So how do you start exploring the age of bacteria, and trying to discover when they developed as a human-infecting species? One way to look for the age and relatedness of strains is by looking at the bacterial DNA and examining the rate of mutations that cause very small differences between bacterial strains (single nucleotide polymorphism – shown in the image below). It is also possible to identify “pseudogenes” within the bacteria – little bits of viral DNA or bacterial genes that became redundant due to a change in the bacterial lifestyle (for example genes for extracellular lifestyle that started decaying and mutating once the bacteria became fully intracellular). These can be dated using the ‘molecular clock’ – which assumes a steady rate of background mutation and can provide approximations of the age of genes.

Image by David Hall (Gringer). Created using Inkscape v0.45.1. Taken from wikimedia commons, credit link above.

The disease leprosy, caused by Mycobacteria leprae, has recently undergone this analysis and raised some interesting questions about its origins and spread. Although first recorded in humans around 600BC in India, the molecular evidence point to it being far older, possibly originating in Africa during the Paleolithic period. The lack of genetic variation between leprosy strains also points to a genetic bottleneck in the past. This is likely to have been caused by the bacteria’s low rate of infection. Despite the huge amount of social stigma associated with it leprosy is not highly infectious and could easily have been almost completely lost among early human societies.

Another bacteria to have gone through the genetic analysis is Bordetella pertussis, the bacteria responsible for whooping cough. Originally thought to have passed to humans via a similar species found in domestic animals, the molecular evidence once again suggests that it has been around since before animals were first domesticated. Instead it may have evolved from the bacteria B. bronchiseptica which was present around 2.5 million years ago with a preference for infecting hominids. This makes a rather neat little story of a bacteria adapting to fit the changing hominids as they became human and evolving specifically to fit the human niche (image below by Nathan Reading)

A rather beautiful picture of B. pertussis colonies growing on agar supplemented with charcoal (to provide extra carbon)

Although this research produces some exciting outcomes, it shouldn’t be taken as the last word on bacterial origins as it does sometimes come up with some questionable results. Trying to combine SNP analysis results with the molecular clock dating of pseudogenes creates some interesting paradoxes, such as pseudogenes within M. leprae that arose over 9 million years ago [EDIT This was originally incorrectly written as 'billion'], when modern humans have only existed since approximately 250,000 years ago! What is clear however is that not all diseases can be blamed on cities and animal domestication, and that some bacteria were infecting humans back when Homo sapiens was still an exciting new species to be. Deeper genome sequencing analysis and further work on dating the pseudogenes could give a fascinating look into the development of human diseases from the times of our earliest ancestors.

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Ref 1: Trueba G, & Dunthorn M (2012). Many neglected tropical diseases may have originated in the Paleolithic or before: new insights from genetics. PLoS neglected tropical diseases, 6 (3) PMID: 22479653

Ref 2: Monot, M., Honoré, N., Garnier, T., Zidane, N., Sherafi, D., Paniz-Mondolfi, A., Matsuoka, M., Taylor, G., Donoghue, H., Bouwman, A., Mays, S., Watson, C., Lockwood, D., Khamispour, A., Dowlati, Y., Jianping, S., Rea, T., Vera-Cabrera, L., Stefani, M., Banu, S., Macdonald, M., Sapkota, B., Spencer, J., Thomas, J., Harshman, K., Singh, P., Busso, P., Gattiker, A., Rougemont, J., Brennan, P., & Cole, S. (2009). Comparative genomic and phylogeographic analysis of Mycobacterium leprae Nature Genetics, 41 (12), 1282-1289 DOI: 10.1038/ng.477

Ref 3: Diavatopoulos DA, Cummings CA, Schouls LM, Brinig MM, Relman DA, & Mooi FR (2005). Bordetella pertussis, the causative agent of whooping cough, evolved from a distinct, human-associated lineage of B. bronchiseptica. PLoS pathogens, 1 (4) PMID: 16389302

Haemoglobin – the molecule that gives blood its red colour and is used to transport oxgyen through the body.

The structure of haemoglobin, by Richard Wheeler (Zephyris) 2007.

The image above (credit link) shows the structure of the haemoglobin molecule. It consists of four sub-chains (shown in red and blue) each of which carries an iron containing “haem co-factor” which you can just about see in the diagram as the spikey green things. These haemoglobin molecules are packed tight into red blood cells, so tightly that the red blood cells don’t even have a nucleus but are just haemoglobin carrying machines. The lack of nucleus means that they can’t grown or divide (or do anything much), so after being put together in the bone marrow and circulating the blood for around three months red blood cells are discreetly removed and replaced.

All of this circulating iron is a great opportunity for pathogenic bacteria, who have developed various systems to get hold of it. Firstly they have to break down the red blood cells, usually by secreting various chemicals that break up the cell membrane, releasing the haemoglobin. Then they have to bind to the haemoglobin via specialised receptors on their cell surface. Once bound, the haemoglobin passes through the bacterial cell wall and into the interior of the cell. For bacteria with two cell membranes (Gram negative bacteria) this is a complex task involving various different proteins, transporters, and use of the proton-motive force. For bacteria with one large thick cell membrane (Gram positive bacteria)  some sort of protein relay process seems to be involved, which uses far less energy. Greater detail on both these processes can be found in the references below.

A very simply schematic of the difference between Gram positive bacteria (top) and Gram negative (bottom). Original uploader was Graevemoore at en.wikipedia.

Once inside the bacterium, the haemoglobin is broken down to release the precious iron that it carries. This is more dangerous than it sounds, because the iron in haemoglobin is carrying oxygen, which means that there is potential for reactive oxgyen species to be released and cause havoc inside the cell. Not only that but in some bacteria the “haem co-factor” itself can be toxic. Some bacteria contain special enzymes called “Haem oxygenases” which deal with the oxgyen species, while others sequester the haem in vacuoles away from the rest of the cell, or turn on exporter molecules. It’s not quite clear whether the exporters are taking away the haem or some other toxic product, but they are vital for preventing the toxic effects of haemoglobin within the bacteria.

The whole process of extracting iron from haemoglobin is actually fraught with dangers for the bacteria. The process requires all sorts of special molecules and transporters which don’t feature in human cells, which makes them a prime target for the immune system to recognise an invading element. In particular the haemoglobin binding proteins, which are a bit like a large red flag labelled “invader” sticking out of the bacterial cell surface. Not only that, but they are quite energy expensive to run, particularly for the Gram negative cells. In consequence, the bacteria tend to only activate this system when they are running particularly low on iron, and there are no other available sources around.

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Ref 1: Pishchany G, & Skaar EP (2012). Taste for blood: hemoglobin as a nutrient source for pathogens. PLoS pathogens, 8 (3) PMID: 22412370

Ref 2: Pishchany, G., McCoy, A., Torres, V., Krause, J., Crowe, J., Fabry, M., & Skaar, E. (2010). Specificity for Human Hemoglobin Enhances Staphylococcus aureus Infection Cell Host & Microbe, 8 (6), 544-550 DOI: 10.1016/j.chom.2010.11.002

Niches of Sunlight

In every environment there will be competition for resources, and there are generally two ways organisms deal with this; generalise or specialise. To generalise, you try to cope with as many different conditions as possible, so that if you get out-competed in one area you can try to cope with the conditions elsewhere. To specialise, you get damn good at using the conditions in your little niche, in the hope that you’ll be better than anyone else who comes along, and be able to out-compete them.

There are many resources that need fighting over, and in the sea one of the major ones for photosynthetic organisms is sunlight. Other nutrients such as nitrogen, phospherous and trace metals such as iron and copper can exist in different forms at different levels in the ocean (as shown below), but once you start getting below a certain depth, sunlight quickly becomes a finite and rapidly diminishing resource:

Different organisms  cope with the lack of sunlight in different ways. Some (especially the larger algae species) have generalised, they contain a whole range of different light capturing pigments which can absorb a range of light wavelengths, including those in the darker depths. But the little photosynthesising bacteria Procholorococcus (which I mentioned in this post) which have the smallest genomes of all photosynthesising organisms, don’t have that option. Instead they have to specialise, so that different strains  within the species are adapted to different levels of light.

Work done by Rocap (paper reference below) looked at two different strains of Prochlorococcus: MED4 and MIT9313 (which I will just call MED and MIT). The MED strain was found only in the surface waters, while MIT was found much lower down; a phenomenon known as ‘vertical niche partitioning’. Despite their genomes differing by only 3%, and despite being technically the same species (although ‘species’ is an uncertain word in the world of bacteria) they have optimised themselves to completely different levels of not just light but also nutrients, trace metals and virus specificities.

Just a quick visual to make it clear - MED lives near the top of the water, MIT near the bottom.

MED (the one near the surface) has a slightly smaller genome than MIT, yet contains twice as many genes dedicated to high-light-inducible proteins, many of which seem to have arisen by gene duplication. It also has genes specialised for the nitrogen sources found near the surface of the water, and organic phosphates (which again are found predominantly on the surface). MIT on the other hand has fewer genes for ultraviolet damage repair (as light-damage is less of an issue deeper underwater!), but more light harvesting genes. This helps it to gather as much light as possible, despite being further below the surface. It’s also adapted for the nitrogen source found at the lower levels, and increased ability to use orthophosphate, rather than organic phosphates.

Both genomes have lost the ability for photoacclimatisation, that is the ability to change to suit different light conditions. By taking up vertical niche positions, they have forfeited the ability to change their response, meaning that a strict horizontal partition between them must be maintained at all times. Any Prochlorocuccus found at lower levels will be of the MIT variety, while those at higher levels will be MED. It’s even thought that there might be further strict niche partitioning; with different ecotypes of MED adapted to use different iron sources, or different temperatures.

For the photosynthetic organisms that inhabit it, seawater is more than just a blue shifting salty mass. It’s a whole range of niches and environments, partitioned in three dimensions depending on the surrounding conditions and nutrients.

Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, & Chisholm SW (2003). Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature, 424 (6952), 1042-7 PMID: 12917642

This is The Gibson Assembly song, written by the Cambridge iGEM team 2010. If you can’t see it, want it in a higher resolution or just want the link to share, find it here.

The technique they are describing is the “Gibson Assembly” which is a fairly quick and painless way of joining two bits of DNA. In more sciency terms, it works by using PCR to make genes with large overlaps (40bp) at the end. You add a Master Mix to the fragments, incubate for one hour, then just transform into whatever cell you’re using. For more details of how it works go here, for the recipe of the Master Mix and detailed protocol go here, and for a program to help you design Gibson Primers, go here.

The video was just made for fun, and took less than a week to put together (not counting the time to write the words!). Filming was done mostly over one day, using one camera and a slightly broken tripod, just using spaces in the lab and the gel room. The green-screen sections were done by throwing a green table cloth over some poster display boards. The music was recorded seperately, and I think each instrument was recorded seperately as well, to get the sound balance right. It was all carried out by about nine undergraduates (and one lab rat!) and massively confused most of the supervisors.

