for - evolution - work to identify non-DNA information passed down to germ line - millions of permutations - fluorescence technique applied to only a few at a time - tedious work - Denis Noble

for - evolution - epigenetic AND new DNA can BOTH be incorporated into the germ line - Denis Noble

for - quote - DNA simply does not replicate like a crystal. You have to have a living organism to enable it to do so. - Denis Noble

for - quote - myth - Richard Dawkin myth - recreate entire organism from DNA - not possible - Denis Noble

quote - myth - Richard Dawkin myth - recreate entire organism from DNA - not possible - Denis Noble - (see below) - As Richard Dawkins told me two years ago in a debate with him: - "Denis, we could inscribe your DNA in blocks of granite, - the C's G's A's and T's, - and we' keep those blocks of granite for 10,000 years and then we'll be able to recreate you." - I said no you can't - why not? - Well, where would you get my mother's egg cell, as it was in1936 - Well you can see that the point here, it led people to a very simplistic idea that from DNA you could automatically recreate a person, an organism exactly as it is in its first, Incarnation if you like - We can all be reincarnated as many times as we wish!<br /> - Well, one one might sort of wish to be a bit of a Buddhist in all of this and get away with that, - but I don't think even the Buddhists would accept that that was the way they were going to do it if they do it at all

for - DNA replication accuracy - 1 in 10,000 - too high for successful replication - another higher level mechanism to correct for these errors - need a whole body for that - Denis Noble

https://web.archive.org/web/20240924124652/https://edition.cnn.com/2024/09/20/business/23andme-board-resigns-nightcap/index.html

23andme postorder DNA profiling is slowly collapsing. CEO wants to take it private, and board has resigned in protest. This is one of the corps that went public using a SPAC to capitalise on the height of hype. Founded 2006, SPAC in 2021. Revenue is down, and money should run out soon. Seems there's no business model on top of the 1 time purchase of a DNA test. Key asset obv is the data, so I think we can wait for it to be sold to whoever bids most.

for - adjacency - DNA - as an engram - as a memory - Micheal Levin

adjacency - between - DNA - as an engram - as a memory - adjacency relationship - Very interesting n way to see DNA

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

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

Refer to this protocol mentioned in the BioRad page, annotation

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.

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.

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.

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.

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

Mezcal Worm in a Bottle: DNA Testing Yields Unexpected Results

Read on 2023-03-10

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

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

Can broadly split the process into three parts. Initiation, elongation and termination

Primase and DNA polymerase A work in close association.

This is the S-phase CDK.

• Replication origin licensing.
• All of this occurs in G1 phase

Orc1-5 complex.

Cdc6 is only present in G1 phase.

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

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.

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.

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

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.

NHEJ and HR can be compared.

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:

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.

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.

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

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.

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.

HGNCID:

Five biggest myths about the COVID-19 vaccines, debunked. (n.d.). Fortune. Retrieved April 29, 2022, from https://fortune.com/2021/10/02/five-biggest-myths-covid-19-vaccines/

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

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

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

Marcus, A. A. (2022, January 13). COVID-19 spike protein paper earns an expression of concern. Retraction Watch. https://retractionwatch.com/2022/01/13/covid-19-spike-protein-paper-earns-an-expression-of-concern/

CohenMay. 6, J., 2021, & Pm, 2:45. (2021, May 6). Further evidence supports controversial claim that SARS-CoV-2 genes can integrate with human DNA. Science | AAAS. https://www.sciencemag.org/news/2021/05/further-evidence-offered-claim-genes-pandemic-coronavirus-can-integrate-human-dna

Wilson, C. (2021, September 9). Blood test could reveal who is most likely to get severe covid-19. New Scientist. https://www.newscientist.com/article/2289718-blood-test-could-reveal-who-is-most-likely-to-get-severe-covid-19/

Who Is Most Susceptible To COVID Misinformation? (2021, August 11). News. https://www.wgbh.org/news/science-and-technology/2021/08/11/who-is-most-susceptible-to-covid-misinformation

Differences between chimpanzees & humans.

“Myths about COVID-19 vaccination - HackMD.” Accessed February 19, 2021. https://hackmd.io/ovEzSQWcRp2bctQn8MYElQ#Myths-about-COVID-19-vaccination.

Infographics for DNA-sequencing technology milestones.

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.

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.

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

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.

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.

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.

This involves taking a DNA sample from a crime scene to compare with a sample of DNA from a suspect via their fingerprint.

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.

lit review

Crespi, S., Wadman, M., (2020). Why men may have more severe COVID-19 symptoms, and using bacteria to track contaminated food. Science | AAAS. https://www.sciencemag.org/podcast/why-men-may-have-more-severe-covid-19-symptoms-and-using-bacteria-track-contaminated-food?utm_campaign=SciMag&utm_source=JHubbard&utm_medium=Twitter

DNA vaccine for SARS-CoV-2 inflammations.

Hiatt, J., Patwardhan, R., Turner, E. et al. Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods 7, 119–122 (2010). https://doi.org/10.1038/nmeth.1416

Varmus, H. (2020, May 9). The World Doesn’t Yet Know Enough to Beat the Coronavirus. The Atlantic. https://www.theatlantic.com/ideas/archive/2020/05/lack-testing-holding-science-back/611422/

This will change everything.

better than BMIQ

extensive review

DNA

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.

(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.