87 Matching Annotations
  1. May 2024
    1. the misconception about the relationship between genes and proteins and the idea that it that causality can only go in one direction from Gene to protein to 00:53:06 functionality and that it cannot go back the other way which and that is the crucial thing that denies agency to the organism and that was Watson and Crick

      for - critique - of Watson & Cricks DNA - agency of organisms

      critique - of Watson & Cricks DNA - agency of organisms - Watson & Cricks advocated the now disproven idea that causality is only one direction - from genes to - proteins to - functionality of living organisms - when in fact, it goes the other way, giving the high level living organism agency

    1. DNA fragmentation by restriction digestion prior to dropletgeneration enables optimal accuracy by separating tandemgene copies, reducing sample viscosity, and improving templateaccessibility for input samples >66 ng per well

      NEB says

      Digestion is recommended whenever DNA input is greater than 75 ng Source

      NEB says that biorad recommends these enzymes: AluI, CviQI, HaeIII, HindIII-HF, MseI

      More guidelines

      • Assemble ddPCR reactions at room temperature, this allows the restriction enzyme to digest the gDNA during the reaction set-up period
      • Prepare reaction mixes as you would for a standard ddPCR reaction. Add 0.5–1 μL of each restriction enzyme (5–20 units, depending on enzyme concentration) to the reaction mixture
      • After set-up, simply continue droplet generation as normal
      • Restriction enzyme will be inactivated during first PCR denaturation step
  2. Jan 2024
    1. Since less alcohol is required for isopropanol precipitation, this is the preferred method for precipitating DNA from large volumes. In addition, isopropanol precipitation can be performed at room temperature, which minimizes co precipitation of salt that interferes with downstream applications
  3. Nov 2023
    1. back to the former 00:02:28 state of Israel

      There was no "former state of Israel" for the European Jews, and that biblical missconception framed the grave consequences of their colonization. Ashkenazies had patrilinear only of M.Eastearn origin - their husbants were convested to Jewdaism:

      Thus the great majority of Ashkenazi maternal lineages were not brought from the Levant, as commonly supposed, nor recruited in the Caucasus, as sometimes suggested, but assimilated within Europe. These results point to a significant role for the conversion of women in the formation of Ashkenazi communities, and provide the foundation for a detailed reconstruction of Ashkenazi genealogical history.

    2. during the nearly 2,000 years this had become very much a place dominated by Arab Muslim communities so the Jews were moving back

      Grave missconception, Arabs did not replace Palestine populations.

      Modern DNA tells that people of Palestine, Jews and Muslims, Christians and Druzes, never left the place. Arab emigration were mostly a spread of their ideology, not in body counts. The admixture of Arab DNA to the Muslims of the Levant is actually lower than expected, and non-existent for other Levantines.

    3. going back 3,000 years state of Israel was um dominated by a Jewish 00:01:26

      Non-Jewish religions (Kebarans, Natufians, Sumerians & Akkads and later Babylonians originating from Levant, Anatolia & Eurates crescent) and non-Semitic races (the biblical "Philistines") all co-existed for millennia before the Bible was even written, 1200-200 BC. Jews being the dominant population probably applies only after ~600BC, when they started returning from the 80y Babylonian enslavement, and started to gradually re-occupy their fatherlands, a significant event that culminated a sense of identity much stronger than that of the neighboring populations.

  4. Aug 2023
    1. https://ecoevo.social/@biodiversity/110790626800847007

      Dr Christina Lynggaard, University of Copenhagen, shows an air sampler for DNA. eDNA as a way to do species observation.

    1. eDNA sampling is dna sampled from the environment, not from organisms. Can be sampled from air. Do I know of eDNA citizen science projects?

