A review to read and enjoy

Posted by Kasra Hassani

I am appointed to do a review paper for a ‘Reading and Conference’ course on Fungi. I chose the opportunistic pathogen Aspergillus fumigatus as the focus of my review. Having studied only on Trypanosomes and innate immune cells so far, my background in mycology is close to zero. So I decided to start from scratch. I stepped upon a surprisingly neatly written review that gave me exactly as much background I needed on Aspergillus before I would go more in depth on the subject. “Aspergillus: A primer for the novice” by Dr. Joan Bennett includes scientifically exciting and still critical detail about various species of Aspergillus, their commercial, historical and culinary(yes!) importance. For once after a long time I read the whole review paper and not only the section that interested my research focus. If interested to learn more about the ubiquitous fungus Aspergillus, you can also enjoy reading this paper alongside your favorite afternoon beverage here.


Bennett JW (2009). Aspergillus: a primer for the novice. Medical mycology : official publication of the International Society for Human and Animal Mycology, 47 Suppl 1 PMID: 19253144



Persistence of parasites in the host: co-evolution of parasitism and immunity

Posted by: Kasra Hassani

Many pathogens are unable to live outside the host. Therefore, before killing or completely using up their host, they should ensure that they will be successfully transfered to another one, or one may say, those who did not never made it through evolution. Depending on their life-cycle and type, strategies to ensure transmission diffes among pathogens. In a comment for Nature Reviews in Immunology Sacks and Yazdanbakhsh comparatively discuss these strategies among air-borne pathogens, protozoan vector borne pathogens and also multicellular pathogens. Air-borne bacteria and viruses can easily spread after an acute infection and do not necessarily need to modulate immune response to avoid the up-coming sterilizing immunity. On the other hand, vector-borne parasites such as Plasmodium or the Trypanosomes require more time for efficient transmission. Therefore, parasites have developed strategies to delay life-long immunity. For instance, in African Trypanosomes (T. brucei) continuous variation of the surface glycoprotein (correctly named the variable surface glycoprotein or VSG) hiders development of a protective immune response and allows the parasite to reside in the blood for a long time. Alternatively, Leishmania infections co-inside with presence of regulatory T cells and considerable amounts of IL-10 which down-regulates the protective Th1 response. In larger parasites such as helminths rapid movement from immune-sensitive areas such as the skin or acquiring and presentation of host antigens are among the strategies that are used for delaying the immune response and buying time for transmission.

What I find more interesting among all of this is the evolution of the host in the same direction. In many parasitic infections, the immune response does not lead to complete parasite clearance, rather to a residual infection with minimum or no pathology yet still transmissibility.  Read et al. have argued in a Primer in PLoS Biology that this ‘tolerance’ is a type of immunity that can arise in the host-parasite co-evolution as an alternative to ‘resistance’ where complete of the pathogen clearance occurs. Firstly, complete clearance of the pathogen can be too costly compared to its control. Secondly, In the dynamic co-evolution of the host and the parasite, genes who confer tolerance against a pathogen could be favored to those who confer resistance. Evolution of tolerance does not harm or might even favor parasite existence since tolerant host are reservoirs of the parasites within the population. Therefore, they do not prompt counter-adaptation by the parasites.

Sacks and Yazdanbakhsh conclude their comment by mentioning that these immune strategies should be taken into consideration when designing vaccines for parasitic diseases. They suggest that instead of trying to override this desire of the immune system for tolerance rather than resistance, vaccines could induce tolerance where minimal pathology is caused by a controlled persistence of the parasites. A classic example of a vaccination strategy in this line is Leishmanization wherein live Leishmania parasites used to be inoculated in soldiers or children in risk of infection and would confer immunity to further infections. With regard to development of immunological tolerance to leishmaniasis, not resistance, these types of vaccines need reconsideration.

Can KTIM be a regulatory site widely used by cytosolic kinases?

