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A Different Kind of Canary April 28, 2010

Posted by ecogeeko10 in Ecology, Environment/Conservation, Genetics.
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timber rattlesnake

What’s the difference between a canary and a timber rattlesnake? Not much if you’re a conservation biologist who is examining the effects of habitat fragmentation on biodiversity.

A recent study by a group of Cornell University researchers shows that even some of the simplest forms of human disturbances are having large impacts on biodiversity. Timber rattlesnakes in particular, have been a major focus in the northeastern region of the U.S. because these scientists have been able to utilize fine-scale molecular genetics and microsatellite markers to track the rattlesnake populations. They are finding that fragmentation caused by small scale road development is having a more than noticeable effect on the genetic diversity of these snakes. For this reason, one could compare the rattlesnakes in this study to canaries in a coal mine.

Of the 500 individual snakes taken from four separate regions and 19 hibernacula, none of the genetic clusters spanned either major or minor roads. This greatly proves to the non-believers that roads are indeed significant barriers that limit the dispersal and other natural processes necessary for species survival. Don’t assume, though, that this is only affecting the timber rattlesnake populations. Countless other studies show that habitat fragmentation is causing the demise of many of our planet’s species. Nevertheless, this study is unique because it only deals with roads. When people think of habitat fragmentation, they usually think of rainforest deforestation or mountaintop removal—they don’t always realize that something as common as a road can be quite detrimental to a species. Hopefully this study will help us to learn to notice the “smaller things” that can hurt the environment and maybe we can be inspired to do something about it.

The Song of the Dodo

Before I end this blog, I just wanted to mention that there are a few books that I hope to read this summer, including a book called The Song of the Dodo: Island Biogeography in the Age of Extinction, by David Quammen. This greatly relates to this recent study that was done with timber rattlesnakes because it talks about habitat fragmentation and its implications on biodiversity. I am hoping to learn something from this book and I was also thinking that it would be cool if others read it too. Perhaps we could even discuss our thought of the book at the end of the summer (via the MU Blog)! I am also willing to take other book suggestions—it could be like an “online summer book club” or something. Let me know what you think!

A Second “Lab Rat” has its Genome Mapped April 28, 2010

Posted by ecogeeko10 in Behavior, Biology, Evolution, Genetics, Health, Neuroscience, Physiology.
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Many behavioral ecologists, geneticists, physiologists, etc. are familiar with the zebra finch (Taeniopygia guttata). In fact, many have considered it to be the avian version of the white lab rat. Because of this, these researchers should be excited to hear that scientists have just recently decoded the zebra finch’s genome.

A genome to explore behavior

The zebra finch isn’t the only bird to have its genome mapped (the chicken was completed first) and it’s only about one-third the size of the human genome. However, this was a unique find because it will greatly help behavioral ecologists to understand the underlying mechanisms that help baby songbirds learn how to sing from their parents. This isn’t something that could have been done with the chicken genome because chickens don’t learn how to “cluck” from their parents—they just do it. Zebra finches, on the other hand, are similar to humans because human children also learn how to speak from their parents.

The zebra finch genome gives us the opportunity to explore the influence of genetics on language development.

Researchers are already analyzing the genome and they are finding that a good portion of the bird’s DNA is actively participating in the hearing and singing of songs. What’s more, these short simple songs are rooted in a great deal of genetic complexity. To date, it has been understood that the very act of singing and hearing songs activates large, complex gene networks in the bird’s brain. However, the current genomic research is revealing there to be many more participating genes than once thought. Right now it seems that there may be approximately 800 total genes that are active in this process!

Genes not acting as genes

New evidence is also showing that many of the activated genes aren’t acting like genes in the traditional sense. Rather than coding for proteins, the DNA from these genes is transcribed into short stretches of non-coding RNA that control the expression of other genes involved in the zebra finch’s vocal communication. Since non-coding RNAs are very influential in the developmental processes in animals and since they are thought to be instrumental in the evolution of higher organisms, the vocal learning that is found in the higher organisms may use non-coding RNAs as their driving force.