It was fun

1) Alkali Metals

The periodic table, with the alkali metals circled in red.

The alkali metals have very few electrons (either one or two) in their outermost shell. As discussed in the post on ionic bonds, one way for them to achieve a full outer shell is to form an ion – loose that outer shell electron to form a positive ion and then bond with a negative ion in a giant lattice. Another way is for all the atoms of one element (i.e all Na atoms or Mg atoms) to form a lattice just composed of atoms, with the outer electons floating around freely in the spaces between. This is the essence of metallic bonding, which is sometimes described as a lattice of positive ions in a sea of electrons (even though they are not strictly speaking actual ‘ions’ – metallic elements will be written as Na metal rather than Na+ ions)

A stylised diagram of metallic bonding, from wikimedia commons, credit link below.

For the alkali metals, there are only one or two electrons from each atom actually participating in this delocalised sea of electrons, which explains why these metals are so soft and can be cut with a knife. It also explains their generally volatile nature, they simply aren’t held together very well, and metals like potassium and caesium will catch fire if you get them wet.

2) Transition metals

Transition metals are the block described as "a little complicated" - circled here in red.

The general idea of metallic bonding is the same for the transition metals as it is for any other metals – a delocalised sea of electrons surrounding a lattice of positive ions. However in order to explain the properties of the transition metals I have to go back a bit and explain why they are complicated and this involves orbitals and a certain amount of quantum. I introduced in the ionic bond post the idea that each shell of electrons has eight electrons in it, and while this is true(ish) for the first three shells, it gets a bit complicated in the fourth.

Without getting too involved for now (I might write a post on orbital shapes later …), the transition metals have a lot more than eight electrons in their outer shell – between the third and the fourth shell extra electron orbitals are introduced. Not only does this allow more electrons to be present, but these orbitals are all at very similar distances from the nucleus and therefore can all participate in bonding. It’s probably easiest just to think of transition metals as surrounded by a blur of many easy-going electrons, as well as some empty orbitals that are happy to accept a few extra electrons.

This means that rather than having one free electron for each atom in the lattice, some transition metals will have around five or six. This is why copper (for example) is so much stronger than magnesium. The metallic bond also explains why metals can conduct electricity; free-flowing electrons are what electricity is. The lattice is rigid, but once melted a little it can be bent and stretched and shaped in a way that ionic compounds like salt cannot, which is why copper can be stretched into wires and aluminium can be bent into cars. It’s a property that we take for granted, but it only happens in metals.

Although metalic bonds are fascinating, they aren’t all that biochemically important. Metals are trace elements in organic lifeforms, but they tend to be bonded to other things, or in ion form rather than as the solid metal. Which is why next month I’ll be covering covalent bonding – the forces which hold together all organic life on earth.

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Credit link for metallic bond image.

The mainstream fronts of synthetic biology

“What I cannot build, I cannot understand”.

This phrase by the genius physicist Richard Feynman is cleverly encrypted into the genetic code of the first bacterial cells with an artificial genome that have ever existed.

Actually the quote says “what I cannot create…”, but maybe the scientists at the JCVI –who are behind this tremendous breakthrough- preferred to save some base pairs to avoid the use of the word “create” and its tricky implications. They published this work in 2010 and opened a whole new world of possibilities and made it completely clear to anyone what we mean when we talk about Synthetic Biology and what its ultimate purpose should be: to understand life by building it.

Although the term “Synthetic Biology” has been around since the mid-1970s, the definition of it has been very vague: some people would call Synthetic Biology anything related to general genetic engineering procedures; others, perhaps more rightfully, would claim to be doing Synthetic Biology because of working with DNA synthesis or making bacteria behave like tiny computers. Even the 2010 report by the US Presidencial Comission for the Study of Bioethical Issues has to define the term considering different points of view (that of the molecular biology, the chemist and the engineer) and states that the activities related to Synthetic Biology are considered by some to be just extensions of already existing fields, like Molecular Biology, Genetic Engineering and Microbiology.

I remember (oh, the shame!) being skeptic about the possibility of something so oxymoronic being, well… true. I still turn red when I recall that I kind of corrected the person who first said “Synthetic Biology” to me by telling her that what she wanted to say was maybe Systems Biology.

So what is it really?

Well, my work in Bio! has been devoted to dig into the deeps of Synthetic Biology and the iGEM competition, and throughout this time I began to notice what I would call “the mainstream fronts of Synthetic Biology”. These are the main orientations that so called Synthetic Biology projects would take and by enlisting them, I think it will be easier to clarify the distinctive characteristics of this field.

Front 1: DNA synthesis

The development of DNA synthesis techniques allows us now to synthesize DNA sequences larger than just PCR oligos; genes and genomes are being fully synthesized; difficult constructions are eased by just synthesizing the needed sequences, without needing sub-clonations to gain a useful restriction site. One of the most awesome accomplishment is the generation of the first replicating cells with a fully synthetic genome, which by the way was dubbed “Synthia”. Moreover, one of the most amazing applications of synthesized DNA has little to do with living cells: they are used as mechanical pieces, because after all DNA is a physical entity and can be used as such, giving place for the field of DNA Nanostructures.

A particular technique called “DNA origami” has been really fruitful (ref1) Since the publication of its invention in 2006, DNA origami custom structures have been employed as mechanical and computational devices; there is software available for generating the DNA sequence needed to construct a wanted shape. More recently, DNA origami structures have been employed as intelligent devices that recognize and deliver drugs to cancerous cells.

Front 2: The standardization school and the iGEM competition

The iGEM logo

One of the characteristics of gene cloning is the messy and sui generis protocols that vary from lab to lab and from construction to construction. What would happen if these procedures were standardized, so that any construction needed could be accomplished by anyone with the same steps and same restriction enzymes?

A group at MIT has been dedicated for the last years to standardization in the biological field. The main drive is to accelerate the development of Biology by mimicking the development ofthe engineering fields, i.e. to have a consensus analogous to what mechanical engineers have with the size of materials and tools. Moreover, if we are using standard parts, the quantitative characterization of them would be also facilitated, making mathematical models and simulations useful as predictive tools.

Accordingly, there is the Registry for Standard Biological Parts, which is basically a collection of DNA sequences that share a particular set of rules that ease their combination with each other. Each of these sequences is a biological part and among the existing parts are promoters, ribosomal binding sites, coding genes and also composite parts made of the combination of single parts; the parts are also referred as “BioBricks” and the organism in which they are meant to work is termed the “chassis”.

The fundamental characteristic of BioBricks is the set of rules that ease their combination; these rules allow the concatenation of DNA sequences by iteratively using the same restriction enzymes in the same order. The basics of this technique are the design of idempotent vectors and were first presented by the Knight group at MIT.

The huge potential of the use of BioBricks is reflected by the number of awesome and creative projects that have been presented at the International Engineered Machine competetion (iGEM), which began at the MIT too. In this competition, undergraduate students are challenged to make the most innovative biological machine by using BioBricks. Among the projects that have been presented since the first iGEM edition are biosensors, bioremediators, light-controlled cells, metabolically engineered cells, synthetic genetic circuits and many others, along with their corresponding mathematical models. Students are also encouraged to make a contribution for the humanities side of the project.

Front 3: Genetic code expansion

There are many amino acids that would give proteins many useful characteristics, but in nature, only twenty amino acids are commonly encoded by the 64 codons found in living beings, plus some organisms that also encode some rare amino acids like pyrrolysine and selenocysteine.

What can be done to exploit all the chemical potential found in the so called unnatural amino acids? One approach would be to chemically incorporate the unnatural amino acids into already existing proteins, but this method is highly unspecific and may have a low efficiency; the ideal way would be to incorporate those unnatural amino acids at the very moment when the wanted protein is translated from its mRNA.

This is actually possible by using orthogonal translation systems and expanded genetic codes. The common 64-codon/20-amino acids genetic code has been expanded to 64-codon/21-amino acids and even 65-codon/21-amino acids, with one codon adapted for an unnatural amino acid. (refs 2 and 3)

The system behind the incorporation of this unnatural amino acid is the presence of a tRNA and an aminoacyl tRNA-transferase (AARS) enzyme from a phylogenetically distant organism; both the tRNA and the AARS have been modified to recognize the unnatural amino acid by directed evolution. Because of the phylogenetic distance with the host machinery, the AARS would charge the unnatural amino acid into the tRNA without interfering with the native tRNAs and AARS from the host, i.e. they would be an orthogonal translation system.

The remaining piece is the codon that would code for the unnatural amino acid. In Escherichia coli, the amber codon (UAG) is the least frequent codon found in its genes, so it has been commonly employed to be recognized by the orthogonal tRNA without having a gross effect on the growth rate of the bacteria. Nevertheless, custom codons have also been generated; most interestingly, four-nucleotide codons have proven to be functional.

Unnatural amino acids in proteins have been used as sites for chemical synthesis (the presence of some chemical groups in the unnatural amino acid increases the efficiency and specificity for some procedures, like click chemistry), so that many different active compounds can be conjugated. In this way, proteins conjugated with fluorescent probes, FRET pairs and poly ethylene glycol have been generated. Also, by incorporating phosphorylated residues, it has been possible to hack the normal signal transduction systems in cells. Finally, recently, genetic code expansion has been used to make “oligobodies”, a mix of DNA oligos and antibodies.

Front 4: Synthetic genetic circuits

If the intricate regulation of gene expression can be broken down to a number of basic processes, then by understanding these basic processes, we should be able to eventually understand what happens when they are combined and how they can make a full gene regulation mechanism.

The generation of synthetic circuits like switches and oscillators in prokaryotic and eukaryotic cells has been an exciting matter of study that has brought together mathematicians, computer scientists, molecular biologists and engineers. Switch-like genetic circuit behavior has been attained by using riboswitches, engineered promoter sites and transcription factors that respond to a particular stimulus, like light or some chemical compounds.

The conception and mathematical study of synthetic oscillating genetic circuits have been active since the early 1960s, but it has not been until recently that in vivo experiments have validated those idealizations. A considerable amount of effort has been dedicated to the mathematical characterization, simulation and in vivo implementation of oscillating genetic circuit topologies.

Synthetic genetic circuits have been employed to elucidate natural circuits by rewiring them or inducing “short circuits” into signaling cascades; properly functioning basic synthetic genetic circuits are the key for composite synthetic systems, like logic gates and synthetic signalling cascades.

Front 5: Metabolic Engineering

The realization that for Metabolic Engineering it was not enough to just mix existing genes to rewire biosynthetic pathways is perhaps the main reason why some Metabolic Engineering studies are considered to be also part of Synthetic Biology. The holistic understanding of metabolic flux, promoter activity, preferential codons and scaffold proteins are the basics for Synthetic Metabolic Engineering.

