Thursday, March 20, 2014

Moonwalking Bird

Feeling down? Watch the Red-capped Manakin do the moonwalk for a nice little pick-me-up during finals week.

"Tentacles" Opens April 12th!

You should all come visit me in Monterey this summer! I am so stoked for the new cephalopod exhibit at the Monterey Bay Aquarium (my old home). Follow link for sneak peek-ish short movie.

http://www.youtube.com/watch?v=4XhidS-VEcg&utm_source=bronto&utm_medium=email&utm_term=See+some+highlights&utm_content=5+Reasons+to+Get+Wrapped+Up+in+our+%22Tentacles%22+Special+Exhibition&utm_campaign=2014_3%3A+March+E-Newsletter

NDM1

Antibiotic resistance is scary, however few papers have terrified me like this one. NDM1 is a product of the misuse and over prescription of antibiotics, and has the possibility to cause major harm. NDM1 stands for New Delhi Metallo-beta-lactamase-1and it is an enzyme that gives bacteria resistance to a large range of beta-lactam antibiotics, including the Carbapenem family of antibiotics (the antibiotics used when nothing else works). The enzyme is encoded in a plasmid easily transferred from one species of bacteria to another, allowing any bacteria in close proximity to a bacterium with the enzyme to acquire the resistance. Bactria that possess NDM-1 are almost untreatable, and in some cases, lethal even with treatment. NDM1 isn't just contained to the lab: it's global.

Wednesday, March 19, 2014

"How Wolves Change Rivers"

This short video is absolutely amazing and explains the massive impacts a single predatory species is capable of having on an ecosystem.

Sunday, March 16, 2014

Plastic surgery is a breeding ground for bacteria?

I noticed that many of the presentations on Thursday had to do with bacteria. Therefore, I felt this was fitting and quite interesting.

A side effect of cosmetic surgery (specifically fillers used for lip injections) that is becoming increasingly popular is the development of lumps or lesions around the sight of injection. With this being the second most common cosmetic procedure, this is quite a relevant topic for discussion. Many doctors previously blamed this on an allergic reaction that the patient had to the hyaluronic acid based fillers. What doctors are now finding is that the lesions are formed due to bacterial growth in the sight of injection. What's more is that the gel that is used in the actual filler encourages bacterial growth; they act as incubators and are very susceptible to infection. These lesions are very hard to treat with antibiotics.

When doctors previously thought that the infection was due to allergic reaction, they treated the patients with steroids, which give the bacteria free rein to grow. This treatment proved to be ineffective and seemed to be doing more damage than good. What they have found the most affective precaution to take in order to treat patients is to inject the sight where filler is being injected with prophylactic antibiotics simultaneously.

So the next time you're thinking about getting your lips done, proceed with caution! :)

To read more about it, you can click here!

Second HIV Baby Case - Cured

http://www.bbc.com/news/world-us-canada-26460221

Rather exciting everyone! Just last week the second case of infancy HIV was cured through early treatment. However there are certain risks because they end up taking the infants off of treatment, but as of now the infant has no symptoms or signs of HIV in its blood or tissues. This is very good news because it gives hope to people who currently have HIV and perhaps early treatment in adult prospects could possibly be cured as well. Over 34 million people world wide are infected with the HIV virus which is an immune deficiency virus, it weakens and virtually destroys the immune system and eventually leads to AIDS which most likely results in early death. This virus is strange, and not much is known about it so the more research and test studies such as this one are very beneficial.

Urban Agriculture

For my presentation, I talked about some innovative new ways of farming in urban areas, here's an article that isn't the scientific paper I read. Its pretty cool to think about the future of farming and the possibility your kids or grandkids could live right next door to a farm in the middle of LA or NYC. The future is looking bright my friends!

http://www.dailycal.org/2014/03/13/campus-community-explores-urban-agriculture/

Saturday, March 15, 2014



Hey guys! While I was taking a break from studying I came across this video of a cat and dolphin interacting. It's really adorable and totally worth watching!

Climate Change and Alaskan Wetlands

In case my chalkboard graphic was not enough, I have put together an even more compelling graphic to better illustrate the findings of Corcoran et al. In their study of Alaskan boreal wetland responses to climate change!

Figure 1: climate change and Alaskan wetlands (Morse, 2014)

In Summary, since late 1980s wetlands have shrunk in size due to increased average temperatures in Alaska of 3-4 degrees Celsius. This decrease in wetland size means a higher concentration of nutrients which leads to phytoplankton blooms. These blooms mean more food for zooplankton and less algae fallout to benthic invertebrates. Since migratory birds rely on benthic inverts for a large portion of their diet, the researchers predicted that we may begin to see shrinking migratory bird populations.

