369 Matching Annotations
  1. Last 7 days
  2. Jun 2020
  3. May 2020
    1. Definition: Unit that can be assigned to a group of living beings according to certain criteria. Most of the time, this expresses itself through a separate name for this group.
    1. In 1970 Michener et al. defined "systematic biology" and "taxonomy" (terms that are often confused and used interchangeably) in relationship to one another as follows:
  4. Apr 2020
    1. I had bookmarked this article in the form of tearing out and keeping a paper copy of it in my to read pile back in 2008. Finally getting around to reading it today. It's still an interesting introduction to the broader area which has moved forward, but not significantly enough to date the entire area.

    2. Ideas on how to analyze and predict network behavior have been informed by concepts arising from the computational and social sciences, which are themselves increasingly concerned with understanding networks. The interesting thing about these ideas is that they work at scales ranging from the molecular to the population level.

      scale free networks perhaps?

    3. Small-scale biological theories, such as those describing membrane and protein interactions, can be predictive because the relevant processes are dominated by physical constraints, such as diffusion, hydrophobicity and entropy. The problem is that these types of theories do not scale, and become far less predictive as we increase the complexity of the system.
  5. Mar 2020
    1. The molecular analysis also show that the SARS-Cov2 virus is active and replicates already in the nasopharynx, unlike other respiratory viruses that dwell in deeper regions of the lung.
    2. Surprisingly, ACE2 expression in the lung is very low: it is limited to a few molecules per cell in the alveolar cells (AT2 cells) deep in the lung. But a just published paper by the Human Cell Atlas (HCA) consortium reports that ACE2 is highly expressed in some type of (secretory) cells of the inner nose!

      Major route of viral entry is likely via large droplets that land in the nose — where expression of the viral entry receptor, ACE2 is highest. This is the transmission route that could be effectively blocked already by simple masks that provide a physical barrier.

    3. SARS-Cov-2 virus, like any virus, must dock onto human cells using a key-lock principle, in which the virus presents the key and the cell the lock that is complementary to the key to enter the cell and replicate. For the SARS-Cov-2 virus, the viral surface protein “Spike protein S” is the “key” and it must fit snugly into the “lock” protein that is expressed (=molecularly presented) on the surface of the host cells. The cellular lock protein that the SARS-Cov-2 virus uses is the ACE2 protein

      SARS-Cov-2 enters the host cell by docking with its Spike protein to the ACE2 (blue) protein in cell surfaces:

    4. Filtering effect for small droplets (aerosols) by various masks; home-made of tea cloth, surgical mask (3M “Tie-on”) and a FFP2 (N95) respirator mask. The numbers are scaled to the reference of 100 (source of droplets) for illustrative purposes, calculated from the PF (protection factor) values

    5. The tacit notion at the CDC that the alveolae are the destination site for droplets to deliver the virus load (the alveolae are after all the anatomical site of life-threatening pneumonia), has elevated the apparent importance of N95 masks and led to the dismissal of surgical masks.

      Why N95 masks are much better over the surgical masks

    6. In the case of the SARS-Cov-2 virus it is not known what the minimal infectious load is (number of viral particles needed to start the pathogenesis cascade that causes a clinical disease).

      Minimal infectious load

    7. Of course many aerosol droplets in the exhalation or cough spray may not contain the virus, but some will do.
    8. droplets of a typical cough expulsion have a size distribution such that approximately half of the droplet are in the categories of aerosols, albeit they collectively represent only less than 1/100,000 of the expelled volume

      Droplets of a typical cough

    9. For airborne particles to be inspired and reach deep into the lung, through all the air ducts down to the alveolar cells where gas-exchange takes place, it has to be small

      Only droplets < 10 um can reach to alveolae (deep into lung). Larger droplets stuck in the nose, throat, upper air ducts of the lung, trachea and large bronchia.

