Chigozie's Fun With Jolecule

Ribonuclease

            Ribonuclease is the enzyme that digests RNA. It is a type of nuclease that catalyzes the degradation of RNA into smaller components. Ribonuclease is small, stable, and easily purified and has been an important enzyme in biochemical research. Ribonuclease can be divided into two groups: endoribonucleases and exoribonucleases. Endoribonucleases break down RNA from the middle through cleaving while exoribonucleases break down RNA from the 3’ or 5’ ends. Ribonuclease cleans cells of RNA that is no longer required and plays a key role in the maturing of RNA molecules such as messenger RNA and non-coding RNA. Also, ribonuclease acts as a first defense against RNA viruses and is the building block of more advanced immune strategies in cells. Because of ribonuclease’s nature to break down RNA, RNA in the cells has to be protected from ribonuclease. Defense mechanisms such as 5' end capping, 3'end polyadenylation, and folding within an RNA protein complex are implemented in cells. The alpha helices in this tertiary structure contain glycine which is the simplest amino acid with just an amino group, a carboxyl group and two hydrogen atoms. The glycine helps maintain structural alignment on the interior of ribonuclease as it breaks down RNA.

This is a close up on the tertiary structure of ribonuclease. Here one can see the alpha helices and the beta sheets that make up ribonuclease.

This is the catalytic part of the ribonuclease enzyme. Asp10, Glu48, Asp70, Asp134, and His124 can all be found in this area. These all contribute to catalysis in the enzyme by coordinating divalent metal ions that need to be present in order for the cleavage of RNA to be carried out. This would most likely be found in endoribonucleases.

This is a close up of an alpha helix in ribonuclease. This alpha helix contains glycine, which is important for the maintenance of structural alignment in ribonuclease. This glycine also adds to flexibility in this region.

Daphne's Fun With Jolecule

To begin, I went to http://jolecule.appspot.com, where I clicked on "Myglobin" to view a sample protein structure. I then decided that during this activity, I would primarily analyze lysozyme, which is a bacterial wall digestor. This enzyme manages to break through bacterial walls by catalyzing hydrolysis through the addition of water molecules. Lysozyme is an enzyme which is quite abundant in fluid secretions of animals, as it acts as a protectorate against bacteria. The function of lysozyme proteins is to break down the polysaccharide chain by the process of hydrolysis. The structure of this protein is what enables it to perform this function. The structure is partially beta strand and partially alpha helices. The differential between the two (which are primarily concentrated on their own) occurs where the molecule bonds to the sugar. The amino acid side chains glutamic acid 35 and aspartic acid 52 are known to be critical in the function of this protein. Because the amino acid Glu35 is located at the end of the beta strand, it is able to break down the polysaccharide train by breaking off molecules to form water molecules. A mature lysozyme molecule contains 128 amino acids. With these amino acids, lysozyme is able to hydrolyze a beta-glycosidic linkage between the N-acetylmuramic adic and N-acetyl glucosamine within the polypeptide chain located in the bacterial cell walls of invading specimen. Lysozyme is an incredibly important enzyme, as it helps to fight off bacterial infections which could otherwise be harmful to the inhabitants.

The full view of the lysozyme molecule. The polysaccharide substrate is at the
bottom right of the image. It is shown here without H2O molecules, as it would
be before it performs hydrolysis on a bacterial wall.

Here, the lysozyme molecule is pictured with water molecules added, as they
would be when the molecule bonds to a bacterial wall through the process of
hydrolysis. The polysaccharide substrate is at the bottom right of this image as
well. Note how H2O Molecules are heavily concentrated near the
polysaccharide chain, where bonding occurs between the lysozyme protein and
the bacterial wall.

This image is showint the polysaccharide chain attatched to the protein
lysozyme

The critical molecule Glutamic acid 35 shown as the bonding site between
the protein lysozome and the polysaccharide

 Works Cited

"Lysozyme." - Worthington Enzyme Manual. N.p., n.d. Web. 08 Nov. 2014.

Rana's Fun with Jolecule

Lysozymes

            In order to explore protein structures I went onto a protein model visualizer, called Jolecule, on http://jolecule.appspot.com/.  Once on the main page, I clicked on the “myoglobin” button, and then the “garden” link in the upper right corner.  This last link brought me to a variety of proteins to select from and learn about.  After I have looked through them, I chose to research the Lysozyme protein. 