  5. Jul 2023
  6. Mar 2023
  7. Feb 2023
  8. Jan 2023
    1. we've just developed a way to measure that 100 times cheaper than it was before 00:02:44 and i'm going to bring this test to the public so that's people can test their biological at home or something or it should be a cheek swab that's what we're developing so you don't have to prick or take blood or anything you do a cheek sweat exactly and then you would ship it 00:02:57 in or something yeah you'll post it in and then you get hopefully just a week later or less here's your credit score for your body well that's cool and then even better here's how you how do you slow it down and reverse it based on 00:03:09 everything we know about you wow that's cool take you on that journey so do this eat this swallow this that is cool i got to take that test yeah well you can get on the wait list if you want 00:03:21 okay there's a website because we are uh taking names right now we may do some studies with early adopters too that's cool what's up where is it it's called tally t-a-l-l-y 00:03:33 tallyhealth.com and uh the reason i'm excited about it is it's very hard to focus on what works because we have no idea you exercise you hope that it's good yeah is it too much too little if i eat this does it help me we need a dashboard for our bodies and 00:03:46 that's what that's what these give you

      !- company to order DNA methylation test : Tallyhealth.com

    2. there's a new type of test that my colleagues and in my lab we've developed it's called the dna methylation test 00:02:20 it's also known as the horovath test named after my friend stephen horvath

      !- New health / aging metrics test : DNA Methylation / Horvath Test

  9. Nov 2022
    1. Can broadly split the process into three parts. Initiation, elongation and termination

    2. DNAPolymerase A

      Primase and DNA polymerase A work in close association.

    3. CDK2

      This is the S-phase CDK.

    4. Assembly of the pre-replicative complex
      • Replication origin licensing.
      • All of this occurs in G1 phase
    5. Orc complex

      Orc1-5 complex.

    6. Cdc6

      Cdc6 is only present in G1 phase.

    7. DNA replication pathway in humans. Orc complex binds the origin of replication.

    1. NER * Helix distortion * ERCC6 and 8 mutation -- Cockayne's syndrome * XP proteins (XPE or DDB2, XPC, XPA) mutated in xeroderma pigmentosum. * TFIIH, the same helicases as seen in DNA replication.

    1. BER * For non-helix distorting base lesions. * Base is not present, a gap is present in DNA. * Specific DNA glycosylases used for identification. * APEX1 and APEX2 (AP endonucleases): responsible for end processing * An AP site (apurinic/apyrimidinic site). * The exposed 3' OH is available to a replicative polymerase. * Ligation performed by ligase * Short or long patch BER is possible.

    1. In HR, * MRN -- begginings of dsDNA resection. * The PARP1 protein is active on ssDNA. * Free 3' ends made available, crucial for later DNA pol binding. * RPA binds, coats, the ssDNA.<br /> * Rad51 searches for strand for invasion. * Strand invasion carried out by sister chromatid, etc. * D-loop formation.

      May have. * DSBR * SDSA * BIR

    2. NHEJ relies on microhomologies. Doesn't require homologous sequence from another source. * Ku protein instrumental in identification of DSB and recruits DNA-PKcs. * DNa-PKcs autophosphorylates. * DNA ends processed by Artemis. * LIG4 and XCRR4 are needed for strand ligation.

    3. NHEJ and HR can be compared.

    1. TEs are transposable elements.

      Transposons are mobile DNA elements.Can move throughout the genome. Can be catagorised as class 1 (retrotransposons) or class 2 (DNA transposons).

      Class 1 comprises TEs with LTRs, retroposons (LINE), SINEs.

      Class 2 comprises TEs that operate under replicative transposition or non-replicative transposition. Replicative transposition (nick and paste) -- a total of two TEs as an end result, one as part of the donor and one as part of the target sequence. cointegrate.

      Non-replicative transposition (cut and paste) - only one TE generated, in the target.

      Examples of DNA-only transposon:

    1. The initial sample consisted of 1 band. F = 0. 1st generation = The sample overall less dense, still one band. Intermediate density. dsDNA made of one strand heavy and one light. After 2 generations, there was a band for intermediate density and for strands of just light, N-14, dsDNA.

