480</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='16' height='16' src='http://img2.blogblog.com/img/b16-rounded.gif'/></author><media:thumbnail xmlns:media='http://search.yahoo.com/mrss/' url='http://1.bp.blogspot.com/_oWpV5UMX-r4/TMX6kelcSXI/AAAAAAAAABU/kR6x211JhPg/s72-c/Donnell3.gif' height='72' width='72'/><thr:total>2</thr:total></entry><entry><id>tag:blogger.com,1999:blog-8752779924787100904.post-4159157549727813309</id><published>2010-10-03T21:57:00.000-07:00</published><updated>2010-10-03T21:57:31.678-07:00</updated><title type='text'>This is a long set-up to a bad pun</title><content type='html'>As our developmental biology class ramps up after P.Z.’s unfortunate illness, we have begun to read and discuss Sean Carroll’s book &lt;u&gt;Endless Forms Most Beautiful&lt;/u&gt;. At the end of the fourth chapter of that book, Carroll writes:&lt;br /&gt;&lt;blockquote&gt;“Francois Jacob has pointed out that all of our explanatory systems, whether mythic, magic, or scientific, share a common principle. They all seek, in the words of physicist Jean Perrin, ‘to explain the complicated visible by some simple invisible.’”&lt;/blockquote&gt;I think that &lt;a href="http://en.wikipedia.org/wiki/Fran%C3%A7ois_Jacob"&gt;Jacob&lt;/a&gt;, a member of the “Indiana Jones society of scientists who fight Nazis”, is likely correct that scientific and religious systems of knowledge attempt to fulfill a similar role. The difference between the two is that science has to provide evidence for the “simple invisible” that it postulates. To do this we must find a way to illuminate the hidden mechanisms that drive our natural world. The experiments that manage to most clearly show these mechanisms are the ones that become famous. The elegance with which finch beaks or a double slit experiment can reveal natural truths is what makes them so compelling.&lt;br /&gt;Carroll recognizes the importance of making invisible mechanisms apparent, and compares it to our ability to visualize gene expression using florescent antibodies or other molecular mechanisms. However I think Carroll sells himself short. Even before there were the means to make pretty pictures of embryos with glowing stripes, we could still visualize the effects of “master genes” such as the hox genes. We did this by making monsters. Although it may be less elegant than the newer molecular tools, one can gain insights into the process of development by fucking up embryos and examining the horribly deformed monsters that result. The second chapter of Carroll’s book is thick with examples of scientists who created monsters to learn about development. Although the experiments may seem slightly macabre, the discoveries that result are often really neat. One of my favorite examples that we’ve discussed thus far is the discovery of the &lt;a href="http://en.wikipedia.org/wiki/Zone_of_polarizing_activity"&gt;zone of polarizing activity&lt;/a&gt;.&lt;br /&gt;While an embryo is developing, how does each cell know where it is in the body? How do pinky cells know to make pinkies, and thumb cells know to make thumbs? Saunders and Gasseling (1968) discovered one clue to this puzzle by creating mutant chicken arms. Birds have lost the digits that would correspond to our thumb and pinky, leaving them with three digits on their limbs. But when these researchers took early embryos (before they developed anything beyond stumpy limb buds) and moved bits of the developing limb around they created some interesting mutants. When they removed the back of a limb bud from one developing chicken and attached it to the front of the limb bud in another, the resulting wing had two hands. The small number of transplanted cells were able to direct the formation of an entirely new hand (see figure).&lt;br /&gt;&lt;div class="separator" style="clear: both; text-align: center;"&gt;&lt;a href="http://www.utm.utoronto.ca/%7Ew3bio380/picts/lectures/lecture19/LIMBDEV6.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"&gt;&lt;img border="0" height="242" src="http://www.utm.utoronto.ca/%7Ew3bio380/picts/lectures/lecture19/LIMBDEV6.jpg" width="320" /&gt;&lt;/a&gt;&lt;/div&gt;&lt;br /&gt;This finding showed that a small number of cells could inform the surrounding cells about their relative positions. In essence, saying, “I’m making a ring finger, if you are close to me, build a middle finger and if you are far away make a pointer finger” (remember that birds have only three digits per wing). Saunders and Gasseling called the area of cells that organized the rest of the limb the “zone of polarizing activity” or ZPA. The ZPA provides information about its position by expressing the &lt;i&gt;sonic hedgehog&lt;/i&gt; gene. This creates a protein that diffuses out to the surrounding cells. If there is a lot of the protein around, a cell knows that it’s close to the ZPA and that it should make the back of a wing. If the protein is scarce, a cell is far from the ZPA and should build the front of a wing. The ability of a small number of cells to organize the development of larger structures through the expression of genes is important throughout development.