Molbio Carnival #11

This is the eleventh edition of the Carnival of Molecular Biology, a travelling goodie-bag dealing with all things small and cellular. When this carnival was first started up I must admit I had more of a hope than a certainty that enough people would be interested in the world of the small and cellular for it to continue, but we've passed the tenth edition, and it's still here!

Long may it remain

For this edition, we'll start off with the all important question, what actually is a biochemist? And is it significantly different to a chemical biologist? My reasoning on this is clear; a biochemist is a biologist who likes the chemical side of things, and a chemical biologist is a chemist who is fascinated with biology. They both may work in the same lab, but will have different training backgrounds and different ways of seeing the world. Chris Dieni gives a more thorough explanation of this over at BenchFly.

Science works by experiment, which is why I'm happy that we have two posts this carnival covering experimental techniques used to explore the intracellular landscape. The Biotechnology blog takes us through the technique of 3-dimensional cellular arrays which build up a picture of the entire cell, rather than just using thin slices through the cell. Psi Wavefunction goes deeper and looks at how to study the DNA within cells, and as she works with protists, it's some very strange DNA indeed.

Lineup of DNA, from Psi's post

As well as biologists and chemists, engineers tend to get involved in this molecular-biology gig and when they do they almost inevitably start talking about lego. Lucas from Thoughtomics shows us how life can be thought of as lego blocks, and how planets with life on them could potentially be found, even if the life is not as we know it.

Back in the realm of pure biochemistry is a brilliant post from It Takes 30 which explores how one pathway within the cell can lead to many different outcomes. It focusses on the pathways of p53, an unassuming little molecule that is one of the most important within the cell, as it responds to cellular DNA damage.

From the It Takes 30 post - a diagram many biochemists

are familiar with!

Finally, we'll finish with a last post from Psi, which is part of a multi-post essay about constructive neutral evolution and is well worth reading. As someone who only dashes of quick little posts, it's great to read a well researched longer post, which goes into a good (and accessible!) coverage of an important topic.

That's all for this edition! If you want to get involved (and I strongly recommend it, carnivals are interesting, great publicity, and also quite fun) submit any molecular-biology related posts here. The next edition will be at PHASED and the more posts it has, the bigger and better the carnival will be.

The MolBio Carnival is here!

The fifth issue of the MolBio carnival is here! We've got loads of great entries in this edition, all focusing on the mysterious world inside cells, so take some time out to take a look and comment on them. The inside of cells is such a fascinating place to explore - and many of these posts were written by the people whose job it is to explore them. I've used a fairly broad interpretation of molecular biology, so in this carnival you'll see everything from the atomic details of protein interactions, to the (comparatively) far bigger world of bacterial colonies in the gut.

All good explorations should start with a map - and you don't get much better than the truly gorgeous pictures spotlighted by E. Campbell of the HighMag Blog. This beautiful picture shows a cell with the actin-binding proteins stained purple in order to see how they interact with a mutant actin motor.

Once we head inside the cell, we can start to explore the many complex and fascinating interactions that help to control it. While the DNA might encode all the information needed to create cellular proteins, it isn't just the DNA that is responsible for cellular behaviour, as explained by Christopher Dieni in "How I Learned to Stop Worrying and Love Epigenetics" (which comes second place in the Lab Rat award for best post name). As well as proteins, DNA expression is also controlled by fragments of RNA, explained beautifully clearly by student blogger Khalil A. Cassimally who looks into whether miRNA might be used to control cocaine addiction. And while we're at the level of molecular interactions for cellular control, we can look at control mechanisms for protein folding as well, as the Computational Biology blog takes us through the consequences of entanglement during protein folding.

Picture from Robert Ezra showing protein (green) binding to DNA (gold)

But the cell does not consist solely of DNA and proteins - it also relies on metabolites such as sugars and fats. These metabolites pass through a complex series of reactions in order to convert them to energy, and research on how these reactions occur and are controlled has been going on for many years. Sigmabioblogs has a wonderful interview with the biolegend Dr. Donald Nicholson, who is now over 80 years old and has been working on metabolic pathways for pretty much his entire life! On the subject of nutrients, there is also a great bilingual post on Knedliky about how flavour-enhancers work at a molecular level.