Some of the data supporting this research is assumed to be the same for all wetlands in the study area. This is problematic because the area that they were surveying has 20,000 wetlands in a 36,000 square kilometer area. However, It is nonetheless interesting to think about the cataclysmic effects that climate change can have on an entire ecosystem.

Corcoran, R.M., Lovvorn, J.R., Heglund, P.J. (2009). Long-term change in limnology and invertebrates in Alaskan boreal wetlands. Hydrobiologia, 620(1), 77-89. 

Splash Cups and 3-D Printing

Hello all,

In case anyone was interested, here is a good video explaining the splash cup mechanism of flowering plants that I discussed in class. For some reason on my computer it won't allow me to fast-forward/rewind, so if you want to go back and read something you have to start it over; just pause and it should work fine.

Also, a link to the older article from 1951 can be found here.

On a separate note, the field of 3-D printing is still a bit in its infancy when it comes to the field of medicine/biology, but in recent years there have been some revolutionary advancements, especially with regards to tissue engineering. I highly recommend putting in a bit of independent research on it if you have time--there's some cool stuff being made out there.

Friday, March 14, 2014

Pick your poison

Researchers have found a strange case in which a woman infected with Lupus was controlling her HIV. Lupus is an auto-immune disorder in which the immune system becomes overactive and attacks the bodies own tissue. In this rare case the women's overactive immune system was producing "Broadly Neutralizing Antibodies," which are not normally present in high quantities. These antibodies are key in controlling HIV. Through the study of this case scientists hope to find a way to increase the bodies production of Broadly Neutralizing Antibodies and help fight HIV

http://www.livescience.com/44020-lupus-patient-makes-antibodies-against-hiv.html

We're under a small barrage of asteroids

Over the past week the earth has had near misses from three separate asteroids. The closest one was just 38,300 miles away, for comparison, the distance between the earth and the moon is 239,000 miles. This asteroid was only 25 feet wide, along with one of the asteroids that flew by just a day before. However the second asteroid of the previous day was 100 feet wide and missed earth by a distance of just 217,000 miles. But rest assured, NASA says this stuff happens all the time.
http://www.livescience.com/43945-small-asteroid-2014ec-earth-close-shave.html

There's supposedly water in the upper mantle.



ringwoodite diamond
A diamond mine in Brazil has found a rare diamond estimated to have been formed 323 to 410 miles below the Earth's surface. What's interesting is this diamond is composed of ringwoodite which is a mineral only previously found from asteroids, and created in labs. It forms under extreme pressure generally accredited to the upper mantle and what's known as the transition zone. Apparently this chemical is also 1.5% water, in the form of hydroxide ions. Read more about it >>>   http://www.livescience.com/44057-diamond-inclusions-mantle-water-earth.html
Hello!

During high school, I took two semesters of writing with a professor who specialized in food writing. Through research papers and such, I collected quite a library of articles and information about different aspects of the food industry such as factory farming, the use of antibiotics in feed, "uneven" agricultural subsidies, high fructose corn syrup, and how all of this relates to our health and the health of the environment.

If anyone wants to delve deeper into the world of the American food industry, I'd really recommend The Omnivore's Dilemma by Michael Pollan and Eating Animals by Jonathan Safran Foer (the same author who wrote Extremely Loud and Incredibly Close, if anyone recognized that). Both are excellent reads, and full of facts. Also, while i'm sure everyone has heard about the documentary "Food Inc." it is an informational source (albeit with a fair dose of pathos) that I would definitely recommend. Along those lines, the documentaries "Frankeinsteer," "King Corn, "Farmageddon," and "Dive!" will give you a good look at different areas of the issue and all are available on netflix!

 Additionally, I'll link to some of the articles I've read and incorporated into past papers:

A great article on the emergence of antibiotic resistance in factory farms
A rundown on corn's place in the American diet and as the feed of animals
Agricultural Subsidies and American Health
More on subsidies in this article by Scientific American
Great info on factory farms and their history

I have way more, so if anyone wants a bit more to read feel free to ask. Also, if anyone has any information in this subject that you think would be interesting, let me know!

Gut Microbial Ecology

Just in case you didn't catch what I discussed in class Thursday or wanted to know more:

The review I read stressed the importance of the microbial community structure rather than "good" and "bad" microbes (bacteria and archaea).  The community is structured by "top down" pressures from the host for functional redundancy and "bottom up" selection from resource partitioning for functional specialization.  Thus, the community is a result of coevolution between the host and the microbes.  With regard to function, diversification is continuous; the product of one microbe becomes the substrate for another.

What I found most engaging, however, was the mechanism that we acquire our gut community.  Researchers showed that we all get our initial community structure from our mothers.  Particularly, we get them from our mother's vagina and feces upon birth.  Babies born by natural birth have different colonization patterns than babies born by cesarean section.

