Friday, August 23, 2013

Blame it on the DNA

This one really gets going around 0:40, and it's pretty catchy.

Wednesday, August 21, 2013

Chandra's Interactive Guide to Stellar Evolution

NASA's Chandra X-ray Observatory is a space telescope specially designed to detect the X-rays that are normally absorbed by Earth's atmosphere. Because Chandra orbits above it, up to an altitude of 139,000 km (86,500 mi), it can detect these X-ray emissions that come from very hot regions of the Universe. Exploded stars, galaxy clusters, matter around black holes. Things that are invisible to the naked eye but show up in X-ray.

Now check out this really neat, interactive guide to stellar evolution from the Chandra X-ray Observatory. Through this interactive guide you can see examples of stars at various evolutionary stages, and what Chandra has learned about them.

Find the guide by going to the Chandra X-ray Observatory Website, clicking the image above, or copy this link ( into your browser.

Chandra also has a Facebook page

Monday, August 19, 2013

Eating and Evolution: Are Prey Preferences Causing the Evolution of Killer Whales?

When I was an undergrad, a lowly freshman who just knew she wanted to study biology, I took an internship at SeaWorld Orlando. I was excited that I got to participate in a real research project doing actual sciency stuff. The project was on the nursing behaviors of captive baby killer whales. Really cool right? Little did I know that actual science is composed of hours upon hours of tedious observation and documentation (2:00pm – melon bumping, 3:00pm – melon bumping, 4:00pm – melon bumping…). Despite that (or, who knows, maybe because of it), it was an neat project that boosted my interest research biology. And I got to watch killer whales for hours every week. So when I came across the paper for today’s post it really reminded me those times.

A new study published in the Proceedings of the Royal Society B, Biological Sciences looks at niche variation within sympatric killer whale populations in the North Sea. Those of you familiar with the terminology I just used might want to skip to the next paragraph. Otherwise, let’s hit a few terms first. We’ll start with the niche variation hypothesis. In the simplest terms, a niche describes where a species lives and the roles it plays in its habitat. The niche variation hypothesis describes differences within a species that are correlated with the variety of foods and habitats that are used by various populations. For example, why do island birds of the same species have different bill sizes? Likely because their bills adapt to the food items they are exploiting on their own island. It conveys a competitive advantage which results in a reproductive advantage that will lead, eventually, to an evolutionary change. This change will likely be a speciation event. This is a lineation-splitting event that produces two or more separate species from one (think about the branching on the tree of life). Usually we think of speciation as occurring via a geographic isolation (birds on different islands, populations separated by a mountain range, etc.), but the niche variation hypothesis allows for sympatric speciation because the exploitation of different resources splits a population within the same habitat. Admittedly, this type of selection would need to be really strong and stable over a long period of time to cause speciation. Now on to the study!

Killer whales (Orcinus orca) are actually members of the dolphin family (Delphinidae). They are the most widely distributed cetacean species in the world and are top marine predators. Males typically live about 30 years on average, and females about 50 years. The diet of killer whales is often geographic or population specific. Populations of orcas are usually defined as either “residents” or “transients.” As the name suggests, residents tend to stay in a more localized area whereas transients travel over large distances, sometimes overlapping with the ranges of resident populations. It has been documented that these different types of populations vary greatly in their diets, each consuming a narrow range of prey. Residents feed primarily on fish while transients feed nearly exclusively on other marine mammals. Considering this, and what we know of how the niche variation hypothesis cause speciation, have or are killer whales branching in to two species?

One of the problems in answering this question is the long-lived nature of these animals. It’s difficult to see a long-range change on a long-lived species. Most evolutionary studies use either comparisons at a single point in time or over timescales representing one to a few generations. Okay, that’s pretty good, and these snapshots have been very informative, but to get a real-time view in a long-lived species you really need to go small. And by that I mean molecular. Ancient DNA (aDNA) and stable isotope data from subfossil (remains that have not completed the fossilization process) specimens can be used to track niche and evolutionary history. The scientists in this study used these methods to look at the evolution in sympatric killer whale populations in the North Sea. First, they sampled 23 subfossil killer whale bones and teeth recovered by dredging or trawling the Southern Bight of the North Sea or from archaeological sites in Southern Scandinavia. Then they dated their samples using radiocarbon techniques or archaeological context. Next, they used stable isotope ratios to provide a long-term measure of what the animals ate during their lifetimes and thereby estimate the orcas’ niche width (it is argued that populations in wider niches are more variable than populations in narrower niches). Additional evidence of these dietary habits was gathered from examining the wear-patterns on the teeth (for example, feeding heavily on herring badly wears down the teeth). Then mitochondrial DNA (mtDNA) sequencing was used to determine the degree of linage sorting (separate populations carry their genetic diversity with them) based on isotopic (prey) niche. And finally, they biopsied the skin of modern orcas, sampling either while the animals fed on fish or on stranded remains with known stomach contents. From this they were able to extract high-quality DNA and conduct an individual-based analysis of population structure. This, combined with the aDNA data, effectively gave them a map of the evolutionary outcome of niche variation.

