Mycoplasma genitalium Updated 2025-07-16
www.lgcstandards-atcc.org/products/all/49896.aspx:
- £355.00 in 2019
- biosafety level: 2
Reproduction time: www.quora.com/unanswered/How-long-do-Mycoplasma-bacteria-take-to-reproduce-under-optimal-conditions
Has one of the smallest genomes known, and JCVI made a minimized strain with 473 genes: JCVI-syn3.0.
The reason why genitalium has such a small genome is that parasites tend to have smaller DNAs. So it must be highlighted that genitalium can only survive in highly enriched environments, it can't even make its own amino acids, which it normally obtains fromthe host cells! And because it cannot do cellular respiration, it very likely replicates slower than say E. Coli. It's easy to be small in such scenarios!
Power, Sex, Suicide by Nick Lane (2006) section "How to lose the cell wall without dying" page 184 has some related mentions puts it well very:
One group, the Mycoplasma, comprises mostly parasites, many of which live inside other cells. Mycoplasma cells are tiny, with very small genomes. M. genitalium, discovered in 1981, has the smallest known genome of any bacterial cell, encoding fewer than genes. Despite its simplicity, it ranks among the most common of sexually transmitted diseases, producing symptoms similar to Chlamydia infection. It is so small (less than a third of a micron in diameter, or an order of magnitude smaller than most bacteria) that it must normally be viewed under the electron microscope; and difficulties culturing it meant its significance was not appreciated until the important advances in gene sequencing in the early 1990s. Like Rickettsia, Mycoplasma have lost virtually all the genes required for making nucleotides, amino acids, and so forth. Unlike Rickettsia, however, Mycoplasma have also lost all the genes for oxygen respiration, or indeed any other form of membrane respiration: they have no cytochromes, and so must rely on fermentation for energy.
Downsides mentioned at youtu.be/PSDd3oHj548?t=293:
- too small to see on light microscope
- difficult to genetically manipulate. TODO why?
- less literature than E. Coli.
Data:
- www.ncbi.nlm.nih.gov/bioproject/97 contains genome, genes, proteins.
- www.genome.jp/kegg-bin/show_pathway?mge01100 all known pathways. TODO: numerical reaction coefficients? Which enzyimes mediate what? Appears to factor pathways across organisms, which is awesome.
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Just add GDB Dashboard, and you're good to go.
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This paper is in the public domain and people have uploaded it e.g. to glorious Wikisource: en.wikisource.org/wiki/On_the_Relative_Motion_of_the_Earth_and_the_Luminiferous_Ether including its amazing illustrations.
Fig 3 from On the Relative Motion of the Earth and the Luminiferous Ether
. Source. Amazing 3D technical drawing from the 19th century!!! Continuous problems are simpler than discrete ones Updated 2025-07-16
Basically, continuity, or higher order conditions like differentiability seem to impose greater constraints on problems, which make them more solvable.
Some good examples of that:
- complex discrete problems:
- simple continuous problems:
- characterization of Lie groups
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Output: another sequence of complex numbers such that:Intuitively, this means that we are braking up the complex signal into sinusoidal frequencies:and is the amplitude of each sine.
- : is kind of magic and ends up being a constant added to the signal because
- : sinusoidal that completes one cycle over the signal. The larger the , the larger the resolution of that sinusoidal. But it completes one cycle regardless.
- : sinusoidal that completes two cycles over the signal
- ...
- : sinusoidal that completes cycles over the signal
Motivation: similar to the Fourier transform:In particular, the discrete Fourier transform is used in signal processing after a analog-to-digital converter. Digital signal processing historically likely grew more and more over analog processing as digital processors got faster and faster as it gives more flexibility in algorithm design.
- compression: a sine would use N points in the time domain, but in the frequency domain just one, so we can throw the rest away. A sum of two sines, only two. So if your signal has periodicity, in general you can compress it with the transform
- noise removal: many systems add noise only at certain frequencies, which are hopefully different from the main frequencies of the actual signal. By doing the transform, we can remove those frequencies to attain a better signal-to-noise
Sample software implementations:
- numpy.fft, notably see the example: numpy/fft.py
DFT of with 25 points
. This is a simple example of a discrete Fourier transform for a real input signal. It illustrates how the DFT takes N complex numbers as input, and produces N complex numbers as output. It also illustrates how the discrete Fourier transform of a real signal is symmetric around the center point. Flatpak Updated 2025-07-16
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React setups:
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Most of these are going to be Whole-genome sequencing of some model organism:en.wikipedia.org/wiki/Whole_genome_sequencing#History lists them all. Basically th big "firsts" all happened in the 1990s and early 2000s.
- 1975 by Sanger et al.: 5 kbp of the single-stranded bacteriophage ΦX174 using Sanger's radiolabelling method
- 1981 by Sanger et al.: 17 kbp of human mitochondrial DNA via Sanger method, known as the Cambridge Reference Sequence
- 2003: Human Genome Project (3 Gbp)
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This form is not really an inner product in the common modern definition, because it is not positive definite, only a symmetric bilinear form.
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