Wallace Marshall
@WallaceUcsf
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professor at UCSF, engineer turned cell biologist, wants to know how cells solve geometry problems
Joined February 2017
Before Twitter shuts down let me just say that you should always verify your RNAseq results using qPCR.
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Has anyone ever done this: use gene editing to replace a bit of sequence with the identical sequence and see if anything happens. It should have no effect of course, but has anyone ever done it? Is it like a standard control for crispr?.
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It’s incredible how densely packed the cell is with organelles and other structures! Just seeing a talk from JLS which brought up this paper using fib-sem
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Where does the structure of mitochondrial networks come from? In a new paper from Greyson Lewis, we review mitochondrial through the lens of graph theory 🧵.
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Delighted to announce our new paper on single-celled learning, In which we show that the gradual habituation to mechanical stimulation seen in groups of Stentor results from step-like responses in individual cells.
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Sorry for maybe dumb question: you know how ppl differentiate iPSCs into all kinds of cells? Can they diff into cell types that don’t normally exist in nature?.
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How do organelles fit together inside a crowded cell? Answering this question requires a way to image many organelles in a whole cell at high resolution with high throughput. Our new preprint shows how to do this in yeast using soft x-ray tomography.
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Delighted to share our new preprint on the cell biology and genome of Stentor pyriformis, a giant ciliate that maintains Chlorella endosymbionts in surface-associated microtubule baskets.
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“Certainly the method is not simple to use. In fact it is difficult to use; but it is intended for the solution of very difficult problems”. -quote from my dad’s book. He passed away this spring but when I read his written words I feel like he is still with me.
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in case twitter goes down this weekend, can we at least all agree that C. elegans is a good model system?.
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@Adrian_Jacobo @BWJones @NeedhiBhalla yeah the problem is that most institutional IT people have absolutely no idea what the actual data needs of scientists are like. its the same problem with computer security where they assume that we only use computers to run word processors and do office work.
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happy to announce our paper on the transcriptional program of regeneration in Stentor! . Stentor is a giant cell with a complex shape that can regenerate. Looking at the genes expressed during regeneration provides a way to learn about the mechanism.
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@Edel_PLopez seriously there is NOTHING WRONG with saying that a manuscript is fine as it is and does not need further changes! I think half the problem with peer review is that we all feel under pressure to find flaws, however minor, to show we are doing our jobs.
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ok sci-twitter - does anyone know of a good (i.e. affordable) web resource for storing cell imaging data where we're talking in the 10-100 terabytes range? have people figured out how to comply with the upcoming NIH data sharing mandates?.
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congratulations to @seemaychou for her 3% score on her NIH R01. for those who aren't sure what this means, suffice it to say that this is an awesome score!!.
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Single cells can learn without a nervous system, but how? In our new preprint, Deepa Rajan and I describe a simple model for habituation in Stentor cells, based on mechanoreceptor internalization and recycling, and test it with quantitative experiments.
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Phase separation in the cytoplasm 1925. Plus ça change, plus c’est la même chose
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thrilled to announce @BEuplotes paper showing that a single cell, Euplotes, coordinates its walking with a computational process implemented using microtubules. We like to think about cells as computers or robots, and this work shows they really are!.
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a lot of the work in enzyme biotechnology is purifying and immobilizing your enzymes. Here we show how you can use the flagellar axoneme to self-assemble enzymes in an immobilized form that is easily purified and stored.
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Where does pattern come from inside cells? in this preprint, @aralbright93 reports a big step towards answering this question by showing that regionalization of mRNA in a Stentor cell depends on an intact microtubule cytoskeleton.
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Trying to upload a manuscript to PNAS takes hours of jumping through stupid hoops. What a PN in the ASs!.
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Variance isn’t just about error bars: it can be a window into biological dynamics. Our new paper uses fluctuation analysis to probe Chlamydomonas flagellar length regulation, a model for organelle size control.
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new preprint on a project we've been working on for a LONG time, using chlamy flagella to study noise . final breakthrough was a new microfluidic device invented by my awesome student @David_P_Bauer . Biological Noise in an Organelle Size Control System
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Hiro Ishikawa bringing up some lab tension about the fact that the model system used by half the lab gets fed to the model system used by the other half
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A joint postdoc position is available in the labs of Prof. Wallace Marshall (UCSF) and Prof. Sindy Tang (Stanford) on single-cell wound healing. We seek candidates with a cell biology or related background to explore how the single-celled ciliate Stentor heals drastic wounds.
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meiotic homolog pairing is the basis of Mendelian genetics, and while a lot is known about the molecular-scale events of meiosis, the question of how chromosomes physically locate each other inside a crowded nucleus, entangled with other chromosomes, is still unanswered
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interested in modeling cell biology? This summer - Finding Your Inner Modeller, August 2-6
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So tonight’s debate makes me wonder - is the fly a good model organism?.