These small and focused intramolecular reactions aren't just used to control the cell, but also to control far bigger systems, or cell-cell interactions and communication. Memoirs of a Defective Brain explains how the bacteria Strep pyogenes uses intramolecular interactions to prevent the immune system recognising an infection. His post "The SpyCEP who cleaved me" not only wins the Lab Rat award for best post name, but also features the BEST diagram I've ever seen for explaining the subtle and complex interactions between cells of the immune system:

While we're on the theme of bacteria (yay!) we'll head over to the stomach. James, of (currently...) Disease of the Week, has written a great two part series on those bacteria in our gut, focusing on the question of how they actually get into our gut, and what they do when they get there. Part 1 deals with babies, and Part 2 with adults. There's also a lovely post from Lucas Brouwers, of Thoughtomics, which looks at the evolution of cyanobacterial toxins - and why a bacteria that lived millions of years before humans were even thought of would need to produce such a powerful neurotoxin.

And lets not forget the plants! They rely on intracellular interactions as much as any other organism. There's an old (but very good) post from Denim and Tweed about how nitrogen fixing bacteria made the leap from being intracellular parasites to mutualistic helpers. We've also got a post from It Takes 30 - about how sex is specified in plants. Unlike humans, who rely on chromosomes, hormones, and a whole host of social norms and pressures to distinguish the sexes, plants might need no more than a single amino acid insertion.

Those are basically just brightly painted sexual organs on display

We'll finish the exploration on a slightly larger, but no less fascinating level, the reproductive systems of marsupials by the amazing piratey Captain Skellet. By labelling gene markers for the development of organs researchers have come to the (not unexpected) conclusion that marsupials are Just Weird, and no one is quite sure why...

The next edition of the MolBio carnival will be hosted at PHASED, so if you've missed out this time, go submit your posts here by the 3rd of January. Blog carnivals are a great way to share information and to get new readers, so it's highly recommended!

Studying Streptococcus - SGM series

The fourth post now in the SGM series, and this one focuses on Streptococci. Streptococci are a genus of spherical Gram-positive bacteria containing both pathogenic and harmless strains, including the flesh-eating bacteria (which cause the delightfully named necrotizing fasciitis) as well as bacteria responsible for making swiss cheese. Commensally they are found on many parts of the human body, including the mouth, skin, intestine, and upper respiratory tract .

Streptococcus - growth and division leads to long chains of bacteria (image from lenntech)

It's quite a broad topic which allowed plenty of speakers to address their favourite issues with these bugs, but as well as discussions of the virulence factors, biofilm properties and various different intracellular survival properties of the Streptococcus there were also some talks covering new research mechanisms. Rather than focusing on the properties of the bacteria, these talks were about new methods used to study them.

The one that jumped out at me the most was about using Bioluminescent imaging to track a Strep infection. This appealed to me because the iGEM team next door are working on Bioluminescence so it's a word I've heard a lot over the last eight weeks. By adding bioluminescent bacteria to a mouse model, the course of the infection can be tracked over several weeks (using small animal imagine machines it can be tracked in the same mouse). This provides a far better understanding of the pathogenesis of the bacteria; how it spreads through the body and at what point it is most infectious.

The process of using bioluminescence to track diseases (image from the reference).

Using luminescence to study disease progressions isn't a new idea, but the use of whole animal scanning mechanisms now means that fewer animals have to be sacrificed in order for the study to done. The luminescent tissue does not have to be extracted, and the more natural disease progression can be followed.

Other methods explored included the by-now predictable whole genome study analysis to organise the different types and virulence levels of a Streptococcus suis which leads to meningitis in piglets. Comparative genome hybridization studies allow many genomes to be compared at once, giving a better idea of the differences and similarities between them. This helps to separate the strains into serotypes (different groups), and to compare the differences that lead to virulence. Genome comparison work was also being done for Streptococcus equi species which cause infections in horses.

In other news (pretend that was a smooth transition!) the latest Carnival of Molecular Biology is out over at Thoughtomics. There are some brilliant articles covering the intra-cellular happenings of organisms from bacteria to frogs to Tibetans. If you've ever wondered about noisy bacteria, zombie enzymes or what micro-RNA is, go take a look and visit the submissions.

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Timothy C. Doyle, Stacy M. Burns, Christopher H. Contag (2004). In vivo bioluminescence imaging for integrated studies of infection Cellular Microbiology, 303-317 DOI: 10.1111/j.1462-5822.2004.00378.x

On writing and blogging

I've written about many things on this blog. Bacteria, antibiotics, um, other bacteria. But one thing I haven't really covered is blogging about blogging. There is a good reason for this, lots of other people are doing it so much better and I wouldn't know where to start, apart from floundering around waving my arms about and talking about how much more I've enjoyed blogging now I'm in this whole 'network' thing.