Identification of Key Cytosolic Kinases Containing Evolutionarily Conserved Kinase Tyrosine-based Inhibitory Motifs (KTIMs).

Posted by: Issa Abu-Dayyeh

I have posted an earlier article to talk about our PLoS NTD paper where we have described a novel strategy by which Leishmania was able to inhibit TLR-mediated macrophage activation through its ability to inhibit IRAK-1 kinase activity by activating the protein tyrosine phosphatase  (PTP) SHP-1.

We have identified the site of binding between SHP-1 and IRAK-1 to be an evolutionarily conserved ITIM-like motif, which we called a kinase tyrosine-based inhibitory motif (KTIM). In this newly-published paper in Developmental and Comparative Immunology, Abu-Dayyeh et al. present evolutinary as well as experimental data that propose that KTIMs could potentially represent a novel regulatory site involved in the control of the kinase activity of many key kinases involved in siganlling pathways of immune cells. Although this work awaits to be further explored by other researches, I believe this work could open various doors towards many important discoveries in the field of immunology.

Here is the abstract of the paper:

We previously reported that SHP-1 regulates IRAK-1 activity by binding to an ITIM-like motif found within its kinase domain, which we named Kinase Tyrosine-based Inhibitory Motif (KTIM). Herein, we further investigated the presence, number, location, and evolutionary time of emergence of potential KTIMs in many cytosolic kinases, all known to play important roles in the signalling and function of immune cells. We unveil that several kinases contain potential KTIMs, mostly located within their kinase domain and appearing predominantly at the level of early vertebrates becoming highly conserved thereafter. Regarding the KTIMs that were found conserved in both vertebrates and invertebrates, we provide experimental data suggesting that such motifs may have constituted readily-available sites that performed new regulatory functions as soon as their binding partners (e.g. SHP-1) appeared in vertebrates. We thus propose KTIMs as novel regulatory motifs in kinases that function through binding to SH2 domain-containing proteins such as SHP-1. Copyright © 2009. Published by Elsevier Ltd.

PMID: 20043942


TriTryp – a database for genomics of Trypanosomatids

posted by: Kasra Hassani

EupathDB in collaboration with GeneDB have started up a database dedicated to genomics and functional genomics of Leishmania and Trypanosoma. The beta version of this website can be found here. It provides us with various tools and resources for genome, proteome and transcriptome browsing and sequence retreival as well as BLAST search and links to pubmed NCBI. I am sure once debugged and fully functional, this database can be very useful for those of us working on Trypanosomatids.

Dawkin’s “extended phenotype”, an extension or a revolution?

Posted by: Issa Abu-Dayyeh

The extended phenotype, a relatively longer and a more difficult reading than Dawkin’s “The selfish gene”, is in my opinion a book worth the reading effort for several reasons:

1-Although a big portion of the book was dedicated to rebuttal critics that showered Dawkins with accusations of being a genetic determinist and a reductionist (Based on his views in the Selfish gene), Dawkin’s replies to those criticisms are pretty logical and organised. In fact, Dawkins almost did not have to retract any of the claims he made 6 years before “the extended phenotype” was written.

2-The rest of the book sets to establish a new vision on the extent to which a gene can act.

Many of us would agree that an organisms’ behaviour is selected to maximize the success of the replication of the genes residing inside this organism. As tempting as this statement might be, this vision definitely pictures the body as the gene’s prison. It is the boundary, the wall,the farthest limit upon which a gene can act.

Dawkins suggests in “the extended phenotype” that the action of genes goes way beyond their ability to produce proteins for the bodies they reside in. In fact, genes can have effects on inaminate objects (such as the type of house an animal would build) or on other living beings. An example given by Dawkins is a trematode that lives in snails. This trematode codes for proteins that drive the snail to produce thicker shells than ususal. This provides greater protection for the trematode while diverting the snail’s energy from practices that could benefit the snail but not the trematode such as: reproduction. The author goes on and on giving examples of how genes can act at a distance!