    2. Three methods of replication were initially hypothesized: * Conservative * Semi-conservative * Dispersive

      Semi-conservative method was eventually determined to be correct based on empirical evidence from Messelson & Stahl, in 1958.

    3. Parental strands consist of N-15 isotopes. Replicated daughter strands consist of N-14 isotopes. The CsCl ultracentrifugation process creates density gradient. This allows DNA fragments of different densities to migrate and form a band at the point at which their buoyant density equals that of the salt.

      1. E.coli grown in an heavy nitrogen, N-15, enriched medium
      2. Then transferred to N-14 based media to reproduce
      3. As several points in the experiment, cells were lysed and underwent ultracentrifugation through a CsCl concentration gradient
    1. la capacidad de “cortar y pegar” el DNA de diferentes organismos

      Considero que esta habilidad es demasiado importante para mi carrera como bioingeniero con énfasis en biotecnología porque representa el pilar fundamente de la recombinación genética.

  10. Jul 2022
    1. New DNA technology is shaking up the family trees of many plants and animals.

      One of Darwin's most compelling arguments in favour of evolution by means of natural selection was just how many different, apparently unrelated phenomena it explained. One of these was 'Classification' (what we now call taxonomy).

      Darwin argued that, when the taxonomists of his day arranged species into hierarchical groups, those tree-like groupings were best explained by genealogical descent.

      Now that biological evolution is accepted as a fact, genealogical descent has become the criterion taxonomists use to place species into hierarchical groups. Ironically, Darwin's explanation of taxonomy means it can no longer be used to justify his theory because modern taxonomy is, in effect, defined by his theory.

      The strongest tool we have for identifying genealogical descent in species is modern DNA analysis. This has helped identify many mistakes in former, non-DNA-based taxonomic classifications. But DNA analysis can't be used in all cases… For example, we do not have access to DNA samples of the vast majority of extinct species.

  11. May 2022
  12. Apr 2022
    1. Eric Feigl-Ding [@DrEricDing]. (2021, November 12). 💡BEST. VIDEO. ALL. YEAR. Please share with friends how the mRNA vaccine works to fight the coronavirus. 📌NOTA BENE—The mRNA never interacts with your DNA 🧬. #vaccinate (Special thanks to the Vaccine Makers Project @vaccinemakers of @ChildrensPhila). #COVID19 https://t.co/CrSGGo6tqq [Tweet]. Twitter. https://twitter.com/DrEricDing/status/1459284608122564610

    1. Edward Nirenberg 🇺🇦 [@ENirenberg]. (2021, November 30). This is also not limited to the vaccine- any infection we encounter will do the same thing. It’s how we evolved to get around a massive genetic and bioenergetic challenge and it’s brilliant and it’s happening all the time regardless of any vaccines we get. [Tweet]. Twitter. https://twitter.com/ENirenberg/status/1465698637434933254

  13. Jan 2022
    1. Paolucci, S., Cassaniti, I., Novazzi, F., Fiorina, L., Piralla, A., Comolli, G., Bruno, R., Maserati, R., Gulminetti, R., Novati, S., Mojoli, F., Baldanti, F., Bruno, R., Mondelli, M., Brunetti, E., Matteo, A. D., Seminari, E., Maiocchi, L., Zuccaro, V., … Ferrari, A. (2021). EBV DNA increase in COVID-19 patients with impaired lymphocyte subpopulation count. International Journal of Infectious Diseases, 104, 315–319. https://doi.org/10.1016/j.ijid.2020.12.051

  14. Oct 2021
  15. Sep 2021
  16. Mar 2021
    1. half of the difference in gene expression between chimps and humans has to do with genes that are coding for olfactory receptors, other differences are related to the size of the pelvic arch, the amount of body hair, immune system recognition capabilities, some aspects of reproductive isolation, etc; those and others account for almost all the genetic differences between chimps and humans.

