DNA methylation in prokaryotes
Introduction I was researching possible failure modes of plasmid transfection in e. coli, and I came across a post that mentioned DNA methylation as a possible problem. I had not dug into this before, and discovered that it is an entire field of study within biology. Before I realized how broad the topic was, I anticipated writing this blog post on DNA methylation; I then reduced its scope to only prokaryotes, though I will talk a little bit about how DNA methylation affects eukaryotic organisms as well in order to provide more context for what it does and how it works.
Which Coronavirus? There are many types of coronaviruses. Similarly to cancer, if we say “she is sick with coronavirus”, there are several questions that are left unanswered. If we were to say “she is sick with cancer”, we might follow up with “what kind of cancer?”. There are 7 known coronaviruses that infect humans
Human coronavirus 229E (HCoV-229E) Human coronavirus OC43 (HCoV-OC43) SARS-CoV Human coronavirus NL63 (HCoV-NL63, New Haven coronavirus) Human coronavirus HKU1 Middle East respiratory syndrome coronavirus (MERS-CoV), previously known as novel coronavirus 2012 and HCoV-EMC.
Gene transfer in plants
Overview Recently, I’ve been thinking it would be really cool to have a synthetic greenhouse; full of plants that could be found nowhere in nature. Flowers that glow in the dark, leaves that fluoresce under UV light, cucumbers that smell like vanilla, potatoes that taste like oranges. I’m getting a little ahead of myself, but it would be cool.
This post will go over some techniques that are used to introduce new genes into plants.
Creating a virus
Overview Previously, I’ve talked about transfection of e. coli using heat shock in my post on plasmids. Transfection into single celled organisms can be relatively simple. Using heat and electricity, we can take an artificial plasmid and add it to e. coli or yeast. This synthetic addition to the DNA in a cell codes for a protein that we want, and the cell will now produce that protein like a small factory.
Overview One project that I’ve had in the back of my mind is inventing new dyes based on colors in insects. Dyes created by biological mechanisms can be much more environmentally friendly than those created with chemicals. Unfortuantely, I have not found anywhere to buy the DNA that I want - in many cases, the genomes haven’t even been sequenced yet. Both of these problems will require me to isolate the DNA myself.
DNA sequencing methods
Overview One of the driving factors behind the recent explosion in progress in synthetic biology has to do with the cost and speed of genome sequencing and synthesis. Here, I’m going to focus on genome sequencing. There are lots of companies that will do this for you, and lots of lab devices that you can buy so that you don’t have to do the sequencing yourself, but I thought it would be worthwhile for me to understand what it takes to sequence DNA.
Why do I care about this? In this post, I wanted to go over what bioinformatics does for synthetic biologists. I’m a software engineer by training, and I’ve even taken some of a bioinformatics course. But I still didn’t understand what the purpose of bioinformatics was. More importantly, I didn’t understand how what I do for a living now - AI - could help with it.
Bioinformatics is an entire field, so I’m not going to be able to do it justice in a single blog post.
Bacterial artificial chromosomes (BAC)
What is a BAC? Previously, I wrote about plasmids as small, circular DNA sequences. The double edged sword of normal plasmids is that they are small. This can make them easier to reason about, but it can make them inconvenient for some uses. For example, if you wanted to study the herpes virus, it might be useful to have bacteria that carry the genome of the virus. BACs allow biologists to study organisms more holistically, but without having to actually raise the organism.
What is this? This is a list of resources that I have found to be useful in my own exploration and learning. I will continue to update it based on what I use.
Resources protocols.io - lots of open protocols openwetware - open protocols Benchling - Bunches of useful tools for labs bitesizebio - Lots of useful articles Thermo Fisher’s list of lab protocols diy-bio - Has tons of links, guides, and help to get people started in synthetic biology bio-hk
What is a plasmid? Whenever I start looking into genes and genomes, I eventually end up at a circular diagram with highlighted sections with gene name labels. I understood that these represented genetic information, but I didn’t really understand why I should care about them.
Being new at this whole biology thing forces me to remind myself of the fundamentals pretty often. In this case, I have to go back to the fundamentals of what DNA actually is.