But then Hannah went and wrote a post about it and that post gave me confidence. I might be just a recently-graduated student with limited experience of both science and science writing, but can still write. I can't write about facultys, tenure-track, post-doc-ness, or give much breadth of experience to my topics, but what I can bring, and what I hope I always will bring is a huge amount of occasionally overwhelming enthusiasm for the bacteria I love finding out about.

What's possibly a benefit to that is that I'm always starting from the point of view that I'm probably wrong. Any comments that ask pertinent questions about what I've written have me scuttling back to the literature. This blog has helped me learn, and helped me discover a new things and most importantly has kept my learning broad. I've just graduated, which means if I go on to do a PhD I will continually be narrowing down my field of vision directed towards whatever I happen to be studying. Even during my degree it was starting to happen, and yet by keeping this blog open I can learn about things like modelling virotherapy for cancer and how plants respond to iron stress despite the fact that it's not really a part of my course. It's all interesting, and I want to keep finding out about it.

As well as giving me confidence with her post Hannah also tagged me for the bloggers with substance meme:

1. Sum up your blogging motivation, philosophy and experience in exactly 10 words.

I can do that in two words: I write.

Ten words: I cannot find a way to stop myself writing. Refrigerator.

I write. I have always written. I have whole files full of masses of paper that I scribbled bad sci-fi stories on when I was ten. Any computer I've ever used will have a folder marked "non-fiction" that is usually more crammed full of things than any other folder. I have bits of fantasy story and fanfic scribbled in the margins of my lecture notes. Every time I go on holiday I usually bring some blank paper and a pen with me, rather than (or as well as) a book to read. My A-level chemistry notes have Star Wars essays covering them and I swear I used to have a school shirt with random phrases from a Harry Potter fanfiction scribbled on the cuff.

I can't ever imagine not writing.

Somewhere around second year university I decided that I should probably channel this force for good and, after finding Ed Yong's blog and realizing that it was possible to write about science online, I started writing about science. It seemed to work well, and it's been working better and better ever since. I have bloggy friends now, and a bloggy community. I tweet stuff. The writing has become something great, and I still very much enjoy doing it.

Yes that was slightly more than ten words. This is a blog-post, not a tweet.

2. Pass it on to 10 other bloggers with substance

I think everyone I'd want to pass it onto has already been tagged, but here's ten bloggers that I enjoy reading and most of whom I'm blog-friends with anyway:

Skeptic Wonder - The Protist Person

Lucas Brouwers - who blogs at Thoughtonomics about all sort of interesting stuff

C6-H12-O2 - a blogger I found recently who writes lots of nice mol-bio articles

Angry by Choice - who won me over by writing a post about a fungi that devours worms by making little traps for them

Schooner of Science - the pirate science blogger!

MolBio Research Highlight - who got the MolBio Carnival running and does awesome tweets.

Disease of the Week - A bacteriologist, a virologist, and a lot of diseases (and currently a poll...)

Oscillator - for synthetic biology goodies

Dr Isis - for all the wonderful advice on science, motherhood and other things that I might end up doing in the future

Games with Words - who makes very good points that I sometimes disagree with

(I would have added Culturing Science to the list as well, but she tagged me so I'm not sure it counts...)

That's probably the most linked post I've ever made, and also probably more information than anyone really wanted to know about me. I am a science student who likes writing, and this blog is where it all comes together as one.

New Carnival!

This is a little late as I've been away, but better late than never! A new carnival has arrived thanks mostly to the efforts of Alejandro Montenegro aided by myself, Lucas Brouwers, Psi Wavefunction and Alexander Knoll.

This carnival will collect articles focussing on all processes that go on inside cells. Every month (starting August the second) a collection of these articles will be gathered and posted on a suitable host blog. Posts from anyone are welcomed, as long as they feature internal cellular happenings.

I really love blog carnivals, as they give an interesting selection of work to browse through and, from a more selfish perspective, they do help to increase readership to your blog. Submissions will be accepted up too the first of August so if you have written, or are planning to write, anything about the Private Life of Cells then go submit your post here.

Also, for those that missed it the latest Carnival of Evolution is up at Culturing Science. It's an absolutely amazing issue, with loads of great articles and little hand drawn illustrations for each section heading.