            Lysozymes are small protein enzymes that bind to polysaccharide chains and break them apart by hydrolysis.  These enzymes protect humans from danger of bacterial infection by attacking and destroying the cell walls of the bacteria.  The bacteria itself constructs a tough skin of carbohydrate chains (sugars) that are interconnected by short peptide strands.  In order to fight the bacteria, the lysozyme breaks the carbohydrate chains of the bacteria, which in turn, destroys the structural integrity of the cell wall and causes the bacteria to burst.  However, as efficient as it is in killing bacteria, the lysozyme is too large of a molecule to travel between cells, that it cannot rid the entire body of disease.  Lysozymes occur in plant and animal tissues and in secretions such as tears, saliva and mucus.  Also it is greatly found in egg whites.  It is found in our tears, and mucus to resist infection on exposed surfaces.  Lysozyme also provides protection in the blood because blood is the worst place for bacteria to grow.  In general Lysozymes protect many places that are rich in potential food for bacteria.  As well, Lysozyme is added to digest cell debris and release the inclusion bodies. 

Furthermore, Lysozyme is a crystal structure with two structural domains.  One is made up of mainly alpha helices, and the other is mainly beta strands.  The boundary between the two domains forms a split where the substrate binds.  Lysozyme adds a molecule of water to the bond between two sugars, which breaks the bond.  This is catalyzed by two amino acid side chains in the active site of the enzyme.  These active sites are glutamate 35 and aspartate 52.  

- This is the overall picture of the lysozyme protein with the polysaccharide substrate in the center.

- This is one of the glu-35 active sites of the enzyme, which would lie next to the polysaccharide.  

- This is one of the asp-52 active sites of the enzyme, which would lie next to the polysaccharide.  

Rameia's Fun with Jolecule

Cyclooxygenase 

Rameia Ramsey 

 The protein I choose to examine and learn about is Cyclooxygenase. Cyclooxygenase, also known as COX, is an enzyme that is responsible for the creating of prostanoids, which are involved in the inflammatory responses. There are three main groups of prostanoids, which are the prostaglandins, prostacyclins, and thromboxanes. Prostaglandins are mediators of inflammatory and anaphylactic reactions, prostacyclins are seen in the resolution phase of inflammation, and thromboxanes are mediators of vasoconstriction, which is the narrowing of blood vessels from contractions from the muscular walls.

There are two forms of the Cyclooxygenase protein respectively named , COX-1 and COX-2. Both of these versions use arachidonic acid to produce prostaglandin but there are certain features that help make COX-1 unfavorable and COX-2 favorable. There are such things called COX-1 inhibitors, these are agents that hinder the action of the enzyme COX-1. The COX-1 enzyme is found in most cells and helps maintain the stomach’s. For example, inflammatory drugs such as aspirin or ibuprofen block the actions of COX-1 and COX-2. The COX-1 inhibitors are able to decrease inflammation but they can also decrease the protective mucus in one’s stomach, which in turn can cause a variety of health concerns such as an upset stomach or ulcers. This is how a COX-1 inhibitor can be seen as undesirable and unfavored. COX-2 inhibitors are agents that block the enzyme COX-2 which causes inflammation. The COX-2 enzyme converts arachidonic acid to prostaglandin which cause pain and inflammation, such as arthritis, in an individual's body. The COX-2 inhibitors relieves this pain. So drugs such as Bextra and Vioxx are examples of COX-2 inhibitors that help protect against the COX-2 enzyme. This is how COX-2 would be seen as more favorable to than COX-1.

Both COX-1 and COX-2 are tertiary structures because of the fact that the amino acids and the binding site and catalytic regions are almost exactly the same.  COX-1 and COX-2 are both homodimers. A dimer is a chemical compound that is made of two identical or similar monomers. A homodimers would be a dimer made of two identical monomers. They also both contain three high mannose oligosaccharides, a fourth oligosaccharide is found only in COX-2 which helps with its degradation. Each monomer of the dimer has three domains, which are the epidermal growth factor, membrane binding, and catalytic domain. On the other side of the membrane binding domain is the peroxidase active site which contains the heme. The active site of COX-2 is larger than the active site for COX-1. There are many differences between the two. COX-1 is produced under all types of physiological conditions, while COX-2 is produced only during specific conditions like inflammation. This would also explain why COX- 1 is found in the kidneys, stomach, and platelets and COX-2 is found in macrophages, leukocytes, and fibroblasts. They are also produced differently, COX-1 is made continuously while COX-2 is only produced when needed. COX-1 is useful to ones body and does not need the aid of inhibitors, but COX-2 plays a major role in inflammation and therefore inhibitors are needed for the COX-2 enzyme.

This is an aspirin molecule in the Cyclooxygenase protein.

This is the bonding site of the aspirin molecule.  This is what prevents the arachidonic acid which eventually gets converted into prostaglandin from binding.

This is the tunnel that leads to the active site.

