Archive for the 'Uncategorized' Category

May 08 2014

Thank You All So Much For A Great Year

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I can’t believe our Freshman year of college is almost over! It has been a whirlwind, a stressful, crazy, amazing mess that I am extremely grateful I got to spend with all of you. I couldn’t have asked for a better group to go through this program with. As finals come to a close, I wish you all the best of luck  with your summer ventures, whether that be research in Houston or simply relaxing at home. It has been a privilege to get to know each and every one of you.–And Dr. Addair and Dr. Gibbon, thank you both so much for all of the time and effort you have invested in us, I think I speak for all of us when I say that I’m eternally grateful for everything you have taught us.

I will see you all at the final!

–Chloë Sells

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May 08 2014

Predicting Global Warming

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As discussed in our last unit of freshman biology (can’t believe its almost over!), there are ways that ecologists and other scientists can predict global warming based on historical trends. In the textbook, the warming preceding the last ice age was characterized by glaciers and trees retreating to the north and south poles. It further states that based on the rate at which the biosphere is warming now, trees would need to retreat at about a 7-9 km rate whereas they are only moving at about a .2 km rate currently. The latest National Climate Assessment, released May 6, outlines the climate changes in the US; I have skimmed through the introduction (the whole document is 840 pages!) and have found a section on melting ice and glacier migration – here is a paragraph I found both relevant to our current unit (tundra biome, chemical cycles, and global warming) and interesting: “Glaciers are retreating and/or thinning in Alaska and in the lower 48 states. In addition, permafrost temperatures are increasing over Alaska and much of the Arctic. Regions of discontinuous permafrost in interior Alaska (where annual average soil temperatures are already close to 32°F) are highly vulnerable to thaw. Thawing permafrost releases carbon dioxide and methane – heat-trapping gases that contribute to even more warming. Recent estimates suggest that the potential release of carbon from permafrost soils could add as much as 0.4ºF to 0.6ºF of warming by 2100.” There are many implications associated with the many areas affected by dramatic climate change, and we must bring them to our attention. Good luck all on your finals! It’s been a great semester.

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May 02 2014

Beginning of the end

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It is unbelievable how fast this semester has gone. I can’t believe we are already here – almost approaching the end. I am really glad that I had the opportunity to be apart of the PHAGES experience this past semester. Not only have I learned a lot, but I have gotten to know you all a little better, and the experience has been amazing .

Flashback to  first few sections of lab, when we watched the Hatful lectures: I remember feeling so overwhelmed with everything that I didn’t know about bacteriophages and the bioinformatics software. Looking back, it’s crazy how much I’ve gained from this research experience, and I am incredibly grateful. For example, we’ve learned how to annotate DNA sequences and blast protein sequences and through these techniques found novel protein sequences, frame-shifts, and a BUNCH of NKFs. These accomplishments are nothing short of awesome!

As we close out this semester, I want to thank you all for including me in your class. Study hard and finish strong!

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Apr 30 2014

Almost the end?!

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I can’t believe that just a few months ago, we were learning how to serial dilute our samples and trying to look for a phage. This semester has been so enriching- from learning how to use DNA Master to going through the research process and developing our independent project. Our group has worked on comparing certain genes between all the known Arthrobacter genomes. It was amazing to realize how well everything came together in the end last week, when we were compiling and synthesizing our data for the final presentation. We started out having so many questions about where to start and how to gather data, but learned so much during the entire process. Good job to all the other groups on great projects as well!

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Apr 29 2014

Lab Project is Almost Completed!

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For the past month the Philosoraptors have been struggling with endless amounts of inconclusive data and confusing results from BLAST matches, but its finally starting to come together. We have actually discovered some pretty cool things regarding the connections between the genes  of Amigo and the other Arthrobacter phages. I’ll save the rest for our presentation. When we first started on this project I was worried we wouldn’t find anything interesting but nevertheless we did and now that our data finding is complete, all there is left to do is put together our presentation. Congrats to all the other teams and their successful research projects as well! I can’t wait to hear your results!

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Apr 29 2014

Comment on “The Final Countdown”

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KATELYN GOD BLESS YOU. YOU ARE A BEAUTIFUL HUMAN BEING.