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Congratulations to Amy Chang for her paper just out in PNAS. surprising conclusion: cell state dynamics, as inferred from morphology, can be described with an equilibrium formalism @NSFbiology.Dynamics of living cells in a cytomorphological state space
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Sci Twitter help - why does differentiation of cells entail both cell fate determination AND arrest of division? Is continued division somehow incompatible with locking in a specific cell fate? Like by erasing chromatin state or something? Sorry if this is a dumb question.
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Feast of Seven Fishes done as a paella this year. Mussels, clams, shrimp, crab, lobster, scallops,& calamari. Seven fish!
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True or false: “Stochastic” means the same thing as “random”.
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Finally out: We usually draw nuclei as being spherical, but they can have many different shapes. In her new paper, @rebmcginvestigated the mechanism of nuclear shape change, using the Stentor macronucleus as a model system.
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are you interested in: heterogeneity, differentiation, decision making, or noise in biology? check out the Stochastic Physics in Biology GRC - you don't need to be a card-carrying physicist!!
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I'll never forget witnessing Mats inventing structured illumination in the Sedat lab - he spent months staring into space and scribbling calculations, and then gradually the machine started to take shape. he was a true genius.
Maria has the distinction of being the last user EVER of the Mats Gustafsson Structured Illumination Microscope. While it pains us to do it, the SIM scope will be dissembled to make way for new instruments. It will live on through its reused components. #Janelia #microscopy
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processing my first Christmas without my dad - currently re-reading a book he gave me as a Christmas present when I was in grad school. he knew I was interested in DNA topology and felt that knot theory would be relevant.
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If you wish you could take th Physio Course but fear your advisor won't like it, I volunteer to talk to your advisor and convince them.
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Barcodes are everywhere, but what about in biology? In our new preprint we propose that somatic homolog pairing could be mediated by non-specific interaction "buttons" arranged in a barcode pattern 🧵.
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This is so cool - motile bacteria leaving behind a trail of colonies of nonmotile progeny due to abortive transduction with P22 phage carrying flagellar motility genes
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How do cells measure? Flagellar length in Chlamydomonas provides a genetically tractable model system to explore this question. In our new preprint, Hiro Ishikawa tests a model based on flagellar calcium levels first proposed by Joel Rosenbaum in 2003 .
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Where does pattern come from inside cells? in this revised preprint, @aralbright93 shows that regionalization of mRNA in a Stentor cell depends on dynein motors and the microtubule cytoskeleton.
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Standing room only for @vfarm15 talk on cell biology of giant (like really really giant) cell of the placenta @GladfelterLab #CellBio2023
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Had a great time giving my talk about Stentor regeneration today at SCDB! I feel very privileged to have been given this opportunity!
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Tremendous privilege to have spent the past two weeks exploring cells with an amazing group of students in the physiology course at woods hole. #MBLphys. #xtremecellbiology
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Example of a non- model model organism breaking open a field: van Beneden discoverrd Centrosomes by looking at dicyemid worms.
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Anyone else have their life changed by seeing a picture? Seeing this picture made me decide to combine biology & engineering when I grew up
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Every night my little dog Bantam jumps on the bed, where he isn’t allowed, and goes to sleep. So then I have to pick him up and move him to his own doggie bed. It seems that no matter how many times I do this, he never learns. He must be a special kind of stupid.
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here's surface meshed renderings of the yeast vacuole and nucleus by @marymirvis using soft x-ray tomography data from our collaboration with the Larabell group at LBL. The mesh makes it easy to quantify distance between organelles and the area of their membrane contacts 1/2
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A major focus of our research, has been the mechanism of flagellar length control in Chlamydomonas. Here I want to draw attention to a review that I wrote which explores this topic "through the lens of math" which I will try to explain below.
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Do you like biology and physics? Do you like microscopes? Do you hate sleep or being bored? Apply to the Physiology course!
The application deadline for many of MBL's Advanced Research Courses is Feb. 1. Don't delay - YOU WANT TO DO THIS! Courses in Embryology, Physiology, Microbial Diversity, Neurobiology, Neural Systems & Behavior, Parasitism. Financial assistance available.
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in case twitter goes away this weekend, I just want to say, I am still shocked at how many of you are wrong.
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oh my god this was my rotation project in Cynthia Kenyon's lab back in 1992. I was never able to get it to work, this is so awesome!.
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Metabolism is really just a list of compounds that Chuck Norris allows to cross the mitochondrial inner membrane
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how much of the proteome is localized relative to global cell polarity axes? to answer this question, Athena Lin cut individual Stentor cells into pieces and Tao Liu's group at PNNL carried out proteomic analysis on the pieces.