Joshua's Fun with Jolecule Blog Post

Joshua Everett
Fun with Jolecule

Antibodies

Antibodies are molecules that search for viruses, bacteria, and other infectious molecules within an organism. These antibodies are commonly circulating in the blood of humans along with examining all objects that they come into contact with. Specifically when an antibody finds a foreign object in the blood, it attaches to the object and fights off any infection the object might bring to the human. This process can only be fulfilled if the object is a virus and an abundance of antibodies attaches to its surface. On the other hand, if the foreign object in the blood is a type of bacteria, the antibody will attach to the bacteria and only act as a marker protein. This marker will alert more powerful defense molecules to fight off the bacteria from causing infection. Antibodies function in direct correlation with the immune system of individuals, for example, without antibodies people would have a weak immune system and would be unable to fight of disease. Without antibodies, there is not a functional immune system in the body, and individuals would be suffering from constant sickness. 

The basic structure of an antibody is simply a molecule that is made of up of several flexible arms that have binding site at the end of each of them. The abundance of arms help ensure that the antibodies are always prepared to fight off any foreign object no matter what the shape consists of. The binding sites of these flexible arms also are able to work symbiotically to be able to attach to viruses and bacterium despite any complications with the shape. Antibodies, however, vary in their properties and distinctions. Some antibodies only have two arms with binding sites, while others may have ten arms with binding sites. Some antibodies even have additional long flexible linkers that are attached from the molecule to the arms with allows some antibodies to have better coverage over the foreign object they are binding to because of the extra length. Various antibodies originate from genes that are recombined in lymphocytes which are the blood cells that create antibodies. The variety of antibodies creates a system in which only certain antibodies are active when different infections are present in the body. Different antibodies have different binding properties which allow for all viruses and bacterium to be fought off with a different antibody. 

Furthermore, all antibodies are composed of four major chains, two long and heavy chains and two short and light chains. Between two of these chains, a heavy and a short chain, there is room for a binding site from a pocket that is formed between them. These long protein chains vary in length and create many loops which allow them to be appropriately called, hypervariable loops. The loops these chains make form these pockets that allow antibodies to attach to foreign molecules that are attacking the body. The other parts of the antibody molecules have many other chains/arms that are connected to a central domain called an antigen (an antibody generator). This formation stays continually uniform with every antibody. In addition, the antibody structure is also on a quaternary level of protein structure because of the many polypeptide chains that are part of an antibody. In Jolecule, the protein structure depicted only shows one immunogloulin. An antibody will have three of immunologists in its structure. A quaternary structure is considered to be any protein that has more that two polypeptide chains in a molecule. An antibody has many chains, two heavy and two light chains and even more when all three immunogloulins are present, which allows an antibody to fit the criteria of a quaternary structure.   

This picture is depicting the overall structure of what an antibody looks like. The immune system forms antibodies that are made up of three major components, light chains, heavy chains, and a central domain, an antigen. All three parts of the antibody work together to be able to fight of foreign particles. 

This picture depicts the top of the binding site where the chains are forming loops in the molecule. In the immune system, antibodies are produced from the mutated residues contributed by the binding site from the loops shown.

This picture depicts a single protein called an immunogloulin. An immunogloulin is only one of the three immunogloulin in a complete antibody. One immunogloulin contains heavy chains, light chains, and an antigen is attached between the chains.  Two immunogloulins act as the Y structure of an antigen and contains a heavy and light chain. A third immunogloulin acts as a base for the antigen because it only contains two heavy chains and not a light chain and a heavy chain. 

This picture depicts the heavy chain of the antibody goes below the antibody into another domain. In this domain, the heavy chain interacts with other proteins. 

Jazmean's Fun with Jolecule

Glucocorticoid Receptor

After playing around in Jolecule, I decided to learn more about the different proteins they had available for viewing. The protein that peeked my interest was the Glucocorticoid Receptor. As presented in Jolecule, this protein is in its tertiary structure due to the folding of the protein.This protein is responsible for controlling stress response in the nucleus. The receptor binds to cortisol (cortisol is a steroid hormone that is produced by the adrenal gland) and then travels to the nucleus and binds to the DNA within the nucleus. This process of binding can trigger either two responses; the expression of anti-inflammatory proteins in the nucleus is up regulated or the expression of pro-inflammatory proteins in the cytosol is repressed. Inflammatory proteins are responsible for the healing of tissue when there is an injury present. These proteins can cause redness, heat, and pain at the site of the injury. If the inflammatory proteins persist for too long, the pain at the injury site can become chronic. Glucocorticoids stop this from happening. Because of this, glucocorticoids (as noted by NCBI) are widely used for the suppression of chronic inflammatory diseases such as asthma. Glucoorticoids receptors are also gaining interest within the field of Psychology as these receptors are also responsible for the response of stress in the brain. Psychologists believe that further understanding how the Glucocorticoid Receptor works will help in understanding how psychological diseases develop such as depression.

