six-month period between November of 52 and April of 53 where we unlocked first the power of the nucleus because we could fuse hydrogen and the other thing we were able to do was uh figure out the threedimensional structure of nucleic acid in the form of the double helix
for - stats - history - Nov 1952 - hydrogen bomb - -April 1953 - discovery of DNA
the only way you can visualize the vaces because they're too tiny to be visualized by standard microscopy labeling with florescent dyes is about the only way we can um easily identify what molecules have been passed down from the vesicles to The Germ cells but that's very restrictive you see because there will be millions of different molecules in a single visle to be faced with only being able to label three or four of those otherwise we can't make out the the differences is it's very tedious
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
epigenetic inheritance of course which would be let's say rnas determining how much of a gene is expressed will be transmitted down through the germ line and and the possibility of actual new DNA being incorporated into the germ line I think both can occur
for - evolution - epigenetic AND new DNA can BOTH be incorporated into the germ line - Denis Noble
DNA simply does not replicate like a crystal you have to have a living organism to enable it to do so
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
as Richard Dawkins told me two years ago in a debate with him Dennis 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
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
we now realize the base pairs come to join each other up together as the system unravels and forms a new pair of DNA molecules well up to a point it does and that point is known to be accurate to about one in 10,000 base pairs now if you and I wrote an article and there was only one typo in a 10,000w article we'd be very pleased but this is nowhere near enough for a DNA sequence of three billion base pairs there would be half a million at least of Errors
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
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.
is DNA in engram or not yeah I think so yeah okay yeah yeah I think so but now now again that that requires that requires a real shift I think most biologists would say no but I think it is because I think that um all memories are just messages from your past self and that what's happening with DNA is that previous previous basically there's this giant lineage agent that's the scale of an evolutionary lineage and the DNA are its engrams where that information is is being passed on the way that any memory would
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
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
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
Refer to this protocol mentioned in the BioRad page, annotation
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
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.
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.
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.
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?
Digestion is recommended whenever DNA input is greater than 75 ng
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
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
Can broadly split the process into three parts. Initiation, elongation and termination
DNAPolymerase A
Primase and DNA polymerase A work in close association.
CDK2
This is the S-phase CDK.
Assembly of the pre-replicative complex
Orc complex
Orc1-5 complex.
Cdc6
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.
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.
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.
What are the functional groups of DNA?
Embryonal rhabdomyosarcoma (ERMS) of the uterus has recently been shown to frequently harbor DICER1 mutations.
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
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.
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.
“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.
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.
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.
histone acetylation
Allows for DNA binding proteins to interact with sites to activate gene transcription and alters the accessibility of chromatin.
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.
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.
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.
DNA 9ngerprinting
This involves taking a DNA sample from a crime scene to compare with a sample of DNA from a suspect via their fingerprint.
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.
DNA damage-induced cell death: from specific DNA lesions to the DNA damage response and apoptosis
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/
generally accepted extinction coefficients for nucleic acids are: • Double-stranded DNA: 50 • Single-stranded DNA: 33 • RNA: 40
Using long-read sequencing to detect imprinted DNA methylation
TaqMan qPCR pushes boundaries for the analysis of millennial wood
Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data
CLARK is a software tool for classifying any type of DNA/RNA sequences
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
Dynamics and function of DNA methylation in plants
Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons
Genome-scale DNA methylome and transcriptome profiling of human neutrophils
Mitochondrial DNA
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.
"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,"
Dnmt3a is an epigenetic mediator of adipose insulin resistance
A resource for the allele-specific analysis of DNA methylation at multiple genomically imprinted loci in mice
Qiagen buffer PB with 9 ml sodium acetate (5M), and 1.25 ml sodium chloride (5M
silica-powder-based extraction
Statistical and integrative system-level analysis of DNA methylation data
Transcription factor–DNA binding: beyond binding site motifs
RCP: a novel probe design bias correction method for Illumina Methylation BeadChip
better than BMIQ
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.
Mass Spectrometry of Structurally Modified DNA
extensive review
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.
right to privacy, while allowing them to make an informed choice about taking reasonable risks to their privacy in order to help advance research
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.