One of the seminal studies was that from the Keasling group, who rewired E. coli with asynthetic metabolic pathway that leads to the production of a precursor of an anti-malarial drug, artemisinin. The field has developed to include also biofuel biosynthetic pathways. (ref 5 and 6)

Another approach for Synthetic Metabolic Engineering, also developed by the Keasling group, is the use of synthetic protein scaffolds. These synthetic scaffolds are made by natural protein binding domains from phylogenetically distant organisms; a synthetic scaffold contains a number of different binding domains. When a set of enzymes from a particular metabolic pathway is genetically conjugated with a ligand domain – each enzyme with a different ligand domain- they will attach to the synthetic scaffold in an ordered pattern. The synthetic scaffold acts then as a spatial anchor for the metabolic pathway that can greatly alter the metabolic flux towards a desired product.

One interesting derivation of the scaffold concept was developed by team Slovenia in the iGEM 2009. Instead of using proteins as scaffolds, the team used a DNA molecule to recruit the enzymes of the metabolic pathway; this was possible by genetically conjugating the enzymes to a DNA binding domain from a phylogenetically distant transcription factors. Thus, the DNA-binding enzymes would attach to their recognition sites in a synthetic DNA construct and enhance metabolic flux through a biosynthetic pathway.

Closing remarks

With the enumeration of the main Synthetic Biology fronts:
1) DNA synthesis
2) biological parts standardization
3) genetic code expansion
4) synthetic genetic circuits
5) metabolic engineering,
it can be seen that something that all the projects share is the drive to gain an increasingly precise control over cellular processes, considering ground elements –i.e., custom DNA sequences, custom proteins produced by genetic code expansion, standard biological parts and basic synthetic circuits- but also higher-order elements –composite synthetic circuits and engineered metabolic pathways.

The degree and the tools with which Synthetic Biology intends and is actually beginning to control cellular processes are what distinguish it from any other field of the biological sciences.

Synthetic Biology is a fast growing and productive field. There is indeed a lot to do, particularly regarding to the precise quantitative characterization of biological parts and circuits; but since the field is attracting many smart and active young minds from different disciplines, the growth and innovation rate will likely increase in the years to come.

MALS/Göttingen
Mar 18, 2012.

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References:
1) Douglas, S., Marblestone, A., Teerapittayanon, S., Vazquez, A., Church, G., & Shih, W. (2009). Rapid prototyping of 3D DNA-origami shapes with caDNAno Nucleic Acids Research, 37 (15), 5001-5006 DOI: 10.1093/nar/gkp436
2) Young, T., & Schultz, P. (2010). Beyond the Canonical 20 Amino Acids: Expanding the Genetic Lexicon Journal of Biological Chemistry, 285 (15), 11039-11044 DOI: 10.1074/jbc.R109.091306
3) Kazane, S., Sok, D., Cho, E., Uson, M., Kuhn, P., Schultz, P., & Smider, V. (2012). Site-specific DNA-antibody conjugates for specific and sensitive immuno-PCR Proceedings of the National Academy of Sciences, 109 (10), 3731-3736 DOI: 10.1073/pnas.1120682109
4) Moon TS, Clarke EJ, Groban ES, Tamsir A, Clark RM, Eames M, Kortemme T, & Voigt CA (2011). Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. Journal of molecular biology, 406 (2), 215-27 PMID: 21185306
5) Nielsen, J., & Keasling, J. (2011). Synergies between synthetic biology and metabolic engineering Nature Biotechnology, 29 (8), 693-695 DOI: 10.1038/nbt.1937
6) Jarboe, L., Zhang, X., Wang, X., Moore, J., Shanmugam, K., & Ingram, L. (2010). Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology Journal of Biomedicine and Biotechnology, 2010, 1-19 DOI: 10.1155/2010/761042

Bacteriophages are viruses that infect bacteria. They come in two different flavours; latent phages, which incorporate themselves into the bacterial genome and lie in wait, and lytic phages which infect bacteria, take over the cell, fill it with their offspring and then all burst out of it like the baby alien in Alien. While latent phages are fascinating for geneticists (not least because they provide a way of getting DNA into a bacteria) lytic phages are even more fascinating for people trying to kill bacteria, as they provide a way of destroying the cells.

Bacteriophage! Image credit below.

The advantage of bacteriophage as an antibacterial treatment is that they are more specific and accurate than antibiotics; antibiotics will simply kill most bacteria they come across whereas bacteriophage are specific for certain species. And unlike an antibiotic, which has to flood your system to have any effect, bacteriophage will replicate specifically within the invading bacteria at the point of infection.

On the other hand, just like any other antibacterial, the bacteria will eventually develop resistance towards the phages. If you attack a bacterial infection with one phage strain specific to that bacteria than very soon the bacteria will be able to withstand attack. One way to counter this is to blast the bacteria with many different types of phage that work in slightly different ways. Researchers working on the bacteria Klebsiella pneumoniae came up with a streamlined method for creating a ‘bacteriophage cocktail’ for a specified bacterial invasion. The cocktail contains different strains of phage, all of which can attack the bacteria in different ways, making it harder for the bacteria to develop resistance against any one of them.

Stylised diagram of a bacteriophage; showing head, sheath and tail sections. Attrib. GrahamColm at en.wikipedia, link below.

Although the diagram above shows a ‘standard’ bacteriophage, there are small differences between strains that can be seen under an electron microscope. Some have different shaped heads, or differently ordered tails. Some of the tails are straighter, or longer, than others. Using the different phage morphologies, the researchers isolated three different strains, and then confirmed the difference by looking at which strains of bacteria they all infected. Although there was substantial overlap between the bacteria they could kill, there were differences between each phage strain.

This three-phage cocktail was shown to be more effective than a monophage therapy in clearing the bacterial infection, and it also worked effectively at much smaller doses. The three-phage mix killed the bacteria much quicker, allowing less time for resistance to develop, and the researchers put forward that they might even have a synergistic effect – one phage lowering bacterial defences and allowing another to more effectively invade.

The development of phage cocktails, either to be taken instead of antibiotics, or to be taken with a lower dose of antibiotics, has the potential to be an incredibly useful area of research. At the moment the few phage cocktails that are used in come countries seem to be a rather haphazard mix of phage strains. A technique for quickly establishing strains for an effective antibacterial-cocktail would be a great help for phage technology and antibacterial treatments.

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Credit link for image 1.

Credit link for image 2.

Ref: Gu J, Liu X, Li Y, Han W, Lei L, Yang Y, Zhao H, Gao Y, Song J, Lu R, Sun C, & Feng X (2012). A method for generation phage cocktail with great therapeutic potential. PloS one, 7 (3) PMID: 22396736

The video above is a 3D model of a tomogram of a single cell of the freshwater protozoan Tetrahymena thermophila that the students produced. The strange otherworldly blobs and crevices are internal cellular membranes, while the red rods are cytoskeletal fibres. The whole video builds up the internal world of the cell as an undeniably busy place, full of membranes and vacuoles and separate compartments.

To produce this video, the students took thin slices from the cell and photographed them using the electron microscope. A computer program was then used to put these slices together into a full 3D image of the cell. A colour model was then rendered, with the original grey micrograph in the background for reference (you can see it in the video above). The video was then able to travel through this 3D landscape, capturing it from different angles.

Side by side - the electron micrograph and the finished model taken by the students (picture used with permission)

Although at first glance, the two images above look very different, a closer look reveals clear similarities. The membrane around the edge of the picture on the left, and running down the middle, has been rendered in green. The dark curved blob on the right hand side is in purple on the right hand side of the model, and all other little purple blobs can be matched to their corresponding marks. However the coloured 3D version has a great advantage over the static thin black and white images – it can be explored in all dimensions and it is much easier to see the connections between membranes.

This image wasn’t just produced as an exercise either, the students were actively exploring the mating of  Tetrahymena thermophila. As well as confirming earlier studies that showed pores forming between two mating cells, they also discovered that each pore was filling with a system of branching membranes. The pores expand during the mating process to allow DNA to pass between cells, which means that these membranes could be helping to guide the DNA, or protect it as it moves between the two mating organisms. EDIT: it has since been pointed out to me that as these are protozoa rather than bacteria it isn’t just ‘DNA’ that is passing through these pores, but the entire nucleus!

It’s a brilliant project for young students to get involved in, and they all had a great time taking part. There really is no better way to find out about scientific research than by actually getting out and doing some!

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Thanks to St. Olaf college for permission to reproduce the video and images. Their press release can be found here.

The original logo for the MolBio carnival! Put together by Alejandro Montenegro-Montero.

So first of all, what is the carnival? It’s a roving collection of regular monthly links, collated using the blog-carnival website. People can submit posts, and they all get sent to the host, who organises them prettily on their own blog. It was first set up in June 2010 as an idea by Alejandro, Lucas Brouwers, Alexander Knoll, Psi Wavefunction and me.  Since then its had an issue every month, either hosted by one of us or other biological bloggers who express an interest.

Are blog-carnivals important? They are certainly a fair amount of work to maintain and sometimes feel a bit like  a giant echo chamber. But from a readers point of view they can introduce people to some fascinating new blogging, and from a bloggers point of view they help to share the readers around. More importantly, they create a sense of community among the bloggers themselves. I might not always have time to catch up with what my bloggy-friends are doing, but once a month I get links to their work all gathered together in one place. Running the carnival has helped me make new bloggy-friends, and find more blogs that cover science I want to read about.

A screenshot of the first edition of the MolBio carnival

So without further ado, in the spirit of linking and sharing great MolBio writing, here are the awesome regular writers, who I’ve met and become friends with through the carnival. Take a look at their blogs, and enjoy the writing, and we’ll be back next month with an actual carnival! If you want to participate, submit any molbio blog posts here (or send me an email).

Lucas Brouwers: One of the first blogs I approached to write comments on was Lucas’s old Thoughtomics blog. To my surprise and delight he came straight over to my blog and commented back. Lucas writes the kind of amazing science posts I can only dream about, covering a range of biological topics that usually have a strong evolutionary focus.

Psi Wavefunction: Psi is the person to go to for all things protist, and I am constantly fascinated by the offhand way in which she can discuss insanely complex protist relationships. Not to mention the amount of memory it must take to remember the names of all of them! A good blog to go to for all things microbiological.

Alejandro Montenegro-Montero: The original mastermind of the MolBio carnival, Alejandro now blogs at the MolBio hut. He covers research, science news, science policy and the science blogosphere. He’s been writing a lot lately about the open-access issue, with quotes and points from a number of sources.

James Byrne: James blogs about all things medical, which means that when he does blog about bacteria, it’s inevitably from the point of view of something horrible that they’ve done to people. It’s not all bacteria though, James writes about all kinds of weird and wonderful diseases.

Connor Bamford: Connor is a more recent bloggy-friend; but someone whose blog I’ll be reading for a long time to come. Connor covers viruses, and writes mostly about primary research in a way which is really accessible to read. I read Connor to catch up on the viral news that I miss with my bacterial blog.

