Monthly Archives: March 2014


Hey Guys,

Great job on the posters. Our group had fun going through the entire year and reflecting on what we have done with phages.

This is an article on chemist who claimed that he can cure autism by balancing the amount of glutamate in the body. A lady named Reid and her autistic daughter wiped MSG from their diet. There were very positive results as her daughter became less autistic. I think it is worth checking out.



Inbreeding possible cause of woolly mammoth extinction

Researchers recently examined the remains of two woolly mammoth remains found in the North Sea. What they found is quite interesting. Both specimens, who were most likely the last woolly mammoths in this area, had cervical ribs (ribs attached to the vertebrae in the neck). Upon further analysis, researches discovered that around one third of the total population of found woolly mammoth remains have this condition. This number is very high compared to their modern day relative, the elephant, in which this event only occurs in about 3% of the population. What could cause this high percentage of abnormal bone structure? In humans, cervical ribs are caused by inbreeding and adverse environmental conditions during pregnancy. Researches believe that the same is true here. Perhaps disease, famine, or the extreme cold  caused a decline in the woolly mammoth population size, causing a higher percentage of inbreeding. Or, perhaps the population size was small from the beginning, causing inbreeding to be a large factor throughout their existence. Either way, this discovery sheds new light on the vulnerability of the woolly mammoth species.  The article is linked below.

Extraordinary incidence of cervical ribs indicates vulnerable condition in Late Pleistocene mammoths

Science is Fun!

Hey y’all!

Over spring break, I went to the Perot Museum in Dallas. It is a museum of nature and science and IT WAS SO COOL! Most of the exhibits were geared toward children, but I had so much fun nonetheless. My favorite exhibit was actually the evolution exhibit, probably because we were just discussing it in lecture. The exhibit was situated so that as you walked through it, you progressed through evolutionary time. First you went to the cells, then the bacteria, then fungi, plants, and animals. They had a lots of fossils displayed to “fill in the gaps” between life. One of the most interesting aspects of this exhibit was at the end, where there was a list of new species discovered in the past couple of years. They all had hilarious names and looked completely different from any animal I have ever seen. The funniest one that I saw was a mushroom named Spongiforma squarepantsii. I guess it just goes to show if you go through all of the trouble to discover a new species, you get free creative license with the names!

Another exhibit I really enjoyed was the Being Human exhibit, just because they had such interesting things! They had a human body sliced a couple millimeters thin so that you could see a cross section of all of the organs and bones. It was so cool! They also had a machine that you could hook up to and you could move balls in a container using your brainpower. I moved a ball with my brain, y’all.

It was great to see so many people having so much fun learning about science. It was so funny to see little kids completely amazed at the different dinosaur teeth or the evolution of wings. If you have a chance, you should definitely visit the Perot Museum.


Preventing Alzheimer’s Disease

Researchers from Harvard University have recently discovered a protein thought only to be used in the womb in elderly subjects. This protein, which they are calling REST, protects the fetal brain during development and was previously thought to disappear after birth. However, their study shows that elderly adults without Alzeimer’s disease have a high level of this protein. It will be interesting to observe what types of therapies come from this discovery.

Here is the article:

Weaponizing Bunnies : A Short How-To

I was reading “The Week” (one of my favorite news magazines) when I came across this article… To be completely honest, I only clicked on it because the picture of the rabbit was so cute, but it’s actually quite interesting! Tell me what you think 🙂

Geologic Time Song

Dr. Adair said that many of us struggled with the geologic time scale on our last test. This video help me IMMENSELY when studying that information for the test, and I thought it might be helpful for the final as well. Also, it has lots of dinosaur animations, which is always exciting.

Fully Annotated Genome

Hey Guys,

I can not believe our genome is finally annotated. I had so much fun finding genes that were important to our genome and conversing with others on these genes. My favorite part of annotation was finding new genes. It was really cool to find things that glimmer missed. I think that this Bioinformatics work that we are doing has great potential in the future.

This is an interesting article about a giant virus that scientist found and resurrected in Siberia. It does not infect humans, but the article brings up a good point that if Siberian ice keeps melting, viruses that did infect humans could be revived. It is an interesting concept to think about.

Human Evolution- Homo Sapiens Became Black to Beat Cancer

This article explains one possible reason why humans have darker skin than chimpanzees (after humans and chimps parted ways). Because of evolutionary pressures, human skin was almost always black. This may be due to the role of melanin in black skin. Melanin helps absorb ultraviolet light, prevents DNA damage and protects mutations, protects against skin cancer. Interesting read!

The “chicken from hell”


Recently, the remains from three different specimens have been put to together to almost completely reconstruct the skeleton of the Anzu wyliei, pictured above. The remains show some shocking findings. This bird-like dinosaur stood roughly  5 feet tall and 11 feet wide at the hip. Think about it: the hip of the Anzu was about as all as my entire body. Resembling a giant, flightless bird, the Anzu had a toothless beak, feathers, and long, slender legs like an ostrich. However, it also had large claws at the tip of its forelimbs. The finding of the Anzu has proven that caenagnathids form a natural grouping within Oviraptorosauria, a theropod group composed of caenagnathids and oviraptorids. Furthermore, the scaring and healing of some of the bones of the Anzu seem to suggest that they were able to withstand quite a bit of trauma. 

