Wednesday, April 25, 2012

Going Mad

The carcass of a California Happy cow lies at Baker Commodities Inc.  The test is positive; it’s infected with Mad Cow disease. This rendering facility preforms tests for animal BSE surveillance programs.

Bovine spongiform encephalopathy (BSE) commonly known as Mad Cow disease is a fatal neurodegenerative disease it causes the spongy degeneration of the brain and the spinal cord.

Mad Cow is a sibling of a series of diseases that spread across species, like scrapies in sheep and Creutzfeldt–Jakob disease in humans. The culprits are prions.

Prions are misfolded proteins. The name is a composition of protein and infection. Now if you remember your biology proteins are composed of a series of bound amino acids, this would be the primary structure then the amino acid arrange themselves in either alpha helix or beta sheet secondary structures, and finally they come together in a 3D tertiary structure.

The structure of a protein is vital, if they change their tertiary or secondary structure they wreak havoc across the body.  Protein misfolding is associated with numerous diseases for which no cure is available at the moment. These diseases are often debilitating, as is the case of spongiform encephalopathy.

In 1997, Stanley B. Prusiner won the Noble Prize in for the purifying and identifying the agent accused of transmission of spongiform encephalopathy.  Why is discovery worth a Nobel Prize? With a great outbreak of spongiform encephalopathy, in Britain during the 1980, there were numerous investigators searching for the culprit.

Prior these outbreak disease infection diseases were commonly and solely accredited to viruses, bacteria, fungi or parasites. When proteins were first proposed as the wrongdoer there was significant debate against the idea. Few of the scientists at the time considered the possibility; most renouncing the evidence declared that it was impossible.

The first clues that lead biologist Tikvah Alper and mathematician John S. Griffith to suggest a protein was that the disease resisted radiation. Now if it had been in fact a living being (let’s not debate the life of a virus) the pathogen particle would have been destroyed with induced radiation. Their findings also suggested that the pathogen must be smaller than a virus.

Let’s peer into the mechanism of destruction.  The name spongiform encephalopathy clearly alludes to a sponge; ence- is the prefix for brain, a spongy brain. The disease spreads and a heap of tiny holes appear in the brain causing mental and physical abilities to deteriorate.

The holes are caused by prions aggregates. The misfolded proteins accumulate outside the disrupting the normal tissue structure and creating the holes.  The incubation time is relatively long while the progression is swift and fatal.

Although the full structure of prion has yet to be exposed, researches do know that mammal’s posses correctly folded prion proteins. Once the healthy prions (PrPC) come in contact with misfolded prions (PrPSc) they cannot resist their influence and fold themselves. Following a catalyst reaction of degenerative proteins.

While it is know that eating flesh infected with PrPSc will infect another animal, there are current studies interpreting other possible mechanisms.

One problem is that PrPSc does not respond to sterilization methods like proteases, heat, radiation, and formalin treatments. Effective prion annihilation relies on protein hydrolysis or reduction or destruction of protein tertiary structure with bleach, caustic soda, or strongly acidic detergents.

This is a grim issue when you consider that prions persist in the environment and could possible infect animals roaming once prion infected lands.

A carcass lies in a laboratory bench, researchers probe for answers to number of questions.  Are there more reliable quantification methods? Can we denature prions by composting the animal? Could plant uptake prions? Can we prevent it? Can we cure it?

Thursday, March 29, 2012

Let’s Concentrate!

In an earlier blog post I mentioned wasteful ineffective packaging. Now I want to show you an example of improving product packaging.

All Small & Mighty 3x-concentrated laundry detergent released in 2006

Laundry Detergent!

What’s so amazing about this? Well the idea of a concentrated solution is that you need less of said solution to obtain the same “working” results. So we get to buy less detergent bottles, hence reducing how many are discarded and made in the first place.

Another neat thing is that concentrated liquid reduces water. Before the laundry detergent came watered down, this increased the water used in production as well as packaging and transportation.

