Bio321 tag clouds

For those headed into Bio321 this Spring - here are tag clouds of the content to give you a view into the course!

The lecture:

The lab:

Genetically altered HIV to battle leukemia

http://www.nytimes.com/2012/12/10/health/a-breakthrough-against-leukemia-using-altered-t-cells.html/ref=science&gwh=D9083766D40AE2F7CE684DB2E7476883&_r=0

HIV attacks the immune system and as a retrovirus it can insert its genome into the immune cells' DNA. This research team is using a genetically modified form of HIV to have it specifically put certain genes into the T cells that cause them to target the B-cells (which are the problematic dividing cells in this case)

The exposure of the modified HIV to the T-cells takes place outside of the body then the newly altered T-cells are returned to the host. Sounds like this is in the promising stage but still needs further work

I especially think it's so amazing to be using such a destructive virus to our benefit

Thanks to Alex Pedicone for bringing this one to my attention!

Living in sub-zero brine

Murray et al. 2012. Microbial life at −13 °C in the brine of an ice-sealed Antarctic lake. PNAS

Lake Vida is in the Antartic, how's this for a place to live:

• sits at -13 deg C
• salt concentrations 6 times that of sea water
• sits under 50-100 ft of ice
• aphotic (little or no light penetrates)
• anoxic (no oxygen)

(taken from Nature journal's website here)

As always though, microbes abound - albeit ~10-fold lower concentrations than lakes, and a lot more tiny cells that normal. Now that doesn't mean the diversity is high - in the survey they found ~32 species in 8 different phyla - but c'mon, give any microbes credit for living down there!

The researchers cored deep, viewed the cells via fluorescent staining and microscopy, and coupled that with rRNA gene sequence analysis.

Link to the original article: http://www.pnas.org/content/early/2012/11/21/1208607109

Link to more general article: http://www.nature.com/news/life-abounds-in-antarctic-lake-sealed-under-ice-1.11884

Holiday soaps

Can't think of a better soap to have around than this

http://www.etsy.com/shop/CleanerScience

Time for the beach?

http://www.motherjones.com/blue-marble/2012/07/dirtiest-beaches-nrdc

It doesn't matter how expansive the ocean is, the beaches aren't always pristine!

I was happy to see that the NC beaches were generally on the "cleaner" end. This was based on coliform bacteria present. Interesting factoid - beaches that meet minimum federal standards would still sicken 1 in 28 swimmers. Not sure how that was calculated but impressive if true.

South Padre Island in Texas was also listed as one of the cleanest - nice to hear given how many students flock down there each Spring

the titantic's second demise - bacteria

http://www.microbeworld.org/index.php?option=com_jlibrary&view=article&id=8629&utm_source=twitterfeed&utm_medium=twitter&utm_campaign=twitter

appropriate timing of this story coinciding with 3D release of the movie!

living in the deep ocean, chomping on iron, not a typical way to make a living but someone's got to do it....

Cleaning/restoring paintings with bacteria

First saw this in National Geographic - another neat application of microbes to treat delicate art pieces where traditional cleaning methods might be damaging

http://www.sciencedaily.com/releases/2011/06/110607063411.htm

Earth Microbiome project (EMP)

there are a group of scientists that are trying to use 16s and metagenomic analysis across all of Earth's ecosystems. The goal is an incredible number of environmental samples (10K-200K depending on the source of the info) expected to generate 15 trillion base pairs of DNA sequence information.

http://www.earthmicrobiome.org/

This is an incredible project that should yield some pretty fantastic insights into microbial life on this planet

For current students: The importance of this project relates back to the fact that so many (an estimated 99%) of the bacteria out there are not easily cultured by our standard techniques, therefore we seldom detect that they are there and in many instance, we have never detected them. By analyzing the DNA we can detect their presence and estimate their diversity by comparing the DNA to microbes that we have already worked with. Expect this project to reveal many new lineages of bacterial life!

Looking for treasure trove of ancient microbes

Lake Vostok is a giant freshwater lake that is entombed beneath 2 miles of ice. It is estimated that this body of water has been sealed off for ~10 million years. Scientists have been drilling for a long time in hopes of reaching the water and to then be able to sample it.

What would they expect to find? Microbes would be the primary form. What would microbes that hadn't intermingled with other microbes in millions of years look like? That's the magic question. My guess is that there will be some really amazing things that come from this and that it will related to environmental metagenomic analysis

http://www.nytimes.com/2012/02/09/world/europe/russian-scientists-bore-into-ancient-antarctic-lake.html

http://www.huffingtonpost.com/2012/02/09/lake-vostok-microbes-unlikely-life_n_1264605.html (this article diverges quickly but for current students I like how it alludes to the extremophiles)

An interesting side note - the world's coldest recorded temperature was at Vostok - minus 128.6 degrees. They had to try to do most of this work in the "summer" when flight into the site was possible

Healthmap getting more use with official groups

Healthmap is one of those resources I've been showing students in class for the past year or two. Here's a nice quick note from Nature Medicine that supports that it's getting more use by official health-related units.

The internet brings massive amounts of data combined with up-to-the-minute changes and flexibility. By culling through this data and tying in geographic mapping, there are some really creative projects that are changing the way we track and predict disease spread.

http://www.nature.com/nm/journal/v18/n2/full/nm0212-185.html?WT.ec_id=NM-201202

trying to understand a microbe that can't be cultivated

BioTechniques - Seawater Microbe’s DNA Demystified

A theme that I put out there all the time in my class relates to how we have been discovering over the years how we often don't even know that the microbes that are most dominant in a system exist, much less what they're doing. In this article, the authors run a metagenomic study - sequencing all the DNA that's in a sample of water they take from some surface seawater. They knew that something noncultivatible dominates that but did not have it in culture. From the metagenomic DNA they were able to sew together all the sequences that presumably came from that dominant organism thereby giving them the genomic data that they could analyze. With that data they could analyze what capabilities that microbe has - metabolic pathways, motility, ability to deal with light, etc. Very fascinating. This kind of approach will become increasing important in the next years

did I mention that the group they studied make up 50% of the microbes in the ocean? And can't be cultivated? That's wild that it could be that important in the system yet we can't cultivate it. It would be like trying to talk about the trees on Elon's campus but not being able to see the oaks....

Here's the link to the original article

http://www.sciencemag.org/content/335/6068/587.abstract