Tuesday, December 22, 2009

Friday, December 18, 2009

Friday fish tank - Dwarf Puffer

Captain Adama sitting high on his leafy perch.

Thursday, December 17, 2009

Congratulations Kevin!

Raising a glass to you for passing your Quals. Good job. Now, how long until you are diagnosed with PQS?

Monday, December 14, 2009

Chris Matthews on climate denial

Visit msnbc.com for breaking news, world news, and news about the economy

I was planning on writing a post about “Climategate” but honestly, it just isn’t worth the effort. These “climate skeptics” are nothing of the sort and they’re not “just asking questions”. They are deniers and arguing with deniers is a fruitless endeavor. No amount of evidence you present them with will ever shake their views. They revel in their alternate reality with a seething disdain for “experts” and a choking air of anti-intellectualism. The sad thing is as Matthews says, is that they’re winning.

...ugh, now I feel dirty for using so many quotation marks.

What? An octupus carrying a coconut?

It could grip it by the husk.

Ed Yong has a really interesting post up about octopuses and their prized coconut shells. They carry around these shells as portable cover when walking (yes, walking) long distances of barren sea floor. Check out his post for some cool videos and a great write-up.

More at the BBC and the actual paper can be downloaded here.

Saturday, December 12, 2009

Skepticism vs. "Storm"



How clearly Tim Minchin has managed to both encapsulate the frustration we experience when dealing with kooks and grandeur we see in this life. Plus, its terribly funny.

h/t
Orac

Friday, December 11, 2009

A dirty bomb


A pretty effective PR poster for UNICEF highlighting the dangers the millions face by not have clean drinking water.

Retardants are Retardants

It has always been suspected that polybrominated diphenyl ethers (PBDEs) might have potential neurological effects much like other halogenated organic compounds. Reported in EHP this month, a study of healthy school-aged children were measured for various motor, cognition and behavioral endpoints and correlated with their mothers’ prenatal levels of various organohalogenated compounds. Exposures to higher levels of PBDEs lead to both positive and negative neurological outcomes.

PBDEs are everywhere. They are used as flame retardants and found in fabrics, textiles, furniture, electronics, foams etc...So from everything including the computer chair I’m sitting on, to the bed I plan on crashing into tonight, are loaded with PBDEs. It has been shown previously that a measurable percentage of the air we breathe indoors are PBDEs (there are reasons why indoor air pollution is worse than outdoors). Now make no question about it - PBDEs save lives. Much like DDT which successfully reduces malaria in some parts of the world, we must not overlook the beneficial impact these chemicals can have. In fact, the federal government requires manufacturers to include these compounds because house fires are common and flame retardants save lives.

Much like any halogenated compound, the bonds in PBDEs are very strong and they do not degrade readily in the environment. In addition, they are hydrophobic, leading to accumulation in fat reserves and their ultimate fate is bioaccumulation and biomagnification. PBDEs are a conservative pollutant, meaning once they are released, they can be considered as a permanent addition to the environment. The frightening thing is, because they are so ubiquitous, PBDEs can be measured in our bodies and the concentration doubling times are as little as 5 years!

But back to the study, this is the first time a cohort study had been performed on healthy school-aged children (5-6yr) looking at prenatal exposure to halogenated compounds. Mothers were first measured for serum background levels of several organohalogenated compounds at the 35th week of pregnancy. What was found in their children, now years later, that exposure to prenatal PBDEs leads to permanent neurological disruption, such as shortened attention span and poor fine motor skills. However, unlike exposure to prenatal PCBs, there was no impairment of cognitive function. In addition, exposure to PBDEs also led to increased coordination and better behavior. Because of the diverse neurological effects seen, both positive and negative, it is difficult to determine the implications of these findings. Also in laboratory studies, it has been found PBDEs can cause worsening neurological impairment with age. So this leaves open the question of how these children will be affected as they grow.

Both Penta- and Octo- BDE have been banned in the EU and US, and Deca- being only banned in the EU. While these are considered the most persistent forms of PBDE, our high volume of production still puts us all potentially at risk, even if we are only exposed to just background levels.

The Friday fish tank: Albino Bristlenose Pleco

Here is my "fish-of-many-moustaches" (as a friend has dubbed him), enjoying a quiet night under a ledge.

Monday, November 30, 2009

Monday morning music



Since I think we'll both be writing mostly for school this week, I'll leave you with some Krautrock to start out this Monday. Can, along with Frumpy, have lead to some pretty productive writing nights for me, let's hope I can manage a few more.

