Tim Yu

phd student @mcbseattle in the @jbloom_lab wondering how viruses evolve

[Bloom Lab @jbloom_lab]

In new study led by @timcyuu, we measure how mutations to H3 flu HA affect cell entry, stability & antibody escape

We find pleiotropic effects of mutations on these phenotypes shape evolution: epistasis alleviates cell-entry but not stability constraints

https://t.co/mZs4KdCvkv

[Bloom Lab @jbloom_lab]

In study led by @CKikawa & Andrea Loes, we use new assay to measure ~10,000 neutralization titers to recent influenza strains & show titers correlate w evolutionary success of viral strains

Similar data could help forecast evolution for vaccine selection

https://t.co/OxwiNnXUuU

[Tim Yu @timcyuu]

Congrats @gracecbower!

[Grace Bower @gracecbower]

Beyond proud of the work that went into our latest story! A big shoutout to @evgenykvon for the incredible guidance.

[Evgeny Kvon @evgenykvon]

How do enhancers work over distances that sometimes exceed megabases? Excited to share our work led by @gracecbower where we uncover a unique sequence signature globally associated with long-range enhancer-promoter interactions in developing limb buds: https://t.co/n0p7BdxSdq 1/

[Bloom Lab @jbloom_lab]

In new study led by @bdadonaite, we measure how all mutations to H5 influenza HA affect four molecular phenotypes relevant to pandemic risk:
https://t.co/QOjVTF4h9L

Results can inform surveillance of ongoing evolution of H5N1.

[Bloom Lab @jbloom_lab]

In new study led by @bblarsen1 in collab w @veeslerlab @VUMC_Vaccines we map functional & antigenic landscape of Nipah virus receptor binding protein (RBP)
https://t.co/EyFWcxzRe9

Results elucidate constraints on RBP function & provide insight re protein’s evolutionary potential

[Bloom Lab @jbloom_lab]

In new study led by Andrea Loes, we develop sequencing-based neutralization assay that measures replicate curves for hundreds of virus-serum pairs per 96-well plate (see image below)
https://t.co/hCkjUEiRpV

We apply assay to characterize response to repeat influenza vaccination

[Bloom Lab @jbloom_lab]

In new study led by Caleb Carr & @khdcrawford, we measure how all mutation to Lassa virus glycoprotein complex (GPC) affect cell entry & antibody escape

Results show how prospective assessment of effects of mutations can inform design of countermeasures
https://t.co/M2LmbTbwKm

[Bloom Lab @jbloom_lab]

In new study led by Frances Welsh, we map how mutations to influenza affect neutralization by antibodies from humans of various ages

We find differences in mutation effects among age groups

Virus has evolved especially to escape antibodies of teenagers

https://t.co/yZR1ryE62j

[Jessie Kulsuptrakul @JKulsuptrakul]

Thrilled to announce my first first-author paper of grad school has been accepted at @eLife! Shoutout to @turcotteea, my 2 awesome labs, and my two amazing advisors Michael Emerman and @psmitchej. Check it out here: https://t.co/vIhW9EANOM

[Bloom Lab @jbloom_lab]

In a new study led by @CaelanRadford in collaboration with @FKlein_lab, we use an improved deep mutational scanning system to map the neutralizing specificities of broad human polyclonal serum antibodies from individuals living with HIV.
https://t.co/GCeUHRyjlQ

[Bloom Lab @jbloom_lab]

Final version of our paper on deep mutational scanning system to measure antigenic and functional effects of mutations to full SARS-CoV-2 spike: https://t.co/DDaCUk1MCx

System uses non-replicative lentiviral pseudotypes to safely map effects of thousands of spike mutations.

[Bloom Lab @jbloom_lab]

In work led by @bdadonaite @khdcrawford @CaelanRadford, we develop pseudovirus system to deep mutational scan full #SARSCoV2 spike: https://t.co/O6MGHXVWdS

TLDR: can now safely measure how all mutations to viral entry proteins affect antibody neutralization.

🧵 below (1/n)

[Jessie Kulsuptrakul @JKulsuptrakul]

First manuscript of grad school now live on bioRxiv! Check it out ;) So excited and thankful to @psmitchej and @memerman for their amazing guidance.

[Tyler Starr @tylernstarr]

Our newest study is up, where we report deep mutational scanning data in the Omicron BA.1 and BA.2 receptor-binding domains https://t.co/NlVGygtQag

[Tim Yu @timcyuu]

Excited to share our preprint on modeling viral escape from polyclonal antibodies. Check out the thread by @jbloom_lab for more details!

[Bloom Lab @jbloom_lab]

In new work, we formulate a biophysical model of viral escape from polyclonal antibodies, & develop software to apply model to deep mutational scanning data to understand antigenic effects of combinations of mutations: https://t.co/6DS5PLqpJp

I explain in 🧵 below.

[Bloom Lab @jbloom_lab]

In new study, we examine how target cell ACE2 expression affects #SARSCoV2 neutralization https://t.co/47RTQ5aeSS

We find high-ACE2 cells emphasize role of RBD antibodies in serum & lower ACE2 cells reveal more neutralization by antibodies to other regions of spike.

🧵 below:

[Bloom Lab @jbloom_lab]

In new study led by @dbacsik, we show single influenza-infected cells produce wildly different numbers of viral progeny: https://t.co/mZSRW3k2iw

Surprisingly, cells that transcribe the most viral mRNA are NOT ones that produce the most progeny virions.

Explanatory 🧵 below

[Tyler Starr @tylernstarr]

🥳 Excited to share that the Starr Lab is coming to the University of Utah @UofUBiochem! Check out the lab website to see where we’re headed in our studies of protein evolution in viruses and immunity https://t.co/J6Dc9pCBK3

[Bloom Lab @jbloom_lab]

We have new data on the effects of all RBD mutations to Omicron BA.1 and BA.2 on ACE2 affinity & RBD expression. These data, which are from experiments and analyses by @tylernstarr @AllieGreaney & Will Hannon are available here for viewing and download: https://t.co/QPXRmQIyZV