The Glucocorticoid Receptor is modular in structure. This means that within the receptor, there are different structural parts that have multiple functions. Like all steroid receptors, the Glucocorticoid Receptor has a variable domain, DNA binding domain, hinge region, and hormone binding domain. The variable domain is different for each steroid receptor. For GR, it has the N-terminus which directs the delivery of the protein to the correct organelle. The DNA binding domain controls which gene will be activated when it comes in contact with the DNA within the nucleus. The hinge region is responsible for the movement of the receptors to the nucleus and the hormone binding domain is responsible for the affect of the response of the receptor.

This shows the DNA Binding Domain. This is the only DNA Binding Domain in the Glucocorticoid Receptor 

This is the Hinge Region.

This is the N Terminal 

This is the overall protein

The Carbon Fixer, Rubisco Protein by Nida Ali

Rubisco, the Carbon Fixer Protein

Through the Jolecule program, I chose the Rubisco protein, which is known as the carbon fixer. Rubisco is used to catalyze the first major step of carbon fixation in the Calvin Cycle. Rubisco is often referred to as the most abundant protein in the world. It goes through the Calvin cycle by undergoing photosynthesis and molecular synthesis, which is seen in all plants. Carboxylation or even oxygenation of RubP, also known as ribulose-1,5-bisphosphate, is catalyzed by the Rubisco protein with carbon dioxide or oxygen. Since carbon is “locked” in highly oxidized forms, carbon dioxide gas, oxidation with carbon will allow it to be "fixed" into organic forms. Rubisco takes carbon dioxide and attaches it to ribulose bisphosphate. Rubisco then takes the chain and shortens them into two identical phosphoglycerate pieces that each contain three carbon atoms. Rubisco produces phosphoglycerate which is then recycled to create more ribulose bisphosphate in order to continue on the process of the carbon fixing cycle.

Rubisco contains a three-dimensional structure and the protein strands coil on themselves in a Quaternary structure which makes their function possible. Rubisco is composed of eight large protein chains, which forms four dimers, as well as eight small protein chains, which assembles the small subunit. A dimer is a macromolecular complex quaternary protein structure. The active sites of Rubisco are located on the large subunits between the dimer pairs. Rubisco's catalytic properties/function relies on the large subunits of the protein. In order for this enzyme to do its job, a Mg2+ ion must be positioned in an active site and a CO2 molecule added. This CO2 then reacts to produce a 6-carbon intermediate molecule. Thus, the specific shape of each active site only allows for the binding of certain molecules which then allows rubisco to carry out its function.

Here is an overview of a version of Rubisco from a photosynthetic bacteria. It is displayed as a Quaternary structure of inter-twist alpha helices with kinks. This complex protein needs the Quaternary arrangement of the polypeptide chain in order for it to be a functional protein.

Carbon is removed from Co2 and is added into ribulose bisphosphate, a short sugar chain with five carbon atoms. Since carbon is “locked” in highly oxidized forms, it must be“fixed” into more organic forms through the oxidation with carbon. Here there are two tertiary forms of the protein which combine to display a functional protein in the form of a Quaternary structure. This zoomed in picture highlights the folds of the protein, which is displaying the various points of attraction from the secondary structure and therefore create kinks within the strands.

In order for Carbon Fixation to occur, the Mg metal ion is required for the coordinate reactions. The Mg ion is positioned in an active site.

Rubisco accepts both Carbon Dioxide and O2 as a substrate, but here Mg ions coordinate with Oxygen atoms in order to undergo Carbon Fixation. The activation site of this enzyme requires the addition and activation of Carbon Dioxide to Lysine.

Jube's Fun with Jolecule

                                                                  Antibody Protein 

        I studied the antibody protein. Also known as immunoglobulins, antibodies are specialized cells of the immune system that work to prevent antigens from attacking the body. They work to detect foreign particles and fight it off to defend the body’s immune system. Using jolecule, I was able to see the specific arrangement of an antibody. Antibodies are Y shaped, and they are composed of two antigen binding sites. Each binding site has a heavy chain and a light chain. This variation allows the binding sites to vary from one antibody to the next. The following figures highlight some of the essential aspects of the protein.