E.E Giorgi: A true molbio blogger, EE writes about viral DNA, and other genetics issues. Also does some really great photography on G+ which is well worth following.

Captain Skellet: The Captain! Skellet’s blog covers a whole range of science topics over at Schooner of Science, and was a very early blog-friend. She also regularly covers Australian science conferences and science news.

[One weird thing I noticed when writing this list; all the male bloggers use their full names. All the female ones have pseuds or use their initials. Funny that...]

So, if you’d like to submit, or host the MolBio carnival in its coming months, just follow the link, leave a  comment, or get in touch!

I have no idea what crossing these two dogs would produce. Possibly some kind of war pompom. Image credit below.

When it comes to the world of microorganisms, however, species becomes even more of a murky concept. For bacteria and archaea even the concept of interbreeding doesn’t really exist. Bacteria don’t require all that squishy ‘sex’ stuff to produce more bacteria, they just divide themselves in half and filch random DNA from their mates, nearby bacteria and the general environment. However at the same time it’s still useful to be able to disinguish bacterial species; for example to recognise that S. aureus is a very different creature from an E. coli. All bacteria are not the same; but if they can share genes so easily, why are there such clearly different species? Why are there any differences between them at all?

Work done on archaea, the sadly ignored cousins of bacteria, is starting to give more of an idea about how a ‘species’ in microorganisms form. Studies done on the thermoacidophilic (high-temperature and low-pH loving) archaeon Sulfolobus islandicus gathered from a hot spring in Russia shows some mechanisms that, in these strains at least, leads to separate archaea species forming rather than one homologous population.

A group of archaea. These ones are halobacteria - salt lovers - rather than the thermoacidophiles in the study. Credit for the image is below.

The paper highlights two main theories as to how species form in microorganisms. ‘Species’ in this instance is defined as lineages with discrete clusters of sequence diversity. Theory one is the ‘niche’ theory, the idea that selection is ecological, and “ecotypes” (i.e almost-species) are kept because they’re specialising themselves to fit into a certain niche. If you’re trying to be the best at living in a hot pond, genes to help you cope with ice-crystals aren’t going to be much use.

The second theory is that there are genetic barriers that cause some clusters of micro-organisms to become genetically distinct and species-like. If the mutations within your own genetic material are more likely to be passed on than genes picked up from nearby organisms then it genetic clusters of species will form. This is all to do with the rates of mutation and recombination, and is explained much better (with many more paragraphs) in the reference below for those who are interested. It can also involve things like restriction enzymes, which chop up DNA. If one archaea line contains enzymes that break down the DNA of another line they aren’t going to be successfully sharing DNA any time soon.

It could also be a bit of a mix between they two. If tiny amounts of DNA are being shared, while large changes are made to the chromosome due to niche-specialisation, then the species fits under theory one. If more DNA is being shared with fellow micro-organisms, and each one is not mutating much, then theory two is clearly more relevant. For different species, in different conditions, speciation may occur using different methods.

For the Sulfolobus islandicus however, there’s now a lot more information on how species and clusters form. The researchers looked at two separate lineages within the hot springs, and found that although the archaea were capable of sharing DNA, they were none-the-less starting to become ecologically distinct and evolutionarily independent. Just to be clear, there was no physical barrier stopping them. They were all just swimming around in close proximity in the same warm springs. There weren’t even biochemical barriers stopping them, the DNA was capable of surviving in both strains without being chewed up by enzymes or otherwise harmed.

An unrelated picture of a Sulfolobus archaea. If you look closely, you can see little white viruses stuck to the surface. Which has nothing to do with this article but is still really cool! Credit below.

So are these two separate strains ‘species’? Not really, they still share DNA, but they seem to be on their way to becoming distinct species. Archaea, like bacteria, will always be capable of sharing DNA with each other. What is fascinating here is that sometimes, it appears, they just don’t want to. It may be that species in micro-organisms form less because of barriers that physically prevent gene flow, and more because the organisms themselves simply don’t want to share DNA anymore.

After all, if you’ve spent the last few hundred years specifically evolving to fit one precise little niche, how much help is DNA from someone who hasn’t?

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Ref 1:Cadillo-Quiroz H, Didelot X, Held NL, Herrera A, Darling A, Reno ML, Krause DJ, & Whitaker RJ (2012). Patterns of gene flow define species of thermophilic archaea. PLoS biology, 10 (2) PMID: 22363207

Credit for image 1.

Credit for image 2.

Credit for image 3.

The immune system protects your body from any invading elements, and because of this it needs a way to distinguish body cells from invading cells. The cells of the immune system do this by recognising bits of bacteria as foreign invaders, and of course the first bit of the bacteria they see is the outer cell membrane. H. pylori has a way of making parts of its outer cell membrane look very similar to human blood group antigens, so the immune cell doesn’t recognise it as an invader.

This image seemed necessary...

The bacterial cell membrane is made up of lipopolysaccharides (i.e lipids, or fats, connected to polysaccharides - sugars). H. pylori has ways to modify the biosynthesis pathway of these lipopolysaccharides to produce different structures. In particular to lipid A, which is part of the structure on the surface of H. pylori.

The bacteria have several different ways that they modify the lipid A. Firstly, they can reduce the lipids overall negative charge, either by adding positively charged substrates, or by removing negatively charged phosphate groups. This makes the bacteria more resilient to certain antimicrobial peptides that bind to negative charges. They can also add extra bits to the lipid A (in particular acyl groups) which make the surface of the  bacteria harder to for immune cells to recognise. This lipid A modification pathway is highly ordered and efficient. Rather than producing all different kinds of lipid A at the surface, each bacterium will be covered in one type of modified lipid  A.

Lipid A from E. coli, with the phosphate groups circled in red. Image credit below.

The reason that H. pylori has this one specific modification pathway is likely  to be due to the fact that it only has one host. H. pylori lives in humans and nowhere else. There is only one type of immune system it has to evade. Once the lipid A resembles human blood antigens, any changes or alterations would be strongly selected against in order to keep the bacteria well hidden.

For a more in-depth biochemical analysis of exactly how these modifications happen, take a look at the paper below!

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Credit for image 2

Ref 1: Cullen TW, Giles DK, Wolf LN, Ecobichon C, Boneca IG, & Trent MS (2011). Helicobacter pylori versus the host: remodeling of the bacterial outer membrane is required for survival in the gastric mucosa. PLoS pathogens, 7 (12) PMID: 22216004

The previous posts covered van der Waals forces and hydrogen bonds (and dipoles!) These forces are both fun, and incredibly important in determining the properties of water (without which there would be no life) and petrol (without which there would be no cars) but they aren’t particularly strong forces. Both van der Waals and hydrogen bonds are relatively weak, and I think it’s about time I started covering the three Big Bads of molecular forces: ionic bonds, covalent bonds and metallic bonds.

Starting with ionic bonds. In order to properly cover these, I need just a little bit of background on what atoms are actually like. Now there are many different models for what atoms are ‘like’ but for the purposes of ionic bonds the easiest way to think of them is as a small nucleus with a positive charge surrounded by small whizzing negatively charged electrons. Electrons don’t just all fly around with no direction, they exist in orbitals, each a different distance from the nucleus. To find out how many electrons are in the outermost orbital, furthest away from the nucleus, you can look at the periodic table.

The periodic table. The number of electrons in the outer shell can be found by looking at which column the element is in. This does get a bit complicated for some of the larger elements, but for the first few rows it works fine.

The outermost orbital is the most important because all the other electrons are a) in orbitals with the maximum number of electrons and b) unable to take much part in reactions due to the outermost electrons being in the way. Atoms in general are at their most stable when they have a full outer shell of electrons. As many atoms don’t have a full outer shell of electrons, they try to find ways of getting one.

Take sodium, for example, with the chemical symbol Na (blame the Greeks for that!) Now sodium is in the first column of the periodic table, so it has one electron in the outermost shell. All the other shells are full of electrons. So the quickest way to get a full outer shell is to loose that outermost electron, leaving you with a full shell underneath. Loosing one electron, however, requires energy, which means that unless this can be combined with a process which produces energy, it is not going to happen.

Loosing one electron also means that rather than having an equal number of positive nuclear charges and negative electron charges. the sodium now has one fewer negative charges. Instead of a neutral sodium atom, it is now a positively charged sodium ion.

So how does the sodium get the energy back? One way of producing a lot of energy in the world of molecular forces is to form a bond. Breaking bonds requires energy, but making them produces energy (ask a physicist about this if you’re unsure why, the explanation might not make you any more sure but it’s nice for physicists to have someone to talk to). Luckily, a positively charged ion is very good at forming bonds with a negatively charged ion.

To see how a negative ion forms, take a look at the other side of the periodic table at the element chlorine. Chlorine has seven electrons in its outer shell (a full shell is eight electrons for the smaller elements). In order to fill its outer shell it can take an electron gaining one extra negative charge and forming the negative chloride ion. It doesn’t just take that electron from anywhere, it will actually tear it away from the sodium atom. Leaving one negative and one positive ion; Na+ and Cl-

A simplified diagram of the electron transfer, with outer shell electrons shown. Image in the public domain, credit below

The bond formed between these ions is called an ionic bond.

The two ions don’t just form a single bond between them, ideally they want to make as many bonds as possible. Ionic bonds create giant ionic lattices of interchanging ions. These are incredibly strong, making ionic compounds very hard to break, melt, or crush.

Not only do ionic forces help to hold elements together, the formation of these bonds can completely change the properties of the elements they bind. Sodium is a soft grey metal (you can cut it with a knife!). Chlorine is a deadly green gas. The giant ionic lattice sodium chloride is salt, a white grainy edible food.

Sodium metal and chlorine gas in elemental form, and magnified crystals of sodium chloride. Credit for all images below.

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Credit for image 2

Credit for images of chlorine, sodium and magnified salt crystals used in image 3

So I do like to write about plants every now and again, and it isn’t a very difficult task because like every other multicellular organism on the planet, plants also suffer from bacterial infections. Unlike humans, they don’t have a blood stream to carry immune cells around, so they instead rely on bombarding bacteria with nasty chemicals, quickly killing off any parts of the plant that get infected and acquiring a kind of plant resistance to stop attacks occurring again. (The three links are to a mini-series on plant immunology on my old blog.)

However in plants, as in humans, prevention is much better than cure and so the plant has all sorts of mechanisms to stop bacteria getting inside and causing infections in the first place. Plants have openings in their leaves called stomata which are used to control water levels inside the plant cells. The stomata open up to release moisture and close to retain it. They aren’t massive holes, but they can be seen with a light microscope and identified fairly easily by your average 16 year old (I remember looking at them during my AS levels!)

A stoma! The two curved things surrounding it are the two cells that control the opening. The small oval-shaped middle bit is the stoma - a hole in the cells covering the leaf. Image credit below.

