Apr 15 2014

The seeming lack of attP sites in Amigo

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In the past week, our group investigated looking for attP sites in our genome but we started to run into complications. First, the attP sites for Arthrobacter are not known so we resorted to running the entire genome through BLAST to find similar conserved sequences compared against the entire Arthrobacter taxa. Surprisingly, even after changing search parameters, few similar sequences were found and none had good e-values. We were looking for short, highly conserved (near 100% identity) sequences but they were not found.

We even considered the possibility that Amigo is not actually an Arthobacter phage and ran it against all kinds of categories – micrococcinae (the family Arthrobacter belongs to), etc., and yet, we still couldn’t find anything with significant similarity. This made it near impossible for us to continue with this particular project so we ended up switching last Wednesday to a new and more doable project. Although it was a little frustrating to hit a dead-end twice, we are confident that we learned a lot from it and that our new project shows a lot of potential.

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Apr 15 2014

Research

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Hey Guys,

So we are working on our project and are having a lot of fun exploring all of the phage genomes. We were going to sequence all of the tape measure proteins and compare their geographic locations, but we scratched that idea. We played around with a few other ideas but we settled on another cool idea. supposedly the first 1600 nucleotides and the last 1600 on Amigo’s genome nucleotides are extremely similar. Today we figured out why Pittsburg placed Amigo’s ending where they did, but there is still much to learn. We are still exploring the subject, and there will be more updates to come.

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Apr 14 2014

Trying to find the lysin

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For the past two weeks Jackie, Scott and I have been trying to find the lysin gene in Amigo but we still have inconclusive results. We thought that due to Amigo being highly lytic that it would not be as difficult as it has been. Using phamerator, we have been going through found genes for ones with the function of a lysin and then looking them up in the NCBI database. We compared each one to amigo but so far the best match had an E Value of .056. Hopefully today we will find something!!

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Apr 14 2014

Independent Projects

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It’s been 2-3 weeks since we’ve started our individual projects, and thus far our (The Minions) project has been making steady process. We decided to investigate whether the proteins responsible for inducing the lysogenic cycle were conserved among phages.

Thus far, we have had a difficult time finding good protein blast matches between Amigo and other phages in the database. Considering the small sample of other Arthrobacter phages to compare to, we figured it would be difficult to find great protein matches. What has taken us by surprise, however, is how the protein blast matches with other phages (e.g. smegmatis) have been relatively poor as well. This week, we will try to take on a new direction and attempt to find matches between nucleotide sequences instead of proteins.

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Apr 11 2014

Ebola

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Isn’t it crazy that given all our technology, all our accomplishments and research, but a little virus can still defeat us? It seems incredible that just because of a difference in genetic code and binding potential, an ebola virus is deadly, while a bacteriophage is just a bacteria lyser.

http://www.ibtimes.com/us-defense-department-spent-140m-ebola-treatment-research-theyre-getting-close-1566666

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Apr 08 2014

Giant Turtle Bones Found Centuries Apart

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In 2012 an amateur paleontologist found a broken half of an ancient sea turtle humerus. What’s interesting about this fossil is that it’s other half was found in 1849. The two halves of the same fossil were found over 160 years apart! Not only was it astounding that the two halves fit, but the missing half drastically changed the size estimations for its species, Atlantochelys mortoni. Now scientists estimate this sea turtle was about 10 ft. long from tip to tail, making it one of the largest sea turtles ever known. However, this find did not just change the size estimations of the Atlantochelys mortoni. The finding one half of this fossil 162 years after the other half was discovered has changed scientists believe about the longevity of fossils. No one believed that the other half could have been discovered after being exposed to the elements for at least 162 years, but this fossil proved them wrong. Now scientists are revising their beliefs about how long exposed fossils can survive. Just one half of a ancient sea turtle humerus had the power to change not only scientists beliefs about the animal itself but also about the survival of fossils in general. The article is linked below.

Paleontologists Assemble Giant Turtle Bone from Fossil Discoveries Made Centuries Apart

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Apr 07 2014

Endocrine System

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Hey Phagers,

So the endocrine project we have been working has been very interesting to me. I have really enjoyed learning about the different types of hormones and their functions in the body.

This is an article on type 1 diabetes. Apparently this molecule Ceramide inhibits glucose uptake and makes the Beta cells of the pancreases secrete more insulin than necessary. This increases the risk of an individual getting type 1 diabetes. This article looks at many ways to hinder this molecule and cure type 1 diabetes.

http://www.hindawi.com/journals/bmri/2014/980815/

 

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Apr 06 2014

Are all lies immoral?

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While searching the internet to learn more about the posterior pituitary gland and the hormones it secretes I came across an interesting study. The work of researchers from the Ben-Gurion University of the Negev in Israel and the University of Amsterdam in the Netherlands focuses on ethical decision making. They designed an experiment to investigate the biological foundation of lying. 60 male participants received an intranasal dose of either oxytocin, a peptide of nine amino acids that functions as both a hormone and a neurotransmitter, or placebo then split into teams of three and asked to predict the results of 10 coin tosses. They knew that for each correct prediction, they could lie and earn more money to split between their group members, who were engaging in the same task.

The coin toss results reported by participants who had taken oxytocin and those who had received the placebo were very different. Among the control subjects, 23% claimed to have guessed the results of nine or 10 of the coin tosses. But in the oxytocin group, 53% of the participants claimed to have correctly guessed this many coin tosses. So it seems fair to assume that the majority of the subjects who claimed 90% or 100% success rates were lying, but it shows that the oxytocin group were more than twice as likely to lie than the placebo group.