However, what I find most interesting about the recent discoveries in the dinosaur way of life is their resemblance to birds in both physical and behavioral attributes. Recently, I was watching a documentary on the evolution of dinosaurs, and the new theories fascinated me. The documentary said that it is believed that dinosaurs, like the Anzu, laid eggs in a nest and protected them much like birds do today. Furthermore, they suggested that the father  may have also played a large role in raising and protecting his children. This new family dynamic is a very interesting discovery, and I cannot wait to see what else science will unveil from the lives of the dinosaurs.

Link to article: Nearly complete ‘chicken from hell,’ from mysterious dinosaur group

Method of Silencing Genes

I found an interesting article on the Science Daily website concerning the method plants use to silence genes.  In Biology class we are just beginning to discuss plants and their methods of growth and formation.  I just read a section in our book over the differentiation of cells in plants.  This differentiation is the result of many things including gene silencing.  Each plant cell contains the same genome, but the cells perform different functions.  Therefore, this must be a result of gene silencing, where certain genes are expressed and others are not expressed.  A team from Indiana University was researching how plants cells know which genes to silence.  They observed that unlike some thought, this ability to know which genes to silence is not “hardwired” into their DNA.  In other words, it is not an inherited trait, built into their DNA.  Instead, the ability to silence genes seems to be a learned characteristic, through “molecular memory.”  The genes recognize heritable chemical marks on the genes, and remember to silence or express these based on past experience.  The chemical marks/tags serve as “molecular memory” to help the gene remember to silence these specific genes in future generations.  This was a very interesting article published on March 20, considering we are currently learning about the basics of plant differentiation in class!

Annotation Debate

On Wednesday in lab, my group and the other group that annotated the same genes that we did debated over certain genes and whether or not they would be the longest ORF or the second longest. My group had picked the longest due to the fact that we wanted to shorten the gap however after discussion with the other group we conceded that the second ORF was a better fit, receiving a closer blast match. I really enjoyed that class period because I liked seeing what their thought process was when they were annotating the same genes as we were and how we thought similarly and how we differed.

Like thrillers? Like epidemiology? This ones for you.

Over the break I read a book that has been on my reading list for some time; The Hot Zone by Richard Preston.  For anyone who is interested in virology, epidemiology or enjoys being freaked out by potential pandemics, this is a must read.  It is an incredibly well documented non-fiction thriller, an account of the rise of Ebola throughout the 20th century.  Did you know the Ebola Zaire strain has a 80-90% mortality rate? Scary.  And there is no known treatment.

The book is absolutely fascinating, and as I find epidemiology really interesting, I could not put it down.  While its is a dramatization, Preston does an excellent job of presenting the story of the Ebola virus, from its mysterious origins in the jungles of central Africa to its near US breakout in a Washington, D.C. monkey house.  He has been praised in academic circles for his depiction of the history of the virus.  A word of caution, this book contains the sometimes gruesome descriptions of the effects a hemorrhagic fever has on the human (and monkey) bodies.  The book is fascinating, frightening and haunting reminder of the power of such a miniscule bundle of protein and DNA.   After all Stephen King did call it ”one of the most horrifying things I’ve ever read.”

Game of Guessing

Today we found a much more efficient method of merging our annotation work.  We got in our groups and discussed our reasoning for extending, inserting, deleting the genes.  This process actually worked wonderfully!  We almost finished and came to a consensus on the entire genome.  However, one thing I learned was just the uncertainty of science.  The importance of educated guessing and asking stupid questions became so much clearer to me in this lab. There were many points in lab today where no of us had any idea of what we were doing.  There was no evidence either way, and we simply had to make an educated guess in one direction.  Because this genome has never been annotated, we are exploring totally unchartered territory.  We are researchers asking stupid questions and making educated guesses, hoping it will lead to further understanding!

Sea anemone is genetically half animal, half plant

Hey guys! Check this out. Its super cool.

Evolutionary and developmental biologist Ulrich Technau and his team at the University of Vienna have discovered that sea anemones display a genomic landscape with a complexity of regulatory elements similar to that of fruit flies or other animal model systems. This suggests that this principle of gene regulation is already 600 million years old and dates back to the common ancestor of human, fly and sea anemone. On the other hand, sea anemones are more similar to plants rather to vertebrates or insects in their regulation of gene expression by short regulatory RNAs called microRNAs. It assumed that plant microRNAs arose independently from animal microRNAs, but their evolutionary origins, as they state in the article, is unclear. This is the first qualitative difference found between Cnidaria and “higher” animals and the findings provide insight on how important levels of gene regulation can evolve independently.

