Looking back on a great year

After a full year in the Biology 1406 class, I’m so glad I got this opportunity. Allow me to list Three Things That I Think I Thought about This year…

1. What a great group!

I absolutely loved getting to know everyone in the class – there’s only been a few times in my life that I’ve been part of a class where everyone (literally, everyone) was excited about the subject matter, extremely quick to pick up the material, and always willing to go the extra mile. This was by far my favorite class peer group of my freshman year.

2. Doing real science

While my friends complained about dissecting rats and memorizing the names of fungi, I had the chance to participate in truly novel research that has significance to science. Furthermore, I actually had the opportunity to work on an independent research project!

3. A true challenge

More than any other class, this class made me really work for my grades and I appreciate that very much. Dr. Adair and Dr. Gibbon made this class interesting and challenging, difficult but also engaging.

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

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.

I love you all!

I just wanted to thank everyone for a great year. You all are such a blessing in my life, and I’m glad to have gotten to know all of you. Good luck on finals, and I’ll see you next Saturday!

The End

I can’t believe this year is coming to a close.  I never would have thought that I would be part of such an amazing research experience.  Our last class is tomorrow, and our last lab is done.  I’ve really enjoyed my time with SEA Phages, and feel like I have grown so much in knowledge and now I have more direction with what I want to do with my life.  It is such a bittersweet feeling to have such an experience end.  Thanks to my classmates for such a great atmosphere and thanks to Dr. Adair and Dr. Gibbon for their passion and dedication to our class.   Phages rule. <3

Sniffing Out The Opposite Gender

Just today a research article was released on the study of chemical cues humans use to identify the opposite gender. It seems that as humans we have similar chemical cues as pheromones. Apparently just using our nose we can smell androstadienone (in males) and estratetraenol (in females) on an unconscious level. After smelling these hormones a person can identify of judge if the walk of a certain person is more feminine or masculine. However, this doesn’t mean that a woman can smell another woman’s estratetraenol and think her walk is more feminine. The study shows that only males smell the estratetraenol and judge the walk to be feminine. Similarly, the women can smell the androstadienone in men and judge the walk as being masculine, whereas men cannot do it. The article is linked below.

Humans Have a Nose for Gender

Dinosaur Blastulas!

Hey guys!

Since the last unit we covered included animal development, I have been doing a little outside reading and came across this awesome article. Scientists have discovered the oldest fossilized evidence of dinosaur embryos. There are many difficulties associated with dinosaur embryos because as you know, dinosaurs laid eggs. There are many examples of fossilized eggs, but being able to find remnants of the actual embryo is extremely rare. This discovery is helping scientists trace the developmental pathways back to some hundreds of millions of years. Here’s the link if you’re interested!

 

http://www.nature.com/nature/journal/v496/n7444/full/nature11978.html

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!

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!

The Final Countdown

As we all continue reviewing for our final, I just wanted to share a study habit that is effective for me. Because I already know the information, I just need to refresh my mind; youtube videos are extremely helpful. Crash Course Biology is one of my favorite channels, but if you type in the name of the chapter you’re reviewing, you will get lots of great videos and lectures. Another one of my favorite finds is the geologic time song video (see my earlier blog post). Good luck studying guys!

Nostalgia and Brain Damage

I suppose it doesn’t make much sense to have some nostalgia before the year even finishes, but at the same time, it is crazy! I’m so glad I got to have this year with all of you guys. It seems like it’s been so long since we were sitting in BSB D310 enriching our third soil sample, trying to figure out why in the world we couldn’t find any phages. But here we are!

On a more scientific note, I came across this article today that talks about how exactly alcohol/other drug stressors can distress a fetus. With a mouse model, they were actually able to isolate the specific gene that fetuses seem to use to protect themselves from these toxins. However, what seemed interesting to me is that the article held a focus to the offspring’s future intolerance of the toxic substance, like alcohol, which is something that I never knew about.

Working on Projects

Hey Guys,

Our group is finding some great information for our independent project.  We are firming up the rest of our presentation on Amigo’s repeated sequence. Amigo’s repeated sequence is very interesting, and it is puzzling why Amigo would double some of its genes. We are having a lot of fun researching this subject.