Further support that the community isn't transmitted genetically: twins have the same level of similarity in their community as siblings.

Community is especially important for interactions with the immune system and with pathogenic communities.  The immune system regulates relative abundances of microbes not individual species and t-cells as well recognize the community not individual species.  Pathogens will interact differently with a healthy community than just a few of the "good" species.  Gut microbe community can therefore be used as a biomarker for health and susceptibility.

Furthermore, the community can influence metabolism of polysaccharides and susceptibility to obesity.  The two dominant divisions of bacteria in the gut are Bacteroidetes and Firmicutes.  Having more Firmicutes andd less Bateroidetes has been linked to obesity.  Microbial diversity in the intestine thus represents another form of heredity that could potentially be reprogrammed (maybe at birth) for a healthier society.

Ultimately, our living style (being fanatics about hygiene) could forecast our disease susceptibility in the future.  This might have huge implications for our society's prescribing of antibiotics that Abby discussed.

This is an easy to read and fascinating paper so if you have the time over break, check it out!

Ley, R. E., Peterson, D. A., & Gordon, J. I. (2006). Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell124(4), 837-848.
Some Brave, Bizarre uses of Botox. 

 In class we briefly mentioned Botulinum toxin type A (Botox), a drug produced from the same toxin that causes a life-threatening type of food poisoning called botulism. Botox is most commonly known for its temporary smoothing of facial wrinkles.  However, there are several other uses for the muscle paralyzing drug. I found research papers discussing the use of Botox treating hyperhidrosis (excessive sweating) and even migraines.  For the website listing additional uses for Botox, click here.  The research papers are cited below.


  •  Marc Heckmann, M.D., AndrĂ©s O. Ceballos-Baumann, M.D., and Gerd Plewig, M.D. “Botulinum Toxin A for Axillary Hyperhidrosis (Excessive Sweating)” The New England Journal of Medicine 2001; 344:488-493. 15 Feb 2001. Web. 21 January 2014.
  • Silberstein, S.  Mathew, N. Saper, J. Jenkins, S. “Botulinum Toxin Type A as a Migraine Preventive Treatment” Headache: The Journal of Head and Face Pain Volume 40, Issue 6, pages 445–450, June 2000. Web. 22 January 2014

Thursday, March 13, 2014


Can Bacteria Be Used to Clean Up Oil Spills?
Yes! New experiments are being conducted which reveal that within the right conditions, marine bacteria can be used to clean up a considerable amount of oil. This idea holds great potential as an environmentally-friendly method to clean up after oil spills.  Read more about it here.


















Where's Waldo? (The Octopus).

It's pretty well known that octopuses use camouflage as a defense mechanism.  But how exactly do they do this?  And what are the limits of their abilities?  Check out this video, complete with over the top science-drama music, to get a better idea of how cephlapod's chromatophores allow them to achieve such impressive camouflage feats, as well as seeking some pretty cool footage.

http://www.youtube.com/watch?v=pVIVIq4F3x0

Traumatic Insemination

Today I presented on polymorphism leading to speciation in side-blotched lizards, but this topic was the runner up when I was picking.  It seems too outrageous and horrifying to waste.  Wikipedia is a great place to start learning about bed bugs that penetrate directly into the abdomen with their penises, penis fencing, and snail's love darts.

http://en.wikipedia.org/wiki/Traumatic_insemination

For a more comprehensive look and much denser reading, here is the scientific paper I read:
http://www.ncbi.nlm.nih.gov/pubmed/23347274

Hygiene Hypothesis


I talked on the Hygiene Hypothesis today briefly. Here is   
the link to the article I read and a wiki page that does
a decent job summarizing it.                                      







More information about Triclosan

Today I spoke about Triclosan in class, however due to time constraints, I was unable to really cite any sources. A few people seemed interested in finding out more information, so I wrote up a little paragraph summarizing some of the main points, and provided links to my sources.

