Tag Archives: bioinformatics

Bowdish lab research on the evolution of MARCO featured in the New York Times

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Our research on the scavenger receptor MARCO was featured in an article “Air Pollution, Evolution, and the Fate of Billions of Humans” by Carl Zimmer in the New York Times. In this manuscript we collaborated with Dr. Brian Golding, an expert in evolutionary biology in order to understand the evolution of this macrophage receptor. MARCO (or macrophage receptor with collagenous structure) is expressed on macrophages where it binds bacteria and particles such as those found in dust and air pollution. We had hypothesized that because it is the receptor for two pathogens, Streptococcus pneumoniae and Mycobacterium tuberculosis, that have played a major part in driving human evolution, that we might find evidence of areas of the receptor that were undergoing rapid evolution to protect us from this pathogen.

In order to determine which regions of the protein were changing we performed a phylogenetic analysis of the sequence of MARCO from humans, our close ancestors, the Denisovians and Neanderthals, and primates. We found a few interesting things. There was one mutation, which we call F282S (282 refers to the 282nd amino acid in the protein, the F = phenylalanine and the S= serine), had changed very rapidly. All our primate, Denisovian and Neanderthal relatives had a serine residue in that position but fully 83% of the human genomes we analyzed had a phenylalanine. The fact that this mutation spread so quickly through the population means that there must have been very strong selection pressure. We cloned both variants and found that the human specific variant was indeed better at binding inert particles and bacteria. There were a few other interesting mutations we characterized (see article below) but the take home message is that some of the evolutionary adaptations we have made to deal with pathogens may have influenced our ability to handle air pollution or, since the savannah was predicted to be a dry and dusty place, the adaptations we’ve made to deal with particulates in the air may have changed our response to pathogens.

To read the full article, see below.

Human-specific mutations and positively-selected sites in MARCO confer functional changes. Novakowski KE, Yap NVL, Yin C, Sakamoto K, Heit B, Golding GB, Bowdish DME. Mol Biol Evol. 2017 Nov 20. doi: 10.1093/molbev/msx298.
PMID: 2916561

Publication: Human-specific mutations and positively-selected sites in MARCO confer functional changes.

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First author on the publication, PhD student Kyle Novakowski of Dr. Dawn Bowdish’s lab.
A common element that links ancient fish that dwell in the darkest depths of the oceans to land mammals, Neanderthals, and humans is the necessity to defend against pathogens. Hundreds of millions of years of evolution have shaped how our innate immune cells, such as macrophages, detect and destroy microorganisms.

In a new study led by Dr. Dawn Bowdish (in collaboration with Dr. Brian Golding) and her PhD student Kyle Novakowski, the team identified novel sites within a macrophage receptor, MARCO, that are under positive selection and are human-specific. The team demonstrated the importance of these sites by site-directed mutation and showed a reduction in cellular binding and uptake of pathogens. These findings demonstrate how small genetic changes in humans can influence how we defend ourselves against pathogens.

Read the full publication in Oxford University Press.

Human-specific mutations and positively-selected sites in MARCO confer functional changes. Novakowski KE, Yap NVL, Yin C, Sakamoto K, Heit B, Golding GB, Bowdish DME. Mol Biol Evol. 2017 Nov 20. doi: 10.1093/molbev/msx298.
PMID: 2916561

Publication: Streptococcus pneumoniae Colonization Disrupts the Microbial Community within the Upper Respiratory Tract of Aging Mice

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Colonization of Streptococcus pneumoniae within the upper respiratory tract (URT) of elderly individuals is a major concern, as it often results in the development of pneumonia, which can be deadly in this population. A study published by MIRC Masters’ student Netusha Thevaranjan, under the supervision of Dr. Dawn Bowdish, examined howNetusha-sm aging can change the composition of the respiratory microbial community and consequently, impact bacterial colonization. Using a mouse model of pneumococcal colonization, the study characterized the composition of the URT microbiota in young, middle-aged, and old mice in both the naïve state, and throughout the course of nasopharyngeal colonization with S. pneumoniae. It was shown that the composition of the URT microbiota differs with age, and that colonization with S. pneumoniae in older mice disrupted pre-existing microbial communities.

Furthermore, the study demonstrated that there were several interspecies interactions between S. pneumoniae and resident microbes. In particular,Streptococcus interacted competitively with Staphylococcus and synergistically with Haemophilus. This work provides insight into how aging influences bacterial colonization, and understanding the relationship between these two factors can help create strategies to protect the elderly from age-associated infections and disease. Read More

Vote/like our video highlighting our NSERC funded research!

