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.

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!

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

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.

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!!

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.

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

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.

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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

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!

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.

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

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!

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.

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!

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.

http://www.the-scientist.com//?articles.view/articleNo/39332/title/Convergent-Fish-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!

Can I just say how nice it feels to be working on genomic annotation? I’ve been relatively un-surprised at the number of genes with unknown functions, but also at the number of genes with oddly-specific fuctions: or portions of a gene that code for things like immunoglobins that have no business being in a phage genome. I’m excited to see where this takes everybody in terms of the independent projects

http://www.genengnews.com/gen-news-highlights/supercomputer-analyzes-240-full-genomes-in-two-days/81249533/

I saw this headline today-
February 20, 2014, 10:30 AM EST.
Supercomputer Analyzes 240 Full Genomes in Two Days

It will probably take us several weeks with all of your brains put together to analyze 1 very small genome. The technology is changing fast.  Sequencing is getting faster and cheaper, but what about the time and expense of analyzing?  Data doesn’t mean much if it is just sitting on the desktop.

Your generation will be analyzing and utilizing genome sequences more and more for diagnostics.  Computers will be doing the analysis.  Who will decide what to do with the results? What do you think?

Did you know that Darwin discovered a frog in South America that is only about 2 cm in size? The male frogs carry the baby frogs in their mouth while they mature.  Watch this!  http://video.nationalgeographic.com/video/animals/amphibians-animals/frogs-and-toads/weirdest-darwins-frog/

Read more about it here.

It may be extinct?

Saw this little guy on the ground in the parking lot today and I totally thought it looked like a phage. They’re out there guys. 

Clovis is a group of what became native americans. Here is a cool short article on the genome they sequenced and some information they were to able to extrapolate from the data.

http://www.sci-news.com/genetics/science-genome-clovis-boy-01760.html

Last week, my group presented a project on genetically modified foods… We focused mainly on the current events and history within the United States (for somewhat obvious reasons), but as I was reading the New York Times this afternoon, I noticed this interesting article about genetically modified corn in Europe! I think it’s pretty cool that they might let this new crop through after such a long time … Also, did I mention it’s about corn? Yes, C-O-R-N, the spirit animal of our Biology class 🙂

http://www.nytimes.com/2014/02/12/business/international/modified-corn-a-step-closer-to-approval-in-europe.html?ref=science&_r=0

Take a look-see and tell me what you think!

I was reading an article today about the progress of gene expression analysis over the years which is very relevant to the topics we are discussing in class! As we know, sequencing has increased from 10,000 bases per day to around a billion base pairs a day and the price has been cut significantly, almost reaching the $1000 mark. With prices and time cut, this allows whole genome sequencing (WGS) to be utilized in diagnoses and treatments like cancer. Currently, WGS is helping in the study of the genetics of acral melanoma (20% lower survival rate than non-acral melanoma) in order to create an effective treatment. With WGS, researchers can now measure tumor-specific alterations in chromosome structure, point-mutations and gene expression via a combination of whole genome, whole exome and RNA sequencing. With these approaches, it is hopeful that treatments will be personalized in the future. The “improvement” of genome sequencing over the years is very exciting, and there will undoubtably be more applications and technologies in the years to come!

I really enjoyed your presentations last week.  All of the topics demonstrated to me that we have only just begun to understand how cells work and communicate, but knowing what we know allows so many good things to occur.

Imagine being the scientists that spend their life designing and testing a prosthetic hand and then learning that the individual trying it out can actually feel with it!  This is the latest of several breakthroughs in this area.

https://www.sciencenews.org/article/prosthetic-provides-sense-touch-man-who-lost-hand

The future looks bright to me!