I happen to think that it's a good looking molecule 
First registered as a pesticide in 1969 (1), Triclosan is widely used as an antimicrobial compound, and is present in everything from hand soap to surgical instruments. Triclosan's main method of action involves inhibiting bacterial fatty acid synthesis at the enoyl-acyl carrier protein reductase (FabI) step (2). Humans lack this enzyme, and the EPA concluded that Triclosan would have no effect on people. A 2006 study (3) demonstrated that Triclosan acts as an endocrine disruptor in frogs, is known to enter the bloodstream of humans through the skin (4), and was found in 75% of peoples urine samples in a 2010 (5) study with concentrations ranging from 2.4-3790 ug/L. More recently, in a August 2012 UC Davis study, Triclosan was found to depolarize L-type calcium channels and reduce cardiac output in mice (6).  California ocean water contains Triclosan in concentrations approaching 732 ppt (7), the highest levels in the nation.
1. Triclosan Facts Pesticides: Reregistration. US Environmental Protection Agency. [Online] http://www.epa.gov/oppsrrd1/REDs/factsheets/triclosan_fs.htm.
2. Mechanism of Triclosan Inhibition of Bacterial Fatty Acid Synthesis. [Online] http://www.jbc.org/content/274/16/11110.
3. The bactericidal agent triclosan modulates thyroid hormone-associated gene expression and disrupts postembryonic anuran development. Science Direct. [Online] http://www.sciencedirect.com/science/article/pii/S0166445X06003407.
4. Moss T, Howes D, Williams FM. Percutaneous penetration and dermal metabolism of triclosan (2,4, 4'-trichloro-2'-hydroxydiphenyl ether). PubMed.Gov. [Online] http://www.ncbi.nlm.nih.gov/pubmed/10722890.
5. Drinking Water Contaminants of Emerging Concern Program. s.l. : Minnesota Department of Health, 2010. http://www.health.state.mn.us/divs/eh/risk/guidance/dwec/cecfy10report.pdf
6. Triclosan impairs excitation–contraction coupling and Ca2+ dynamics in striated muscle. s.l. : UC Davis, 2012. http://www.pnas.org/content/early/2012/08/08/1211314109.full.pdf+html

7. Revised Environmental Fate Science Chapter for the Triclosan. s.l. : UNITED STATES ENVIRONMENTAL PROTECTION AGENCY.
http://www.oehha.org/prop65/public_meetings/052909coms/triclosan/ciba7.pdf

Jurassic Park: Dinosaurs only?


Was John Hammond prejudiced when he welcomed us to Jurassic World? That is, were more than just dinosaurs inside the park and in that era? This Reuters article talks about the presence of feathered-birdlike dinosaurs, flying reptiles, a gliding mammal, a swimming mammal, and salamanders during the Jurassic Era (Their proof behind this theory comes from recent fossil evidence from China) Read to find out more (and watch the movie because it's really good).

Summer Research Scholarship!


CCS sent out an email about this, but I thought I'd post it here in case any of you didn't see it. For anyone involved in research or who wants to research over summer, the SURF (Summer Undergraduate Research Fellowships) scholarship application is open! It's due April 7th, and all you need to do is a short application and get two letters of recommendation. All the info is HERE! The one downside is that preference is given to sophomores and juniors, but it's always worth a try. Good luck!

Are Lazurus Species the Real-Life Zombies?


Just as Jesus raised Lazurus from the dead, some animal species that were thought to be extinct are being sighted again. Here is a link that lists the top 10 species that have been rediscovered lately. However, because of the existence of the Lazarus species, there are also Elvis species, that is there are species that "impersonate" the great species that went extinct. To see some examples of Elvis species click here. The big question is, how can we distinguish the two apart? Are these Lazarus species zombies or are they simply just an adapted version of the original species?

Polydactyly in the Amish Population


The Founder Effect is felt heavily in the Amish population with Ellis-van Creveld syndrome, which causes polydactyly. When the original small population of a community contains an unusually high amount of one gene, this gene is spread throughout the population as it increases, thus creating the Founder Effect. This occurs within the Amish, as the original founders contained genes for Ellis-van Creveld syndrome, and as the population grew within its small borders the gene was kept in close quarters and is therefore far more common than in average global populations. Ellis-van Creveld syndrome causes polydactyly, short ribs, disproportional short stature, short limbs, small trunk, dental anomalies, dystrophic nails, congenital cardiac disease, and genu valgum (knock-knees). These symptoms are detailed here. In short, a syndrome you do not want to have. In average populations, rare genes such as this are filtered out through a large proportion of dominant genes which override it. However, because of the small population size and occasional interbreeding of the Amish communities, Ellis-van Creveld syndrome has become common.
Hello!

I spoke in class today about bacterial conjugation. I didn't have enough time to really say much about it, so if you're interested:

This website has a nice video about the basics of the process

This pubmed article does a wonderful job explaining bacterial conjugation in more detail 

Also, this is a good resource for learning about plasmids and some more info on conjugation

Otherwise, if you have any questions let me know!

Tomatoes: Fruit or Vegetable?

Legal Solutions Blog: Tomatoes

More Tomato Stuff!