The evolution of language

It is also worth noting that when comparing the newly mapped zebra finch genome with the chicken genome, there seems to be some obvious differences that may point towards the evolutionary pathway that gave rise to birds that are capable of vocal learning. For instance, the evolution of the ion channel genes—which are important players in behavior and neurological function—in the zebra finch brain were greatly accelerated; the expression of the male sex chromosome genes seems to have been modified; and the production of new variants of neurobiologically important genes have taken place. It is amazing to see how much has learned in such a short period of time!

From birds to humans

It took the combined effort of more than 20 institutions to map out the genome of this song bird and now everyone has the opportunity to reap the benefits from this work. The newly gathered information should prove to be instrumental in helping us to better understand how humans learn language and perhaps it will help neuroscientists to identify the genetic and molecular causes of certain speech disorders that are associated with various illnesses such as Parkinson’s disease, strokeautism, etc. With the parrot genome scheduled to be completed by the end of this year, who knows what all we can learn about our little feathered friends and even ourselves!

Research Conferences are Cool! April 25, 2010

Posted by ecogeeko10 in Behavior, Biology, Ecology, Evolution, Genetics, Neuroscience, Physiology.
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A couple of weeks ago, I was fortunate enough to be able to attend the Association of Southeastern Biologists’ 71st Annual meeting held in Asheville, North Carolina. This is a pretty neat conference because every year over 1000 biologists get together and present the research that they have been working on in the past year.  The reason why I made the trip is because I did a poster presentation for my research on beaver dredged canal function and development. However, the types of questions that other researchers addressed ranged from topics such as the role of estradiol in courtship displays of Collared Manakins to the best management techniques for mountain lions in New Mexico. This conference was definitely geared towards a wide range of interests.

One particular oral presentation that I attended and thought was pretty interesting was by a graduate student named Jennifer Carman from Western Carolina University. In her study, she was investigating the morphological variation in song sparrows. What was so fascinating about this research, though, was that she was seeing real/statistically significant morphological differences between birds in rural areas and birds in urban areas. Just as Charles Darwin saw that there were many variations in the beaks of finches on the Galapagos Islands, Jennifer was seeing that the urban populations of song sparrows had larger and strong beaks than the rural populations that are just a few miles down the road. What’s more, the urban birds seemed to be much bolder than their neighbors. Jennifer was sure to let us know that this is only a preliminary study, but she is hoping to eventually find out what is causing these morphological differences. Are the urban population exposed to different food sources that require stronger beaks? She is also interested in seeing if the urban populations have higher levels of testosterone. If so, how are these populations benefiting from being more aggressive? I am interested to see how this study turns out.

A second talk that I thought was interesting actually relates a lot with what we have been doing in our own molecular genetics class. In the presentation, titled Detection of Misidentified Plants in the International Cocoa Geneback, Trinidad, James Bardsley (Towson University-Maryland) explained how he and his class used SSR analysis in order to find that 31 out of the 123 individual cocoa plants that they brought back from Trinidad were actually mislabeled. The reason for this high level of error comes from the fact that breeders are constantly trying to create new hybrids with desired characteristics. For instance, one person may decide that he was to create a crop that has a high yield and is disease resistant. He would achieve this by obtaining a “high yield” gene and a “disease resistant” gene from the gene bank and then breed them into the crop of interest. This constant intermixing of genes makes for much difficulty when trying to tell plants apart. Many of these hybrids have very similar morphological characteristics! James and his lab proved that the best way to fix this problem is to utilize molecular techniques when trying to identify a species. This is indeed a relatively expensive technique, but it is unfair that the consumers are being sold the incorrect product 25% of the time. Hopefully the cocoa companies takes this information to heart.

I’m really happy about being given the chance to attend one of these meetings. I was able to gain experience in presenting my own work, I was able to network with other scientists in the field, and I was able to learn about some pretty cool studies that are going on around the country. I highly recommend that anyone who is interested in research should go to a conference like this because they are great resources for anyone who wants to get their name out there so that they can obtain a job or go on to graduate school. This meeting was definitely worth the eight-hour drive!