Water is a very important resource, vital for life. We use freshwater water more than we think. We can categorize water use as direct and indirect. Direct would be drinking, cooking, swimming pools, ect., indirect would be food, electronic devices, manufacturing,  etc. (WaterFootprint)

So next time you go shopping for laundry detergent take the concentrated bottle, and remember to read how much you need. It will be far less than the un-concentrated version, adding more than you really need won’t make your clothes any cleaner the detergent will just wash away, which is wasteful. So read the labels, and add just enough because more won’t help the environment nor your pocket.  

Friday, March 23, 2012

If you ever visit Puerto Rico you would hear the sounds of my fauna. Among those there is a little slimy cold amphibian called coquí. It is onomatopoeically named, and coquí is commonly used to describe seventeen species of Eleutherodactylus. The little guy fill our ears with its song and children sing to them thinking the coquís respond. The song serves as a warning and a mating call. It is a warning to other males not to enter their territory and an open invitation to females.  

Globalization is not a solely a human phenomenon of communication, trade and travel. The world fauna and flora have been trans-located from endemic lands for centuries. The framboyan traveled from Madagascar, and who would ever imagine the island without the beautiful spectacle this tree provides. Breadfruit it also another plant species that traveled far, it was introduced from Polynesia to the Caribbean colonies.


The seventeen species of coquís  live in diverse habitats through the island. Some live in the drier climate, while others in more humid areas and then some in the elevated mountains. Of the known species of coquís  in Puerto Rico three are already thought to be extinct coquí dorado, coquí de eneida, and coquí palmeado. The coquís  suffer ant the hands of human development, climate change, and invasive species.

There is not a clear path for each invasive species that settle in a new territory. But once they arrive they affect the natural ecosystem. The fungus Batrachochytrium dendrobatidis arrived in Puerto Rico around 40 years ago; the estimate is given relating the appearance of the chytridiomycosis illness. This illness causes skin infection and the fungus proliferates in humid areas.

Coquís  are an important national symbol and entertainers during the night. They boast more than just esthetic importance. They are important predators of small insects, responsible of controlling mosquito’s population and other pests.

Climate change aggravates the situation. The winter season is characterized by lessen rainfall, years back rain was seen around every three days while now it can go nine straight days without raining. This is not an arbitrary occurrence rather the new average. One of the consequences is the migration of coquís  to more humid areas where they are exposed to the fungus and develop the skin infection that causes their premature death.

We can observe the travel patterns of other invasive species. The easiest ones to track are product of human pompous behavior. The selfish need to own exotic animals. The problem is that these species are abducted from their land and introduce into new habitats. Sometimes they cannot survive in the strange lands and sometimes they thrive due to the lack of predators.

Iguana iguana native of Central and South America was introduced to Puerto Rico as an exotic pet. It was introduce into the wild because people tired of them and they escaped captivity. It was considered harmless to animal species because iguanas are commonly herbivores. They are also thought to eat bird eggs, small insects, and coquís . There is some debate upon the matter. Some investigators suggest that they only do so if there is no edible plant option in their diet, if they are in captivity. Iguanas only have three know predators in Puerto Rico, and they have multiplied their numbers, becoming a threat to plant species they eat. If their number rise and the plants they feast on diminish they would become prone to eat small animals.

Juancho II eating a hibiscus flower. Captured in Fajardo, PR.

El coquí himself is an invasive species. It was introduce in Hawaii in the 90’ where it song its considered a cacophony, it threatens the Hawaiian insect population and competes for food with other native predators. The Hawaiian government has tried various techniques to eliminate coquís such as citric acid, concentrated caffeine, water vapor and traps. The problem is that the use of insecticides to control the species is harmful to the environment. 

Wednesday, March 14, 2012

Matryoshka Dolls

A box arrives; you open it to find a second box surrounded by air bags. After jumping on the air bags to startle your lab mates, you open the second box to find a small bottle nested by foam peanuts. But I lied it was not just one box. How many boxes do we receive daily in one particular laboratory?  I could not say. I do know that the size of a box could tell me how big an object can never be. Otherwise there is no correlation between the size of the object and that of the box.