I was curious as to why the Supreme Court found tomatoes to be a vegetable, so these are the explanations I found. It has to do with how tomatoes are commonly thought of and used as vegetables despite technically being fruit. They compared tomatoes to things like squash, beans, and peas, which are also thought of and used as vegetables even though they are all fruits. The court case was brought about when a tariff was imposed on vegetable imports and a family attempted to import tomatoes as a fruit. When they were charged the tariff, they sued to regain their lost revenue. The Supreme Court ignored the dictionary and botanical definitions of tomatoes, focusing instead on the common conception of a tomato in everyday use.

The Terror of the Megalodon


The Megalodon, a prehistoric shark with size greater than the almighty Tyrannosaurus Rex, lived in the Cenozoic Era. Discovery channel's infamous "Shark Week" dubs the tale of "Megalodon: The Monster Shark Lives" and twitter goes crazy with people thinking that this monstrous creature was actually real and demands an apology. National Geographic does the world good by explaining this creatures disappearance and the mystery behind it. Click the link here to learn more!!

Dunkleosteus: Nightmare Fish of the Devonian

Imagine a great white shark wearing full body armor, and you have a good idea of the Devonian Period's apex predator. Reaching 8 meters in length, this four-ton fish possessed one of the most powerful bites in history. It's diet consisted of anything unfortunate enough to crossed its path, as virtually no fish alive during the Devonian could withstand a bite from its crushing jaws. To read more about dunkleosteus,visit the following link:

Summer Course Resources

In case some are interested in getting some coursework done over summer as a fallback if any research opportunities are not available, I highly recommend looking up the UC Extensions program. It's similar to community college courses but offers somewhat more advanced courses as well as some specialized ones which may coincide directly with your research interests. Some are a bit more expensive than normal community college courses but many I think are cheaper than taking classes at the UC directly. Also, transferring the credits through them is a breeze obviously. I recommend checking them out. Some might be in your area, as they are not always directly within the corresponding city.


If you don't care about getting the 'official credit' as much but want some very handy extra learning through your summer, if you don't know about Coursera it is a great tool. You can enroll online for courses offered at universities throughout the world and do the work and the tests alongside the class for free. At the end you get a certificate verifying you have completed this class. While it is not as official as the UC course it is a good tool to force yourself onto another academic schedule that is more flexible and less stressful. Hope this helps!

Global Warming and Malaria

http://www.bbc.com/news/health-26470755


 So pretty scary guys, Malaria due to higher global temperatures has gained the ability to move to higher altitudes such as in Ethiopia where over half the population lives at around 5,000 feet. Current studies say that just a 1 degree change in celsius could lead to 3 million additional cases of Malaria in children under the age of 15. In 2012 alone over 600 thousand people died from Malaria related causes. If you don't care about the environment, perhaps this could be some inclination to decrease your carbon footprint. Check out more on this story at the link on the top.

Wednesday, March 12, 2014

Gambian Giant Pouched Rats as Mine Detectors

Hey everyone! Here's an article on why you should love Cricetomys gambianus, This cat-sized African rodent may be responsible for saving many human lives and limbs, due to its efficiency as a landmine-detector. The following link tells about Britain's efforts to recruit these furry fellows in clearing minefields in Mozambique. ,

Protocells!!!!!

So I just gave a talk tonight on Abiogenesis and Protocells, and I ended with discussing how we can use protocells in a biotechnology sort of way.
There is a TON of really cool things going on right now, for example,

Running shoes that can repair themselves overnight
New potential cancer therapy
and, self-repairing architecture

I'm personally very excited by all this technology and building the bridge between life and non-life. The idea that you can program a very simple cell to do whatever you want it to is a novel idea that could have very positive, and also perhaps negative consequences if people use protocells to create more powerful and deadly bio weapons. It's something very important to consider, but something that also shouldn't hinder us from potentially world-changing technology.
Protocells have more use than just biotechnology though- creating life from abiogenesis --> protocells can help us better understand the origin of life on earth, which is something humans are constantly questioning.
Craig Venter has claimed to create life in a lab, and he did, but I personally don't really think it counts because he didn't start from scratch- he created life from parts of living things instead of life from non life. Hopefully in the near future someone (probably a brilliant ccs student) will able to create life from scratch in a way that mimics the early earth.