Tuesday, November 24, 2009

Another reason to avoid tuna and sushi

That firm flesh in your sushi roll may not be what you think. A new survey published in PLoS one showed that in NYC sushi restaurants, 25% of what was labeled as “tuna” was actually endangered bluefin. Combined this with the still insufficient quotas set by The International Commission for the Conservation of Atlantic Tunas, which just voted to lower quotas from 22,000 to 13,500 tons this year, bluefin tuna stocks are being driven to extinction. I’m not one to criticize others about which foods are “ethical” to eat but selling and eating endangered species is simply beyond the pale.

Though I guess there was some good news to be taken out of this study. 5 out of 9 fish labeled as “white tuna” was actually escolar, an oily fish that causes temporary but severe orange(!) diarrhea. The actual name of the condition caused by these fish is known as keriorrhea and boy, do I wish some of those symptoms on those peddling off and consuming this fraudulent meat.

Monday, November 23, 2009

Излел е Делю хайдутин


I'm going to try and make it a Monday morning habit of posting some music, a good way to start the week. For the first installation, I present to you the Bulgarian folk singer, Valya Balkanska, ambassador of the Earth. You see, back in 1977 we launched a satellite to reach outside of our solar system to hopefully one day be found by some extrasolar intelligence. The Voyager 1 satellite also contained a golden disc- a phonographic record with images and sounds, greetings of diverse languages, and a sample of the music from many cultures to represent our planet. Put together by a committee chaired by the great Carl Sagan, it is works like these that show the accomplishments and bonds we share as the human species. Of all the songs on the disc, it is this moving piece that I wonder most about what some other being will think of us; calling out from our home, Earth.

J.

Sunday, November 22, 2009

Introducing Resistance

I guess before we really get the blog rolling an introduction is in order. What is Tracing Resistance? This blog is the unholy amalgamation of to totally different fields, marine toxicology and an HIV research. When you put us together you get supertoxic HIV (er…or something like that), and hopefully an interesting read. A common theme between our research is how the cell resists challenges from the environment. We trace the cell’s resistance in different ways and from different points of view. Although we are big enough nerds to blog about what we do this will not be 100% science all the time. We will bring our personalities and
other interests to our posts.


Kevin: What Tracing Resistance means to me. I am a second year PhD student in virology. My thesis work is focused on understanding the cross species transmission of HIV and HIV-like viruses (Simian Immunodeficiency viruses, SIV). Work in this area has identified numerous proteins that have evolved to prevent infection of these viruses. HIV has evolved ways to evade and counteract these proteins and is therefore successful in humans. However, if you take HIV-1 and put it into some species of monkey they will not get sick. This is because those monkeys have evolved genes that can specifically block things that look like HIV. The protein I focus on is called Trim5α, it binds to and destroys viruses after they enter the cell. In order to understand Trim5α mediated resistance we look at the natural diversity between humans and non-human primates and the viruses that infect them. To me tracing resistance is tracing millions of years host and virus coevolution.

John: Help! I'm surrounded by fish tanks! Currently, I am a second year Masters student in marine science. My research so far has been looking at functional responses in organisms to environmental contaminants. This has included measuring toxic metabolite production, accumulation of toxicants and the affects of hypoxia. Currently, I am studying one way organisms express resistance to contaminants through the use multixenobiotic efflux transporters. These are the first line of defense a cell has to foreign chemicals and sees to it that none get in. An emerging contaminant in the last few years, are chemosensitizers which shut down these defensive pumps, compromising resistance and increasing toxicity from contaminant exposure. I study this in fish embryos. Expect to see some sciencey posts on fish, pollution and other environmental issues.

African Cichlids: evoluton for the home aquarist

I hope to fill my next fish tank with cichlids, the bright and colorful fish native to South and Central Americas (oscars, angelfish, discus) and to African lakes (including the delicious tilapia). Those familiar with Africans will know that each species has special water requirements depending on the lake they originate from. African cichlids, besides being important in the aquarium trade, are understood by biologists to be a prime example of rapid evolution and speciation.


Speciation of large animals (like fish) is often an incredibly slow process, happening on time scales not relevant to the human mind’s perception of the world. Within African lakes, notably, Lake Victoria, Malawi and Tanganyika, the number of cichlid species have exploded in the last few hundred thousand years. There are an estimated 1,600 species of cichlid inhabiting Africa alone. Since these lakes are also ephemeral over geologic time, they evaporate and fill again cyclically, so this rate of speciation is simply astounding. Lake Victoria for example was completely dry 12,000 years ago, and yet is now home to over 300 species of native cichlids. This indicates colonization from surrounding satellite lakes (in flood events perhaps) and rapid speciation. There have been questions raised whether our taxonomic grouping of these fish is correct. That is, whether these are truly different species, or just a variety of morphs of a few species. Genetic evidence supports the former.