      Differences between chimpanzees & humans.

    1. The TURBO DNA-free™ Kit contains reagents for the efficient, complete digestion of DNA along with the removal of the enzyme and divalent cations post-digestion.
  17. Feb 2021
  18. Nov 2020
    1. if the magnetic tape remains tightly wound, you can’t read the information on the cassette. Epigenetics works by unspooling the tape, or not, to control which genetic instructions are carried out. In epigenetic inheritance, the DNA code is not altered, but access to it is.

      An interesting way to describe epigenetics. It is like magnetic tape on a cassette, you have to unwind it to be able to read its content. Epigenetics, by analogy would be controlling the spooling of the DNA for accessibility.

    1. Genomics

      The study of whole genomes of the organisms and incorporates elements from genetics. The genomics uses a combo of DNA, DNA sequencing, and bioinformatics to sequence, assembly, and analyze the structure and the function of the genomes.

    1. histone acetylation

      Allows for DNA binding proteins to interact with sites to activate gene transcription and alters the accessibility of chromatin.

    1. transcriptionalleve

      This is the process of a complementary mRNA copy of a single gene on the DNA that is created in the nucleus. The mRNA is smaller than the DNA so it can carry the genetic code into the ribosome and into the cytoplasm that enables the protein creation.

    1. reading fram

      The reading frame is the way of dividing each sequence of nucleotides in the DNA or RNA molecule into a set of consecutive, non-overlapping triplets.

    1. Single-strand binding proteins

      These bind to single-stranded regions of the DNA and during DNA replication they bind to newly formed DNA strands. They help keep the DNA strands in place as a framework for new DNA synthesis.

    1. Tumor suppressor genes

      These are genes that slow down cell division, repair DNA errors, and/or tell cells to terminate. If these Tumor Suppressor Genes fail to function properly, they go rouge and become cancer cells.

  19. Oct 2020
  20. Jul 2020
  21. Jun 2020
  22. May 2020
  23. Jan 2020
    1. generally accepted extinction coefficients for nucleic acids are: • Double-stranded DNA: 50 • Single-stranded DNA: 33 • RNA: 40
  24. Nov 2018
  25. Sep 2018
  26. Jul 2018
    1. repeat expansion at IIL1 leads to increased accumulation of 24-nt siRNAs in a temperature-dependent manner that correlates with the iil phenotype. We show that DCL3 and other components of the RNA-dependent DNA methylation (RdDM) pathway are essential for this siRNA-directed epigenetic gene silencing
  27. Apr 2018
  28. Mar 2018
    1. Excessive mutation will often stop a gene from working, yet somehow the sand rat’s genes manage to still fulfil their roles despite radical change to the DNA sequence. This is a very difficult task for genes. It’s like winning Countdown using only vowels.

      This will change everything.

    1. "Interestingly, though our results are preliminary, there are no major traces of genetic ancestry in these early inhabitants of Bavaria that might have come from soldiers of the Roman army,"
  29. Jan 2018
    1. A resource for the allele-specific analysis of DNA methylation at multiple genomically imprinted loci in mice
  30. Dec 2017
  31. Jul 2017
    1. global dye-bias equalization step to control for the different average intensities in the red and green channels. This procedure scales the background-corrected intensities, dividing by the average intensity of the positive control probes in the same channel, red or green, and multiplying by the average intensity of all positive controls in a reference array.
  32. Jan 2017
  33. Nov 2016
    1. Two new molecular catalysts of water oxidation have been synthesized by a team of brilliant scientists from the U.S. Department of Energy’s Brookhaven National Laboratory. These new molecular catalysts – complexes of ruthenium which are surrounded by the binding molecules, and they contain phosphonate groups.

  34. Mar 2016
  35. Feb 2015
    1. tests

      (We should be thinking...)

      What kinds of "tests"? When?

      The answers are available in the Cease and Desist letters and later in the article -- DNA Barcoding.