Now reader, you might be thinking “Silly girl, of course chemicals require additional protection during shipment”. I will ease your mind, harmful chemicals come in a bottle, wrapped in thick absorbent towels, inside a thick plastic bag suspended in absorbent foam, inside an aluminum air tight cylinder (very difficult to open I should say) inside a box, surrounded either by packaging paper, air bags, foam or other. Oh and I forgot, sometimes you are lucky and get multiple cylinders. I’ll tell you now about space, say the chemical bottle is two inches tall, the cylinder might be more than a foot tall; can you guess the size of the box? The box will most likely be able to fit two of these cylinders. Since the box is too big it creates the need for additional snubbers. Then I wonder, wouldn’t it be nice if we had smaller boxes?

Small box, Danbo

However, we also order other stuff. Harmful chemicals are not the only ones being subjected to numerous entrapments. Last week we killed a pH electrode and needed to resuscitate it, I mean replace it. Once again, we can observe the Matryoshka effect, the electrode itself is small, but since it’s made out of glass and any scratch to the functioning surface would render it useless it must be protected. Clearly, it comes in a foam bed within a “small” box. When the electrode arrives you get a box that could easily fit about twelve of the small boxes, with room to spare because they don’t concur in length. What’s the purpose for that second box, when the electrode rests protected in its foam bed?

Ever since I started grad-school, shipments of supplies have perplexed me. Often I have joked that if I don’t become a research professor I would certainly go to work for any of these companies and manage the boxing and shipping department. I would save so much money from my innovative boxing ideas that I would become their hero. Because, think about it, boxes and snubbers are not the only resources being wasted. You have to ship them, and to ship them you have to put them in a transportation device, which can only hold so much space and weight for that matter. For each trip, an x amount of fuel is used and parts are damaged, which must be repaired or replaced.

The associated cost is not merely monetary, it also has an environmental impact.  Where did the cardboard box come from? If you sum all of the energy invested, what was emitted to the atmosphere, to the land, to water sources? And after all that process, when you have the box in your hands, will it be reused, recycle, thrown away? But we are missing one R, reduce. The amount of packaging is an excessive Matryoshka that must be reduced. So I should change my major, study industrial engineering, and eliminate unnecessary boxes. 

Mafalda. The last panel reads "In the space era everything is possible"

Wednesday, February 29, 2012

1986: In the Footsteps of Scott
Robert Swan walked the desolated Antarctica landscape. Blue eyes and burned skin where gifts received from the encounter with the ozone hole. His team stood at the South Pole, achieving the longest unassisted march ever recorded in history.

Robert Swan. Image from The Journey So Far

Ozone is an important component of the atmosphere. It’s a highly reactive compound, which concentrates in the stratosphere. As sunlight travels across the universe, it interacts with various materials. The same can be said of its travels in the Earth’s atmosphere. This trajectory shields certain wavelengths from reaching the troposphere. When sun light hits the ozone layer, UV rays are absorbed by ozone and then dissipated as heat. As a result, we receive a lower percent of UV rays than those that are present above the stratosphere.

Anthropogenic sources of chlorine can cause dire ozone depletion. Chlorofluorocarbons, commonly known as freons, turned out to be a greater threat than expected. In 1930, freons were widely used in aerosols and air conditioning systems. It was not discovered until 1971 that most of the synthesized freons were still present in the environment. During the 1970s, a decade of  investigations, it was shown that freons reach the stratosphere and react with, and deplete, ozone.  In 1978, the use of freons in aerosols was banned in the U.S. Later, Freon-12 was isolated as a mayor threat and it was not until 1995 that its production was terminated and replaced by Freon-13a. 

1989: Icewalk
Certainly, walking to the physical South Pole is not enough. Robert Swan headed to the northern equivalent.  Due to the effects of global thermal change, the explorer‘s life was once again in peril. While walking through the Arctic, the expedition almost drowned due to the ice cap melting.
Melting of the ice cap is a natural phenomenon. April marks the beginning of the “melting season” and it ends in September when it starts freezing again. The problem is that the melting season is becoming longer. Ice melts earlier in the year and freezes later. Once the ice starts to melt, the water underneath absorbs heat from the sun, promoting further melting. Absorbed heat also affects the time it takes for the ice to start freezing. Since the ice melts earlier, it allows water to absorb heat for a longer time deferring the freezing period

Image from

One of the effects of increased melting, is clearly an overall smaller ice cap region in the surface. Polar bears are one of the many species affected by the smaller ice cap during the summer, as they need the ice to hunt.