Jen Casselle and Michelle Ferraro: Marine Invertebrate Recruitment Lab

[Biology-U-L] PISCO LAB Opportunities Biology Undergraduate List biology-u-l at lifesci.ucsb.edu Thu Aug 22 11:23:10 PDT 2013 Previous message: [Biology-U-L] CCBER Vertebrate Collections Internship Next message: [Biology-U-L] Fwd: Medical Assistants Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] *Marine Science Volunteer Opportunities in the PISCO Lab!* Are you looking for an interesting place to gain valuable lab and field experience in a progressive environment? The Partnership for Interdisciplinary Studies of Coastal Oceans Lab is in need of patient, motivated, committed, independently minded undergrads to conduct ongoing marine intertidal and subtidal monitoring and research projects. These projects are basically focused on understanding how individuals, communities, and whole ecosystems interact and are affected by regional near-ocean processes and climate change. PISCO is a science consortium based out of four universities, and comprised of the very best principle investigators, science coordinators, analysts, post-docs, and graduate students collaborating across many disciplines and a latitudinal gradient stretching from Baja to the Pacific Northwest. Immediate work that needs to be done in the lab includes a host of projects related to the sorting of recruitment samples that are worked up using dissecting stereomicroscopes. Students who work in the lab will also have the opportunity to do field work from Spring to Fall. Field work consists of full day trips (6am – 5pm) out to the Channel Islands aboard University and Channel Islands National Marine Sanctuary (NOAA) research vessels. Collections are all done via free diving, so AAUS SCUBA diving certification is not required but strong swimming skills and free diving experience are desired. Requirements: I prefer 2^nd and 3^rd years with some lab experience, and BIO/AquBIO/ENVS/EEMB majors. Be prepared to commit to *six to eight hours a week for at least two quarters*. If you feel like you are a particularly detail oriented and motivated 1^st year don’t hesitate to apply. Here is what I need and in the following order: 1.Name 2.Major 3.GPA 4.Class Standing (1^st /2^nd /3^rd /4^th) 5.Resume/C.V.(can be covered in by #6) 6.Tell me a little about yourself and why PISCO Lab is a good fit. Send all applicable information to: Michelle Ferraro PISCO Lab/Project Manager michelleferraro88 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: Previous message: [Biology-U-L] CCBER Vertebrate Collections Internship Next message: [Biology-U-L] Fwd: Medical Assistants Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Pretty Worms

For those of you that want a break from reading scientific papers and studying for finals here are some fantastically beautiful pictures of obscure marine worms.  This continues to be one of my favorite aspects of biology: pretty things.

http://www.thisiscolossal.com/2014/03/worms/

Whale Graveyard

Talking about fossils yesterday reminded me of an article I saw fairly recently. A large graveyard filled with fossilized marine life was found in Chile in four distinct layers, suggesting four separate mass strandings between 6 and 9 million years ago. Researchers uncovering the bones are speculating that the mass die-offs occurred due to harmful algal blooms that poisoned many marine species and caused them to die and wash ashore on this tidal flat. Orange splotches found on rocks near the bones where examined and found to be fossilized organisms similar to dinoflagellates, which are known to produce red tides today, suggesting a algal bloom similar to a red tide occurred and lead to the mass strandings. They found several dozen baleen whales, aquatic sloths, walrus-like toothed whales, 2 different types of phocid seals, and an extinct species of sperm whale. (Journal: http://rspb.royalsocietypublishing.org/content/281/1781/20133316.full)


"Skin pigmentation provides evidence of convergent melanism in extinct marine reptiles"

Our class discussion yesterday reminded me of a paper I came across that was recently published in Nature. It discusses possible coloration of an ancient leatherback turtle, an ichthyosaur, and a mosasaur. The researchers found that the ancient reptiles' skin likely contained eumelamin (melanin that produces brown/black coloration). The extinct leatherback turtle and mosasaur may have even been countershaded! Comparisons to modern marine organisms, such as the extant leatherback turtle, make it seem likely that these animals were dark colored or countershaded and could provide potential insights as to why these animals may have been colored this way. The article is very interesting and totally worth reading! Here's a link for anyone interested! There's a link to a PDF under the author list if the images don't show.

Potato Chip Addiction

For all of you eating those late night study snacks, there's a scientific reason you can't just eat a few chips. I just found this paper because I ate 2 bags of chips and wondering why I couldn't stop myself. Your brain is actually stimulated by these endocannabinoids which give you a sense of euphoria and essentially tell your brain "That was good, give me more!" Some scientists believe this recent discovery could potentially be used as an anti-obesity drug.

The body is an incredible thing and so are CHIPS!

Check it out for yourself: http://www.pnas.org/content/early/2011/06/27/1104675108

Tuesday, March 11, 2014

Hello Everyone!

If anyone is interested, the first topic I chose to research this quarter was the origin of viruses. Apparently, there are a bunch of different hypotheses on how exactly they came about. If anyone is interested, this post on nature.com is really thorough and insightful. The various hypotheses are summarized quite well. Also, he uses over ten citations that lead to great papers on the subject.

One especially interesting paper that was listed as a citation is one that argues that the eukaryote nucleus came from a DNA virus!

If anyone is interested in discussing the nature.com article or any of the cited papers, or if you find some other interesting papers about viruses, be sure to let me know!

Human Fossils!

