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.

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!

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

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

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

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!

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.

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

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!!)

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.

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

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

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

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!

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.

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.

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

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

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/

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