Archive for April, 2014

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 28 2014

The Final Countdown

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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!

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Apr 28 2014

Nostalgia and Brain Damage

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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.

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Apr 28 2014

Working on Projects

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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

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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 25 2014

Maize!

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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!!)

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Apr 23 2014

Effect of Environment on Health

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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.

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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 21 2014

Living Organ Regenerated for the First Time

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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

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Apr 20 2014

New Fertility Proteins Identified

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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

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Apr 19 2014

Pretty Cool

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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

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Apr 17 2014

Independent Project

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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!

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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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