1959: The last great wilderness on earth 
Robert made a promise to Jacques Cousteau and Sir Peter Scott in 1991: to use his story to preserve the Antarctic. He started the 2041 mission in order to ensure the preservation of this last great continent for generations to come.
The mission to protect the Antarctic started in 1959 with the signing of the The Antarctic Treaty, originally upheld by 12 countries. Now it boasts the support of 44 nations. 
Further protection is granted by the Madrid Protocol, singed in 1998, naming the land “A Natural Reserve Land for Science and Peace”. The protocol clearly states the conditions in which expeditions or research can be conducted in Antarctica. It also places a ban on mining and mineral exploitation for 50 years. Hence, the name of Robert's mission, "1941", which is the year the debate returns in full swing. What to do with this untouched land?

2008: E-base goes live!
Robert uses the greatest tool at hand in order to fulfill his mission, education.
“As the last unspoilt wilderness on earth, Antarctica is currently protected by the treaty prohibiting drilling and mining until 2041. Decisions made by today's youth will impact our entire planet's ecosystem and the future of life on earth” Robert Swan (2041).

Image from The Journey So Far
With the aid of 35 youngsters and the Russian government, Robert headed to Antarctica in order to clean scattered debris in King George Island. A journey that required seven years before completion. The island had been previously used as a research facility, and had accumulated waste over the years.  Forgotten in the island was a scientific station, and with Robert's envision it became a learning station.

Penguins reclaiming King George Island. Image from The Journey So Far

In 2008, E-Base broadcasted live the efforts of Robert and a small team to live in Antarctica, for two weeks, sustained solely by renewable energy. The idea was to demonstrate the use of clean technology and energy saving techniques.
Another growing experience is the Inspire Antarctic Expedition program, which focuses on leadership, teamwork and personal development. It allows very lucky educators, students, entrepreneurs, and corporate leaders to travel in organized expeditions to Antarctica. Traveling the cold terrain will grant the explorers experiences and stories that they can share with the world, a vessel to communicate the importance of protecting the environment.

Wednesday, February 15, 2012


In my head, as a child, winter had no connection with seasons. Winter was a time to get presents, tasty food, and time off from school. But more than anything winter has always been the best time to enjoy the beach, sure the water is a bit colder, but given that most people are frighten by the abundance of jellyfishes and the high waves you don’t have to worry about beaches being overcrowded. And then I decided to pursue grad school in Wisconsin…

Now you must think I’m crazy, if I wanted to achieve academic diversity there are plenty of other schools I could have gone to, but we are not going to talk about that now, there is something more crucial.

Lets concentrate of my change of perspective.

If you ask me now the first thing that flies into my head when I think of winter the answer would be static shock. Yes static shock. This is a cruel phenomenon. You want to protect yourself from the chilly wind so you layer up then as you walk to a building and open a door zaaap! You’re shoked, you think it’s weird, then you go to the lab bench to do some experiments and zaaap! your hit again.

There must be something terribly wrong, all day you’ve been shocked opening doors, turning on instruments even turning on the lights. There is nowhere to seek refuge from this horrible sensation. As it goes on, you wonder how to diminish this health hazard (mental health that is).

Then, after weeks of torture, somebody decides to be nice and tell you that fleece is one of the culprits. My mind wanders. Obviously fleece is an enemy, since, even in my extremely humid home (Puerto Rico) I could see static sparks when I moved my fleece throw.

The fleece jackets are thrown out the window, no more fluffy boots either. I embrace sneakers and frozen feet. I refuse to be constantly bested by the element of surprise.

Friday, September 30, 2011

The game Katamari has inspired me to create a miniature katamari!

I found some clay and decided to start working with it. After half an hour of trying to make the clay edible without any success, I started to work.

I managed to make a hollow ball by covering a small balloon with clay. Three days later it was dry and ready to mold and paint.

A few holes to organize the scattered pens around my desk. 

Molded some small items to be picked up by the katamari.

After a grand fight against super glue and stuck fingers, I managed to glue all of the little things to the katamari and mend a few of the broken ones.

Mmmm yummy pizza. Of course the katamari grows by picking up stuff so I'll be adding more items soon.