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Monday, March 18, 2013

I'm back!

Hello friends!

Wow! It has been a while since I posted something in this blog!

I guess it is time that I talk about something... or at least update you on what I am doing currently.

This is my current obsession, the hellbender.

Last August I got started on my PhD in conservation genetics at Purdue University. I currently am working with the creature in the picture above. It is known as North America's giant salamander, or hellbender. Populations of this species have dropped more than 70% accross its range within the past 30 years. Reasons for its decline include habitat loss, pollution, collection, and disease. I am particularly interested in observing the immunogenetics of this species, due to the fact that one of the subspecies of hellbenders (the Ozark hellbender, native to the Ozark region of Missouri and part of Arkansas), suffers of pathogenic infections on the skin. Most infections occur in the extremities causing necrosis, and most adult Ozark hellbenders have no feet because of this. Pathogens (such as chytrid fungus and ranavirus) have already threatened the health of many of the world's amphibians. My goal is to look at one set of immune genes (Major Histocompatibility Complex or MHC) of both hellbender subspecies (Ozark and eastern hellbenders), and try to see if there is a genetic cause behind the Ozark hellbender higher risk for infection. MHC genes are involved in the recognition of self and non-self. Your body uses these genes in order to recognize pathogens, and present them to the immune system. They have also been found to be involved in mate selection, kin recognition, and pregnacy success. High diversity in the alleles within your MHC protects you against a large array of pathogens, and low diversity limits the amount of pathogens that you are protected against. Diversity within these genes is maintained by heterozygous andvantage or frequency dependent seleciton. My theory is that because of their small population size, Ozark hellbenders have a low diversity within their MHC genes, and thus have a decreased immune response to pathogens.

Picture of an MHC molecule presening a pathogen to a lymphocyte
Similar results have already been seen in the axolotl. The axolotl is an aquatic salamander endemic to the Xochimilco Lake, MX. It is the model specimen for caudata (order of salamanders), and its MHC genes have been well studied. These studies have shown that there is no diversity within the genes. This animal is immunosuppressed. However, my reseach goal is to find at least one allele that confers resistance to a common pathogen in hellbenders. Zamudio et al. 2012 were able to detect an MHC class II allele that provided resistance to chytrid in frogs, which gives some hope for the hellbender. If we are able to find such alleles, we might be able to direct breeding programs to artificially select for such traits and increase the beneficial allele frequency in the population. 

The journey just begins, but I will try to keep you posted on how this adventure goes!

I'm holding an eastern hellbender from Missouri, with permision of Jeff Briggler MDC Herpetologist

Thursday, October 7, 2010

Sancha, Mota #2, and Birria

Sancha posing for the camera on the day I bought her.

First of all I would like to start by saying... HAPPY BIRTHDAY SANCHA! It has been a year since I bought my oldest mouse, Sancha. I have always had a fascination for rodents. I really never knew why, maybe it has been the fact that they are small and furry or so just ecologically diverse. Beavers, squirrels, mole rats, and yes even mice, have always been at the top of the list of my favorite animals. I had just gotten an apartment, had no roommate to oppose, and felt lonely, so the natural thing was for me to buy a female mouse. Her coat attracted me immediately, a soft short hair fur colored white a light brown. Why a female? Males release pheromones in their urine to attract females, a fragrance that I do not appreciate. Shortly after getting Sancha, I noticed that her behavior seemed very passive compared to how she acted they day I picked her in the store. I had learned that mice like to live in communities, especially females, so I decided to purchase her some company two weeks later. Her two new roommates were Birria, a black colored short haired mouse and Mota, a pear colored mouse with dark brown spotting. Mota passed away in March due to illness, and was recently replaced by Mota #2 who looks just like her. I try to maintain the characteristics of the original group; I did not want to change things too much for my poor mice.

The reason why I am introducing my mice to this blog is due to a recent knowledge I have acquired in animal learning. In this case, I am more interested in individual and social learning. Learning is costly to individuals in nature. It tends to be evolutionary adaptive only when animals inhabit environments with high predictability within generations and low predictability between generations. In other words, learning happens only when the environment may change from the lifetime of parents to that of their offspring, and when the environment within an individual’s life does not change much. In other situations, behaviors that can be inherited through genetic means are far less costly and more efficient than learning capabilities. Knowing how rapidly mice reproduce, and their short life spans (1-2 years) it is reasonable to assume that a mouse fits the qualifications needed for learning to be possible in a species. Yes, I understand how common mice studies are, but I am an amateur scientist still and in my attempts to increase my knowledge of the scientific process I will perform this experiment.