As stomata are basically a hole from the inside of the plant to the great bacteria-ridden outdoors, it is important that they remain well-regulated. Plants can recognise bits of bacteria and when they do they can change internal conditions to close up the stomata, bolting the doors to prevent bacteria getting in. By sensing parts of bacteria such as (say) flagella, proteins are activated that change the concentrations of salts inside the cells surrounding the stomata, and cause them loose their curved shape and come together, effectively closing off the opening.

When plants were infected with the bacterial strain of Pseudomonas syringae the stomata closed up within 1-2 hours of infection, which for a plant is fairly rapid. However around 3-4 hours later the stomata started opening up again, and it wasn’t due to a bacterial protein, but a plant one. The protein in question was LecRK-V.5 and plants without the gene for this protein developed fewer disease symptoms and contained lower levels of internal bacteria than the non-mutated wild-types. The figure below shows the wild-type leaves at the top, with more disease symptoms than the healthier mutants below.

Figure from ref. 1

As stomatal opening is only one factor in the antibacterial plant response, the researchers then explored whether LecRK-V.5 was affecting any other responses. The main one being the production of dangerous Reactive Oxygen Species (ROS) which are often produced to damage invading bacteria. Both wild-type and LecRK-knockout-mutant plants showed no difference in levels of ROS, LecRK-V.5 only seems to affect the stomata.

The point about ROS also gives a clue as to just why the plant chooses to activate this protein following infection, seemingly making it easier for bacteria to gain access to the interior. In the mutant plant cells, with no LecRK-V.5, high levels of ROS started building up in the cells surrounding the stomata. ROS are dangerous to any cell they come into contact with, so by dampening down the response to bacterial infection around 4 hours following entry, the plant might be saving itself from being damaged by its own immune response. If the infection is still spreading after four hours, it may be more prudent for the plant to abandon the dead tissue and try and salvage what’s left. Leaves are not desperately important to plants after all, they can always grow more!

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Ref 1:Desclos-Theveniau, M., Arnaud, D., Huang, T., Lin, G., Chen, W., Lin, Y., & Zimmerli, L. (2012). The Arabidopsis Lectin Receptor Kinase LecRK-V.5 Represses Stomatal Immunity Induced by Pseudomonas syringae pv. tomato DC3000 PLoS Pathogens, 8 (2) DOI: 10.1371/journal.ppat.1002513

Ref 2: Nicaise, V., Roux, M., & Zipfel, C. (2009). Recent Advances in PAMP-Triggered Immunity against Bacteria: Pattern Recognition Receptors Watch over and Raise the Alarm PLANT PHYSIOLOGY, 150 (4), 1638-1647 DOI: 10.1104/pp.109.139709

Credit for image 1.

The bacteria that cause Tuberculosis are nasty little beasts. The white blood cells that clear infection in your body work by ingesting bacteria and then breaking them up, and the TB escapes this by letting itself get ingested and then sitting inside your white blood cells. They don’t sit passively, however, they burst out of the cell and recruit a whole host of other blood cells which surround the infection and form what’s called a granuloma. The bacteria stay inside the granuloma and become dormant, but if they escape they can set up other sites of infection throughout the body.

A granuloma caused by Mycobacterium avium (related to TB). In the pale circular granuloma, you can see lots of white blood cells. The white-blood cells have lots of nuclei inside them (many dark purple dots surrounded by a purple membrane)

The white blood cells that first ingest the TB bacteria are macrophages, which kill invading particles (be they cells or bits of cells, or even dead parts of your own cells) by ingesting them into a vacuole and then breaking them down. The TB gets ingested fine, but once inside the cell, it stops the cell from breaking it down. That means that you now have a white blood cells infected with a TB bacterium.

In order to create the granuloma, the TB bacterium needs to bring other white blood cells to the scene. The best way to do this is to rupture the cell that it’s currently in, because bits of broken up cell are a great way to get the immune system rushing over. A recent paper in PloS (reference below) shows that in order to do this, the TB must break out of the vacuole holding it following ingestion, and then kill the host cell once it’s in the cytoplasm:

A VERY SIMPLISTIC diagram of the bacterium (purple) being ingested by the white blood cell (blue) and then breaking out of the vacuole.

This model is not a fully accepted one within the TB community, and there’s still some conflict as to whether the bacterium actually breaks out of the vacuole it gets ingested into (as shown above) or whether it stays within the vacuole and wrecks havoc from there. The paper explores this using a technique called FRET. FRET works by using two fluorescent probes which, when they get close to each other, light up. If the two probes are far apart, no fluorescence is seen, but if they’re in close proximity they light up like a fairy light and can be detected.

One half of the probe was attached to a protein found in the white blood cell cytoplasm, while the other was attached to a sugar found on the bacterial cell surface. What they found was not only does the bacterial sugar end up very close to the cytoplasmic protein, it does it relatively quickly. Within 24 h to 48 h after infection fluorescence could be detected in almost all the infected blood cells. A bit of tinkering around with knocking out bacterial protein activity also discovered a set of proteins that were vital for this process to occur: ESX-1.

ESX-1 gene codes for a secretion system, not surprising seeing as there job seems to be to get the bacteria out of the vacuole! Bacteria without the ESX-1 system stayed inside the vacuole for ten days and no FRET fluorescence was seen. Not only that, but it was only the cells with functional ESX-1 systems that were causing cell death. When the bacteria stayed in the vacuole (which is technically called a phagolysosome) the white blood cells remained alive, whereas once they managed to get out, the cells started dying. This seems to indicate that bacteria need to be in the cell cytoplasm before they can start killing off your cells and forming a granuloma.

The reference is open access so for more information, and for some great pictures of the FRET results, go take a look!

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Ref: Simeone R, Bobard A, Lippmann J, Bitter W, Majlessi L, Brosch R, & Enninga J (2012). Phagosomal Rupture by Mycobacterium tuberculosis Results in Toxicity and Host Cell Death. PLoS pathogens, 8 (2) PMID: 22319448

Credit for image 1.

Image 2 (c) me. Linkback if you want to borrow it.

There are several advantages to this. For a start, other things like food and nutrients tend to accumulate at surfaces as well, bringing the bacteria a regular supply of food. A surface is a more stable environment, the bacteria that adhere to your teeth do so because to get swept away into the stomach is to be pulled down into a very literal lake of acid. For bacteria that form biofilms, sticking to a surface is the first stage in this process.

Most of the bacteria that live on your teeth are harmless. They become rapidly less harmless if they get into your bloodstream though, so keep brushing your teeth! Image credit below.

So how do the bacteria know when they reach a surface? They can’t see it, after all, and they don’t really have a sense of touch. It’s been proposed that they react to deformation stresses – i.e they notice when parts of their membrane are being squashed on a surface. Enough of these membrane deformations can act to switch the bacterial phenotype, turning it from a free moving bacteria into a bacteria stuck onto a surface.

Work done to study this involved looking at how well bacteria stick to different surfaces, and seeing how much of an adhesion force is produced. Surfaces such as polymer brushes or hydrogels don’t exert enough pressure and the bacteria (in this case E. coli) doesn’t even recognise that it’s near a surface. The strongest adhesion forces are found  with positively charged surfaces. As the outer membrane of bacteria is usually negatively charged, this extra charge attraction helps with adhesion.

Bacteria faced with a polymer brush (left) and a solid surface (right). Bacteria are in brown. Silly picture (c) me.

Once the bacteria has attached to the surface, the adhesion forces increase dramatically to permanently fix the bacteria in place. The first adhesion event is likely to be not with the surface at all, but to a film of water covering the surface. Once attached to that, the bacteria can pull itself closer and start sticking to the actual surface of the object. The paper points out that these changes in force strength are unlikely to be changes in genetic expression, or metabolism, but instead are just the strengthening of the connection at the membrane surface. This will be followed by changes in bacterial metabolism and gene expression to best support this attachment.

The reference for this paper (below) is taken from PLoS Pathogens. As there’s been a bit of a thing lately about journals and scientific publishing, I thought I’d join in by limiting my blogging exclusively to open access journals. From now on anything I blog about, you will be able to read. And if you’ve written (or read!) anything bacterial related in an open access journal feel free to get in touch if you want me to cover it.

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Ref: Busscher HJ, & van der Mei HC (2012). How do bacteria know they are on a surface and regulate their response to an adhering state? PLoS pathogens, 8 (1) PMID: 22291589

Credit link for first image

The article is by Michael Shermer, and you can read it here. It’s about human deception and deception-deception (the process by which we deceive ourselves into believing our deceptions). Called “the lies we tell ourselves” I’ll do a quick summary here:

It starts off the main argument with the quote: “A selfish gene model of evolution dictates that we should maximise our reproductive success through cunning and deceit”. It then points out that due to game theory we are aware that everyone else is also using cunning and deceit, which means the best way to go is to “feign transparency and honesty and lure them into complacency before  you defect and grab the spoils”. He finishes off with the idea that this is where morality comes from: “It is not enough to fake being a good person … you actually have to be a good person by believing it yourself and acting accordingly.”

So that is how human behaviour works. If you’re a cunning, sneaky, nasty person it’s because that’s how your genes tell you to be. If you’re a good, honest and truthful person it’s because you’ve successfully managed to buy your  own con.

Is this way of thinking justified?

No.

Starting at the beginning then with that wonderful “selfish-gene model of evolution”. The “selfish gene” was a metaphor used by Dawkins to explain gene-based evolution. Genes are not literally selfish any more than rocks are. And selfish was just one word, “opportunistic” might have been a better one, because genes don’t work alone. Many of them need other genes, or entire gene clusters in order to function. They need proteins, and the study of protein evolution and epigenetics is an exciting subject in its own right. There’s been some interesting work as well into lipid evolution and how the composition of the cell membrane when cells divide can determine their fate. No gene is an island.

And even if ‘selfish’ is a useful metaphor to explain genetic behavour, why on earth is it a sensible idea to abstract that up to human behaviour? Sure our genes help to determine our behavour, but so do our proteins, our neurons, our cells, our social surroundings and a whole host of other factors. Individual cells in the human body are not selfish, they are in fact highly cooperative and communist. Each cell must obey orders exactly, and if it doesn’t it must commit suicide instantly. There are some cells that break away into an individualist life of freedom but these are cancer cells.

Why must the selfish-gene model predict human behavour, why not the communist-cell one?

In fact, why not go further down? Why not look at the way atoms, or quarks behave, and then say that humans must behave like that!

Two glances around in any human society will tell you that humans are manifestly not selfish individuals all waiting for a change to “defect and grab the spoils”. Human society doesn’t work like that. If you break down society, people don’t just scatter to the selfish winds, they form new little societies to survive within. Look at the internet – a great anarchic gathering of people from all societies, with no rules thrust upon them, and what are the most popular sites (disregarding pornography)? Social networks, social forums and online communities. People like being social, they like being with others. Sure they exhibit selfish behaviour within those societies, but they also show behaviour which is loving, altruistic, angry, excited, and a whole range of emotions that the “selfish-gene” model does not abstract too. There is no reason to arbitrarily decide that any conventionally ”Good” emotion is a deception-deception.