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Here is a review about regeneration in Stentor, but I wanted to take this moment to relate how I got interested in Stentor in the first place! . Regeneration in Stentor coeruleus
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At the Allen Institute for Cell Science, hanging out with the scientific advisory council at the Cell Representation Summit where the goal is discussing how to define cell state at different scales and levels of abstraction. Cell bio +math+physics+CS+…
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Nice morning running the Oakland half marathon. Finished in 2:48:09 which is pathetic but at least better than my last half marathon time last fall, which was 3:11:06. waaay better than my first attempt at the Oakland half back in 2016 or so where I walked the last 3 miles
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in case twitter goes down this weekend, what do people think, should peer reviewers sign their reviews?.
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Evolution of yeast into humans was driven by declining availability of YPD in the pre-Cambrian environment.
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let's take guesses: if you exert tension on the cell membrane, to what extent does that tension propagate around the whole cell? now read this amazing paper from the Weiner lab and find out what actually happens! @C3STC.
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has anyone published a single-cell RNAseq atlas of a single cell type, like budding yeast or RPE1 cells, and made a u-map type plot? does it look like a nice compact sphere or something, or does it show a higher complexity? i know I should know but. i don't.
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another example of how tightly the organelles are packed inside a cell, this time, the marine alga Ostreococcus. beautiful paper from Grant Jensen's lab taking advantage of the tiny size of Ostreococcus to image the whole cell all at once by cryo-EM.
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quick question for twitter biology ppl: what distinguishes a multicellular organism from a colony of individual cells? I have heard ppl say if it develops from an embryo then its multicellular. is that a formal definition? can anyone point me to a ref?.
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Marshall lab retreat watching @ASCBiology #Cellbio2021 talks in Salinas - trying to capture some aspects of an in person meeting as best we can!
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hey sci twitter any suggestions for good Masters programs for a student interested in the intersection of biology and computer science, with a strong research component?.
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maybe this is a dumb question: if you have RNA inside granules (phase separated) and you prep the cell for ssRNAseq, will the RNA inside the granules be well-represented among the reads? its hard to imagine RT could get inside the granules. has anyone looked at this?.
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This is what happens when you invite a seminar speaker whose work is literally on fire @NeedhiBhalla 🔥#UCSF
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When Stentor regenerates (or divides), its macronucleus does from an elongated shape, to a sphere, and then re-elongates. if you look at enough of these image sequences (made possible by laboriously mounting cells in a Schaeffer rotocompressor) you notice something weird 1/2
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Congratulations Ulises Diaz for his HHMIGilliam fellowship for research on re-use of cytoskeletal structures during Stentor regeneration.
HHMI is proud to announce the 2020 #GilliamFellows! They’re bound by a shared passion for science and will join a growing and diverse community of graduate students and their advisers.
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In biochem we usually assume processes are isobaric so everyone uses Gibbs free energy etc. are there good examples of hydrostatic pressure changing in a cell during a process of interest s.t. it’s not isobaric? Muscle contraction? Is biochem affected?.
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True or false: cancer cells in general have an increased water content compared to non cancer cells? I read this somewhere but is it actually the case? If so, WHY???.
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now at Amazon: Introduction to Quantitative Cell Biology by Wallace F. Marshall via @amazon.
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I want to thank everyone who weighed in on r vs python, SUPER helpful! here is what I am hearing: .A. for ML & image processing use python, for statistics use r.B. Rstudio is better IDE.C. python runs faster.D. more libraries for python.E. r maybe better for bioinformatics.
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As much as I value the unique opportunities created by non-standard model organisms like Stentor, when it comes to automating genetics, you just can’t beat budding yeast. With basic robotics, a single lab can do genome-wide strain constructions and other genetic experiments.
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Talk by @BEuplotes at #CellBio2022 where he was awarded the ASCB Keith Porter postdoc award for his research on cytoskeletal computations controlling cell walking
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Announcing the 2019 Gordon Research Conference on Stochastic Physics in Biology - check it out! Student travel funds are available, just email me for details.
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Stentor moves into the age of high-throughput automation! amazing images by @Connie_Yan0102 on the Opera Phenix high-content confocal platform
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Most impressive thing I have ever seen - @KateAdamala instead of a regular talk is doing a live demo!! #SynCell2022
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Happy to be teaming up with @jiexiao_lab to organize the new Faculty Opinions (formerly F1000) subgroup in cell biophysics. Stay tuned!.
We're delighted to announce an exciting addition to @Facultyopinions, the Biological Physics Faculty! This Faculty will contain expert-recommended #research from this important discipline. Learn more about the launch & the experts heading up the Faculty👇.
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@boehninglab i also don't get the original tweet - is he saying that in his family some people get told they must leave, like "sorry your services as my uncle are no longer required but we wish you all the best in finding another family to join"?.
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Cellbio question: when vesicles bud off of an organelle are they all same size? Do different organelles produce different size vesicles?.
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