Here is an article about clustered, regularly interspaced short palindromic repeats (CRISPRs). I posted an article about this before, but this article shows that CRISPRs actually are phage resistant genes. It is defiantly worth checking out.

http://www.nature.com/nrmicro/journal/v6/n3/full/nrmicro1793.html

“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

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.

Maize!

Hey guys! I really think that everyone should take time to read this!

http://www.jyi.org/issue/identification-of-dna-sequences-of-long-terminal-repeat-retrotransposons-in-maize/

During September of 2005 Joseph L. Wezenter analyzed maize sequences at Montclair University. The goals of his project were similar to that of Phoenix’s group project- to determine what Long Terminal Repeats retrotransposons and what genes are present in maize (for us Amigo), to find the start and stop locations of both, and to ultimately create physical maps depicting their locations.

With the raw sequence from the FASTA file, a web-based piece of software called GenScan was used. GenScan predicts the locations and exon-intron structures of genes in genomic sequences from a variety of organisms such as maize. By being organism–specific, the results are more precise. The FASTA sequences were loaded and maize was selected as the organism. From this the one letter amino acid sequences of the predicted genes were generated and uploaded into BLASTp (protein-protein) of the NCBI website for further analysis.

TIGR (http://www.tigr.org/tdb/e2k1/plant.repeats/) is another piece of web-based software Joseph used. It is a collection of curate databases containing DNA and protein sequences, gene expression, cellular role, protein family, and taxonomy of microbes, plants, and humans (TIGR 2005).

A phylogenetic analysis was also preformed on these LTRs. It was depicted in a TreeView diagram that represented a pedigree of inherited relationships among molecules, organisms, or both. (Like I know one of the other groups did!!)

Effect of Environment on Health

Since we are studying ecosystems and populations, I thought it would be interesting to learn about the effect of ecosystems on organisms.  I was reading through Science Daily and there is some research being done on the effect of environments on individual’s health.  Duke University performed a study on the poor health results of people living in poor Chicago neighborhoods.  I found this very interesting.  It is incredible just the amount of evidence they have found in the correlation between one’s living situation and one’s health.  This applies directly to what we are learning in class pertaining to the spread and dispersion of populations throughout areas (with much dependence upon environment).  This research makes me wonder about public health systems that can be implemented in poorer communities to help the health issues of communities.

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.

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

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.

Living Organ Regenerated for the First Time

This past month scientists at the University of Edinburgh regenerated the thymus gland of a living mouse. They did this by increasing levels of FOXN1, a protein produced by the thymus, which helps to control how important genes are switched on. This could mean so much for the future of medicine. The same team’s research suggests that targeting the same pathway in humans may improve thymus function. Not only does this impact elderly patients, whose thymus has deteriorated with time, but it also affects those born with an underdeveloped thymus. Furthermore, if scientists can regenerate a thymus by just targeting a single transcription factor, then could they regenerate important organs, such as the heart, through the same or similar processes? This new research opens up an entire world of opportunities for doctors and patients alike. If you would like to read the article, it is linked below.

Regeneration of the aged thymus by a single transcription factor

New Fertility Proteins Identified

Researchers from the Sanger Institute have recently identified two of the proteins involved in mammalian fertilization. The sperm protein, named Izumo after a marriage shrine from Japan, and the egg protein, named Juno after the Roman goddess of fertility, are two key components to having the egg and the sperm bind. Twenty percent of infertility cases have no known cause, and lack of these proteins might help to explain these mysteries. Researchers also theorize that Juno has a role in the formation of the fertilization envelope. Since we just studied this, I thought it was very interesting!

http://www.ncbi.nlm.nih.gov/pubmed/24739963

Pretty Cool

Okay, I’m reading this for my chemistry honors paper and I’m getting pretty excited cause it’s talking all about the genomics of Ebola and at least in the first few paragraphs, it’s all stuff that we have worked with in Arthrobacter! Not exactly the same things but it is so cool to be able to understand it!

http://emedicine.medscape.com/article/216288-overview#aw2aab6b2b2

Independent Project

Today, Olaf’s Fan Club finished making the presentation for the final project. We researched Arthrobacter clusters, and I’m very excited to share what we found with the class. I’m so thankful for my group and for this class. Y’all are the best, and I love you guys!

The seeming lack of attP sites in Amigo

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.