This is one of those studies where the results are all variable. *sigh* ‘Tis science. From the isotopic analysis, the researchers found  a lot of overlap in the results, mostly likely explained by among-individual differences. Because this type of analysis represents what an animal ate over its lifetime, differences in prey items within the diets of individuals are not apparent. This and the analysis of tooth wear suggests some overlap either in the diet and/or foraging method of the specimens studied. The result is consistent with the observations of the modern whales. Fish eating pods are often found with mammal remains in their stomach contents. Lineage sorting of mtDNA sequences based on the isotopic values revealed that there “has been multiple diversifications [sic] in isotopic niche” and “an indication there was relatively stable transmission of isotopic niche along matrilineal lines within some clades, in particular those that were dominated by samples from Norway.” The incomplete lineage sorting they found seems to be consistent with relatively recent divergences in niches, and their models indicate panmixia (random mating) between at least some groups that feed on fish and some groups whose diet includes seals.

To sum up, we know that there is niche variation in populations of killer whales. But all of that variation and overlap that the researchers found suggests that any speciation is still at an early stage in this system. And while the results of this study seem to be all over the place, it does add more information to the story while providing a useful long-term evolution study methodology. It also strengths the argument that sympatric speciation is difficult to achieve.

Also check out this great presentation on this study!

ResearchBlogging.orgFoote, Andrew D., Newton, Jason Newton, Ávila-Arcos, María C., Kampmann, Marie-Louise, Samaniego, Jose A., Post, Klaas, Rosing-Asvid, Aqqalu, Sinding, Mikkel-Holger S., & Gilbert, M. Thomas P. (2013). Tracking niche variation over millennial timescales in sympatric killer whale lineages Proceedings of the Royal Society B, Biological Sciences, 280 (1768) DOI: 10.1098/rspb.2013.1481

Science's article "North Atlantic Killer Whales May Be Branching Into Two Species"

For more information and explanation of some of the evolutionary terms discussed this post see:
Understanding Evolution via Berkeley, particularly the page on sympatric speciation
and for a nice description and examples of niche variation see
Soule, M. and Stewart, B.A. (1970) The "Niche-Variation" Hypothesis: A Test and Alternatives. The American Naturalist, 104(935): 85-97. (LINK)

Some useful resources for information on killer whales:
NOAA Fisheries Office of Protected Resources page on Killer Whales
National Marine Mammal Laboratory's page on Killer Whales
Cascadia Research Collective's "Studying the diet of fish-eating killer whales"

(image via National Geographic, photo credit Gerard Lacz/Animals Animals—Earth Scenes)

Thursday, August 8, 2013

Teaching Science Through Rap

Two podcast events collided for me to produce today's post. The first was a 2-part interview on Neil deGrasse Tyson's show Star Talk. This interview included clips from Neil's discussion with GZA from the Wu-Tang Clan where they talk about how he thinks of his music, how fans relate to it, and how science has influenced his lyrical prose. Neil then listens to and comments on this discussion with Columbia Assistant Professor of Science Education Dr. Christopher Emdin. In his work, Chris uses rap to connect inner city youth to science. His erudite elocution put together with his expertise of hip hop culture is really inspiring.

You can hear this interview on Star Talk's website, just look for Season 4 episodes 20 and 21, or by clicking HERE.

Next, check out this video where Chris explains how urban students would learn more effectively if their teachers understood and spoke the language of hip hop.

The second podcast event was an NPR story called "Science Rap B.A.T.T.L.E.S. Bring Hip-Hop Into The Classroom." This story includes the two videos below, and it discusses Chris's teachings as well as how students research and wrote rhymes for the Science Genius B.A.T.T.L.E.S competition. This program is part of a national push to boost science education among minorities. Senior Jabari Johnson won the competition with his rap "Quest for Joulelry," but you can see all of the lyrics HERE.

In the San Francisco Bay Area, Tom McFadden also teaches science through music via Science with Tom and The Rhymebosome. You will recognize his work from my Monday video post Covalent Love. His approach with students is teaching them to write about conflicts from the history of science.  Here's a video he created with a group of seventh-graders from Oakland California.

Since it directly pertains to this subject, I'm going to throw in a video trailer for Baba Brinkman's Rap Guide to Evolution. I've actually seen him perform live, and he is a great.

If you've been following my blog long enough then you know I like to post good sciency music videos, many of which are raps. Here are a few to look at or revisit when you have the chance:

The Photosynthesis Rap
The LHC Rap
The Grad Student Rap
The Meiosis Rap
Epic Battle of Electricity
Rapping ATP
Rappin' Science

You can also click on the videos label over there on the right side of your screen to see all the wonderful sciency music I've come across in my Internet travels.

Want more information? Just click through the links peppered thoughout the post and look for more science rap video posts on my blog.

Wednesday, August 7, 2013

Covalent Love

You don't have to be a chemist to love this video.