Human societies evolve by human cooperation. By the sharing of knowledge and resources, by the protecting of those more vulnerable, and the slow and shaky development of general morals. These morals are decisions made by the society (or occasionally by the one tyrant in charge of the society, but nothing is perfect) about what behaviours are acceptable. Looking at society this way isn’t it just as justifiable that cooperation and sharing are the “natural” human behaviours? That people who cheat are somehow deceiving themselves into believing that they don’t need society, and have deceived themselves so well that they believe it?

These  aren’t identical to the way our genes behave because people are not genes. Behaviours are emergent properties of humanity, not dictated attributes of our component parts. People are largely made up of water, yet no-one suggests that lying down and sort of sloshing around is natural human behaviour.

If you want to study human morality, you really need to start asking philosophers. That’s what they’re there for. Historians, anthropologists, even literature students and theologians are equipped with the understanding and the tools used to discuss human society, emotions and behaviour. This is an area that scientists can find interesting, and even contribute too, but in studies of behaviour and morality science is simply not the major player.

I’m sure there are great ways to build a secular civil society. But basing your foundations on the unjustified abstraction of a dodgy metaphor is not a good way to go about it.

Microbes and Madness

At first glance, it would be reasonable to assume that my profession and that of the author of this fabulous blog are poles apart. However, everything in nature has a connection, and so it is not surprising to discover a fascinating area where psychiatry and bacteriology overlap.

A broad range of pathogens are known to cause psychiatric sequelae, including worms (neurocysticercosis), protozoa (cerebral malaria, toxoplasmosis), viruses (HIV, herpes simplex encephalitis, rabies), prions (Creutzfeldt-Jakob disease, kuru), and, of course, bacteria (neurosyphilis, Lyme disease, post-streptococcal syndromes). However, in the spirit of this blog, this post will be focusing on bacteria.

There are essentially four mechanisms through which bacteria cause psychiatric symptoms in humans:

I. Bacteria can infect the central nervous system and cause direct damage to brain cells.
II. Bacteria can trigger a powerful systemic inflammatory response that results in a disruption in brain function.
III. Bacteria can trigger an adaptive immune response which produces antibodies that cross-react with host central nervous system proteins.
IV. Bacteria can be the objects of a phobia.

Syphilis and Lyme disease are examples of infections which involve the first mechanism. Syphilis is caused by spirochaetes of the species Treponema pallidum, and is sexually-transmitted. Lyme disease is caused by spirochaetes of the genus Borrelia, and is vector-borne, with ticks from the genus Ixodes being the commonest vector. Both diseases are associated with widespread dissemination of infection of multiple organ systems, and are notorious for their protean manifestations.

The range of possible psychiatric presentations is vast. Syphilis, in particular, can mimic any psychiatric syndrome, and was a common diagnosis in psychiatric inpatients a century ago. The possible range of presentations include delirium, dementia, psychosis, mania, and personality changes. Lesions of the frontal lobes are associated with personality changes and disinhibited behaviour, whereas those of the temporal and parietal lobes are associated with cognitive decline. Lyme disease can also mimic several different psychiatric syndromes, but typically affects the limbic system, causing disorders of emotional regulation, including panic attacks, phobias, depression, and obsessive-compulsive behaviour.

The second mechanism listed refers to sepsis-associated delirium. No human organ system is a closed system, including the central nervous system. Bacterial infections with a focus outside the outside the brain are capable of causing a systemic reaction, which affects the brain. The result is an acute confusional state, or delirium.

Common causes are pneumonias and urinary tract infections, although infections of other organ systems are also frequently implicated. Delirium presents as a transient global disorder of cognition. Typically, there is clouding of awareness, disorientation, impaired attention, fluctuating alertness with agitation or drowsiness, hallucinations, illusion, and vague delusions. The state is thought to be caused by a global disruption of brain function, which may result from the effects of a systemic inflammatory response to infection. These effects may include systemic vasodilation causing cerebral hypoperfusion, increased permeability of capillaries allowing toxins to cross the blood-brain barrier, the action of inflammatory cytokines on the brain, and increased body temperature resulting in an increase in neuronal oxygen demand.

The third mechanism is seen following infections with group A beta-haemolytic Streptococcus pyogenes, such as scarlet fever and tonsillitis. In response to infection, the adaptive immune system produces antibodies against antigens on the invading pathogen. However, some streptococcal antigens are similar in some way to antigens on host tissues, and so the antibodies produced mistakenly recognise and attack the host tissues. Examples of post-streptococcal autoimmune diseases include rheumatic fever, glomerulnephritis, and Sydenham’s chorea.

A psychiatric syndrome caused by this mechanism is PANDAS, which stands for paediatric autoimmune neuropsychiatric disorder associated with streptococcus. This typically presents as a dramatic onset of obsessive-compulsive disorder, tic disorders, or Gilles de la Tourette syndrome following an infection with group A beta-haemolytic Streptococcus pyogenes in childhood. It is thought to be a result of autoimmune damage to the basal ganglia, which is the part of the brain involved with the initiation and regulation of motor commands. Interestingly, it has also been suggested that encephalitis lethargica, a mysterious syndrome which caused an epidemic during World War I, may also be caused by a post-streptococcal autoimmune reaction.

The fourth and final mechanism listed refers to mysophobia, or the pathological fear of germs. Behavioural symptoms include repeated washing of hands, excessive cleanliness, and avoidance of social contact. Anxiety and panic attacks also occur. Although the behavioural manifestations are similar, mysophobia is not to be confused with obsessive-compulsive disorder. The former is a phobic disorder, in which the fear of germs underlies the behaviour, and the function of the behaviour is avoidance of the phobic object. In the latter, the behaviour is compulsively carried out in response to the obsession that the behaviour must be carried out.

I hope to have provided an comprehensive overview of some of the interesting ways microbes can cause mental and behavioural disturbances in humans. The function of this ability is open to speculation. The film 28 Days Later tells the story of an artificial ‘Rage’ virus. When a human is infected, he or she becomes uncontrollably aggressive, attacking other humans and infecting them with viruses in the process. Thus, the viruses’ effect on human behaviour is clearly advantageous to their spread and propagation. However, outside of fiction, the advantages of pathogens’ effects on human behaviour is less obvious. Even with rabies, on which the symptoms of the ‘Rage’ were based, there has been no documented human-to-human transmission through bites. In fact, the only documented cases of human-to-human transmission of rabies were of transplant recipients receiving corneas from infected donors! It is therefore not known what evolutionary advantage, if any, the psychiatric sequelae of infection convey to the pathogens. It is possible that they are epiphenomenal.

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References:

Pfister D, Siegemund M, Dell-Kuster S, Smielewski P, Rüegg S, Strebel SP, Marsch SC, Pargger H, & Steiner LA (2008). Cerebral perfusion in sepsis-associated delirium. Critical care (London, England), 12 (3) PMID: 18457586

Neurosyphilis: Considerations For A Psychiatrist Mark A. Ritchie, Joseph A. Perdigao, Mark A. Ritchie

The Neuropsychiatric Assessment of Lyme Disease

A. Mazzola, G. Mazzola (2006). OCD And Beta Haemolytic Streptococcus: A Nasty Association. Priory publishing link

Credit link for featured image.

This post came to light due to Captain Skellet (whose been around SciAm lately!) alerting me to Hatena. I’ve heard of several organisms containing proto-plasmids; symbiotic chloroplasts which haven’t completely been endosymbiosed, but the strange life-cycle of  the protist Hatena was a new one so I went to look it up. And I’m very glad I did, because it’s pretty amazing.

Hatena, taken from the reference (link below).

The picture above shows a micrograph of Hatena. The green blob is the symbiont living inside it and the scale bar is 10um. As a quick point of background information chloroplasts are the little membrane enclosed vesicles in plants which carry out photosynthesis. The current theory for how they developed is that they were once free-living bacterial type organisms (cyanobacteria) which were engulfed by a larger cell and over time lost their own identity to become photosynthesising factories inside the larger cell.

Hatena arenicola doesn’t have a chloroplast, but it does have a symbiotic relationship with another organism; nephroselmis. The nephroselmis is always found in the same place in the Hatena, and carries out photosynthesis to provide energy for both of them. Unlike regular chloroplasts, nephroselmis has its own proper nucleus and even its own mitochondria although most of the internal cellular organisation and any kind of motile apparatus (such as flagella) has been lost. Nephroselmis is a sort of half-symbiont, with enough of it’s own machinery to be a clearly distinct organism, but once it gets inside its host organism, it’s happy to stay there and mutually benefit the both of them.

The weirdest thing about these two organisms though, is their replication cycles. When Hatena replicates, the nephroselmis doesn’t, and as a result only one of the offspring gets the photosynthesising symbiont. The other organism remains colourless and develops a complex feeding apparatus at the apex of the cell, presumably as it can no longer rely on the symbiont for food. This wierd ‘half plant, half predator’ lifecycle is shown below. (Picture taken from the reference, scale bar 10um):

The replicating life-cycle of Hatena. Ref link below.

That’s just weird. Seriously odd. The Hatena is able to move seemingly freely between being a predator consuming other cells for food, and being a plant-like organism once it settles down with its symbiotic partner. The grey non-symbiont organisms can be induced to take up free-moving nephroselmis and (in the words of the paper) “tentitavely” maintain a symbiotic relationship with them but it also seems perfectly happy to survive on its own.

The paper suggests that Hatena cycles between these two modes of living, depending on circumstance. Thus the ‘predator’ grey cell shown above will continue eating fellow cells until it consumes a nephroselmis, at which point it degrades its complex feeding apparatus, accepts energy from the symbiont until it’s ready to divide. One of the daughter cells will then go through the whole cycle again while the other remains as a non-predating plant. The authors freely admit that there is little evidence for much of these stages, but it seems a reasonable way to explain what is going on.

As this is clearly a very early stage in symbiotic capture it has important implications for the endosymbiotic theory of chloroplast evolution. Along with various other ‘intermediate’ symbionts (such as Karenia mikimotoi and Lepidodinium viride) the Hatena helps to show how chloroplasts might have first formed in the cellular ancestor of plants. Hatena and its symbiont have already acquired an intimate structural association, only the coordination of their cell cycles would be required to turn the nephroselmis into an internally replicating plastid.

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Ref: OKAMOTO, N., & INOUYE, I. (2006). Hatena arenicola gen. et sp. nov., a Katablepharid Undergoing Probable Plastid Acquisition Protist, 157 (4), 401-419 DOI: 10.1016/j.protis.2006.05.011

Although bacteria live as isolated cells they are constantly communicating with surrounding bacteria, particularly those of the same species, and can often band together to form large groups of bacteria surrounded by a sticky mesh. These are known as biofilms (which I cover in more detail here). One of the main ways that bacteria communicate with each other in order to organise structures like this is by quorum sensing.