An Alternative Use for Twitter…

I was looking at my twitter account the other day and found this article posted by Scientific American. Being the nerdy person I am, this is basically the only stuff on my twitter feed.

While the end of this article does point out possible selection bias on the part of the researchers, I found this to be extremely interesting. Until reading this article, it had never occurred to me that all of the autistic individuals I know or have heard of are male. This is definitely something good to read if you are interested in genetics!

University of Leeds’ study on early life on Earth

A group at The University of Leeds is working with a jet propulsion lab at NASSA to study some of the chemistry that could have possible led to the earliest life on earth. In the video on the link below he is talking about the chemistry of the vents at the bottom of the ocean that could have led to the production of this life! super cool.

Heartbeats Help People See

I thought this article was so interesting. Everything is connected! This article highlights this very fact. According to this article from Nature Neuroscience, each heartbeat creates a blip of neural activity, and this helps us better detect things in the world. Another theme that is talked about in this article is how all bodily functions have some kind of an effect on the brain. Enjoy!

“YEARS”, A song written by nature

So this guy had an awesome idea to design and create a type of record player that can read tree rings!

The actual sound is connected to what’s called a trigger. The trigger takes the frequency’s read by the scanner and play those same frequencies in a more familiar timbre. So in this case, it sounds like a piano!

There are some really interesting minor sounding harmonies in the areas of the tree where the rings show abuse. Check it out! Its pretty amazing.


Annotations Complete?!

It seemed like just yesterday that we were struggling to learn how to annotate a gene. It’s safe to say that we have come a long way! Our group decided to split our portion into two. Bethany and I annotated the first 12 genes plus 2 tRNAS, and Jeremy and Chloe annotated the rest of the gene assigned to our group. The main thing Bethany and I had a hard time with was a huge gap (over 200 bp). We added genes where we thought they would be appropriate, although we are not 100% sure they are right. We merged our files during the last lab, and I can’t wait to see what other groups have come up with! Hope everyone is having a great break!

Pithovirus sibericum

Scientists recently discovered a 30,000 year old virus in north-eastern Siberia, Russia. This virus has been shown to closely resemble the Pandoravirus, but the Pithovirus has significantly less genes (500), and only one or two proteins similar to the Pandoravirus. The Pithovirus also relies less on the ameba nucleus and more on its components in the cytoplasm. Although this virus infects only amebas, its discovery may hint to future public health risks as global warming melts the permafrost where we now know preserve such ancient, and harmful, viruses. Discoveries such as these remind us of the discoveries we are making in lab currently! Of the genes my group has identified, only a couple have remotely matched any known proteins. We have such a great opportunity in our hands to make significant scientific discoveries! Its so very exciting.

Happy Spring Break!

Came across this while I was looking for my speciation article. I thought it was pretty interesting. Plus a pretty picture of a phage for your viewing pleasure. imageHave a great spring break everybody!

Annotation Complete!

Hey Y’all!

I am so excited that Amigo is finished! I feel like it came and went so quickly! We just got Amigo and now his annotations are almost complete. Our group, Olaf’s Fan Club, divided our section of the annotations into two groups, and Sierra and I annotated the last 18 genes of Amigo’s sequence. Most of the genes we had were fairly easy to annotate. Glimmer and GeneMark called the longest ORF, all the coding potential was covered, but there were no BLAST matches. This, though somewhat disappointing that we do not know what any of those genes do, made annotating a pretty quick process. The bulk of our time was spent on the large gaps in between genes. Between a lot of genes, there were 60-100 bp gaps, which is larger than expected for a bacteriophage but too small to have a gene in between. Sierra and I decided that Amigo had a less dense genome, so it will be interesting to see if other schools had the same type of problem with their genomes. Some of the gaps were over 200 bp and had little blips of coding potential, and in those we added genes. We are not entirely sure if some of the added genes are actually valid, but we used the guidelines and tried to do what looked the best. I cannot wait to see what the other groups came up with and if we are consistent in our annotations throughout the class!

I hope everyone has a wonderful and safe spring break!

Good luck on the test tomorrow!

Amigo is annotated!

downloadAfter four straight lab periods of staring at “No known functions” and 1200 bp gaps with no coding potential, we are finally done! I don’t know about any of you guys but I know that I certainly did not expect there to be so many genes with no matches or known functions. It really helps show just how little is known about these little guys and how much new information can be derived from a single phage’s DNA. While it may have been frustrating for us to have so little definitive knowledge as to what the genes do, what we just did will help connect puzzle pieces so that in the future these gene’s functions can be determined and the database can be expanded. Yay us, go team!

Adipose fins


Some researchers are looking at another morphological structure of modern day fish to investigate fish evolution.

“Adipose fins are small, fleshy and usually not as elaborately structured as other fins. Although some 6,000 species of fish—including trout, catfish, and salmon—have them, relatively few researchers have studied these structures in the last half-century.”

They plan to explore early changes that may be linked to the transition to tetrapods.  The beauty of cience is there is always another question!