Synchronized E. coli

http://ucsdnews.ucsd.edu/video/0110geneticclock.mov

Neat experiment Showing bacterial coordination in a cool visual way. All done with E. coli modified to carry a green fluorescent protein

comments open on Micro course blog

Hi all - just set it up so that any of you can comment on articles/posts. Please feel free to participate long after you are done with the course!

along those lines, please feel free to share anything that you find that you think may be of interest to the group

cheers

http://www.atcc.org/CulturesandProducts/PhotoContest/tabid/2007/Default.aspx

Thought this was very relevant to our class - ATCC is holding it's imaging contest. Check out their entries at the above URL - click on "view entries". I think if we had had official ATCC cultures then some of the microbial art pieces you put together would have easily had a shot!  The shot from their page shown below is actually Serratia marcescens - a species that we used this semester too

Thanksgiving micro moment

I love making a turkey soup after our main meal. I go through a ritual of boiling things down, fishing out the bones, seasoning it, etc. It takes a lot of time but man, I look forward to that first bowl of soup.

This year I made a classic microbiological mistake. After a long day I forgot and left the soup out overnight. Yes, earlier it had been boiled but since the boiling a number of us had dipped a nonsterile ladle in. Students should be able to think about how long it took their nutrient broth inoculations from this semester to go from clear to cloudy. I left the soup out for 24 hrs before realizing my mistake - the room was at a good 70 deg F (~20 degC). And yes, essentially this soup was a beautiful nutrient broth.

It broke my heart but I dumped the soup.

Bacteria always win....

Current top 7 in Micro

Who doesn't like a top 10 list, right?

Current top 7 microbiology papers as ranked by the Faculty of 1000. Many of these topics relate to things we've been talking about in class this past month!

http://the-scientist.com/2011/11/15/top-7-in-microbiology-4/

Anti-malarial target, Yeast genome, septin cages as a way of trapping bacteria, mRNA's from bacteria as PAMPs, evolution of mitochondria, microbiome affecting viral infections, apoptosis

E. coli at the fair

Elon's student TV station did a bit on the E. coli outbreak and interviewed me for a few biological tidbits

http://phoenix14news.wordpress.com/2011/11/08/e-coli-outbreak-develops-following-nc-state-fair/

I thought they did a good job - remember that few people who haven't taken a microbiology course appreciate what you guys do. The typical person on the street sees bacteria as an invisible menace and only understands that there are bad ones, not the good side of the story. Heck, even microscopes seem pretty high tech to the general public...

Flu Near You service

sponsored by HealthMap, based on weekly voluntary surveys their goal is to map out and track how flu spreads through the region this year. Free registration to participate. Should be really interesting to monitor this

https://flunearyou.org/

Ancient genomics sheds light on past plagues

This caught my eye as I had just talked a bit about Yersinia pestis in class about 1-2 weeks ago. This species is generally assigned as the causative agent of the plague that wiped out 1/3 of Europe in the mid1300's. Researchers obtained DNA from Black Plague victims from the 1300's and were able to pull out and sequence the genome of the bacterium that caused it. Their initial questions were 1) was Y. pestis actually the cause and 2) if so, how did this strain relate to today's strains?

When they compared the genome to modern Y. pestis, they found that 1) it was indeed Y. pestis, and 2) there is little change between the ancient strain and the current strain suggesting that it wasn't necessarily a abnormally virulent strain.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10549.html

A few posts ago I noted the use of genomics to track modern epidemics. This study adds a unique component by analyzing ancient genomes. Took a peek at the methods - they had to enrich the DNA by using modern Y. pestis fragments to pull out the ancient bacterial DNA, otherwise it's a needle in a haystack! 

Megavirus chilensis takes current award for biggest virus

From Oct 10, 2011 issue of PNAS

http://www.pnas.org/content/early/2011/10/04/1110889108.abstract

isolated from the sea near Chile, somewhat related to the prior record-holder Mimivirus, contains 1120 protein-coding genes, 1.26 Mbp of DNA, and size of ~0.2-0.3 uM

(image from geekosystem.com)

next generation sequencing strikes again

A while back I noted a "proof-of-concept" study where researchers took a problematic strain of E. coli from an outbreak, pumped out the genomic sequence and analysis in a few days and were able to make great strides in understanding the nature of why this particular strain was a problem.