Quorum sensing uses small molecules that bacteria can both excrete and sense. When enough bacteria are in one place then the surrounding concentration of these small molecules reaches a critical level and can activate the genes for a variety of different responses including luminescence, virulence (in pathogenic or disease-causing bacteria) and the formation of biofilms:

From "Looking for Chinks in the Armor of Bacterial Biofilms" Monroe D PLoS Biology Vol. 5, No. 11, doi:10.1371/journal.pbio.0050307 via wikimedia commons.

It turns out that there are a whole range of different types of biofilms, that bacteria use for many different purposes. Although many species formed biofilms when bany cells joined together some species stopped forming biofilms when they reached a certain cell density. Biofilms are carefully controlled by bacteria, they do not just start growing when a certain number of bacterial cells gather together and then never stop, each biofilm is tailored specifically to the needs of the species making it.

Using models of mostly infectious biofilm-forming bacteria (such as Vibrio cholerae which causes cholera) they found that as well as helping to bind the cells together and resist attacks from antibiotics the biofilm was also a defense against competing bacteria and may have helped to out-compete them by covering all available living surfaces with slime. The ability to produce biofilms not only helps the V. cholerae against other invading bacteria, it also helps it gain a hold against the body’s own internal bacterial defenses that line the internal gut.

However once the levels of V. cholerae became too high the bacteria often stopped generating the biofilms. This could be for two reasons, firstly the biofilm takes up valuable resources that could be used in growth and division and secondly it prevents the bacteria within it from travelling very far. V. cholerae infect the body by having periods of growth followed by periods of mad colonisation, which works best if the biofilm actually disperses at high cellular density to allow the cells to spread.

This can be contrasted with more sedentary bacteria like P. aeruginosa which likes to settle down once it finds a place to live and occasionally disperse colonies into the body. Rather than loosing its biofilm this bacterial species retains it even at high cell densities. This allows it to out-compete any other bacteria that may be at the site of infection, and hold off both the body’s natural defenses and any chemical antibiotic drugs meant to kill it.

Comparisons of different V. cholerae strains revealed a wide range of different biofilm formation patterns between strains, all linked to Quorum sensing signalling. This is likely to depend on the internal environment that specific strains occupy, the amount of competition they face and the necessity for quick and frequent bouts of dispersal.

Biofilms are often seen as being a final living space, a giant bacterial ‘city-base’ from which offspring can spread while the old-timers stay and develop antibiotic-resistance to new challenges. It’s interesting to see that this is not always the case. That the biofilm can just as easily be a short-term shack for travellers as well as a city for settlers.

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Credit for image 1

Reference: Nadell CD, Xavier JB, Levin SA, & Foster KR (2008). The evolution of quorum sensing in bacterial biofilms. PLoS biology, 6 (1) PMID: 18232735

Luckily a great paper (reference below) came out recently that explores three different types of antibiotic treatment and how bacteria have evolved to protect themselves from the antibiotic attack. Bacteria can evolve quickly, as they reproduce relatively fast, and can support a larger number of mutations within their cells than the average human or eukaryotic cell. This means that by the time most antibiotics officially hit the market somewhere in the bacterial kingdom a method of resistance already exists.

The antibiotic novamoxin. From wikimedia commons credit link below.

In order to study how bacteria evolve resistance, the researchers used a tool that they named the “morbidostat” (presumably “Death-counter” was already taken) to adjust the antibiotic concentration in the experimental growth media to ensure that the bacteria were always under a high evolutionary pressure to evolve resistance. This is important for studying bacteria that require multiple mutations in order to evolve the highest form of resistance. Using a fixed concentration of antibiotics would produce maybe one of two helpful mutations that give the mutated bacteria enough advantage to outcompete the non-mutated ones. Constantly adjusting the antibiotic concentration means that the bacteria are in a constant struggle for that extra edge of resistance to give them a selective advantage.

Using the morbidostat also means that the bacteria are kept at a low concentration (rather than the resistant bacteria out-competing everything else and then growing exponentially). This prevents nutrients from becoming a limiting factor as the culture only ever contains a managable number of bacteria.

Growth curves for bacterial population. Without the morbidostat resistant populations will grow exponentially. With the morbidostat the continuing increase in antibiotic concentration helps to control the population under fierce selection pressure. Image (c) me.

Using the morbidostat to control the cell cultures, they then set up five parallel experiments for three different antibiotics; chloramphenicol, doxycycline and trimethoprim. Every day, they took a sample of the culture to examine the levels of resistance within the culture. They found that while resistance to chloramphenicol and doxycycline increased smoothly over time, resistance to trimethoprim increased in a stepwise fashion, with no changes for a couple of days and then a sudden jump in resistance.

On the final day of the experiment they took one colony from each sample and sequenced the whole genome to see what genetic changes had occurred. Despite the fact that both chloramphenicol and doxycycline target the ribosome, no mutation to the ribosome was seen. This is not surprising as the ribosome is an important piece of cellular equipment and not to be tampered with! Instead, all the mutations in these bacteria were involved in transport and membrane proteins. The bacteria were acquiring mutations that allowed them to shuttle the antibiotic out of the cell. Not only that but the shuttling mechanism wasn’t hugely specific either; bacteria with chloramphenicol resistance were also resistant to doxycycline.

For trimethoprim on the other hand, all the mutations were found in the region of the protein that the antibiotic affects (the synthesis pathway of an important metabolic enzyme). Trimethoprim resistance therefore was not transferable, bacteria resistant to trimethoprim were unable to survive when challenged with chloramphenicol or doxycycline. The step-wise evolution was seen as the area for mutation was so small. Whereas there are many small mutations that can occur to improve the ability of the cell to shuttle antibiotics away, mutations that affect such a small specific area of DNA are quite rare. Hence the stepwise resistance rate; all the bacteria would be equally susceptible until one small mutation happened prompting the sudden fast growth of the resistant population and a sudden increase in resistance.

The full genome sequence of the bacteria doesn’t just allow researchers to find out which genes have mutated, it could also help to explore the exact order in which they did, putting together a developing resistance profile for the antibiotic response. That kind of detail would require many more cultures and experiments, but the techniques are all in place!

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Credit for image 1

Ref: Toprak, E., Veres, A., Michel, J., Chait, R., Hartl, D., & Kishony, R. (2011). Evolutionary paths to antibiotic resistance under dynamically sustained drug selection Nature Genetics, 44 (1), 101-105 DOI: 10.1038/ng.1034

Major problems start to happen, however, once bacteria get through that epithelial barrier and into the tissues of your body. Which is why the first bacteria of the new year is the oral bacteria Fusobacterium nucleatum, which has a trick to open up little doors in blood vessels. These aren’t massive holes, not big enough to cause bleeding but large enough to let it and other bacteria into the bloodstream.

The bacteria in all their blobby glory! These are actually the related Fusobacterium novum. Image taken from the CDC Public Health Image Library (link below).

This is a big issue, because once the bacteria get into the blood-stream they can travel around anywhere within the body. It’s not  just the blood-vessels in the mouth that the F. nucleatum can get into, it can also bypass a lot of other cellular barriers such as the blood-brain barrier that keeps bacteria out of your brain, and the placental barrier that guards the passage of substances between a pregnant mother and the foetus.

The bacteria works by releasing a chemical which is picked up by the cells that make up blood vessels (endothelial cells) and causes the cells to become more permeable. More technically the bacterial chemical (a FadA adhesin) binds to a protein on the cells (vascular endothelial cadherin) that helps to keep the endothelial cells joined together and causes it to migrate away from the cell-cell junction. This opens the junctions up slightly and makes the whole vessel more permeable.

Endothelial cells that form a lining around the blood-vessels. Cell-cell junction in blue and nucleus in red. Pic (c) me.

FadA (the bacterial chemical) is an interesting little molecule, and while it’s highly conserved in F. nucleatum and related oral bacterial species, it has been lost in many closely related species which do not populate the human mouth. This is a protein with one specific purpose – to open blood vessels – and where that function is not needed the bacteria has no need for the protein. When it’s first made by the cell it exists in a form called pre-FabA which anchors to the bacterial membrane with the soluble part (the actual FabA) on the outside of the bacteria ready to be deployed.

To test whether the FabA and the cell cadherin could bind, the researchers carried out a whole range of different binding tests (more information in the  reference below). First, they did a yeast-two-hybrid screen, a sort of sciency quick and dirty method to see if two proteins can bind each other. Then they took both proteins out of the cell to see if they could bind separately, by sticking one protein to a column and seeing if it could ‘catch’ the other as it was washed through. Finally they put both proteins back in the cell with coloured markers attached to see if the coloured markers appeared in the same places. All of these results, along with the actual structures of the two proteins, suggest very strongly that they bind.

One of the most interesting tests they did was to see whether the F. nucleatum was just opening the floodgates for itself, or whether other bacteria were sneaking in at the same time. They did this by making little wells with endothelial tissue between them. Sure enough, those cultures containing E. coli along with F. nucleatum showed that both bacteria could travel through the endothelium together, whereas in cultures containing only E. coli the bacteria remained on one side of the membrane.

The researchers don’t suggest any way to combat this, they’re more interested in the exciting science, but regularly and gently brushing your teeth can’t hurt! (I should point out here that non-gentle brushing of teeth can damage the gums and open blood vessels anyway, making the clever bacterial tricks somewhat redundant)

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Credit for image 1.

Reference: Fardini, Y., Wang, X., Témoin, S., Nithianantham, S., Lee, D., Shoham, M., & Han, Y. (2011). Fusobacterium nucleatum adhesin FadA binds vascular endothelial cadherin and alters endothelial integrity Molecular Microbiology, 82 (6), 1468-1480 DOI: 10.1111/j.1365-2958.2011.07905.x

1) The First Post – electric bacteria

This was the first post I ever wrote for SciAm, and as such it felt like my first chance to prove myself on a shiny new network. I’m not totally pleased with the handmade drawings (they are somewhat confusing and the large marker doesn’t help) but they were my first attempts. Hand-made, or custom-made art is something I want to get a lot more into in the future.

2) The Joint Post – bacteria that stop at the blue light

This was part two of a two-part set written by me and James Byrne. Having two separate people writing about the same paper gave two different perspectives, which was a really interesting exercise. I would love to do more of these in the future, they help to introduce readers to new blogs, and also to create a sense of network within the science blogs. And they’re fun!

3) The Chemistry Post – hydrogen bonds

For a network wide Chemistry Day, I decided to write about the intramolecular forces that hold water together. I enjoyed it so much that I wrote a second one slightly later, about van der Waals forces. Although I try to primarily focus on bacterial and microbiology in this blog, I must admit to a small secretive love for chemistry and chemical forces. I’d love to write more chemistry posts in future; not an overwhelming number but one or two a month would be nice.