I am going to teach Mota #2 a trick through the use of associative learning. Associative learning occurs when one manipulates an individual’s instinctive behavior in order to acquire a conditioned response to a neutral stimulus that the animal would not have otherwise. For example, if you are scared of snakes by instinct, it will be natural for you to seek cover at the sight of a snake. Now, if every time I show you a snake a introduce a red light, you will learn to associate the red light to the snake and eventually you will only behave fearfully when I introduce the red light alone. Sounds familiar? Yes, this is what Pavlov proposed when he trained his dogs to salivate to a bell.

So, Mota #2 will be given a piece of a sweet cookie along while I make clicking noises with my mouth. Eventually, I will test if she responds to my clicking alone. Of course, her responding to the clicking will also include some operator conditioning style of learning. Why, because looking for food in my hand is not a instinctive behavior, but an association that looking for food in my hand in response to the clicking usually results in her getting a treat. The experiment does no end here, since I will see if Mota #2 is able to teach this behavior to her cage mates. If all of them respond to the clicking is a similar manner, then they will have learned the behavior by copying their tutor.

I will keep you all posted on how this progresses. This is an interesting field of animal behavior and psychology since it can be applied to many aspects of life. How exactly does one learn to avoid foods that we do not like? How can we increase our educational learning skills through these primitive examples of learning? Learning how learning takes place is not only interesting but can be extremely helpful. Stay tuned for more!

Sancha, Mota, and Birria staring up from their cage.

Monday, September 20, 2010


We were doing a personal culture activity today in my LCG class and I came to realize something really interesting that was happening within my students. There was a clear split between individuals who believe in creation and those in evolution. It seems as though individuals who are religious seem to be skeptic regarding science because of this division. I consider myself somewhat religious. I believe in God, and I am currently on the process of becoming a catholic. However, I do believe on evolution. How can this be possible? Well my friends… I rely on the Theory of Non-Overlapping Magisteria (NOMA). Created by Stephen Jay Gould, it advocates the idea that neither religion nor science are more important than each other. In other words… there is a strict separation between both ideologies. Each magisteria holds its own questions, and these are the questions that they are capable of answering. For example: medical science answers questions regarding illness, whereas the bible answers questions regarding sin. “The bible is not a biology book,” is one of the quotes that I remember my Biology professor, Dr. Michael Dini, say as he explained the theory to our class. “Where do we come from?” is a measurable question which can be answered by science. ‘Why are we here?” is clearly defined in the bible and can not be measured by the realm of science. Thus, these questions are best answered by each realm that has the resources to do so. One is free to study nature in any way. However, because of my scientific backgroud this blog is designed to do so through a scientist's perspective. Everybody is welcomed to read it. I am just asking for tolerance and understanding. Maybe you do not believe in evolution, but that does not mean that science is out of your reach.

Tuesday, September 7, 2010

What is place?

I am taking a class with Dr. T agian! Here is a post of my latest assignment.

El Paso, TX is a location that derives a lot of sentiment within me. I often try to associate these feelings with its definition of a place; however, is a place something that creates sentiment. My current home, Lubbock, TX generates distinct emotions that are different from those of El Paso. If so, do different geographical locations deserve equal or different categorizations? I am asked to define a place, yet in order to do so I will have apply this definition in an non-subjective manner. In my perspective, a place is a location capable of sustaining a unique aspect of life. Life can be defined as nature or human activity. El Paso is home to nearly 600,000 individuals along with numerous desert species of plants and animals. It is an international border town that is shaped by three distinct cultures: Mexican, Texan, and Native American. The customs of these three sources influence the society of the city by affecting the way the people interact with their environment and with each other. Unlike the rest of Texas, El Paso retains a more liberal perspective on environmental and moral issues. The Franklin Mountains, surrounded by the city, retain the original desert ecosystem of the urban location.
All the physical and cultural characteristics of a site seem to be the contributing aspects that define it as a place. We can argue that a place is somewhere you hear about, a locality you can visit, or even an area that basically exists. Yet, in order for one to know it as a place, there has to be certain characteristics that get impregnated within the human mind. How can point-A be a different place than point-B if they are exactly alike? It is when there is a difference between the two that one can distinguish them apart. One can utilize human or even natural based characteristics of point-A, El Paso, versus point-B, Lubbock, to recognize that they are different and attain the ability to relate to their literature, art, traditions, and importance in the natural and human directed perspectives of what the world is.