Save the Whales! April 23, 2010

Posted by ecogeeko10 in Biology, Environment/Conservation, Genetics, Policy.
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We are having a great time in our Molecular Genetics class (BIO 415) right now because we are currently underway on a project genetically analyzing different fish products being sold in local markets and restaurants. Apparently there has been a real problem with the mislabeling of these fish products throughout the country, which can lead to the illegal sale of endangered species or the misrepresentation of the demographics of  fish sold making it hard to police sustainable fishery methods.   We wanted to see if this problem is prevalent in our hometown of Indianapolis, IN.  It was for this reason that I was excited to see that the same experiments and techniques are still being used elsewhere.

Just recently, a team of filmmakers, Oregon State University scientists, and environmentalists investigated some sashimi being sold at sushi bars on the west coast and found that there is whale meat illegally circulating in this market. Through genetic analysis, the team was able to find that these sequences were genetically identical to whale products that have been previously purchased in Japanese markets. Unfortunately, these products are most likely coming from what is supposed to be Japanese “scientific whaling” expeditions. This means that whale meat is being traded as a food product even though the commercial hunting of whales was banned by the International Whaling Commission (IWC) in 1986. The restaurants have subsequently been shut down as a result of these findings.

This illegal trading activity isn’t just occurring between the United States and Japan, though. Further studies have revealed there to be a total of 13 whale products being sold in places as far as Seoul, South Korea. However, the samples can’t be conclusively linked to an individual whale unless the genetic identity records of the “scientifically killed” animals are released by the Japanese government. As of now, Japan is conveniently refusing to release this important information. Therefore, one of the major focuses of the researchers, right now, is to obtain these records because it is only with this information that they can provide resource managers with the best possible science.

Though it is very sad to see that such illegal activity is still going on around the world, I think it’s cool to see that certain tools and techniques that we are using in our Molecular Genetics class is up to date and is still being used throughout the scientific community. It also amazes me that science has become so advanced over the years that we are now able to do the unimaginable. Who would ever thought, fifty years ago, that we would be able to narrow down the source of a particular piece of whale meat being sold in Los Angeles to a single whale population off the coast of Japan. Hopefully our newfound abilities in molecular genetics will continue to help scientists in uncovering various illegal activities and will help to better prevent such activities from continuing. Now, however, it seems like our biggest problem is trying to get the necessary information from the appropriate individuals (e.g. the whaling records from the Japanese government). It is with these tools and information that we can achieve our ultimate conservation goals.

Something New About Something Familiar April 14, 2010

Posted by ecogeeko10 in Biology, Genetics, Health, Medicine.
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Hey! Remember that one little concept in biology that you learned in your 8th grade science class? That one little process that really has no other function…except to make life happen! Anyways, I’m talking about mitosis. Well just recently, scientists have found and identified the genes that are involved in this cell division process! This was no small task, though. In order to find these genes, the researchers had to sort through the 22,000 genes contained in the human cell. They did this by silencing or inactivating the genes and filming them—one by one—for 48 hours under a microscope. This was made a little more possible, though, through the help of a newly formed computer program that was able to help analyze the footage. This computer program was able to analyze 200,000 time-elapsed movies of mitosis (I really envy that computer…) and ultimately pin-point the 600 genes that play a role in the cell division process. Cool huh?

With this newly gained knowledge, scientists can now better understand how cell division works in normally functioning cells, but most importantly, researchers can potentially pin-point what makes mitosis go array in abnormally functioning cancer cells. This will greatly help medical physicians to more accurately diagnose patients and it will also help them in making decisions on the best way to treat certain illness.

Unfortunately, researchers have yet to find out how these genes act at the molecular level, but when they do, they will be sure to make this data freely available online—just like they did with the recent mitosis research!

…everyday it seems like we are getting closer and closer to finding a cure for cancer.