3) The Perfect Post – unculturable bacteria

Somewhere around September/October time I started to get into a proper rhythm with blogging. Read paper, understand paper, find two images for blog, formalise introduction, write post. This happened around twice a week, didn’t seem to take up too much time and had a positive effect on my page views. I love a lot of the posts I produced around this time, but my favourite is the  one on unculturable bacteria. There’s nothing I don’t like about this post. I could certainly make it better with more information, or a maybe a quote from the researchers, but as it stands it’s one of my favourites.

5) The Silly Post – bacterial X-men

During the run-up to Christmas I wrote two of the funnest posts I’ve ever done, finding bacteria to compare to X-men and sticking a little bit of interesting science information down for each one. The list form made writing a lot easier at a time when I was quite busy, and they were quite popular with readers as well. I certainly don’t want to turn this blog into “Cracked.com with added bacteria” but there might be the odd list going up every now and again. Particularly when I’m overworked.

It’s been a great year for me blogging-wise. Joining the SciAm network has been an amazing experience and I’m very much looking forward to blogging through 2011!

It isn’t just one clear species of bacteria that has magnetotactic ability, rather there are several different groups of bacteria of different  shapes and sizes. Some of these are large multicellular bacterial groups, while others are single-celled large and rod-shaped. It is these large rod-shaped bacteria that the paper has been exploring, putting together a comprehensive description of them as a group.

The magnetotactic bacteria will swim along the field lines. Image from wikimedia, source link below.

Samples of magnetotactic bacteria were collected from brackish water in the wonderfully named Death Valley Park in California. While many different types of magnetic bacteria were found, the rod-shaped ones were by far the dominant group. Having isolated a sample of exclusively rod-shaped bacteria, researchers could then examine the physical properties. All of the bacteria had a flagellum, a single little ‘tail’ used for propulsion. They contained different forms of the internal magnetic nanoparticles as well; some of the nanoparticles were made up of magnetite (Fe3O4 – iron and oxygen complex) and some made up of greigite (Fe3S4 – iron and sulfur complex). The greigite nanoparticles were a range of different shapes while the magnetite crystals formed bullet shaped particles.

The type of nanoparticle that formed was found to be strongly related to the outside surroundings. When the bacteria were put into high sulphur growth medium, more of the greigite nanoparticles were formed. Conversely, when the hydrogen sulfide concentration was artificially reduced, more magnetite crystals formed.

The two different types of nanoparticle in the same bacteria. Image adapted from the reference (below).

These samples were collected from brackish water rather than the marine environment that most magnetotactic bacteria are found in, which means that magnetic bacteria have diversified into a greater range of habitats than previously thought. Although some of the bacteria isolated  contained exclusively magnetite or greigite nanoparticles, it seems a fairly safe bet that under different environmental circumstances they would be able to change which nanoparticle was made, to reflect the available elements. In both cases, an iron compound is required, but there seems to be no appreciable fitness difference between bacteria with the iron-sulfur compounds, or the iron-oxygen ones.

Genetic analysis showed that the genes for producing magnetite and greigite appear to be in two separate groups or clusters on the genome. Comparing these clusters to other bacteria that produce magnetite or greigite nanoparticles supports the idea that one contains genes that code for proteins required for manufacturing the bullet-shaped magnetite nanoparticles, while the other contains genes related to greigite production. Keeping the two different types on two seperate gene clusters allows them to be regulated differently, and respond individually to different environmental stimulus to ensure that whatever the surrounding environment, the bacteria will always be able to swim along geomagnetic field lines.

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Credit link for fig. 1
Ref: Lefevre, C., Menguy, N., Abreu, F., Lins, U., Posfai, M., Prozorov, T., Pignol, D., Frankel, R., & Bazylinski, D. (2011). A Cultured Greigite-Producing Magnetotactic Bacterium in a Novel Group of Sulfate-Reducing Bacteria Science, 334 (6063), 1720-1723 DOI: 10.1126/science.1212596

4) Multiple Man

Multiple Man’s power is that he can replicate himself, splitting his body into two or more identical copies in clear violation of the laws of conservation of mass. When he wants to get rid of these extra bits he can sort of return them to his body, reforming as one person. It’s strongly suggested that he remains in control of all the extra multiple men as well, one of them can’t go off and (say) rob a bank without him controlling it.

The bacteria: E. coli
[Edited due to serious reading comprehension error!]

Bacteria are the masters of dividing quickly and unlike multiple man, they aren’t constrained by how many copies they can produce. E, colis is one of the fastest dividing bacteria in the world, splitting into two once every 15-20 minutes. While this might be slower than multiple man can manage, the end results are far more spectacular:

For those that can’t get the sound, that’s five thousand billion billion bacteria produced in one day, just from a single dividing cell. (link to video on youtube)

5) Berzerker

Berzerker is one of the lesser known X-men having appeared in only one of the comics. He did, however, make it onto two of the animated series (X-men: Evolution, the one where everyone is a teenager, and Wolverine and the X-men, which I’ve never seen). His power involves the manipulation of electrical energy; he can throw balls of electricity at people, convert his body into raw electricity, and change the channels on the TV without needing a remote.

The bacteria: Geobacter

I covered the amazing powers of Geobacter in my first ever post on this blog, but it’s well worth reiterating because they are awesome. Geobacter might not be able to shoot balls of lightning at people, but they can certainly run a current through themselves, and more excitingly, they can run an electrical current up through a whole column of bacteria, essentially converting a chain of bacteria into a piece of electrical wiring.

A chain of bacteria running an electrical current from the base of the mud to the top of the water. Picture (c) me.

The electrons are needed for the redox reactions that all organisms need to carry out to survive. By picking up electrons from the mud, and then transferring them up through pili to the surface the bacteria create an electrical current. You can read more about it on the old post.

6) Mystique

Raven Darkholme, aka Mystique. In the film she’s naked and blue with strategically placed scales. In the comics she’s still blue but wears a little black two-piece for dignity. Head (or second in command depending on what universe you’re in) of the brotherhood of evil mutants, her power is the ability to change form, to shape-shift into the features of another person.

The microorganism: Trypanosoma Brucei

I’ve cheated here a little. T. brucei isn’t actually a bacteria, instead it’s a single-celled protist, one of those organisms which are two large and structured to be a bacterium, but too weird to properly be a eukaryote.

False colour SEM of T. brucei, from Zephyris via wikimedia commons (credit below).

T. brucei causes sleeping sickness, and has a fairly complex lifecycle involving humans and tsetse flies. Once inside the human it travels around in the blood, and can occasionally make its home inside various organs. Floating around in the bloodstream, however, is dangerous as it won’t be long before part of the human immune system will recognise the intruder and start to rally a force to attack it.

The T. brucei deals with this by periodically changing its skin. Like Mystique, it can change form so that by the time the immune system gets back all ready to attack the recognisable intruder the intruder is no longer recognisable. The outer surface of the T. brucei is covered with a molecule called VSG (variable surface glycoprotein) and the T. brucei genome contains the information for an entire archive of VSGs, with only one being expressed at any one time. By switching to a new VSG, the T. brucei can remain hidden inside the body, constantly changing form and escaping capture.

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Source for T. brucei picture.

1)  The Blob

Like many of the X-men, the Blob has gone through several incarnations of character but the one main continuous feature is that he’s big. That’s pretty much it. The size gives him supernatural strength, the ability to be ‘immovable’ (although you could probably shift him with a few tanks if it came to it) and occasionally he has his very own gravitational field. His name is usually Fred Dukes.

The Bacteria: Thiomargarita namibiensis

Image from NASA, credit below

Thiomargarita means “sulphur pearl” and this bacteria is a gram-negative little beasty found in the oceans. It can grow up to 0.75 mm wide, which may not sound much compared to the bulk of Freddy Dukes, but bear in mind that even at his height the blob was no more than 10X bigger than the average person. Thiomargarita is over one million times larger than the majority of bacteria. Although it can drift around on the tides, it has no way of propelling itself around, which means that once it stops it’s pretty immovable as well.

The reason most bacteria don’t grow this large is because they rely on diffusion to get nutrients inside the cell, and 0.75mm is a very large distance in terms of diffusion times. In most bacteria, the inside of the cell would starve. Thiomargarita survives by having lots of large vacuoles which are filled with nutrients. These vacuoles are also what help to make it larger; they act as a nutrient-holding network inside the cell.

2) Magneto

Magneto is one of the Big Bad of the X-men. His mutation allows him to manipulate metal and not necessarily magnetic metal either (that sort of varies with the plotline). Any metal he comes into contact with he can bend, shape and distort. He can manipulate bullets, twist up helicopters and in one memorable movie scene pull all of the iron out of a guys body through his torso.

The bacteria: Magnetosome-containing bacteria

I’ve written about this once before, and will in all likelihood cover it again sometime,  but there are some bacteria that contain little organelles called “magnetosomes”. These particles contain magnetite crystals which although they don’t allow bacteria to attract metal, they can act like little compasses, which means the bacteria can all line up in the direction of the earth’s geomagnetic field.

Magnetosomes lined up inside a bacteria, paper reference below

Several species of bacteria are also capable of eating metal, including Halomonas titanicae which was found working it’s way through the remains of the titanic. There aren’t yet any bacteria that can make someone’s blood come flying out of their chest, but the Ebola virus comes pretty close.

3) Toad

Toad’s main mutational power is “being a bit like a Toad” so it’s not surprising that he’s gone through several different incarnations as the comics change and evolve. Since his original creation as a bug-eyed Renfield-like lackey he’s been an English punk in Ultimate X-men, a strange bald Shakespearian actor in Age of Apocalypse to finally being played by Ray Parks in the film. His powers vary; while he usually keeps the leaping ability and long tongue he can also occasionally spit slime, excrete slime, and stick to walls. Sometimes he is given the ability to speak to frogs, or to be really good with computers.

The bacteria: Thiobacillus ferrooxidans, leptospirillum ferrooxidans

Both of the above are iron-bacteria that live in stagnant water. They smell bad, they’re slimy, and they’re quite hard to get rid of once they establish themselves in a water-pipe.

Orange-coloured iron bacteria living in a puddle. From the NH Estuaries Project, link below.

It isn’t so much the bacteria themselves that are slimy, but the remains of the things they eat. In order to live and grow they oxidise dissolved iron in the water, producing ferric oxide. As ferric oxide is insoluble, it hangs around as a sort of brown gelatinous slime that gets stuck in the water and stains everything it comes into contact with. As the bacteria spread, they leave behind them a trail of brown slimy stuff that can build up inside pipes and plumbing.

It’s a bit of a stretch, but it’s Toad-like enough, and Toad is my favourite X-men so I wasn’t about to leave him out.

Part two coming soon: Multiple Man, Berzerker and Mystique.

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Credits:
Source for fig. 1, NASA image in the public domain.
Ref. for fig 2: Komeili, A. (2006). Magnetosomes Are Cell Membrane Invaginations Organized by the Actin-Like Protein MamK Science, 311 (5758), 242-245 DOI: 10.1126/science.1123231
Source for fig. 3 – all rights released by the NH estuaries project.