After our discussion today about human fossils, I decided to look more into it and I found that the Smithsonian has an online catalogue of their collection of human fossils. You can search by species, bone type, and age range and they give some general information about each fossil (Where & when it was found, how old it is, etc). I thought it was pretty interesting to look through some of them! Link!



Cool Video!

My Geology professor showed us this video and, after today's lecture, I figured you all would enjoy it too!

"Chimpanzees empathize with group mates and humans, but not with baboons or unfamiliar chimpanzees."

 A newly reported study on Science Daily discussed an interesting behavior of Chimpanzees.  Just like us, Chimps show a "flexibility" in empathy, meaning that empathy can be expressed for more than just close family or group members.  Using contagious yawning (don't lie, you've all done this), the researchers found that "chimpanzees showed contagious yawning to familiar chimpanzees, familiar humans, and unfamiliar humans, but not to unfamiliar chimpanzees or an unfamiliar species (gelada baboons)."  Yawning was shown to be a sign of connectivity between individuals not just from being tired or bored in a 2011 study.  Using this trait, Chimps might be able to be convinced to empathize with "out groups" and increase chances of survival and genetic diversity.  Understanding these social and emotional interactions will also help scientists explore human barriers.

M. W. Campbell, F. B. M. de Waal. Chimpanzees empathize with group mates and humans, but not with baboons or unfamiliar chimpanzees. Proceedings of the Royal Society B: Biological Sciences, 2014; 281 (1782): 20140013 DOI: 10.1098/rspb.2014.0013

http://www.sciencedaily.com/releases/2014/03/140311124202.htm

River Otters

When we hear about otters, we almost instinctively think how adorable and innocent looking they are. But if seen in the wild and hungry, those adorable eyes could be intent on catching their prey. Like catching an alligator for lunch. Typically, when we think of alligators versus river otters we would tend to associate the larger, more rugged animal with being the higher predator; however, that it not necessarily the case here. As said in the article, most otters are close to top predators in their area. Take a look at the article to read about how the otter actually kills the alligator with additional pictures of the attack.
Next time you're in otter territory, be cautious, because they're feisty when hungry. And apparently running onto land does not mean you're safe. Keep in mind otter attacks are rare, but do happen. Here is a report of a teen being chased by an otter on land and being bitten. If you're interested on how fast an otter can run, conveniently there's a paper on that: Running energetics of the North American river otter: do short legs necessarily reduce efficiency on land? You can find it on Web of Science.

To end on a cute note, watch this man cuddle with two otters here.

Monday, March 10, 2014

Origin of Life Refresher

In case anybody is interested in reviewing the class a bit, one of my earlier topics provided a very good summary of the first few weeks of class. The article, titled, On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. discusses how life came about, the key differences between prokaryotes and eukaryotes, and through those differences infers the basis of their common ancestor and its corresponding characteristics.

While the article is fairly lengthy, its laid out well into specific sections if you're interested in particular topics such as chirality. Many of the figures will be familiar as similar ones were used in lecture. Additionally, all of the theories presented (and also challenged) are well-reasoned and supported with common evidence. I encourage you to skim through it--it's extremely well written!

Parasitic Wasps

      Kind of scary... but recently there was a discovery of over 200 new species of parasitic wasps in Costa Rica. When discoveries like this happen I get really excited because it just proves to me that we don't know all the Earth has to hold. People often have the notion that everything has been discovered, and that we already know everything there is to know about what abides on our glorious planet. What I find most interesting about this new discovery is the process by which these wasps reproduce; they inject their eggs into the eggs of other insects. Not only do they plant their eggs, they also plant a virus in the eggs of the inhabitant that will protect their offspring. Reminds me a bit of the movie Alien....

Just thought you guys might find it interesting! Below is the link if you want to check it out!


http://news.nationalgeographic.com/news/2014/03/140304-parasitoid-wasp-costa-rica-new-species-conservation-diversity-science/

"Missing Link"?

A few months ago, my dad sent me an article on a new discovery, and I thought it was super cool. A new fish fossil found in China has been attributed to being a possible "missing link" (see picture to the right) between placoderms (an ancient fish group) and modern fish (yes, like Nemo). Apparently, it was a bigger news topic than I had originally thought, as, a few days after I had read it, it was brought up in one of my EEMB classes, Biology of Fishes. The topic of fishes, as suggested in the name, was discussed in depth in the course and opened my eyes to how cool this discovery really was. A little insight into fish evolution: jawless fishes (generally termed "Agnatha"), including the lampreys and hagfish, are thought to have come first. Then, Placoderms, these huge, ancient fishes with bony plates on the outside are thought to have come next. Placoderms had jaws (see left photo), but they were not like hinged jaws today. To open their mouths, Placoderms completely lifted the top part of their head up. Modern bony fish evolved last (like the tuna, in the bottom picture, observe the jaw differences). The jaws of the tuna can open by simply moving their bottom jawbone, without lifting the top of their head. How did we get from this weird, head lifting mechanism thing to having the type of jaws that is generally seen today? Well, this discovery of Entelognathus (try saying that three times fast) provides a possible transition between the bony plated Placoderms and the bony fishes. If this wasn't cool enough, I was again reminded of the news when our class began discussing missing links. Then I realized, a "missing link" had just been found, within the last few months! They called this discovery "one of the most exciting fossil discoveries in the past century..." (see article), and it happened so recently. It was super exciting to see that extremely important scientific discoveries are HAPPENING RIGHT NOW.

