A growing team of groundbreaking scientists around the world are now sharing their lab notebooks online
Hi, my name is Ellie Williams and I’ve been working at the SGC since 2010 in the lab of Alex Bullock. I’m funded by FOP Friends to look at the development of new drugs that target ALK2 and to study the disease Fibrodysplasia Ossificans Progressiva (or FOP). In the last couple of years a new Read More …
I was away on leave last week, but happily, before I left, I set up 25 crystal plates of ACVR1 with various compounds. The details of the protein purification, the compounds used and some of the crystals obtained are here, on Zenodo. So I was able to at least come back to something after my Read More …
Over the past few weeks I’ve been perfecting a method for screening a small set of therapeutic compounds on DIPG cell lines. Before starting I made sure to discuss the techniques used in other groups to make sure that I design an assay that is comparable to theirs, although I may make my own changes Read More …
I’ve put the Molprobity stats for the model I have refined to run my fragment screening datasets against in Zenodo. It looks pretty good, and I was happy when the parameters finally all went into the green. I have about 90 datasets with resolution lower than 2.6 Å, so hopefully I’ll get at least one Read More …
As mentioned in my Zenodo post here, I fine screened ACVR1 with the three compounds in the title. I got loads of hits for co-crystallisation with K62821a. I mounted almost two pucks’ worth of crystals (31 crystals) and sent them to Diamond for Monday’s run. Unfortunately, none of them diffracted better than 3.5 Å, so Read More …
Whether or not a cell line can be transfected efficiently is an important factor to consider when designing experiments. Often times scientists would like to deliver into the cells DNA or RNA with the instructions to produce specific proteins or to delete away specific proteins. Transfection via liposome (eg: Lipofectamine 2000) is a relatively simple Read More …
Kinase activity of ALK2 and ALK5 in the cells can be quantified using specific antibodies that bind to target proteins once they are phosphorylated. However, conventional detection in Western blot requires large amount of samples and processing time (proteins are extracted from a large number of cells, linearized, separated in electric field and blotted onto a Read More …
There are concerns that compounds that are effective in inhibiting ALK2 by occupying its ATP-binding pocket might have reduced efficacy against mutant ALK2. That will be undesirable since the compounds should also target the gain-of-function mutant ALK2 in DIPG cells. The following experiment takes advantage of the fact that Activin A activates ALK2-R206H mutant but Read More …
Well, it’s been another week of not too much actual lab work and quite a lot of computer work. The lab work I did do was incredibly frustrating due to spending time searching around for reagents and then having a water problem with the liquid handler that is used to set up the fine screens. Read More …
Repeatability is a cornerstone of science, but cells behaviour can change quite significantly if you aren’t careful when looking after them. To ensure that I have the right number of DIPG cells to complete an important experiment, and that they’re all growing healthily, I want to record how fast they grow, and at what density Read More …