&lt;br /&gt;&lt;br /&gt;After Saunders discovered the ZPA, he left the scientific world and started a restaurant franchise. The tagline was: “Colonel Saunders, the chicken wing that twice as good as the competition!”&lt;div class="blogger-post-footer"&gt;&lt;img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/8752779924787100904-4159157549727813309?l=developmentfromanaiad.blogspot.com' alt='' /&gt;&lt;/div&gt;</content><link rel='replies' type='application/atom+xml' href='http://developmentfromanaiad.blogspot.com/feeds/4159157549727813309/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/10/this-is-long-set-up-to-bad-pun.html#comment-form' title='3 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/4159157549727813309'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/4159157549727813309'/><link rel='alternate' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/10/this-is-long-set-up-to-bad-pun.html' title='This is a long set-up to a bad pun'/><author><name>Logan</name><uri>http://www.blogger.com/profile/04166352677595317480</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='16' height='16' src='http://img2.blogblog.com/img/b16-rounded.gif'/></author><thr:total>3</thr:total></entry><entry><id>tag:blogger.com,1999:blog-8752779924787100904.post-256824403057319661</id><published>2010-09-12T19:30:00.000-07:00</published><updated>2010-09-13T10:59:43.489-07:00</updated><title type='text'>Fertilization</title><content type='html'>Because this is a blog about development, perhaps the first post should be called fertilization.&lt;br /&gt;&lt;br /&gt;My name is Logan Luce; I am a senior biology major at the University of Minnesota Morris. I am taking a developmental biology course from &lt;a href="http://scienceblogs.com/pharyngula/"&gt;P.Z. Myers&lt;/a&gt;, a man who moonlights as a horrible amalgamation of scientist and atheist, blogger and firebrand. P.Z. has decided to have all of his developmental students start blogs, presumably for the purpose of mocking the diminutive number of hits that we can eke out of the internets. He has hinted that the final exam will be crashing a poll.&lt;br /&gt;&lt;br /&gt;&lt;br /&gt;A bit about me and the name of this blog: I am primarily interested in ecology and evolutionary biology, and am fascinated by insects and dinosaurs. If you assume that my interests are the same a prototypical 8 year old boy, you would be close to the mark. A naiad is the larval stage of an insect in the orders &lt;a href="http://en.wikipedia.org/wiki/Odonata"&gt;Odonata&lt;/a&gt;, &lt;a href="http://en.wikipedia.org/wiki/Ephemeroptera"&gt;Ephemeroptera&lt;/a&gt; or &lt;a href="http://en.wikipedia.org/wiki/Plecoptera"&gt;Plecoptera&lt;/a&gt;. These insects exhibit incomplete metamorphosis, so the larvae appear similar to the adult except for the lack of fully developed wings or genetalia. Unlike the larvae of other some related insects (such as grasshoppers) naiads do not live in the same environment as the adults that they later become. A naiad may begin as a badass killing machine that hunts in the bottom of a lake, but it will become a badass killing machine that hunts in the sky. Development from a naiad involves moving from freshwater into the air, losing gills and gaining wings, while still maintaining a similar sort of form. As an undergrad that hopes to become a grad student doing cool research on neat bugs someday, I commiserate with the naiad. I don’t want to change too much, but I’m looking foreword to moving to a new environment and the possibility of gaining wings...&lt;br /&gt;and 360 degree vision...&lt;br /&gt;and the ability to hunt and kill on the fly.&lt;br /&gt;&lt;div class="separator" style="clear: both; text-align: center;"&gt;&lt;a href="http://www.martinpustelnik.com/wp-content/uploads/aeshna-affinis-5-1000.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"&gt;&lt;img border="0" height="320" src="http://www.martinpustelnik.com/wp-content/uploads/aeshna-affinis-5-1000.jpg" width="213" /&gt;&lt;/a&gt;&lt;/div&gt;&lt;br /&gt;(That's what grad school is like, right?)&lt;div class="blogger-post-footer"&gt;&lt;img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/8752779924787100904-256824403057319661?l=developmentfromanaiad.blogspot.com' alt='' /&gt;&lt;/div&gt;</content><link rel='replies' type='application/atom+xml' href='http://developmentfromanaiad.blogspot.com/feeds/256824403057319661/comments/default' title='Post Comments'/><link rel='replies' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/09/fertilization.html#comment-form' title='15 Comments'/><link rel='edit' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/256824403057319661'/><link rel='self' type='application/atom+xml' href='http://www.blogger.com/feeds/8752779924787100904/posts/default/256824403057319661'/><link rel='alternate' type='text/html' href='http://developmentfromanaiad.blogspot.com/2010/09/fertilization.html' title='Fertilization'/><author><name>Logan</name><uri>http://www.blogger.com/profile/04166352677595317480</uri><email>noreply@blogger.com</email><gd:image rel='http://schemas.google.com/g/2005#thumbnail' width='16' height='16' src='http://img2.blogblog.com/img/b16-rounded.gif'/></author><thr:total>15</thr:total></entry></feed>