Coelacanth Genome

Coelacanths are currently comprised of two living species, the West Indian Ocean coelacanth (Latimeria chalumnae) and the Indonesian coelacanth (L. menadoensis), but are present in the fossil record from about 390 to 70 million years ago when they were thought to have gone extinct. The West Indian Ocean coelacanth was rediscovered in 1938, followed but the Indonesian coelacanth in 1999. The Indonesian coelacanth is threatened, but the West Indian coelacanth is critically endangered with a population estimate of fewer than 500. The modern coelacanth's appearance has remained largely unchanged when compared to its fossilized ancestors and it was found in a recent article published in Nature that L. chalumnae also have a lower protein evolution rate, but a relatively high abundance and activity of transposable elements. In the article "The African coelacanth genome provides insights into tetrapod evolution" other genomic insights and implications are discussed, including genetic differences between terrestrial animals, bony fishes, and coelacanths.

Sunday, March 9, 2014

Summer REU Santa Barbara Coastal

Interested in a summer internship?  If you are AAUS dive certified, the Santa Barbara Coastal Long Term Ecological Research lab has a place for you!  You would mainly be involved in the under water surveys, so be ready for a summer of diving and learning marine research techniques. $4500 stipend for working June 16th, 2014 through September 30, 2014.

Contact Clint Nelson or Shannon Harrer with any questions: 805-893-7295
Email: clint.nelson@lifesci.ucsb.edu, harrer@msi.ucsb.edu

The application is due on or before March 21st to room 3003 of the MSRB.

If you are interested, comment on this post with your email and I will send you the application.



Thursday, March 6, 2014

HIV-Positive Newborns "Cured"

A baby who was born to a mother with advanced AIDS is now, 9 months later, reported to be HIV free. The mother was allegedly "prescribed drugs to protect her baby" while still pregnant but had not taken them. Immediately after birth, the baby tested positive for HIV and was soon started on the drugs typically used to combat the virus in non-newborns. The baby is still on the drugs and has, according to doctors, "sero-reverted to HIV-negative" but is technically not actually cured (Full story here!) This is the second case in the US of a newborn being "cured" of HIV.

The first case was a child born in Mississippi who is now 2 and a half years old and is described as being "functionally cured" in that the child no longer takes antiretroviral drugs and the virus is no longer actively replicating in cells. The story started the same with this child as well; they were born to an HIV-positive mother and tested positive immediately after birth and were started on full-dose drugs some 30 hours after (Full story here!)

As described in the first news article above, a clinical trial is set to take place with 60 babies who are born infected and will be put on drugs within 48 hours after birth. The trial's success could be shocking to the medical community. It would illustrate that if treatment is started early enough, a cure is indeed possible.

Posting problems

A couple of people are having problems posting. Probably the most common problem is that you are signed into Google but have not accepted the invitation to be an author on the blog. Or you are signed into Google using a different e-mail address than the one you used to accept the invite. The outcome is the same - you can see the blog, it says you are signed in but you cannot post.

If you have accepted the invitation to join the very top right of your screen should look like this with a link for 'New Post'.

If you need me to send you a new invitation (they do expire after a while) then just let me know.

Otherwise continue the great posts!

Wednesday, March 5, 2014

30,000 Year Old Virus

Scientists recently discovered a virus in Siberia called Pithovirus sibericum. It was discovered frozen and underground in the permafrost and was found to be frozen for the past 30,000 years. This means that this virus existed around the time of the Neanderthal man extinction. Don't worry, this virus is not harmful to humans or animals (only amoeba), but it has scientists concerned with what other viruses could potentially arise again from the melting permafrost.
This virus is very large and resembles the Pandoravirus; however, there is no evidence in their genetic makeup that proves any relation. Pithovirus is the first of its kind, making it the first member of a new family of viruses and bringing the number of distinct families of giant viruses to 3: Pithovirus, Pandoravirus, and Mimivirus.
If you want to read more about this virus and what measures scientists are taking next, click here!