    10. Droplets can (for this discussion) be crudely divided in two large categories based on size

      2 categories of droplets:

      a) Droplets < 10 um: upper size limit of aerosol. Can float in the air/rooms by ventilation or winds and can be filtered (to 95%) by N95 favial masks (droplets < than 0.3 um). Here the surgical masks cannot help.

      b) Droplets > 10 um (reaching 100+ um): called as spray droplets. Can be even visible by human from coughing/sneezing (0.1+ um).

    11. Droplet larger than aerosols, when exhaled (at velocity of <1m/s), evaporate or fall to the ground less than 1.5 m away. When expelled at high velocity through coughing or sneezing, especially larger droplets (> 0.1 micrometers), can be carried by the jet more than 2m or 6m, respectively, away.

    1. Ancestor of all animals identified in Australian fossils

      Summary:

      • First ancestor of most animals, including humans, has been discovered—Ikaria wariootia had a mouth, anus, gut, and a bilaterian body plan.
      • Bilateral symmetry was a critical step in evolution, enabling organisms to move purposefully, but so far the first organism to develop it wasn’t known.
      • Ikaria wariootia was discovered through careful analysis of 555 million-year-old samples.
      • It was a wormlike creature, up to 7mm (0.27in) long, with a distinct head and tail, as well as faintly grooved musculature.
      • This discovery confirms what evolutionary biologists previously predicted.
    1. Typically, double terminators are used to stop transcription. Because these parts can be up to ∼168 bp of DNA, this use of double terminators can lead to homologous recombination when used at multiple locations in a design

      double terminators

      Did you test the double terminator strength against your library?

  6. Feb 2020
    1. there is littleelse on this list which can be considered part of a life history strategy if ‘life history’ is meant to be anchored in evolutionary biological research

      Isn't altruism, the willingness and ability to sacrifice for kin, the rate of drop-off of willing altruism, etc all directly connected to evolutionary biology?

  7. Jan 2020
    1. A spacer could compensate for any steric hindrance effect on recruiting the transcriptional machinery at the promoter of the next module in the assembly line; such an effect could be induced by the supercoiling that results when the transcription of the previous module is taking place. However, there is no direct evidence that this may cause a problem, and therefore the argument in favor of using a spacer remains speculative.
    1. More broadly, we hope that others, especially the hundreds of new startups in synthetic biology, consider sharing pre-competitive ideas, methods, tools, etc. We think the community will be stronger as a result.

      This is a great initiative. Hat's off to this company - Octant-bio for encouraging open sourcing of their hard work and optimization.

    2. we usually need 400-1200 colonies, it’s still easier and faster to do this manually than by colony picker. Also, colony pickers typically cost >$100K and don’t seem appropriate for our scale. 
    1. Chemical inducers such as carbon sources, metabolites, and antibiotics, environmental signals such as light, pH, oxygen, or temperature, and autoregulatory quorum-sensing molecules can all be sensed by TFs

      Common inducer molecule types

    1. A final word: when we do not understand something, it does not look like there is anything to be understood at all - it just looks like random noise. Just because it looks like noise does not mean there is no hidden structure.

      Excellent statement! Could this be the guiding principle of the current big data boom in biology?

  8. Dec 2019
    1. blood circulate

      The early modern English physician William Harvey (1578-1627) made several valuable contributions to the medical sciences, including the circulation of blood in the human body. In De Motu Cordis (1628), Harvey sets down his landmark experiments; in these, Harvey used ligatures to stem blood flow to better understand how the heart works to pump blood throughout the human body. This knowledge will be critical for Victor's creation of the Creature.

    2. physiology

      By 1818 physiology had become a controversial branch of medicine at the center of the dispute between vitalism, the idea that a divine spark energized animal life, and materialism, the argument that chemical processes alone give rise to life. Mary Shelley was well aware of the dispute since the Shelleys' family doctor, William Lawrence, was vigorously taking up the materialist argument in works like An Introduction to Comparative Anatomy and Physiology (1816). For a full view of this controversy as it relates to the novel, see Marilyn Butler, "Frankenstein and Radical Science" [1993] reprinted in J. Paul Hunter, Frankenstein, Norton Critical Edition, second ed. (New York: Norton, 2012): 404-416.

  9. Nov 2019