           Figure 1: Y Shaped Structure                     

   Figure 2: Constant Region  

Figure 3: Antigen Binding Site

Figure 1 shows the Y shaped structure of the antibody. This structure is beneficial because it can be modified so that the antibody can attach to the specific shape of the protein or sugar molecules attached to the antigen. Furthermore, figure 2 shows the constant region of the structure which functions to communicate with the other proteins in the immune system to determine how to get rid of the antigen. The ends of the heavy (green) chain and light (purple) chain are the constant regions of this structure. In contrast, the tips of the antibody (where the chain labels are in figure 1) represent the antigen binding site as depicted by figure 3. Figure 3 shows an overhead view of where the antigen binds to the chains. When binded, the immune system will be able to attack the antigen to protect the body.

Evidently, all three figures show the tertiary structure of the protein because the light chain and heavy chain are both apparent. To add, the polypeptide chains have folded into their functional shape. As a result, interactions between the chains allow for them to stabilize so that they can function efficiently. Essentially, the presence of both chains contribute to the function of the protein because both chains work together to attach to the antigen present so that it can, ultimately, be destroyed.

Sara Fun with Jolecule Article

Sara Bearden

Cyclooxygenase

        After playing around in the program Jolecule I chose to learn more about the protein Cyclooxygenase.  This protein is know to be the site of pain-killing.  This protein is involved in the first step of creating postaglandins from a common fatty acid.  These postaglandins are what deliver and strengthen pain signals, induce inflammation, and control the constriction of muscle cells. There are different postaglandins that control different processes but, they are all created form the cyclooxygenase protein.  In order to create postaglandins the cyclooxygenase adds two oxygen molecules to arachidonic acid to start a set of reactions that will create a host of unusual molecules.  As we know the drug aspirin is used as a pain killer well, that drug blocks the binding of the arachidonic acid in the cyclooxygenase active site. That leads to a different product so new messages are delivered and we end up not feeling pain and don't launch an inflammation response.  There are two isomers of this protein and they are used for different purposes.  COX-1 is used for creating postaglandins in order to send basic housekeeping messages to the body in different cells.  COX-2 is used only in certain cells in order to signal pain and inflammation.

         The quaternary structure of this protein is a dimer of identical subunits so there are two active sites of cyclooxygenase and two peroxide active sites ( activate the heme groups that participate in the cyclooxygenase reaction). By having this structure the active sites are close by allowing the reaction to occur quicker and smoother. Each subunit has a knob that is covered with hydrophobic amino acids which allows anchorage to the membrane of the endoplasmic reticulum.  Therefore, the structure doesn't move and the acid that is used for the reaction can find the protein to do the reaction. The cyclooxygenase active site is reached by a tunnel in the protein which leads the arachidonic acid to the enzyme for processing and starting the reaction.  Aspirin can block this site so the reaction cannot occur and leading to different messages being delivered where we end up with feeling no pain. 

 This photo shows how the active site of cyclooxygenase is deep inside the protein.  The ribbon in front of it is the tunnel that would lead the arachodine acid to the active site to bind and start the set of reactions.  At that site is also where the aspirin would go and stop the binding from happening.

 The two active sites of the protein are shown in this photo.  The top one would be the the cyclooxygenase active site where the bottom would be the peroxide active site.  As shown in the photo the two sites are near each other and this is due to the structure of the protein.

 This screenshot shows some of the structures the atoms formed within the shape of cyclooxygenase.  These pentagon shapes are showing how they are non-polar because there are no water molecules around them.  Therefore, the bonds are equally sharing the electrons. Also making the whole protein non-polar which, means it's hydrophobic.

The last screenshot is an overview of the structure of the protein.  You can see the alpha helices intertwine with each other to form the the quaternary structure of a dimer.  There is are two identical subunits that are apart of the dimer which allows for double the active sites and with the alpha helices as a tertiary structure the active sites are in proximity of each other.

Rameia's Phylogeny Article

Phylogenetic Article

My question for my investigation is how are leopards(Panthera pardus) and tigers (panthera tigris) related to wild deer mice(Mus musculus)? My hypothesis is that the leopard and tiger are more closely related to each other than to the wild deer mouse, and that the wild deer mouse would be the outgroup organism.  This question was interesting to me at first because I was curious about how the leopard and tiger obtained their color patterns. Further down in my research it also interested me that the same gene that determines color patterns in the leopard and tiger is the same gene that colors a wild deer mouse, which is the Agouti gene.  Overall I was curious as to what genes and mutations in the genes were responsible for the colors and patterns of these organisms.

To figure out which genes are responsible for the color pattern of each organism, I initially used google to search for the names of the genes.  After discovering the gene name, I procceded to use www.ghr.nlm.gov to understand the specifics of the gene and how it works in organisms.  By doing this I also discovered that I would be using only protein sequences in order to compare the organisms I had chosen.  Knowing this I used www.ncbi.nlm.gov to find the protein sequences I would need in order to compare and create a phylogentic tree for all of the organisms.  By using the program Clusterx, I copy and pasted the sequences into a plain text file in order to align them.  After aligning the sequences, I was able to use Njplot to create a phylogenetic tree which compares the relationships off all the organisms I had chosen.