Haha I definitely needed something else to try for study tactics and this just might do the trick 🙂

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Apr 27 2014

“Chernobyl’s birds adapting to ionizing radiation”

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Birds in the exclusion zone around Chernobyl, a city in Ukraine which was the site of the worst nuclear power plant accident in history, are adapting to and benefiting from long-term exposure to radiation. The explosion that occurred in 1986 resulted in large quantities of radioactive particles to remain in the atmosphere, as well as numerous other environmental consequences. Ecologists have found that with increasing background radiation, the birds’ body condition and glutathione levels increased and oxidative stress and DNA damage decreased. These results are important, as they explain to us more about different species’ ability to adapt to different environments that have been sites of environmental catastrophes. Here is the link to the article-

http://www.sciencedaily.com/releases/2014/04/140424223057.htm

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Apr 26 2014

The boys are losing their genes… uh oh

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According to research studies done recently, the Y chromosome is in a state of genetic decay. The Y chromosome apparently once had 600 genes in common with the X chromosome, but over the duration of its evolution throughout the years, lost all but 19 of them. There is a debate in the science world about this currently, but many scientists, called the “rotting Y” group, believe that since the chromosome has lost so many genes already, its extinction is likely if not inevitable. Another group of scientists has chosen to view this data in a completely different light and see it as the Y chromosome shedding all but the genes completely necessary for survival . Scientists Dr.Bellott and Dr. Page argue that XX cells are “subtly but fundamentally different” from the XY. And, “they are different throughout the body in tissues and organs that show no obvious anatomic differentiation.” They are using this knowledge to try and customize medicine to tailor to the differences between the cells, a concept that could possibly lead to major developments in the medical world.

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Apr 23 2014

Comment On “Depression Leading to Heart Failure”

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As an additional note, I was reading an article a while ago that was similar to this, except it focused more on how survival is largely to do with the will of the mind. This is why people who are stranded in the desert or are seriously injured are able to survive longer than they were expected to. Even though their bodies may be giving out, their will power is what is keeping them going; they literally are keeping themselves alive when medically, they should be dead,  by sheer willpower. It is incredible what the mind can do. The article also pointed out that this lines up with the statistic you mentioned, Abby, about people who are depressed being 40% more likely to develop heart failure. Even though their bodies were relatively healthy to begin with, the lack of will to carry on, coupled with the lifestyle that results from that mindset often lead to the body giving out.

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Apr 23 2014

It Doesn’t Take High Tech Machines To Discover Something Groundbreaking

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This past week scientists from Ireland discovered a new  way to make the “wonder material” graphene…. by using a kitchen blender. The team put powdered graphite, dish washing soap, and water into a kitchen blender and proceeded to blend it at high speeds; the result was the formation of the incredible material. Graphene is unique in that while it is only one atom thick it is very strong, flexible and electrically conductive. Because it has the potential to be used in such a wide array of fields including electronics, there have been many attempts to find a quick and cheap way to make it (In 2004 scientists were using Scotch tape to take the top layer of graphite off to make it). I’d say these scientists found just about the cheapest and easiest way to do it. Personally, what I find most puzzling about this entire thing is why top tier scientists decided a common kitchen blender would be the best way to try their experiment, but hey, it just goes to show that you don’t have to have the latest technological equipment in order to develop or discover something revolutionary.

 

If any of y’all want to read about it more in depth you can use this link to the article.

http://www.bbc.com/news/science-environment-27113732

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Apr 22 2014

This one’s for the guys.

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http://www.the-scientist.com/?articles.view/articleNo/39730/title/Hip-to-Be-Rare/

Yup. Someone wrote a scientific article about whether or not beards are attractive.

The article also talks about negative frequency dependent selection. It’s the principle that the rarest phenotypes can often be advantaged by their uniqueness. That sounds like the most Hipster biological principle ever.

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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 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

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 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 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

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 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 21 2014

Annotation Debate

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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.

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Mar 15 2014

The Next Step…

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Hey guys,

I hope all of you had a safe and restful spring break! Before our Monday lab, I just wanted to share my reflections on our lab time thus far….

After two weeks of intense annotating, it’s hard to believe that we’re officially done the preliminary stages of learning about our phage, Amigo! Quite frankly, I’m surprised how efficient we have become as a class. I remember when we were first introduced to annotating and how lost everyone was (it may have been just me…), so to say that we finished the entire genome is really amazing.

Now comes the more tedious part – proofreading and tying everything together. Even now, we have so much information that needs to be verified and analyzed. I think it will be good to get more than one perspective on our annotations, so that we know we are submitting the best possible product. Moreover, I’m excited to see how all of our hypothetical proteins and unknown protein functions fit together as a whole. Perhaps we will be able to deduce patterns or find something entirely new.

Whatever is in store, I’m looking forward to sharing it will all of you!

Scott Lee

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Mar 15 2014

University of Leeds’ study on early life on Earth

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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.

 

http://www.leeds.ac.uk/site/scripts/news_article.php?newsID=3504

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Mar 13 2014

Heartbeats Help People See

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https://www.sciencenews.org/blog/science-ticker/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!

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Mar 12 2014

“YEARS”, A song written by nature

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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.

 

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