But how influential is this extended phenotype argument? After reading the book, my initial thought was that it is really no revolution! This is simply an extension of our vision of how far genes should be seen to go. On a deeper thought, I believe this book is revolutionary from a different perspective. First, it places more emphasis on the interactions of genes (regardless of the organism that carries them) on the overall evolution of complex traits and the natural selection they undergo. The principle also explains how a parasite can alter the host’s behaviour to its advantage (therefore suggesting what was formerly thought as mal-adaptation of a host gene as good adaptation of the parasite gene), and how some parasites can end up as symbionts and ultimately interested in increasing the reproductive success of the host and, soon, very difficult to even be seen as  parasites (ex: the mitochondria and chloroplast endosymbiont theory).

This book simply modifies a vision: from behaviour maximizing the success of the genes inside the organism to behaviour maximizing the success of genes that code for that specific behaviour, no matter in whose body those genes are found. This definition reorganizes the genetic vision in a way highly compatible with dawkins’ selfish gene view of evolution and natural selection. Is he right about the extended phenotype or is he wrong? I think most of us would agree it is a logical extension of what we perceive as a direct effect of a gene, but what really matters is that it is different… and a different view is sometimes what we need to reevaluate our current vision and devise new experiments to expand our knowledge. Not to mention the importance of such a vision on the mathematics of genetic contributions to phenotypes. In a nutshell, this is a book worth reading!

MHC I and MHC II, simple and clear, once and for all!

posted by: Issa Abu-Dayyeh

Every couple of months I ultimately get into a discussion about the role of MHC class I and II in the activation of immune functions. What drives their transcription/translation, what cells produce them, how are the peptides found and loaded on them; these are many questions that do not seem to go in the long-term memory section of my brain as well as many others.

Here I decided -once and for all- to summarize the dogmas in the aspects mentioned previously.

MHC class I are molecules produced by all nucleated cells, their production is augmented by IFN-alpha, IFN-beta, IFN-gamma, and TNF-alpha. They are loaded with peptides that result from proteasome-mediated degradation of proteins found in the cytosol, they are transported to be expressed on the surface of cells, and MHC I molecules bound to foreign peptides activate CD8+ T cells by binding to their TCR.

In other words, these MHC molecules keep the internal contents of molecules in check. This is consistent with the fact that such a mechanism is very useful against cancer cells and cells infected with viruses that are actively producing their proteins inside the cells.

On the other hand, MHC class II molecules are produced by antigen presenting cells of the immune system: mainly dendritic cells, macrophages, and B cells. Their production is primarily driven by IFN-gamma (and not the other interferons), they are loaded with peptides that are generated by peptidases found inside phagolysosomes, and upon their translocation to the cell surface, they activate CD4+ T cells.

Two main comments come to my mind upon writing those “facts”:

1- It is impressive how those two MHC types seem to complement each other’s function. MHC I screens for internal “problems”: viruses, cancer, and other antigens that are hiding inside cells away from immune detection, while MHC class II are directed against obvious intruders that go inside the cells by phagocytosis (or any surface detection mechanism ex: TLR) such as:  bacteria and parasites. Together, those two molecules work hand in hand in keeping the organism as alert as possible to all sorts of invaders.

2-Although it is interesting per se that interferons and other pro-inflammatory cytokines upregulate the production of those molecules, it is even more interesting to see that molecules such as IFN-gamma which is not typically involved in counter-acting viral infections can upregulate MHC type I molecules. To me, this suggests that an invasion of the immune system by viruses must somehow lead to the production of danger signals recognized by IFN-gamma producing cells (or their activators) and ultimately leads to a response against those viruses through MHC I upregulation (Future work in the field will be the judge!)

In the end, it is as if the immune system is on “code red” and asks each cell to rapidly disply its ID card to the immune police….Normal cells will show the good ID and pass, suspicious cells will display a “wanted” ID and are destined to be eliminated.

Isn’t it amaizing???