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The Bowdish lab is thrilled to participate in NSERC’s “Science, Action!” video contest. An undergraduate team of videographers (Yung Lee, Karanbir Brar, and Tony Chen) filmed our lab discussing our NSERC funded work on discovering the evolutionary origins of phagocytosis. Please “like” and share our video to help us move on to the next level of the competition.

Our NSERC funding has been integral to the lab. This was one of the first grants that got the lab up and running and to date we have had 5 NSERC funded graduate students and 10 undergraduate students including 3 NSERC Undergraduate Summer Research Assistants in the lab. This funding has also been instrumental in developing new techniques, technologies and collaborations that have extended our research capacity.

What are we studying with our NSERC funded research?

Our NSERC Discovery Grant  entitled “Uncovering mechanisms of phagocytosis by class A scavenger receptors” allows us to use bioinformatics and molecular biology to understand the very origins of immunity.

Our lab studies macrophages, which are sentinel cells of the innate immune response. They patrol the body and engulf damaged tissues or pathogens and destroy them. This Pac-man like ability to eat microbes is called “phagocytosis”. We study a particular class of receptors that macrophages use to phagocytose called the scavenger receptors.

Phagocytosis is an ancient process that is central to defence and nutrient acquisition in single-celled organisms and embryonic development, clearance of modified host proteins and innate immunity in multi-cellular organisms. During phagocytosis a phenomenal amount of information is transmitted to the cell including the size and shape of the particle, its composition, and potential toxicity. How this information is transmitted is not really understood but is the focus of our work.

All the major discoveries in immunology (e.g. toll like receptors, intracellular sensors, signalling pathways) began with studies in comparative or evolutionary biology and my program of research continues this tradition. Indeed, the process of phagocytosis is believed to be the prototype function of the immune system as acquisition of nutrients developed into a mechanism of self- versus non-self recognition. The process of uptake is so ancient that it must have occurred prior to or in conjunction with the expression of protein receptors on the surface of the cell. The scavenger receptors, being primitive but effective uptake receptors may rely on membrane dynamics and lipid interactions more than their more evolutionarily recent counterparts (e.g. Fc receptors).  We use bioinformatics to study the genomes of ancient and modern animals to study how the scavenger receptors change over time. Parts of the scavenger receptor gene or protein that haven’t changed over time, are likely very important for function. We use molecular biology to uncover how these particular regions of the protein work.  Studying these processes will uncover novel mechanisms of signalling and contribute to our understanding of the cell biology of endocytosis and phagocytosis, which are processes integral to embryonic development, immunity, homeostasis, implant recognition and adhesion and consequently essential to many fields of biology.

Check out the other videos of the “Science, Action!” video contest here.

http://www.nserc-crsng.gc.ca/ScienceAction/index_eng.asp

To read more about our NSERC funded work click here.

Manuscript: The evolution of the scavenger receptor cysteine-rich domain of the class A scavenger receptors

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Do you work out? Cause you’re built like a rock! A rock like Dwayne “The Rock” Johnson! You have an impenetrable body thanks to your complex immune system. So how did you get such a sophisticated immune system?

In the Bowdish lab, we do more than just macrophage biology; we also study the evolution of the immune system! The scavenger receptors are a group of receptors that play an important role in your immune system by binding harmful bacteria. Our most recent publication by Yap et al., looks at how these receptors evolved and how evolution has changed their function. These receptors are found in various forms of life such as sharks, frogs, and mammals, but the function and appearance of these receptors has changed over time. Check out the open access….

A guide to Bioinformatics for Immunologists

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Congratulations to Fiona Whelan (MSc, Bowdish lab; PhD student, Surette lab) for publishing the review article “A guide to bioinformatics for immunologists” in Frontiers Immunology. The idea of this article spawned from the research that Fiona conducted in the Bowdish lab on the elucidation of the evolutionary history and relationships between the members of the class A scavenger receptors, proteins required for host defense and homeostasis. During this time, Fiona used multiple bioinformatic techniques and tools to form hypotheses as to the function of one under-annotated member of this family, SCARA3.  Even though most of these tools are easy-to-use and require little computational knowledge, Fiona and Dawn discovered through their interactions with other immunologists that these tools were being under utilized.  Thus, they decided to write a review of how bioinformatic techniques can help the average immunologist in their quest for knowledge about the structure of their protein of interest, how to find SNPs that may correlate with disease phenotype, and how to conduct sequence alignments in order to find areas that are conserved across various genes.