One tool biologist have to study speciation is through changes in mitochondrial DNA (mtDNA). Mitochondria organelles within cells have their own unique DNA, from a very early endosymbiosis event where a bacterial cell was engulfed by a cell and co-opted to perform a particular function. mtDNA has a mutation rate higher than the genomic mutation rate in animals so changes can be measured over smaller scales, ideal for trying to determine variation within related species. By comparing the number of changes in a set region of mtDNA, scientists can determine the common ancestry of these species assuming a fixed rate of change of 2.5% every million years. Between the three major African Lakes, it was found is that Lake Victoria and Malawi species were much more similar (1-2 million year common ancestor) than compared to Tanganyika (2-4my). For a comparison, the Victoria and Malawi stock have only a 5% difference in mtDNA, while within South American cichlid stocks, the different is 11%. This low difference supports the hypothesis of very recent speciation. In addition, the mtDNA sequences of Lake Victoria cichlids indicate a monophyletic origin – meaning the founding of the stock was from a single species.

The genetic data also disproves a previously held belief about cichlids. It was found fish within the same lake are more related than to other fish that look alike within a different lake. Similar morphological adaptations in different lakes may be the result of convergent evolution. Convergent evolution is when different species can develop in parallel ways to adapt to their environment; think sharks and dolphins- morphological very similar but genetically unrelated. Speciation and convergence seen in African cichlids may be due to adaption to niche habitats. Within a single lake, there are cichlids that inhabit cavernous rocky shores, open sandy lake bottom, and others even living in discarded shells. Lake environments also have limited resources which put pressure on species to form niche diets as well. While some cichlids are omnivores, many species specialize in grazing on algae, insects on the surface, or some hunting other fish.

African cichlids are a prime example of evolutionary theory in action. Though we may not have much longer to study these wonderful creatures. There are 265 species of cichlid on the ICUN red list, with 109 of these listed as either “endangered” or “critically endangered.” Several cichlid species have been driven to extinction, and others only being kept alive in aquarium. Environmental degradation and introduced species are a serious threat to the population of these fish, particularly in Lake Victoria…a topic I may come back to at a later date.


Johnson, T. C., C. A. Scholz, et al. (1996). "Late pleistocene desiccation of Lake Victoria and rapid evolution of cichlid fishes." Science 273(5278): 1091-1093.

Meyer, A., T. D. Kocher, et al. (1990). "Monophyletic origin of lake victoria cichlid fishes suggested by mitochondrial-dna sequences." Nature 347(6293): 550-553.

images: wikipedia

A familiar argument...wait what?

Friday, November 20, 2009

Emerging Contaminant Alert: Nanosilver

There are known health risks involved with nanomolecules, most notably carbon nanotubes which can be highly toxic. Since the emergence of nanotechnology, metals such as gold and silver are being used in colloidal solutions for a variety of industrial and biomedical applications. Colloids are small particles….really small. They range from 10^-6 to 10^-9m (1um-1nm) in diameter. For reference, that’s about 100x smaller than a virus. Probably the most common colloid we are familiar with is milk, though I doubt anyone ever thinks of their morning cereal as a bowl of nanofat globules floating in suspension.

New research published in the journal Small, demonstrates that colloidal silver has teratogenic, or developmental, defects on zebrafish embryos. Silver, being a Class B metal, has a tendency to form ligands with sulfur complexes, such as those in amino acids (Cysteine for example). Once bound to protein structure-building acids, silver can accumulate within muscle tissues with a high residence time. While gold too is a Class B metal, it is biologically inert and nontoxic. In colloidal form, silver can be easily transported throughout the body (through the circulatory system, through the blood-brain barrier, etc) and its small size affords it’s a high surface-to-volume ratio, making it more chemically reactive, or in this case, biologically.

Zebrafish were used in this study because they are a powerful model for studying development of vertebrate species. So what happens when you mix zebrafish embryos and colloidal silver? Well, mainly death, at higher concentrations at least. It was not until embryos were dosed at less than 250uM were non-lethal effects seen. Zebrafish embryo malformations were scored 0-4 with 0 being normal(control) and 4 being death. “Some of the fish became extremely distorted, almost making a number nine or a comma instead of a linear fish,” said Dr. Darin Furgeson, author of the study in article written for Scientific American. Exposure to colloidal silver caused cranial and spinal deformities, pericardial edema (swelling around the heart) and in addition, toxicity was not only related to dosage, but also to the size of the colloids. By 24hrs of exposure, silver particles with a diameter of 3nm killed 80% of the embryos while particles of 100nm in size, only 3%. So the smaller the colloidal grain size; the more lethal it becomes.