Oxytocin promotes group bonding, so were the subjects who received the oxytocin lying in order to benefit their group? Dr. Shalvi said that the results suggested that people were willing to bend ethical rules to help the people close to them. He goes on to describe how the results highlight the role of bonding and cooperation in shaping dishonesty:

“Together, these findings fit a functional perspective on morality revealing dishonesty to be plastic and rooted in evolved neurobiological circuitries, and align with work showing that oxytocin shifts the decision-maker’s focus from self to group interests.”

The researchers concluded that when dishonesty serves group interests, oxytocin increased lying as well as extreme lying, and when lying served personal self-interests only, oxytocin had no effects.

So not only did I learn that oxytocin is linked to pregnancy and childbirth, among other things stimulating milk production and maternal bonding, but also that it can actually make people more dishonest. Wow!

http://www.latimes.com/science/sciencenow/la-sci-sn-oxytocin-lying-to-help-groups-20140331,0,3284673.story

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Apr 06 2014

BCM

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A few weeks ago, I went to Baylor College of Medicine with SIGHT, and spent the day with the National School of Tropical Medicine. We toured their lab and I was pleased at how well I knew the things that they were talking about! From PCR to synthesizing vectors, it was very exciting to see all of the things we have worked hard at learning applied in real life settings. As an aspiring doctor and researcher, I am grateful for experiences like these to keep me with a vision of what to look forward to, and motivation to keep doing well in school! The opportunity to learn first-hand research methods in our lab has truly built a foundation for us to engage in further research, as the methods we have used will surely be applied in future settings.

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Apr 06 2014

Depression leading to Heart Failure

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I was reading a little about research done in the medical field on Science Daily.  It was very interesting.  The more and more I read, I realize just how related our physical and emotional states are.  It is incredible just how great of an effect emotional instability (as seen in depression) can play on one’s life.  For example, people with depression have a 40% higher chance of developing heart failure (according to research done by Ms. Gustad – see article on Science Daily).  At first glance this seems like a shocking statistic.  However, upon closer examination, it is quite self-explanatory.  If one is depressed, their lifestyle completely changes.  They are less active and tend to eat unhealthy foods.  It just continues to amaze me how much affect one’s mental state can have on their physical state.

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Apr 06 2014

New Virus Found in Russian Tundra

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I found this interesting article on the Economist, and thought I’d share. A group of virus-hunting scientists thawed a 32,000-year-old slab of Siberian permafrost and discovered a virus that infects a species of amoeba. While an average virus has 9,000 bases, this virus (named Mimivirus) has more than 1m bases in its genome. It is also huge physically – 600 nm across. Scientists claim that even though this virus is enormous, it is not very dangerous to people/humans. The full article link is- http://www.economist.com/news/science-and-technology/21598612-exotic-giant-virus-thawed-russian-tundra-siberia-strain

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Apr 03 2014

Z is for Zebra: Why Zebras have Stripes

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Tim Caro and his colleagues from the University of California at Davis believe that they have answered the age old question of why zebras have stripes–they believe the stripes ward off bugs. These scientists did extensive geographic testing on different equis species, using phylogeny to compare the major hypothesis for cause behind the stripes. After determining that the stripes were likely insect repellents, they did testing with tsetse flies and tabanid biting flies, discovering that there is indeed correlation between pattern and where the bugs landed. Apparently flies do not like stripes.

 

Read their article here: http://www.nature.com/ncomms/2014/140401/ncomms4535/full/ncomms4535.html

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Apr 01 2014

Developing our own project!

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Apr 01 2014

Comment On Kaitlyn’s “Geologic Time Song”

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1) That is really helpful and I wish I had found it before that last test! Bummer 🙁

2) It is now stuck in my head and I can’t stop humming it so thanks for that haha 🙂

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Mar 31 2014

Posters

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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.

http://www.foxnews.com/health/2014/03/20/chemist-claims-reversed-daughter-autism/

 

 

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Mar 30 2014

Inbreeding possible cause of woolly mammoth extinction

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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

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Mar 28 2014

Finding Plant/Animal Origins through Enzymes

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I was looking through ScienceDaily, and I found this interesting preview about the ancestral origins of plants and animals. In this publication, researchers are now studying the 2-HAOX enzyme, an catalyst that breaks down fats in plants and animals, and  are trying to trace a common ancestral gene that gave rise to this enzyme. From their studies and phylogenetic tree analysis, the researchers were able to ultimately conclude that this particular enzyme evolved independently between plants and animals. 

From this preview, I found it interesting how scientists are currently looking at all aspects of molecular biology when searching for common ancestors. It’s very exciting to see that scientists are drawing from a wide range of topics, such as metabolism to better understand the early evolution of plants and animals. I would definitely be interested in reading the full publication of this topic.

Here is a link: http://www.sciencedaily.com/releases/2014/02/140214111111.htm

 

 

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Mar 24 2014

Science is Fun!

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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.

I

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Mar 24 2014

Preventing Alzheimer’s Disease

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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:   http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13163.html

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Mar 24 2014

Weaponizing Bunnies : A Short How-To

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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 🙂

 

http://theweek.com/article/index/256780/how-do-you-weaponize-a-rabbit

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Mar 24 2014

Geologic Time Song

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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.

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Mar 23 2014

Fully Annotated Genome

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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.

http://www.foxnews.com/science/2014/03/04/giant-virus-resurrected-after-30000-years/

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Mar 23 2014

Human Evolution- Homo Sapiens Became Black to Beat Cancer

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http://www.economist.com/news/science-and-technology/21597881-homo-sapiens-became-black-beat-cancer-skinny-skin-colour

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!

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Mar 22 2014

The “chicken from hell”

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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

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Mar 22 2014

Method of Silencing Genes

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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!

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