Jesse Shapiro

@bjesseshapiro.bsky.social

1867 Followers 829 Following

Macrobe qui aime les microbes http://www.shapirolab.ca/

Photo of 3 minidiscs with handwritten labels. They are show recordings of The Weakerthans and Neko Case from the early 2000s.
Slip of paper with text: “Vous venez d'obtenir un visa de long séjour valant titre de séjour vous permettant de séjourner en France, bienvenue !”
Photo of a car flying mini flags of both Colombia and Brazil
Photo of a rooftop covered in wildflowers and grasses. There are some buildings and an old church in the distance. It’s raining.
Photo of a MatLab software box being used to prop open a door
A group of people standing in the woods on a sunny day on a large boulder, or on a wood ramp leading down from it.
Photo of a group of people standing around a camp fire at night
Photo of a hockey arena with people milling about looking at posters on what would normally be the ice surface.
Photo of a backpack strapped to the front rack of a BIXI bike share bike in a bike lane
Video of the Canadiens flag flying atop the McGill Arts building.
Photo of a bike with a 1.5kg vanilla sheet cake strapped to the front
Photo of an empty cappuccino cup stained with coffee rings of different sizes
Screenshot of a computer cluster monitoring dashboard showing 92% of storage used, with a sticky note on it reading “BLAME NICOT.”
Photo of the boards of an outdoor hockey rink, with ice completely melted and hair grass left. Mont Royal looms in the background.
Restaurant scene with a Canadiens jersey displayed (Caulfield 22) displayed outside the kitchen
Handwritten letter on university letterhead from an emeritus professor in the department congratulating me on my promotion.
Screenshot of text reading: Describe the applicant's weaknesses: Kryptonite
'Doodle' logo with an infinity symbol as the two Os.
Photo taken from above of a wood table set with a bowl of bagels, cream cheese, and lox with capers, red onions, and sliced tomatoes.
Email from McGill university purchasing department reading: I wanted to update you on the situation shared in recent announcements to the McGill community related to the availability of key computer components. It has become increasingly difficult to purchase computer equipment. Manufacturers across the industry are facing significant constraints as increased demand from large cloud infrastructure providers that is affecting the global supply chain. Impact on HP Orders Due to these circumstances, HP has suspended the processing of orders for laptops and desktop computers. As a result, MicroAge-DIL (McGill’s supplier for HP computers) will be temporarily blocked as a supplier in McGill MarketPlace (MMP) until further notice. This a difficult situation that will require careful management and ongoing monitoring. Alternate supplier options Given the extent of this worldwide shortage, we are authorizing orders for new computers that would normally be placed with HP to instead be submitted to alternate suppliers such as Lenovo, Dell, or Insight (for Apple products). However, similar delays may occur with these suppliers as we have been advised that other manufacturers are also impacted. We can expect delivery and response times to be longer than usual.
Species in the Bangladesh cohort with a significant increase in P:H ratio between patients exposed vs. not exposed to ciprofloxacin. Statistical significance was assessed with a Wilcoxon rank-sum test with Bonferroni multiple correction. Only species with corrected P ≤ 0.05 are shown.
P:H ratio across ciprofloxacin exposure status in the Bangladesh cohort (left). Statistical significance was assessed with a Wilcoxon rank-sum test. P:H ratios in healthy US volunteers before (pre), during (days 1, 3, and 5), and after (post) ciprofloxacin exposure (right).
Conceptual visualization of the prophage to host (P:H) ratio as calculated from metagenomic reads mapped to assembled contigs containing prophages.
A big screen TV livestreams a bald eagle sitting in its nest. The TV is above a bar stocked with beer, chips, etc
Marie-Philip Poulin smiling on the bench after scoring her 19th career goal at the olympics. She’s wearing a Team Canada jersey with the captain’s C.
Photo of a bike with a bunch of firewood on the front rack and paniers on the back rack.
There are at least two biological mechanisms that could underlie the general observation of an association between HGT and co-occurrence. First, taxa that are physically closer could simply have more opportunities for HGT, which must be true to some extent. For instance, taxa in completely isolated environments, with no gene flow or possibility of DNA transfer, cannot undergo HGT. In regions of the ocean stratified by geography, depth, and environmental factors, it is reasonable to expect that taxa would undergo HGT more frequently with other taxa sharing the same local environment. Second, an alternative causal explanation is that HGT of habitat-specific genes allows species sharing those genes to thrive in that habitat, and thus to co-occur. In this alternative explanation, co-occurrence is a proxy for unmeasured environmental variables that define cryptic microbial habitats. Distinguishing between these explanations for the observed associations is an avenue for future research, potentially harnessing time-series sampling to infer causal relationships. Although we cannot formally distinguish between these explanations, our results are consistent with both physical proximity driving HGT and, potentially, HGT contributing to shared niche preferences. We consistently found evidence for increased HGT among genomes in larger particle-associated filter fractions. This suggests that physical proximity on particles, in contrast to reduced encounter rates among planktonic prokaryotes enriched on the small filter fractions, could drive HGT. The larger filter fraction could also share common selective pressures, associated with a particle-attached lifestyle, which may also explain the association with HGT independently of physical proximity.
Breakdown of HGT and related feature prevalence across 43 Tara Oceans samples. The same biological samples are matched based on whether they were enriched for small or large particles based on the fraction filter (i.e. to enrich for free-living or particle-attached prokaryotes). The y-axis for all panels is the proportion of genomes in a sample with at least one instance of that category (e.g. the proportion of genomes in a sample with at least one gene identified to be either acquired or transferred through HGT). Asterisks indicate significant comparisons (adjusted P values <0.05) based on paired Wilcoxon tests.
