Various writings

Below are a selection of scientific articles I published during my stint as an immunologist. You can see a full list here.


IRG1 and inducible nitric oxide synthase act redundantly with other interferon-gamma-induced factors to restrict intracellular replication of Legionella pneumophila.

How does our immune system protect us against pathogens we've never encountered before? Redundancy, my dear... and also redundancy. Using the "accidental pathogen" Legionella pneumophila, we showed that macrophages turn on multiple redundant antimicrobial pathways in response to interferon gamma, an infection alarm signal. Using CRISPR, we identified six interferon gamma-dependent genes that appear to have an overlapping restrictive effect on L. pneumophila during infection. This article was published in mBio in 2019. Art by Kyle Gabler. PDF


Legionella pneumophila is directly sensitive to 2-deoxyglucose-phosphate via its UhpC transporter but is indifferent to shifts in host cell glycolytic metabolism.

Sometimes a postdoc goes down, down, down the rabbit hole chasing something he just can't get out of his head. In my case, it was a drug called 2-deoxyglucose and its effect on Legionella pneumophila replication in macrophages. 2DG is sweet, 2DG is seductive, 2DG is deadly... and of course, 2DG is highly relevant to both L. pneumophila biology and host/pathogen interaction! At least, that is the case we tried to make in this article, which was published in the Journal of Bacteriology in 2018. Cover art by Kyle Gabler. PDF


Cell death and cell lysis are separable events during pyroptosis.



Yes, I dipped a toe into the burgeoning and explosive - spoiler alert: maybe not-so-explosive! - field of the inflammatory cell death known as pyroptosis. "Pyro" = fire; "ptosis" = falling/dropping... "pyroptosis" = fiery cell death... (but it's all Greek to me)

In the early days of my postdoc, I had visions of discovering the mechanism of pyroptosis (pause for laughter), a form of cell death that many people at the time, and to this day, describe as "lytic". Lytic meaning cells that die by pyroptosis are thought to burst, explode, bust open, rupture, lyse... pop!

We thought that imaging individual cells as they die by pyroptosis would help us figure out the mechanism, and while we were tinkering with an old and crotchety microscope, other labs figured everything out. Cue sad gay music. However! All was not lost! We were able to show that lysis, aka cell "popping", can be decoupled from cell death during pyroptosis. In other words, a long-standing assumption in the field is likely not correct: pyroptotic cells don't die because they burst open - it seems they burst in the artifical conditions of the lab after dying.

In other, other words: pyroptosis is not necessarily a lytic form of cell death, and in vivo, cells may not lyse as a consequence of pyroptosis. This could have implications for how the immune system regulates inflammation during infection and in other situations when cells undergo pyroptosis. Here is a link to the article, which was published in Cell Death Discovery in 2017. Panel from figure 2, above, generated by Lucian DiPeso. In fact, Lucian generated all the data and all the figures in this paper! He is a rockstar. PDF


The Macrophage Paradox.



Why do so many pathogens survive and replicate inside immune cells called macrophages, which are supposed to hunt, eat, and kill pathogens? My postdoc advisor, Russell Vance, and I speculate about the "macrophage paradox" in this review article, which was published in the Immunity in 2014. Cover art by Kyle Gabler. PDF

Figure 1 from the article. Why do so many bacterial pathogens make macrophages, a menacing cell type, their home? Illustration by Kyle Gabler.

Also... kinda cool that the Wikipedia entry for the journal Immunity (at least as of 2020) features Kyle's cover!


Protein microarray analysis reveals BAFF-binding autoantibodies in systemic lupus erythematosus.



This article, published in the Journal of Clinical Investigation in 2013, reflects the main project I worked on during my Ph.D. thesis in PJ Utz's lab. The aim of this project was to create a protein microarray to detect antibodies that bind to the communication factors of the immune system: cytokines, chemokines, growth factors, and other secreted molecules that circulate in blood and other body fluids.

We hypothesized that people with human autoimmune diseases, like systemic lupus erythematosis (aka "lupus" or "SLE") might attack their own immune communication factors in addition to more widely known self-targets. My project was to expand upon existing array technology in the Utz lab to test patient samples for these "anti-cytokine autoantibodies". We demonstrated that this expanded array platform is able to detect antibodies to immune communication factors with excellent sensitivity and specificity, that it detects known and novel antibodies in human samples previously studied in other labs, and that it can be used to detect known and novel antibodies in samples from people with SLE.

The SLE results were exciting because we revealed a spectrum of previously uncharacterized antibodies in SLE patients that may be interfering with immune signaling and could contribute to disease pathology. The rainbow heatmap above shows immune communication factor targets of auto-antibodies in SLE patient samples vs. healthy control samples. PDF


Characterization of Influenza Vaccine Immunogenicity Using Influenza Antigen Microarrays.



During my time in the Utz lab, I had the chance to participate in a large consortium project studying the immune response to influenza. Our part of the project involved developing a peptide microarray to determine which parts of the flu virus are targeted by antibodies following influenza vaccination. We divided the influenza protein hemagglutinin into 24 overlapping "chunks" (see figure above). We synthesized these chunks, called "peptides", and spotted them onto an array, which we used to screen patient samples taken pre- and post-vaccination.

In this article, published in PloS ONE in 2013, we discovered regions of the viral protein that are associated with a strong, protective antibody response, and regions associated with a weaker response. A cool aspect of this project was that our samples came from both young and older people before and after vaccination. Young people tend to generate a strong immune response to influenza vaccine, and older people tend to make a poorer immune response to the vaccine. We identified regions of the virus which seem to "distract" the immune response in older adults, meaning that older people appear to make immune responses to parts of the virus that don't end up being protective during infection. These results could help guide vaccine development. PDF


On silico peptide microarrays for high-resolution mapping of antibody epitopes and diverse protein-protein interactions.



Perhaps fittingly during my graduate school years in silicon valley, I got the opportunity to work on a project using actual silicon wafers. My lab collaborated with Intel Corp. to construct peptide microarrays using photolithography directly on silicon chips with the ultimate goal of creating a biological screening tool that can interface in real time with a computer. P.J. called these arrays "On silico" peptide microarrays, which demonstrates why P.J. is so iconic.

Turns out that these arrays work beautifully! The precision of Intel's photolithography process enables the creation of incredibly detailed, high-content microarrays, which we used determine the exact epitopes (aka binding sites) of all sorts of antibodies, including from SLE patient samples. This was an exciting project to work on as a graduate student and the Utz lab has continued to develop these arrays in collaboration with Intel and other academic labs. This article was published in Nature Medicine in 2012. PDF

Above is a picture of an array that reveals the binding sites of antibodies from a person with SLE.

Fig. 1: Intel array design and construction:

I spent hours making a 3D visualizaton of one of the Intel array grids, which nobody else thought was very impressive. But for posterity, here you are:


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