As you can see in the phylogenetic tree, it has came to the conclusion that the leopard and the wild deer mouse seem to have the most similarities with each other.  As seen in the phylogenetic tree the leopard and the mouse branched off of the tiger.  This means that the leopard and the mouse share the most recent common ancestor between all three organisms.  I believe my question of how the leopard and tiger are related to the wild deer mouse was answered, but I do not believe that my findings and the phylogenetic tree are an accurate representation of the evolutionary relationship between all three organisms. The tree shows that the tiger is the outgroup organism.  The leopard and tiger should be more closely related to each other than to the wild deer mouse.  I am basing this off of the fact the the leopard and tiger both share the same genus.  But, by using the Agouti gene which codes for the color pattern in all three organisms, it is possible that the protein sequence of the leopard and the wild deer mouse are more similar to each other in that sense.  

According to an article on www.dailymail.co.uk, scientists had discovered that the Agouti gene is responsible for the color pattern on the deer mice.  In the mice, the  Agouti gene is very active on the rodent's stomach where it causes a delay of the maturation of cells that produce pigment.  Scientists believe that this gene is also responsible for the color patterns of other vertebrates, such as the spots on a leopard, and the stripes on tigers and zebras.  Another article on www.blogspot.com states that the Agouti gene is found in variety of organisms that determines whether or not they have patterned fur.  The gene causes a range of pigmentation, for example the darkening of patches and fur, as well as giving a tiger its stripes.  Based on these articles, the phylogenetic tree that was made is an accurate representation of the relationship based on the Agouti gene of these three organisms.  But, if this is the case then all three organisms should come off of the same branch point and share the same recent common ancestor.  Again, the phylogenetic tree seems inaccurate in this sense.  

Improvements that could have been made to ensure the accuracy of the evolutionary relationships shown in the phylogenetic tree could have been to use longer protein sequences.  Using longer protein sequences could have been a make or break factor in the evolutionary relationships.  Even though all of the protein sequences were not the same length, using longer sequences as well as sequences with similar number of proteins could have provided more balance between the organisms.  Another improvement that could have been made is the addition of other organisms who also possess the Agouti gene.  This also could have gave the phylogenetic tree some balance, possibly creating a variety of outcomes.  

Works Cited

• The Blue Tiger Sightings - Unsolved Mysteries In The World. (n.d.). Retrieved October 24, 2014.
• Fiona Macrae for the Daily Mail. (n.d.). How the leopard REALLY got his spots: Scientists identify gene that determines patterns of colour on mice. Retrieved October 24, 2014.

Jazmean's Phylogenetic Analysis Article

Jazmean Williams

AP Biology

Phylogenetic Analysis

How Closely Related are Dogs to Humans?

The basis of this Phylogenetic Analysis revolves around the domestication of dogs (Canis lupus familiaris) by humans (Homo sapiens). While there is no clear date as to when dogs were domesticated by humans, scientists know that dogs have been domesticated for a long time. Scientists also know that early human hunter-gatherers used dogs to perform many roles such as hunting, herding, and providing protection. This leads to the conclusion that humans domesticated dogs in order to improve their style of living. But why dogs? Why not choose another animal to domesticate? The answer lies within the idea of companionship. Dogs are known today as being man's best friend, however, becoming someone's best friend takes time and an immense amount of effort. Could it be that early humans were willing to put forth the effort in order to find another species they could relate to besides their own? Could the domestication of dogs begun with the intention of companionship instead of the completion of menial labor and protection?

To figure this out, three genes that exist in both dogs and humans will be analyzed and compared on a Phylogenetic Tree to see how closely related dogs and humans are. The closer in relation the dog and human are in the tree, the more alike they are, and the more likely they are to develop a bond with each other. The three genes that will analyzed are the PHOX2A gene, the TGIF1 gene, and the PROP1 gene. The PHOX2A gene deals with the development of the nervous system which affect bodily functions such as heart rate and breathing. The TGIF1 gene provides instructions to develop the front part of the brain. The PROP1 gene helps the pituitary gland release hormones that aid in growth and reproduction (along with other bodily functions). If the nervous system and front part of the brain develop in a similar fashion , then one an infer that there will be similar bodily and brain functions between the human and the dog. This applies too if the human and the dog grow and reproduce in a similar fashion. Also, in the tree, an outlying animal (the Zebrafish) will also be used to further help compare the dog with the human on the tree.