Coefficients in logistic regression model based on all pairwise genome comparisons. The response is whether those genomes have at least one called horizontal gene transfer event (based on the cluster-based approach) between them or not. Co-occurrence (based on the hypergeometric approach) is a binary variable indicating whether those genomes significantly co-occur. “Free-living” and “Free-living and particle-attached” indicate whether the genomes being compared are both enriched in samples filtered to enrich for small particles, or those with little or no size filters. The other variables are ordered quantile normalized continuous values. Variables with “diff.” represent the median inter-sample difference in each environmental variable for all samples encoding the two genomes being compared. Coefficient values less than 0 indicate that decreases in those variables are associated with increases in horizontal gene transfer, whereas a positive value represents the opposite. The intercept for this model was −14.35. Error bars represent 95% confidence intervals (1.96 × standard error). All variables were significant (P values <0.05) except for “small particle enriched”.
Email from workday with subject: A task awaits you: review documents - update academic appointment… (what does it mean?!)
Photo of a projector screen showing a hockey faceoff between Swiss and Canadian women.
A photo of a dumpster in a snowy alleyway with several large white buckets labelled “poutine Québecoise traditional sauce” strewn over the ground
Still shot of Catherine O’Hara and Eugene Levy in Best in Show
Danish flag flying from a flagpole on a red brick house facade.
A selfie of a group of smiling people around a table
Selfie of a bearded man in sunglasses and tuque grinning. He is in skis (not shown) with a snow-covered park in the background.
Two people smiling and holding up golden goblets
Photo of a winter scene with a groomed Nordic ski path running alongside.
First-person video of a bixi bike being ridden through a snowy street.
Photo of a bixi bike share station covered in fluffy fresh snow
A group of smiling people around a restaurant table.
View of train tracks out a train window. Snow is falling and there is a light dusting of snow on the tracks and platform.
Two Oxford nanopore promethion sequencers sitting on a lab bench, each sequencing two flow cells each. One is labelled “Kassen” with red lab tape.
Window of a takeout restaurant advertising pad thai with an AI-generated image of noodles with circular shrimp. It’s been defaced with the text “FUCK AI” in red marker.
A mural of road cycling racers and the inclined tower of the Olympic stadium are illuminated by the golden light of the setting sun. In the foreground, orange cones casually delimit an intersection under construction.
A photo of a cycling map of France on a table beside a glass of beer on a table in a bar.
A corner grocery store with a plethora of pumpkins spilling out on the sidewalk, draped with fake cobwebs and other Halloween decorations.
Photo of construction (and notably demolition of 1960s era wings) of the old Royal Victoria hospital
Photo of the back of the car obscured by 3 bikes piled onto a bike rack.
Coefficients in logistic regression model based on all pairwise genome comparisons. The response is whether those genomes have at least one called horizontal gene transfer event (based on the cluster-based approach) between them or not. Co-occurrence (based on the hypergeometric approach) is a binary variable indicating whether those genomes significantly co-occur, and “free-living” and “less-filtered” enriched indicate whether the genomes being compared are both enriched in that sample-type. The other variables are ordered quantile normalized continuous values. Variables with ‘diff.’ represent the median inter-sample difference in each environmental variable for all samples encoding the two genomes being compared. Coefficient values less than 0 indicate that decreases in those variables are associated with increases in horizontal gene transfer, while a positive value represents the opposite. The intercept for this model was −14.35. Error bars represent 95% confidence intervals (1.96 x standard error). Note that all variables are significant (P < 0.05) except for “free-living” (enriched).
Distributions of the difference in median value of each environmental variable between genome pairs, split by genome pairs connected by HGT and not. The median value for each variable was computed for each genome based on all the metagenomics samples it was found within.
Summary of putative horizontal gene transfer events based on sequence identity cutoffs. (a) Counts of putative horizontal gene transfer (HGT) events based on the cluster-based approach, by the lowest taxonomic level at which the compared genomes differed. The total number of genome comparisons per level is also indicated. These cells are coloured by the percentage per column. (b) Proportion of putative horizontal gene transfer events per taxonomic level, after normalizing by the total number of genome comparisons per level.
Summary of significant coefficients (P < 0.05) in generalized linear mixed model with singleton and doubleton (ultra-rare) element state (intact or pseudogene) as the response. This model was based on 213,912 separate elements. The predictors were each element’s annotated COG category, whether the element is redundant with an intact gene of the same COG ID (i.e. gene family, not COG category) in the same genome, and the interaction between these variables. The non-redundant coefficients represent the sum of the overall non-redundant coefficient and the interaction of non-redundancy and each COG category. Estimates correspond to logit (log-odds) values: estimates > 0 indicate an increased probability of an element being classified as a pseudogene. Error bars represent one standard error.
Schematic of evolutionary scenarios. Scenario 1 represents the situation in which mobile genes Tajima’s D is negatively correlated with gene mobility because HGT is faster than fixation of mutant alleles (red stars). Scenario 2 represents the situation in which Tajima’s D correlates positively with mobility. These genes maintain intermediate frequency mutations (blue stars) despite being frequently transferred to new species. Note that the gene copies (dots or stars) illustrated here could come from members of the same or different species in the microbiome.