Thursday, December 17, 2015

Break Announcement- 2


Thanks to all the people who made blog writing an enjoyable experience for 4 consequtive years. Its time for me to take another short break. The graph here shows the number of posts since this blog page has started.

I will see you again in 2016. Wish all readers a Happy Year Ending and a Happy New Year in advance.

Meanwhile take the time to go through my earlier posts that you have missed.

Varun C N

Friday, December 11, 2015

Antibiotic Catastrophe- MCR1: Follow up


Fig 1: MCR-1 detection in China. Source
Just a couple of weeks ago, I wrote a blog-post on MCR-1 (Mediated Colistin resistance). The first time demonstration of the gene in plasmid has pulled the attention of Clinical microbiologists worldwide. There was a lot of discussion on what this means. Fig 1, from original paper summarises the surveillance data, the extent of spread in China.

The hope was that this hasn't spread as of yet. A study team from Denmark discovered the presence of the new resistant bacteria by searching for it in a database containing the genetic sequences of about 3,000 E. coli samples. According to the announcement MCR-1 was found in one patient, who suffered from a blood infection in 2015 and in five food samples that have been imported from 2012-2014. The Patient was Danish who hasn't travelled outside and the other 5 samples are from poultry that was imported from Germany. That means there are at least 4 countries where this plasmid gene is sitting- China, Malaysia, Denmark and Germany. Paper yet to be published

Frank Aarestrup, head of the genomic epidemiology group at the National Food Institute, comments, “I was not surprised but I had really sincerely hoped not to see it”. In a statement issued by  Antibiotic Resistance Action Centre, Source

The news that the dangerous colistin resistance gene has been found in Denmark is alarming. This newly identified gene, called MCR-1, is on a mobile piece of DNA that can make copies of itself and then jump to from bacterium to bacterium, spreading resistance. History shows that these mobile resistance genes can spread around the world quickly, silently riding in people, animals, and food. The news that MCR-1 has been discovered in Denmark suggests that this scenario is playing out in real time.

In the latest, there is a lot of discussion about surveillance and many different groups have already started to look into evidence of this gene in their colistin resistant strains. Some people are calling it the next NDM and have opinions on the likely global spread already.

Fingers Crossed.
Liu, Y., Wang, Y., Walsh, T., Yi, L., Zhang, R., Spencer, J., Doi, Y., Tian, G., Dong, B., Huang, X., Yu, L., Gu, D., Ren, H., Chen, X., Lv, L., He, D., Zhou, H., Liang, Z., Liu, J., & Shen, J. (2015). Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study The Lancet Infectious Diseases DOI: 10.1016/S1473-3099(15)00424-7

Friday, December 04, 2015

The Red and Black Queen- Hypothesis


I have so often talked about in this blog about the microbe-microbe interaction and often have presented with an idea on how there is a lot of competition with each species trying to get ahead of the other species. For example, Pseudomonas aeruginosa is a highly competitive organism and usually tries to dominate other species nearby, thereby providing a survival advantage. We often consider infections as uni-microbial in nature. It is my understanding that for the majority of the cases it does, but not always. In natural habitat polymicrobial act is a common feature.

Nature has a lot of examples of Multi-microbial interactions. Let us take well known examples of symbiosis. The tie up between the 2 organism is so unique that one doesn't survive without the other. An extreme case of this is endosymbiosis. One of the finest example, I recall is from an article called "Bug in a bug in a bug". The organism in discussion is Planococcus citri which has an endosymbiont- Tremblaya princeps which in turn harbours an endosymbiont of its own- Moranella endobia. Interestingly none of the can survive independently without the other. There are many such examples outside endosymbionts where organisms interdepend on each other for survival.

Illustration 1: The Red Queen Hypothesis.
“Now, HERE, you see, it takes all the running YOU can do,
to keep in the same place.” Source
Perhaps, everyone has heard of the Red Queen hypothesis. Its one of the most famous theories of evolution. The hypothesis states that for a species to survive it has to constantly evolve, which is just enough to stay in the competition for survival. There are books written on this concept. Let us take a quick simple example. Let us assume we have 2 bacterial species (X and Y) in a petri-dish, well mixed with an equal interest in proliferation. The survival advantage for both the species is kind of 50-50. By the course of mutation (Check my earlier posts here and here), let's say X is able to produce a bacteriocin which potentially attacks Y. Logically, Y evolves overtime a defence mechanism. X further evolves a counter defence mechanism and Y evolves a counter-counter defence mechanism. This process can infinitely loop out just to survive. There are extra genes and control mechanisms evolved by both species just to keep themselves in competition but the net effect is "Nothing". As good as each were at the start of competition. The more number of variables you add to this equation more complicated it gets but the idea will remain the same. There is no doubt as to if the above scenario is true, since this has experimentally demonstrated to be the case in a huge set of examples.

Illustration 2: Black Queen
Now think about this for a moment. If the two organism decide that they are not fighting each other, but rather share their work then each of them would get better share. Let us build another scenario with X and Y bacteria. X decides that it is going to do all the amino acid building stuff and Y decides that it will do all the lipid stuff (both in excess of requirement). So X is going to drop all those genes that is required to manage lipids and Y will drop of amino acid part. Once again the species are interlocked but in a symbiotic manner. X supplies its extra to Y and vice-versa. This has a special advantage, there is no competition to build genetic systems at an extra cost (Since you could drop some genes) which anyways is of little value over a longer period of time. This is the basis for Black queen hypothesis.

Black Queen Hypothesis, as per Morris etal; 2012 argues a theory on how organisms become dependent on each other. As Richard Losick comments "It's a sweeping hypothesis for how free-living microorganisms evolve to become dependent on each other. The heart of the hypothesis is that many genetic functions provide products that leak in and out of cells and hence become public goods". The idea is termed black queen to reflect the Heart- cards game where you need to have a minimum points to win. In microbial terms, you harbour minimum set of genes and still survive with the help of other. There is some mathematics in the original paper but let us ignore it here.