But silver has never been a huge human health concern, with most commonly known affects being altered skin pigmentation. In the environment though, silver pollution from industry has been serious issue. Another characteristic of Class B metals is that they have a tendency to bind to particles and be transported via the atmosphere. So silver waste generated in coal production and burning in China, can adsorb onto particulate matter and be transported globally. That’s why atmospheric deposition is the major source of silver in the oceans. Colloidal silver is becoming more commonly used each year with its major use as antimicrobial to prevent bacteria growth on many consumer products. The fact that it has been shown that these colloidal silver solutions are not removed from standard waste treatment process should be of major concern. Anytime there is a potentially hazardous chemical mass produced and not removed before being discharged into the environment, red flags should be shooting up all over the place.

From Dr. Furgeson again, “I think we jumped the gun…[we] should take more time and really look at these new nano-systems before we start to throw them into personal products and shoot them into these ecosystems.”

So the question stands, just what lingering effects may we be seeing ten years from now? What concern is it to human health, environmental health? Like most emerging contaminants, we would expect to see the effects first in aquatic organisms because once something taints their environment, they are exposed via gills (respiration), diet, dermal contact…a combination that makes their health the first proxy we have for other organisms, and why fish embryo studies like this so imformative.

Bar-Ilan, O., R. M. Albrecht, et al. (2009). "Toxicity Assessments of Multisized Gold and Silver Nanoparticles in Zebrafish Embryos." Small 5(16): 1897-1910.

XMRV the next craze?

So for my first official post on this blog I am going to draw on inspiration from Abbie’s erv blog from Science Blogs. Xenotropic murine leukemia virus-related virus (XMRV) is a new retrovirus that has been found in some patients that have chronic fatigue syndrome (CFS) and in some prostate cancers. Remember: correlation does not mean causation (read below). Although we understand some of this virus’ cousins, it has not been fully characterized. Due to its detection in some high-profile diseases, this virus has been kicked around in the media, bounced around in blogs, and has now become the catchall for conspiracy theorists and general nutjobs. There are a few things that need some clarification:

1. Attributing the virus to many unrelated diseases. There is no evidence that this virus causes any disease, yet. There is an association of this virus being in people with a defective antiviral gene (RNAaseL), but this could mean that they are more susceptible to infection. Unlike the most well-known retrovirus HIV, this virus cannot infect cells that are not rapidly dividing. People with CFS have markers of chronic immune activation, rapidly dividing immune cells that are good targets for this virus. Prostate cancers are groups of rapidly dividing cells. It will take a lot of work to determine what relation XMRV has to both of these stories, but there are three possibilities. A.) The virus is a causative agent. B.) The virus is marker of an underlying condition, meaning the virus happens to preferentially infect people who have certain conditions. A good example is how people with AIDS display high prevalence of specific opportunistic infections. C.) The virus infects many different people and the infection has nothing to do with the disease. It is best not to jump to any conclusions until some large-scale studies have been done. Study of this virus is very much in its infancy.

2. The anti-vaccine movement. If you give some of these people any new observation they will latch on like a leech. Some argue this virus came from contaminated cells used to produce vaccines. These are some of the facts. There are very few full-length sequences of this virus, but they are remarkably similar. Normally one associates retroviruses with lots of sequence diversity. Some people see this as proof that these viruses had a common origin. There are other retroviruses that do have more conserved sequences. In the patients where they detect this virus there are generally few copies of the virus floating around, unlike HIV, where there could be millions of copies per ml of blood. A lower error rate combined with low replication rate can cause low diversity. In addition, these viruses are rather streamlined when compared to HIV, so they do not have the same sequence-wiggle room in accessory genes. Similar viruses XMLVs were common contaminants in labs. Some may argue that that this provides an avenue to get into production lines of vaccines. However, all this shows us is that these viruses are very good at infecting rapidly dividing human cells in the absence of an immune system. Contamination in a vaccine would kill a lot of the cells, drastically lower production, and would likely be noticed at some point. Furthermore, there are very low levels of infected people (if it were in a common vaccine the rate should be much higher). Immune-compromised people have received vaccines, and this virus has not popped up and killed them.

3. No the government did not make it. I have no evidence to say someone said it but I am heading this one off.

Hopefully this clears the air on some issues.

Kevin