This review article is written as a case study that follows Fiona’s research into SCARA3 that begins with obtaining the NCBI Reference FASTA sequence of the protein, predicting post-translational modifications, identifying conserved motifs, hypothesizing as to the structure of the protein, examining SCARA3’s transcriptomic profile in different immunological cell types, and analyzing any potential SNPs within the DNA sequence of SCARA3 that may correlate with disease. The article is written with the immunologist in mind and includes the use of only “point and click” tools that require no computational background whatsoever.

Is Fiona’s paper is Open Access? Of course it is! Enjoy reading it here and reading the description on the Surette lab website here.

The laboratories of both Dr. Bowdish and Dr. Surette are always interested in undergraduate and graduate students interested in exploring the impact bioinformatics can have on immunological and microbiological research.

Extra, Extra, Read all about it! The Bowdish lab elucidates the evolution of the class A scavenger receptors.

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Congratulations to Fiona Whelan (MSc) for publishing her first manuscript “The Evolution of the class A scavenger receptors” in BMC Evolutionary Biology. The scavenger receptors are an evolutionarily ancient family of proteins required for host defence and homeostasis but teasing apart their function and even their structure has been challenging. The goal of this manuscript was to use evolution as a guide to discover how the class A scavenger receptor family was formed and to identify regions of conservation and hence probable functional importance for future study. Phagocytic receptors such as the class A scavenger receptors are integral members of the innate immune response, which is conserved in all classes of life and after reproduction and nutrient acquisition is probably the major most fundamental requirement for survival.

There are essentially only four basic mechanisms of the innate immune system – agglutination (e.g. lectins), lysis/neutralization (e.g complement, antimicrobial peptides), phagocytosis (e.g. scavenger receptors), and pro-inflammatory signalling (e.g. the toll like receptors). The fact that these processes are ancient and have been so strongly preserved is a testament to their importance. Of these, phagocytosis is likely the most ancient process and was probably adapted from its original purpose of nutrient ingestion . One might hypothesize that phagocytosis was truly the genesis of the immune system since our single celled ancestors had to distinguish  between “self” and “non-self” in order to distinguish between food and their own daughter cells.  From there phagocytosis became essential to fundamental processes such as embryonic development, pathogen recognition, and homeostatic clearance of senescent cells. Without phagocytosis, the transition to more complicated life forms could not have occurred.

Although there have been excellent evolutionary analyses of the lectins, toll like receptors and complement pathways, very little is known about the evolution of the phagocytic receptors. The class A scavenger receptors are an excellent example of these multifunctional receptors as they are involved in both host defence and homestasis. Since the phagocytic receptors in general and the scavenger receptors in particular are a diverse group of proteins,it has been challenging to understand how members within a group are related. Indeed, the first goal of this manuscript was to definitively demonstrate that the members of the class A scavenger receptors, which had been grouped together based on a ragtag combination of ligand binding and some degree of amino acid similarity, were actually a family at all.  Since we were able to trace a probable path of gene duplication and consequent functionalization, we are confident that the 5 members (SRAI/II, MARCO, SCARA3/4/5) are actually related.  Interestingly the class A scavenger receptors may have acquired their long stalk like form with a single scavenger receptor cysteine rich domain (SRCR) around the time of the evolution of fish since, although SRCR domain can be found in invertebrates and single celled organisms, we could not find anything that resembled a modern class A scavenger receptor in any genomes of evolutionarily more ancient organisms such as jellyfish, lampreys and insects.

Because elucidating the function of the specific domains of the scavenger receptors has been so challenging (even the function of the SRCR domain is unclear), ultimately we want to use evolution as a guide to which domains are functionally important (i.e. conserved). In this regard we found that there is a common conserved region in the collagenous domain, which in the type member SRAI, is believed to be the ligand binding domain. In addition conserved domains were identified in the cytoplasmic tail and the coiled-coiled domain. Future experiments will be performed to determine if these domains are necessary for structure, expression, cellular localization or phagocytic function.

The best part of our paper is that it is Open Access so you can enjoy reading it in provisional form today at http://www.biomedcentral.com/1471-2148/12/227/abstract. If you have questions, comments or thoughts, please feel free to contact Dr. Dawn Bowdish at bowdish@mcmaster.ca or on her Google+ account. Dr. Bowdish is always interested in talking with undergraduate or graduate students interested in pursuing studies that use bioinformatics to answer questions about the scavenger receptors, phagocytosis, and structure/function relationships.

A summary of the common motifs in the class A scavenger receptor protein sequences. Conserved motifs present in the protein sequences of these receptors are indicated with coloured boxes at their approximate position within the protein with shout out boxes used to show the level of conservation across the aligned Homo sapiens sequences. From Whelan et al. BMC Evol Biol. BMC Evolutionary Biology 2012, 12:227