This airs a fresh new question. This theory looks ok when we talk about a couple of organisms involved. What happens to the scenario where one organism is helping a lot of others by taking up their function. This idea is well explained in the paper as "Shooting the moon strategy". Though it appears that this is a risky move for the universal helper (since it is the one that is doing everything needed), it can be a great move in ensuring survival. So even if such a helper is rare in the system, its survival will be ensured by others who are benefiting from the helper.

In summary, The Red queen hypothesis is a statement of competition while Black queen hypothesis is that of coordination.

Here is an interesting thought that I had been thinking about- Viral evolution. There is a huge debate on evolution of viruses. A great deal of scientists agree that viruses are involuted living organisms and another set of scientists argue that Viruses have evolved from chemical bags. I will present here some arguments from both sides and then come back to why I'm talking about it here.

First let us consider the argument that Viruses are previously living organisms that have lost multiple genes (If virus as we know it now are alive, is a totally different debate) . The idea goes something like this. Viruses where once intracellular parasites that had all the necessary genes for self replication. As evolution passed viruses relied more on the cellular machinery and started loosing genes, some of which was still available in host cell. The assumption in this argument is that loosing a gene is easier in comparison to gaining. Further, recent findings of viruses with very huge genomes is in support of this theory. It is argued that they lost a few genes. The other side of the argument is viruses are simple bag of chemicals that evolved to a certain extent and then found that it doesn't need to add up more genes since they could use it from host. One of the best arguments in this side of the prediction is viroids which can be simplified no further as a replication unit. The assumption here is gaining genes is quite easy. According to me we can avoid the assumption of timescale in both arguments since the evolutionary time that we are talking in each case is very high and thus will not effect our current observation. A good summation of the arguments is presented here.

It is commonly argued that virus follows the Red queen hypothesis. Virus competes with host for survival. This to me, is consistent with the idea that viruses have evolved from simpler chemicals. But if I consider that viruses have involuted, then it kind of looks like a negative black queen hypothesis. The virus must have started loosing genes as a mode of sharing but somewhere cheated, since it allowed them to replicate at a really low cost. And now has turned out to a Red queen strategy. Just a thought.
Morris JJ, Lenski RE, & Zinser ER (2012). The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. mBio, 3 (2) PMID: 22448042

Tuesday, December 01, 2015

BtB#5- Defining Immune privilege


Recently, I had a conversation with a person on the topic of "Immune previlege sites". Often the textbooks teach us that there is some kind of special areas or tissues in the body where immune system doesn't seem to be active. How can the immune system not do its regular business in some sites? One of the best example that the classic textbooks cite as Immune previleged is the Central Nervous system. Yet Neuroimmunology is a well defined concept. For a start, that makes a pretty good concept for a "Back to basics post".

The idea of immune privilege arises from original experiments showing that allograft transfer of tissue was not always rejected by the recipient and it depended on site of graft. It was proposed that these site are somehow devoid of an immunological surveillance and action, and was considered as privileged, hence the name. Following are considered as the immune privileged sites
Table 1: Immune Privilege tissues
  1. Central Nervous system
  2. Eye
  3. Placenta and fatal tissues
  4. Testis
Immune privilege is defined classically as tissue site that is protected from immune attack. It should be noted that immune privilege is a context term as per the modern definition. CNS inflammation is a common feature, in cases of infection illustrating that the immune system can still be active in CNS. Paradoxically, tumour cells can secrete immune suppressive factors and thus can have a local privilege environment. Hence the modern contextual definition.

An important point of understanding is the question- "What is the relevance of immune privilege in physiological context?". Immunological reaction is aimed at destroying a target, that is considered as non self. That means anything that is considered as non self based on antigenic display, immune system will be called into action. There are a couple of considerations. During the period of immune training, there are some antigens that are never shown to the immune system (even though they are self) and hence the immune system is not tolerant to these antigens. Such antigens are called as sequestered antigens. One classic example is the eye lens protein. Sometimes the immune system is not allowed to patrol with because of a barrier. Example is Blood-Brain-Barrier protecting the CNS.

Immunological reaction is often like a battlefield. Higher the severity of reaction stronger is collateral damage. This is why immune system is often referred to as "Double edged sword". If Inflammatory activities are allowed in region such as brain where neurons may be damaged it is safer to restrict the activity. It must be remembered that neurons don't regenerate. Thus the restriction and privilege. Another case is that of testis where sperms are produced. Sperms are recombinant haploids derivatives of male cells (If I can put it like that). This means, there are going to be antigens on sperms that may look different from the parent cell. If the site is not privileged, sperms would be immunologically attacked even before they got a chance to do what they were meant to do. When this mechanism goes wrong, testicular autoimmune disease may result. In short immune privilege is a physiological mechanism of protecting tissues where collateral damage due to immune activity is to avoided.

There is a great deal of debate on if the concept of privilege is true as we understand it, especially based on recent findings at least on few cases. For example, it was universally accepted that the brain is heavily protected against immune access. The recent findings evidencing that the brain itself has a lymphatic system has toppled the idea.
Forrester JV, Xu H, Lambe T, & Cornall R (2008). Immune privilege or privileged immunity? Mucosal immunology, 1 (5), 372-81 PMID: 19079201

Louveau A, Smirnov I, Keyes TJ, Eccles JD, Rouhani SJ, Peske JD, Derecki NC, Castle D, Mandell JW, Lee KS, Harris TH, & Kipnis J (2015). Structural and functional features of central nervous system lymphatic vessels. Nature, 523 (7560), 337-41 PMID: 26030524