Say Cheeeeese!!! February 24, 2010

Posted by ecogeeko10 in Biology, Genetics.
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So I’ve been noticing a recent trend in the scientific world lately. Researchers are getting better and better at figuring out the fine details of organisms that occurred many years ago. Take dinosaurs for, for example. It was once thought that all of these “terrible lizards” were only covered with scales. However, it wasn’t too long ago when paleontologists first began finding evidence that some species of dinosaurs actually had feathers. Not many people believed that we would ever get to figure out the actual colors of these feathers, but it turns out that this is also possible.

Historic Portraits

Jakob Vinther, a graduate student at Yale University was studying the ink sac of an ancient squid, when he discovered microscopic melanosomes in the fossil. Melanosomes are cellular organelles that contain melanin, which is a light-absorbing pigment that is found in certain animals such as birds. Once researchers heard about this discovery, they quickly began examining the fossil remains of other organisms such as Anchiornis huxleyi. We can now conclude that many dinosaurs like A. huxleyi were not necessarily dull and gray, but rather, they were quite colorful (see figure 1). The fact that this species of dinosaurs was so colorful could prove that feathers may have had multiple adaptive uses at that time. Not only were they good for warmth and flight (eventually), but they were instrumental display features. What dinosaur wouldn’t want to mate with such a beautifully adorned creature?  This was a very important discovery because it gives evolutionary biologists much more insight into the evolution of birds. We now have more evidence that birds did indeed evolve from theropod dinosaurs.

Anchiornis

But wait!!! I’m not done!!!

It also turns out that we are able to take “snap-shots” of people who lived thousands of years ago! Just recently researchers were able to analyze the complete genome of a 4,000 year old Greenland resident—a Saqqaq. Simply by analyzing the DNA in this old man’s hair, geneticists were able to conclude that this man had brown eyes, dry ear wax, was genetically prone to have thicker hair (thicker than most Europeans and Africans), and yet he was also at risk of growing bald (see figure 2 for “snap-shot”).

What’s most important about this discovery, though, is that these findings help to shed new light on the settlement of North America. Apparently, through analyzing this man’s genome, researchers were able to determine that his closest living relatives were the Chukchis—who lived on the easternmost tip of Siberia. What’s interesting is that the Saqqaq man’s ancestors diverged from the Chukchis around 5,500 years ago and that helps geneticists to believe that this man’s ancestors must have traveled across the northern edges of North America to Greenland.

Neat!

Saqqaq Man

Dolphins and Bats… are they really THAT different? February 8, 2010

Posted by ecogeeko10 in Behavior, Biology, Evolution, Genetics.
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Hey fellow molecular genetics/behavioral ecology students (i.e. Kyle)! Remember when we were discussing how bats and dolphins independently developed similar abilities to use echolocation after diverging from their last common ancestor (which was a looooong time ago)??? Well anyways… Recent (I mean REALLY recent) studies are showing that they might be sharing more than what was once thought!

The evolutionary genetics of hearing

It has been assumed that it was different mutations of different genes that resulted in the “coincidental convergence” of certain traits in different species (I can write sentences like these because this is a blog). However, two studies (here and here) that were published in the January 26th issues of Current Biology suggest that the evolution of echolocation in bats and dolphins were brought about by identical genetic changes.

According to Yang Liu et al, dolphins and bats developed the ability to echolocate because they both experienced similar mutations in their prestin genes. Prestin, which can be thought of as being amplifiers in the inner ear, were mutated in a way so that these species of animals could have a refined sensitivity and selectivity for certain “echolocate-able” frequencies. The evidence shows that these changes in prestin were selected for, so it is likely that they are critical for the evolution of echolocation in animals. The scientists are still working on why this may be.

The researchers were sure to point out, though, that there are still differences in how bats and dolphins echolocate. Dolphins can use echolocation at a range of >100 meters, while bats have a range of only ~3 meters. It is also worth noting that sound travels much faster in water. Therefore, bats and dolphins have had to adapt these differences in order to be successful in their unique environment.

A dolphin/bat superhero.....COOLAnd yes, that is an illustration of a bat/dolphin superhero…. it’s well known for its echolocation superpowers….