The same research group have now applied that to Klebsiella pneumoniae Oxa-48 - a bacterial strain responsible for hospital infections in the Netherlands. This really seems to support the importance of DNA technology advances and how genomic level information will be used in the future.

Got them "antimicrobials in my boots" blues

Bought a pair of hiking boots today and noticed that they had "Microbe Shield" on them. I couldn't resist - I had to find out what they were doing that made it antimicrobial. Obviously with something like a boot you don't exactly impregnate it with ampicillin. Here's what I found out about that

The companie's name is Aegis. They've synthesized an interesting molecule that has 3 main components. The first part of the molecule is bound to the material. The second part of the molecule is positively charged and therefore attracts the negatively charged bacteria to it (quiz - what makes the bacterial wall negatively charged?). The third part of the molecule is rigid and "stabs" the cell. The molecule doesn't get consumed in the interaction therefore it can act for a long time.

They have an interesting interactive about the mode of action of the molecule at:

http://www.microbeshield.com/index.php?option=com_content&view=article&id=31&Itemid=3

update 3/15/13 - looks like the business has been restructured

http://www.microban.com/americas/english

the tech video can now be found at http://www.youtube.com/watch?v=UmQy0AunWGo

slime molds as models

http://www.nytimes.com/2011/10/04/science/04slime.html?_r=1&ref=science

neat stuff about a great group of eukaryotic microbes.

Here's a link to the map experiment that is referred to in here. 

http://www.wired.com/wiredscience/2011/05/slime-mold-iberia/

Anaerobic soil bacteria fighting cancer

Interesting article sent to me by Dr Vick

http://www.bbc.co.uk/news/health-14761417

The bacteria they refer to is Clostridium sporogenes. Many of you will recall that this genus is one of the endospore-formers, and that this genus is primarily anaerobic. The general idea is that the C. sporogenes can grow within the tissues because it is anaerobic. This is not necessarily intuitive to me because I seem to recall that vascularization (and hence blood/oxygen supply)  is an important feature of a tumor - but there must be more to it. 

Anyhow, to those currently in the course - I thought this was timely considering the material that has been covered in this first section

Want to share microbial profiles?

A research group in Europe is looking for participants in a microbial gut profiling study. One of their side enticements is that they will - if you want - put you in contact via social networking with other people worldwide who share your microbial profile. Sounds weird but really I think this is brilliant. Gut microbes impact us in ways that we don't fully understand yet. There may be many other people who have figured out good balance with their microbes that you can learn from. OK, that still sounds weird, but cool in a sciency way

http://my.microbes.eu/

Here's the more sensationalized interpretation....
http://www.mnn.com/health/fitness-well-being/stories/new-social-network-matches-people-based-on-gut-bacteria

Changing role of clinical work in Microbiology

http://www.microbeworld.org/index.php?option=com_jlibrary&view=article&id=7429&utm_source=twitterfeed&utm_medium=twitter&utm_campaign=twitter

Highlights:

• advances in molecular biology are what's changing things (Microbial Renaissance #2, right?)
• cost and accessibility of these tools is still somewhat of an issue, limiting widespread use

Quick staining technique to view endospores

Quick staining technique to view endospores was noted on MicrobeWorld. Presumably they would need to be out of the cell already, and it helps that there are some fully intact bacteria for size comparison. We'll need to give this a try in class!

http://www.microbeworld.org/index.php?option=com_jlibrary&view=article&id=7411&utm_source=twitterfeed&utm_medium=twitter&utm_campaign=twitter

New tech sequences bacterial genome in 2 hrs

http://www.iontorrent.com/technology-how-does-it-work-more/

How it works (if you're into this kind of thing): 

many miniwells, each with strand of DNA (stands that you want to sequence) anchored. Wash specific nucleotide (ex. dATP) over the slide. If that specific nucleotide gets incorporated, sensors detect the release of H+ ions from the reaction which lets you know "yep, that was an A". Generates 100 bp length reads - of course it's 1.4 million of them. They sequenced bacterial genomes (5x-10x coverage) in 2 hours with just 6 hours of prep time for each sample. 

