Dynamic semantics is a theoretical approach to understanding the meaning of linguistic expressions that focuses on how context and discourse evolve over time during communication. Unlike static semantics, which views meaning as fixed and derived from the lexical and grammatical properties of expressions alone, dynamic semantics considers how the meaning of sentences can change based on the discourse context and how they interact with previous statements.

Dubnium is a synthetic chemical element with the symbol Db and atomic number 105. It is named after Dubna, a town in Russia where the Joint Institute for Nuclear Research is located, and where the element was first synthesized in 1968 by a team of Russian and American scientists. Dubnium is a member of the actinide series, and it is placed in the d-block of the periodic table's group 5, which makes it part of the transition metals.

Lawrencium is the chemical element with the symbol Lr and atomic number 103. It is classified as a synthetic element and belongs to the actinide series of the periodic table. Lawrencium was first synthesized in 1961 by a team of scientists at the University of California, Berkeley, and it was named in honor of Ernest O. Lawrence, the inventor of the cyclotron.

Isothermal means "at fixed temperature".

This is to contrast with the more well established polymerase chain reaction, which requires heating and cooling the sample several times.

The obvious advantage of isothermal methods is that their machinery can be simpler and cheaper, and the process can happen faster, since you don't have to do through heating and cooling cycles.

Like PCR, but does not require thermal cycling. Thus the "isothermal" in the name: iso means same, so "same temperature".

Not needing the thermo cycling means that the equipment needed is much smaller and cheaper it seems.

Trade-offs question: biology.stackexchange.com/questions/92172/what-are-the-trade-offs-between-polymerase-chain-reaction-pcr-vs-loop-mediated

Caused by slipped strand mispairing.

oriC = Origin of Chromosomal replication.

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.

Experiments that involve sequencing bulk DNA found in a sample to determine what species are present, as opposed to sequencing just a single specific specimen. Examples of samples that are often used:

One related application which most people would not consider metagenomics, is that of finding circulating tumor DNA in blood to detect tumors.

Sequencing the DNA tells us what the organism can do. Sequencing the RNA tells us what the organism is actually doing at a given point in time. The problem is not killing the cell while doing that. Is it possible to just take a chunk of the cell to sequence without killing it maybe?

The by far dominating DNA sequencing company of the late 2000's and 2010's due to having the smallest cost per base pair.

Illumina actually bought their 2010's dominating technology from a Cambridge company called Solexa.

To understand how Illumina's technology works basically, watch this video: Video 1. "Illumina Sequencing by Synthesis by Illumina (2016)".

The key innovation of this method is the Bridge amplification step, which produces a large amount of identical DNA strands.

This is one of the the key innovations of the Illumina (originally Solexa) sequencing.

This step is genius because sequencing is basically a signal-to-noise problem, as you are trying to observe individual tiny nucleotides mixed with billions of other tiny nucleotides.

With bridge amplification, we group some of the nucleotides together, and multiply the signal millions of times for that part of the DNA.

They put a lot of emphasis into base calling. E.g.:

After filtration, all DNA should present in the filter, so we cut the paper up with scissors and put the pieces into an Eppendorf: Video 1. "Cutting vacuum pump filter and placing it in Eppendorf".

Now that we had the DNA in Eppendorfs, we were ready to continue the purification in a simpler and more standardized lab pipeline fashion.

First we added some small specialized beads and chemicals to the water and shook them Eppendorfs hard in a Scientific Industries Inc. Vortex-Genie 2 machine to break the cell and free the DNA.

Once that was done, we added several reagents which split the solution into two phases: one containing the DNA and the other not. We would then pipette the phase with the DNA out to the next Eppendorf, and continue the process.

In one step for example, the DNA was present as a white precipitate at the bottom of the tube, and we threw away the supernatant liquid: Figure 1. "White precipitate formed with Qiagen DNeasy PowerWater Kit".

At various stages, centrifuging was also necessary. Much like the previous vacuum pump step, this adds extra gravity to speed up the separation of phases with different molecular masses.

In our case, we used a VWR Micro Star 17 microcentrifuge for those steps:

Then, when we had finally finished all the purification steps, we measured the quantity of DNA with a Biochrom SimpliNano spectrophotometer to check that the purification went well:

And because the readings were good, we put it in our -20 C fridge to preserve it until the second day of the workshop and called it a day:

More generic PCR information at: Section "Polymerase chain reaction".

Because it is considered the less interesting step, and because it takes quite some time, this step was done by the event organizers between the two event days, so participants did not get to take many photos.

PCR protocols are very standard it seems, all that biologists need to know to reproduce is the time and temperature of each step.

We did 35 cycles of:

This process used a Marshal Scientific MJ Research PTC-200 Thermal Cycler:

We added PCR primers for regions that surround the 16S DNA. The primers are just bought from a vendor, and we used well known regions are called 27F and 1492R. Here is a paper that analyzes other choices: academic.oup.com/femsle/article/221/2/299/630719 (archive) "Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment" by Yuichi Hongoh, Hiroe Yuzawa, Moriya Ohkuma, Toshiaki Kudo (2003)

One cool thing about the PCR is that we can also add a known barcode at the end of each primer as shown at Code 1. "PCR diagram".

This means that we bought a few different versions of our 27F/1492R primers, each with a different small DNA tag attached directly to them in addition to the matching sequence.

This way, we were able to:

Input: Bacterial DNA (a little bit)
... --- 27S --- 16S --- 1492R --- ...

|||
|||
vvv

Output: PCR output (a lot of)
Barcode --- 27S --- 16S --- 1492R

Finally, after purification, we used the Qiagen QIAquick PCR Purification Kit protocol to purify the generated from unwanted PCR byproducts.