After doing the Phylogenetic Tree for each gene, it shows that the dog and the human share a recent common ancestor. Because both the dog and human share a more recent common ancestor, they share common structures and even patterns of behavior. All three animals share a common ancestor, but it is the dog and human that is most closely related due to both species having a more recent common ancestor with each other.

The results and inferences of this Phylogenetic Tree Analysis is similar to the information presented in scholarly articles. In the National Geographic, Jane J. Lee wrote an article about how the dog and human genomes evolved together in parallel evolution. Weiwei Zhai, a genetics researcher Lee references in their article, used genes that helped in the transport of neurotransmitters and cholesterol processing to compare the two species. He found that those genes were selected for in both humans and dogs. Zhai also found that there are cancer-related genes that are evolving together in humans and dogs. Weiwei Zhai believes this parallel evolution occurred due to the fact that dogs and humans lived closely together in the same environment. There is still debate however on whether the parallel evolution between humans and dogs are unique or if they exist in other domesticated animals as well.

The Huffington Post also reported an article about how dog brains process voices and emotions like humans which further supports the idea of humans and dogs being alike. Attila Andics, the researcher cited in this article, proposes that voice recognition between humans and dogs can explain why communication between the two species is so successful. He also proposes that this discovery can lead to an explanation of the “unique bond” humans and dogs have together.

The evidence provided from the Phylogenetic Tree and from the researchers aforementioned can solidify the possibility that dogs were domesticated with the intention of companionship and not labor. The companionship between the dog and the human could then lead off to a symbiotic relationship between the two species which is shown to have happened due to present day conditions. This way of thinking supports the idea that two species that live in the same environment will not always result to competition, but can work together to form a relationship that benefits the both of them.

PHOX2A Gene Tree
TGIF1 Gene Tree
PROP1 Gene Tree

Primary Sources for Discussion

http://www.huffingtonpost.com/2014/02/21/dogs-brains-process-voices-emotions-like-humans_n_4830393.html

http://news.nationalgeographic.com/news/2013/13/130514-dogs-domestication-humans-genome-science/

Gene Sequences Used

http://ghr.nlm.nih.gov/gene/PHOX2A

http://ghr.nlm.nih.gov/gene/PROP1

http://ghr.nlm.nih.gov/gene/TGIF1

http://www.ncbi.nlm.nih.gov/nuccore/545536496?report=fasta

http://www.ncbi.nlm.nih.gov/nuccore/545506324?report=fasta

http://www.ncbi.nlm.nih.gov/nuccore/66472853?report=fasta

http://www.ncbi.nlm.nih.gov/nuccore/188536104?report=fasta

http://www.ncbi.nlm.nih.gov/nuccore/3360341?report=fasta

http://www.ncbi.nlm.nih.gov/nuccore/522838236?report=fasta

http://www.ncbi.nlm.nih.gov/nuccore/46309510?report=fasta

http://www.ncbi.nlm.nih.gov/nuccore/41054648?report=fasta

http://www.ncbi.nlm.nih.gov/nuccore/213389538?report=fasta

Software Used

http://doua.prabi.fr/software/njplot

http://www.clustal.org/clustal2/

Joshua Everett's Phylogenetic Anaylsis Article

Joshua Everett

AP Biology  

Mr. Hammer

October 24, 2014

Phylogenetic Analysis Article

For this phylogenetic lab, I studied different species of animals that I thought would be similar to one another, not only based on appearance but on the type of gene they all had in common. The question I was addressing in this lab is how are Mus musculus (house mouse), Pan troglodytes (chimpanzees), and Sus scrofa (wild boars) similar to Ambystoma mexicanum (Mexican salamander). To make this comparison, I looked at the msh homeobox 1 gene, also known as MSX1 in each of these species. The MSX1 gene provides instructions to make a protein that regulates the activity of other genes. Specifically, the MSX1 gene controls the normal development of fingernails, toenails, teeth, and other structures of the mouth. I formulated this question based on interesting characteristics of these species like their differences in appearances and their homologous structures. In prior knowledge, I was aware that humans and chimpanzees are very similar to each other not only through their shared structures but also through their DNA sequences. In this lab, however, I wanted to find another species of organisms that were also similar to chimpanzees. Although none of the species I chose to analyze in my lab seem very similar based on their appearance, structures, and ecological locations, that is what makes this lab interesting. This lab will reveal how similar these different species really are to one another based on the MSX1 gene that they all share.