Interestingly enough, they also sequenced Gordon Moore's genome as a test. He's the guy who developed Moore's Law which describes how technology doubles. His genome coast $50K to do but they think that this technology will advance quickly to get close to that target $1000 genome that everyone talks about. Not sure how much the bacterial genomes cost each

Link to the Nature summary

Long term diet affects your gut microbe composition

http://www.sciencemag.org/content/early/2011/08/31/science.1208344

the food you eat acts very much like an enrichment disturbance to your gut microbes!

Evidence of ancient antibiotic resistance genes in bacteria

"Researchers Find Antibiotic Resistance in Ancient DNA"

link to NYTimes article

Highlights

• researchers isolated and sequenced DNA from bacteria in 30,000 yr old permafrost
• by comparing the gene sequences to current databases they were able to identify some of the ancient genes as genes involved in antibiotic resistance

for current Micro students - so given that 30,000 years precedes human use of antibiotics (considerably I might add), why did those bacteria have antibiotic resistance genes? (let me know if you think you have an answer...you'll find out later this semester but it's an interesting one to think about in the meanwhile.)

Squiggly virus

from my favorite satire site:

Deadly New Virus Found To Be 'Real Squiggly

vaccines not cancellations for flu?

Study of the UCSD campus during a 2009 H1N1 outbreak

http://www.asm.org/index.php/news-room/how-flu-virus-spreads-to-college-community-major-implications-for-control.html (also has link to original journal article there)


highlights:

• quite a diversity of flu strains coming into the campus
• influx of strains has enough impact on the student community that they end up recommending that perhaps vaccinations are more important than doing something like cancelling classes as a way to prevent spread

would this be a pattern seen consistently enough to apply to our school? Neat application.

fun with micro numbers

Some numbers pulled off of the Twitter feed #microbiologybynumbers

• Viruses
• if all viruses on earth laid end to end they'd stretch for 100,000,000 light years (not sure if I believe this one)
• 8% our genome is thought to be comprised of defunct viral DNA
• viral lysis in surface waters kill off 20-40% of oceanic prokaryotes daily
• more bacteria in the oceans (10^28) than there are stars in the universe
• 400 g of botulism toxin (produced by Clostridium botulinum) could wipe out all humans on the planet
• Gut bacteria
• gut flora genes outnumber our gene set by 100 fold (same thing I had noted in an earlier post)
• there are more bacteria in the gut than total number of people who have ever lived
• human excrete their weight in faecal bacteria every year
• you have ~1 kg bacteria in your gut

This led me to another interesting website that attempts to catalogue crazy information like these: http://bionumbers.hms.harvard.edu/default.aspx

Isolation of a cellulase enzyme capable with optimal temp of 109 deg C

http://newscenter.berkeley.edu/2011/07/05/hot-springs-microbe-yields-record-breaking-heat-tolerant-enzyme/

highlights: 

• Isolated from a hot spring
• an archaea
• metagenomics later used to implicate a few other archaea as well

whole genome sequencing of E.coli in outbreak

Article in Genome Technology this month: (click to see it)

stresses the power of the genomics age. Check out this timeline:
- received sample on May 30
- completed genome sequencings on June 1
- Genomes assembled and submitted to NCBI by June 2

Findings
- that E. coli was a new strain
- that E. coli had many antibiotic resistance genes

concept of "Genomic epidemiology"discussed

Another part of this article looks at MRSA and genomic sequencing of 63 isolates - identifying 6700 SNP (single nucleotide polymorphisms) that accounted for the variability seen and related to the microevolutionary changes being seen.

E. coli outbreak resources from NY Times

http://topics.nytimes.com/topics/reference/timestopics/subjects/e/e_coli_bacteria/index.html

tidbits from the metagenome

tidbits from June'11 issue of Microbe

- "metagenomic analysis suggests fourth domain within tree of life"

- gut microbiome contains 3.3 million genes!! Humans have ~20-30K so as the article points out human genes account for less that 1% of the gene types that are active in the body.

Bio321 Blog

Welcome to the Bio321 blog. I'll be using this to enhance the course by bringing different articles, etc. to your attention.

Here's a test of a few features so ignore this

a link to the HMP

a linked picture from the HMP

an inserted YouTube video