[HN Gopher] Simulating a minimal cell in the browser
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Simulating a minimal cell in the browser
Author : agnosis
Score : 96 points
Date : 2024-01-20 10:22 UTC (12 hours ago)
(HTM) web link (technistuff.com)
(TXT) w3m dump (technistuff.com)
| agnosis wrote:
| Have you ever wondered how life's most basic units, cells,
| operate? As a programmer and cell biology enthusiast, I embarked
| on a journey to simulate the simplest cell using TypeScript.
| ClaraForm wrote:
| In biology, there's a whole field of research dedicated to
| minimizing cells and their complexity. If you message "John
| Glass" he might be interested in having you model his work!
|
| Edit: oops you've already modeled John's work! That's awesome.
| :D I've attended a few talks by John and I think he'd still be
| interested in seeing whether the modeling side of things can
| explain why he can't get the minimal cell smaller.
| mtekman wrote:
| This is really amazing. I wonder if confounders such as
| transcriptional bursting[1] are modelled too? I did not check but
| I assume cell-cycle is readily modelled.
|
| 1: The tendency of a single cell to perform transcription in
| bursts of activity/inactivity, which averages in bulk tissue as a
| continuous variable.
| bglazer wrote:
| They use a master equation for transcription, so they could
| theoretically get bursty behavior. But, my understanding is
| that the most well understood cause of burstiness is caused in
| eukaryotic cells by rearrangement of histones allowing
| transcription. Since this happens on a slower timescale than
| transcription you get bursts when the histones periodically get
| out of the way.
|
| Bacteria (like this minimal cell) don't have histones but they
| do have bursty transcription, which is weird. Apparently it
| might be caused by DNA supercoiling and uncoiling [1], which is
| weird and cool. That said, they definitely don't model that, so
| I'd be surprised if they got bursting transcription. If they
| did, I'd be interested in knowing what mechanism is causing the
| transcription bursts in the model.
|
| 1. https://www.cell.com/cell/pdf/S0092-8674(14)00739-9.pdf
| 331c8c71 wrote:
| Fascinating stuff, thanks! A recent workshop with recorded talks
| on such cells https://www.jcvi.org/events/minimal-cell-workshop
|
| I am wondering if other researchers can procure or produce these
| cells or these are rather a know-how of JCVI?
| koeng wrote:
| I gave a talk at that workshop! (I'm making the 61 codon
| version of JCVI-Syn3a)
|
| You can get the cells as a researcher, but basically forget
| about it for a commercial user or hobbyist. They're also
| annoying as hell to grow. I'm trying to synthesize it from
| scratch for the precise reason of freeing it from MTAs
| (material transfer agreements)
| DylanSp wrote:
| Sounds like you're doing good work! Out of curiosity, can you
| give a layman's explanation of what makes them hard to grow?
| koeng wrote:
| Their media is real complicated and expensive (plus
| difficult to prepare: can't just throw everything in an
| autoclave), and they don't grow very fast, and they don't
| grow to a high concentration. Basically that means that you
| can easily get contamination (like you would growing human
| cells), and even when you do get growth, it's dilute.
| gus_massa wrote:
| Does this model have operons like
| https://en.wikipedia.org/wiki/Lac_operon [1] ? I guess they are
| skipped to reduce the complexity of the model.
|
| [1] This operon was the first that was discovered, the idea is
| that the cell produce the enzymes to eat lactose only if there is
| lactose and there is no glucose.
| agnosis wrote:
| At the moment it does not. As per the paper[1]:
|
| > We do not simulate any operonal structures for protein-coding
| genes and transcribe each gene individually. Once
| transcriptomics data becomes available for Syn3A to determine
| operonal structures, we can incorporate transcription of
| operons into this model.
|
| [1] https://www.cell.com/cell/fulltext/S0092-8674(21)01488-4
| koeng wrote:
| We don't even know what like, 20% of the genes do. Simulations
| are neat, but they miss a lot of underlying biology that actually
| makes an impact on engineering.
|
| One of my favorite papers was published 40 years ago on this
| topic https://pitp.ias.edu/sites/pitp/files/morowitz-
| completeness_...
| hobofan wrote:
| If you read the article you'd know that that's exactly why
| organisms such as JCVI-syn3A were created, where we know the
| (or at least some) function of 80% of the genes.
| bee_rider wrote:
| Oh wow, a RISC (reduced instruction set cell).
| koeng wrote:
| I'm well aware. I was in charge of designing and synthesizing
| the entire gene set, optimized for E.coli, in order for
| scientists to easily try to discover the function of these
| genes https://stanford.freegenes.org/collections/gene-
| sets/product...
|
| Out of the 100 or so unknown genes we had/have, only like 3
| unknowns were actually used for research. Such is science
| sometimes.
| ramraj07 wrote:
| I thought you posted "Can a biologist fix a radio?" It's also
| very pertinent to this topic:
|
| https://www.cell.com/cancer-cell/pdf/S1535-6108(02)00133-2.p...
| DylanSp wrote:
| Interesting blog post, based on an interesting paper.
|
| For a bit more background, there's been a couple of posts on the
| "minimal cell" concept on Derek Lowe's venerable In the Pipeline
| blog. This 2016 post [1] talks about the initial development of
| the JCVI-syn3.0 cell; this 2023 post [2] goes over a paper that
| studied the evolutionary dynamics of these minimal cells.
|
| [1] https://www.science.org/content/blog-post/smallest-viable-
| ge...
|
| [2] https://www.science.org/content/blog-post/ground
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(page generated 2024-01-20 23:00 UTC)