In order to compare the Mexican salamander, the mouse, the chimpanzee, and the wild boar, I decided to compare their nucleotide sequences, or specifically their mRNA sequences. The MSX1 gene is found on the short end of chromosome four at position 16.2. Because this gene is found on a chromosome and is found from base pair 4,859,664 and 4,863,935, it would make more sense to compare these species based on their nucleotide sequences rather than, possibly, protein sequences (http://ghr.nlm.nih.gov/gene/MSX1). Before I performed my experiment I looked up organisms that had the MSX1 gene and I picked the ones that I knew the least information about. I did this because I wanted to be able to discover something new and interesting about these species instead discovering information I already had prior knowledge about. After I found my different species, I found each of their mRNA sequences by using the NCBI database that could be found at http://www.ncbi.nlm.nih.gov/nuccore. In order to align these sequences to view similarities and differences between all these types of organisms and to draw a phylogenetic tree, I used the program ClustalX2. To view the results in a phylogenetic tree, I used the program njplot to view the phylogenetic tree which allowed me to form conclusions and make inferences on the relatedness of these species.

After forming conclusions and making inferences, my results showed that chimpanzees and wild boars are more similar in the way that they develop teeth, fingernails, and toenails from the MSX1 gene. According to my phylogenetic tree, it seems are if chimpanzees and wild boars share a more recent ancestor than the mouse and the Mexican salamander. The Mexican salamander is the outgroup in my tree which means that they are the least similar to the chimpanzee, mouse, and wild boar. The mouse, however, is more similar to the chimpanzee and the wild boar than the Mexican salamander. The reason in which the mouse is not as similar to the chimpanzee and wild boar is because I am able to infer from the phylogenetic tree that they have a less recent common ancestor. The chimpanzee and the wild boar branch off at a more recent point which could mean that they have a more recent common ancestor which makes them more similar. My question is answered from the phylogenetic tree because it shows that the mouse, the chimpanzee, and the wild boar are not closely related to the Mexican salamander. The most closely related species, however,  are the chimpanzee and the wild boar.

Chimpanzees and wild boars, also known as wild pigs, are the two most closely related species based off of the phylogenetic tree. There is a report that was done by John Hewitt that supports that chimpanzees and wild pigs could actually be more related than what individuals might think. Dr. Eugene McCarthy specializes in hybridization in animals and he hypothesized that it would be possible for a male boar (Sus scrofa) and a female chimpanzee (Pan troglodytes) to cross and reproduce and have offspring. McCarthy proposes that” hybridization between pigs and apes produced the earliest hominids millions of years ago and that subsequent mating within this hybrid swarm eventually led to the various hominid types and to modern humans” (http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html). Scientists believe that humans arose from multiple generations of chimpanzee crossings and or reproducing. McCarthy is newly introducing that wild pigs could have contributed to the earliest hominids as well, based on nucleotide sequence data comparisons (http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html). The fact that wild pigs and chimpanzees are able to reproduce and have hybrid offspring, means that both species of organisms would have to be similar in a way in which they had compatible reproductive parts. Another hypothesis that McCarthy proposed was that chimps and wild pigs had separate crosses that led to the production of separate hominids (http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html). If pigs and chimps cross separately and produce hominids, regardless of the differences between them, scientists and other individuals can deduce that wild pigs are similar to chimpanzees because of the similar organisms that can be produced by both of them. This report would support the results from the experiment because it proves that wild boars and chimpanzees are indeed similar as represented by the phylogenetic tree.

An experiment was performed to see if a mouse, a chimpanzee, and a wild boar are closely related to a Mexican salamander. Nucleotide sequences were found using the NCBI database and  data comparisons were done between all the organisms using ClustalX2. A phylogenetic tree was made from njplot  and the results came back revealing that chimpanzees and wild boars are the most closely related and that the Mexican salamander is the outgroup, or least similar out of the four species. The mouse was similar to the chimpanzee and wild boar but a more recent common ancestor was shared between the chimp and the wild boar which made the ultimate difference between the two groups. The conclusion that chimpanzees and wild boars are more closely related and similar is supported by the hypotheses made by Dr. Eugene McCarthy about hybridization in animals. Overall this experiment proved that comparing DNA sequences or other types of sequences can lead to formations of phylogenetic trees which can reveal common ancestry and relatedness among species of organisms.

Phylogenetic Tree:

https://docs.google.com/document/d/1oSbQSqXWk0lBaO993JiMu8Ze6UK7yCOv8fZx4ET0gn8/pub

Work Cited

Hewitt, J. (2013, July 3). A chimp-pig hybrid origin for humans? Retrieved October 24, 2014, from http://phys.org/news/2013-07-chimp-pig-hybrid-humans.html

MSX1 gene. (2014, October 20). Retrieved October 24, 2014, from http://ghr.nlm.nih.gov/gene/MSX1