Thursday, August 1, 2013

Heavy Metals in Fish: Toxicity and Tolerance

Today I found an interesting paper that fits right in to my new job in the field of aquatic ecotoxicology. As the name suggests, this field is a combination of ecology and toxicology that deals with the nature, effects, and interactions of harmful substances in the environment. In my case, it is aquatic, freshwater systems in particular. The paper I came across looks at the effects of metal contamination and tolerance in freshwater fish.

Metal contamination is something that occurs worldwide. A number of industrial metals (particularly copper, cadmium and nickel) have been well studied in freshwater systems. These studies have used gradients in contamination to demonstrate correlations between chronic metal exposure and physiological changes that occur as a result of the toxicity. These changes can include alterations in various metabolic processes as well as impaired growth and reproduction. This study focuses on how wild brown trout (Salmo trutta) respond when exposed to a water-borne mixture of metals.

The researchers looked at the brown trout that inhabit the River Hayle in Southwest England. Historically, this area has been mined, peaking during the 1800s. The drainage from these mining operations contaminates the river with a mixture of metals, and the middle region of the River Hayle is known to have extremely high metal concentrations. So high that few fish or invertebrates are able to live there. However, brown trout migrate between the upper and lower sections, including this area. Trout found in the lower regions of the river have been shown to have acute metal toxicity, including total zinc, copper and iron which average 639, 42 and 200 ug/L respectively. Despite these high levels, the fish are able to sustain a population with no evidence of reduced genetic diversity. The aim of this study is to figure out how this tolerance of metals is possible.

To answer this question, the researchers used an integrative approach, combining genomics with the analysis of metal accumulation in tissues. They collected embryo and adult fish from the metal-polluted River Hayle and their control, the River Teign. In the adults, the researchers sampled portions of gill, gut, kidney and liver tissues and processed them to measure the concentrations of seven metals: copper (Cu). lead (Pb), zinc (Zn), arsenic (As), cadmium (Cd), iron (Fe), and nickel (Ni). Since there is relatively little gene sequence information on brown trout, they then had to sequence, assemble and annotate transcriptome (the set of all RNA molecules [mRNA, rRNA, tRNA, and non-coding RNA]). I think you'll thank me for not going in to how they do that (if you are interested in these methods, the paper lays them out nicely), but suffice it to say it is laborious but informative. Then they performed a functional analysis for differentially expressed genes from each tissue.

When the researchers compared the metal concentrations they found all seven metals to be significantly higher in the Hayle trout than the Teign trout. Across all metals the fold change was highest in the gills (62.6-fold change) followed by the liver (33.7-fold change) then the kidney (18.5-fold change). They found no significant differences in the gut. This suggests that the gills are the primary uptake route for these metals. That makes sense considering the large surface area in direct contact with the water and the abundance of uptake carriers and transporters for these metals. After the metals are taken in by the gills, they are transported in the bloodstream to the rest of the body, accumulating in the liver and kidney. As these organs are responsible for processing, detoxification, storage and excretion it is easy to see why accumulation might happen here.

In both rivers, zinc was the most abundant metal in the gill, gut, and kidney, while copper was found to be highest in the liver. They also found zinc and copper to be the ones that increased to the greatest extent in the gills, liver and kidney. That's logical when you consider that these two metals were the ones elevated to the greatest extent between the two rivers (60- and 40-fold, respectively). They also found evidence that may link the uptake, storage and metabolism of iron, cadmium, and arsenic.

In order to identify potential mechanisms of toxicity and/or tolerance to these metals, gene expression patterns for the four selected tissues were examined in fish from both rivers. A total of 998 transcripts were differentially exposed in at least one tissue. You should expect the activity of the components involved in the body's metal homeostasis system (that ensures an adequate supply of essential [trace] metals) to change with increased metal exposure. And indeed, the researchers found at least one MT (glutathione and metallothioneins; act as buffers for metal ions entering cells and have an affinity for most metals), particularly metallothionein b, to be the most strongly up-regulated genes in the Hayle trout. This suggests that the trout's metal tolerance mechanism may be as a result of the sequestration of metals by MT. And although zinc and copper were found to be in the highest concentrations in tissues, only the zinc transporter gene was differentially expressed (down-regulated in the kidney). However, they did find changes in iron-metabolism related genes.  Since metals also disrupt the balance of ions in the body causing oxidative damage, the researchers also looked at the ion homeostasis system. They found differential expression of enzymes and a number of other genes encoding proteins that are important in maintaining ion balance.

All of this put together gives some interesting mechanisms of metal toxicity, demonstrating that these fish have developed strategies for dealing with the pollution in their environment.

ResearchBlogging.orgUren Webster, T. M., Bury, N.R., van Aerle, R., & Santos, E.M. (2013). Global transcriptome profiling reveals molecular mechanisms of metal tolerance in a chronically exposed wild population of brown trout Environmental Science & Technology DOI: 10.1021/es401380p

(image via Biopix)
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