Friday, June 25, 2010

Natural Science Research Sampling

It has been a while since I have posted anything in this blog, but I must admit that school has kept me very busy. After Junction, I went back to Chihuahua. I had a good time, even though it lasted too little. I have been taking microbiology and organic evolution at Tech this summer and have been able to acquire some knowledge over what was done at Junction in my mammalogy class. Those samples that we gathered are used in research on disease, evolutionary processes, and even animal characteristics themselves. How can we study disease from animals gathered in the field? This is a very interesting process that covers many aspects of biology. Epidemiology, ecology, evolutionary sciences, and even biotechnology are tools that us scientists can utilize in order to acquire data that we can use to treat, prevent, and even understand pathogenic disorders. By acquiring the tissues, one can identify organisms that serve as carriers of disease, which can be spread to humans. Below I will explain the process to acquiring these samples, preserving the skins and skulls of the animal. As a model I will be using a Peromyscus pectoralis. This is a common deer mouse found throughout much of the American continent.
As I had said in earlier entries, the rodents are collected in the field via the use of live traps (in our case Sherman Traps). Once collected, the mouse is brought to the lab where it is paralyzed. We collect blood form the eye socket through the use of capillaries while the mouse is still alive. After the animal is sacrificed, it is usually frozen and set a aside until one is ready to prepare the specimen.

When the specimen is ready to be prepared, one acquires measurements of the animals total body length, tail length, fore foot length, and ear length. If you are working with a bat, you will also measure its tragus (a small structure in front of the ear). Also, one needs to acquire the weight of the animal. Once these measurements are taken and annotated, you are ready to begin the skin removal.

You begin to remove the skin by creating a delicate incision within the abdomen, being careful not to puncture the abdominal cavity. You begin by removing the legs first to the feet, where you would cut the tibula and fibula at the base where it meets the foot. Then you remove the tail, being careful to first cut off all muscle, urethra, and large intestine. You pull the tail by grabbing the buttocks with one hand and the skin at the base of the tail with the other. You continue to remove the skin throughout the body which is easy until you come to the arms. The arms are easily removed if you pretend that you are taking off a “sweater” then cutting off at the base of the hand where it meets the ulna and radius. The head is a little tricky to skin since there is a lot of connective tissue, but if you cut it with scissors at base of skull you should be able to remove your skin without damaging it.

Once you have skinned your mouse, you want to rub the skin in corn meal. This will absorb most of the fat and moisture that can damage the look of your skin. You continue to remove the organs from the carcass. The heart, kidney, lungs, liver, spleen, and a piece of muscle are collected in order to perform DNA studies or any other that are needed. The samples are stored in liquid nitrogen in order to preserve the delicate RNA which begins to degrade immediately after the animal dies. When the carcass is empty, you can wrap it in string and dry it. It will later be exposed to flesh eating beetles that will clean it of all flesh.

The skin is then filled with cotton and wires and sown shut. When you prepare the skin, you want to make it look real. The specimen is likely to last up to 200 years, and you want to make it look its best for future scientist to study.

An evolutionary scientist can utilize your sample in order to acquire clues when building phylogenic trees. These are hypothetical depictions of the evolutionary processes. These trees have a lot of purposes since they can be utilized in many ways to answer many questions. The great thing about this process of specimen collection is that it allows one to explore both biology and natural history. One acquires a small representation of the species available in an area at a certain time. If you are interested in this, you can visit the Texas Tech Museum in Lubbock, TX. They currently present an exhibit regarding this process. I myself have 10 specimens stored within the museum that I was allowed to prepare in Junction. Although one is not allowed to freely experience the mammal and ornithology collections, the museum allows the public to view a few specimens within the museums exhibits. Above all, knowing that an individual will be utilizing your work for research in nearly 200 years makes you feel that the hard work was worth it.

Tuesday, May 18, 2010

Mammalogy Class #2

For my classmates in Mammalogy at Junction, here are the materials for the second lab test. Rami made some practice quiz slides, that only contain the pictures, that you can also utilize. I encourage you to quiz yourself on the different taxonomic levels of each picture and any other characteristics that Cody might have mentioned in class. (such as type of teeth, fur, ect.) Enjoy!

Mammalogy Lab 7 Power Point:
Mammalogy Lab 7 practice quiz:
Mammalogy Lab 8 Power Point:
Mammalogy Lab 9 Power Point:
Mammalogy Lab 10 Power Point:

Friday, May 14, 2010

Mammalogy Class

For the members of my Mammalogy Class in Junction. Here are the pictures of the Coyote Skulls we need to ID.

Here is the slide for the mammals in Lab 3:

Here is the slide for the mammals in Lab 4:

Here is the slide for the mammals in lab 5:

Here is the slide for the mammals in Lab 6: