Balance of the 2020
Contents
3. Balance of the 2020#
3.1. Main acivities/tasks/things done in 2020#
Experimentally related
1st SATAY round on ylic133 (WT) and ylic136 (nrp1::HYGRO)
Send those samples to sequence in Oxford establishing a collaboration with Agnes Michel from Benoit group. She offered to me that possibility and I accepted it.
Construction of new strains for SATAY bem3::NAT and bem3::NAT nrp1::HYGRO (still they haven’t been checked)
Theoretical/software related
Machine learning model to predict whether a gene pair will be synthetic lethal or not based on the shared protein domains from their protein products. This was a hands on exercise to get into this topic and learn the methods and the context of application. This was a successful replication study from a paper.
Application of open science principles in my daily practice in a more explicit way.
Experimental journal publication in the web as a static web site using Jupyter Book integrating utterances and hypothesis plugins that allows the interaction with other people . Every page has a window where you can write comments and they are automatically converted to issues in the github repository is based the journal.
Structure and publish the code in a github repository respecting certain guidelines : using readme , python modules and scripts. If there is something I would like to document further then use the jupyter notebooks.
Use of boards in Github to manage group projects like the satay group where I have track of the tasks that need to be done , what is in progress and what is finished. These tasks are organized in the shape of issues where you can document in your own.
More use of git and continuous integration for web deployment using github actions and also for machine learning models.
dig into data version control (dvc) for 2021
Daily practices
Keep using and improving my local electronic labnotebook in Visual Studio Code, using the same experimental template as before.
I moved from VuePress to JupyterBook which is handier , and easier to customize (https://leilaicruz.github.io/Experimental-journal-jupyterBOOK/intro.html)
Capacities acquired
Python programming for experimental data analysis and visualization.
Machine learning methods with the python library : sklearn
Cloning of yeast strains
successful first SATAY workflow
PhD practicalities
Successful Yearly meeting.
Discipline related skills ECTS: 15
Transferables related skills ECTS: 8
Research related skills ECTS: 6.5
3.2. Reflection from the outlook to the 2020 (in the Balance from 2019)#
3.3. Reflections#
This year has been the corona year where many things got paralyzed , and all the meetings have been held online.
I have taken few courses from the Graduate School.
3.4. Retrospective from the tasks proposed for 2020#
3.4.1. Designed plan to accomplish in the next 3 years#
3.4.2. Perspective on the next three years (Project Plan)#
Finish the Fridtjof paper, about the evolution of self organization related functions,and integrate this results with my original PhD.
Sent to Elife and rejected because of lack of match between the paper title and aims and the experimental back up.
Working on more suplementary experiments to back up some important controls associated with demonstrating that the sfGFP does not influence the behaviour of the strains with/without the Gal promoter.
Write a paper with the results of the mapping of essential/non essential genes from the bem1\(\Delta\) , bem1\(\Delta\)bem3\(\Delta\) and bem1\(\Delta\)bem3\(\Delta\)nrp1\(\Delta\) backgrounds. (\(\Delta\) - symbolyze knockout)
Still working on that. So far I have done SATAY from \(\Delta nrp1\) and WT. Next one can be \(\Delta bem3\) and \(\Delta bem3nrp1\).
\(\Delta bem1\) is a tricky strain due to its high instability. A master student from Enzo , called Wessel, has been working on that , and managed to do a SATAY experiment in this background using an auxin degradable protein system . With this , bem1 gets degraded in situ just before the reseeding , which is the fitness step (regrowth of the libraries) in SATAY. Still the results has not been sequenced.
Write a paper about, how gene expression can influence genetic interactions in bem1\(\Delta\) strains. Specifically, how Cdc42 changes in gene expression can alter the SATAY map of essential and non-essential genes of the Bem1 deleted strain. Or perhaps, engineer a bem1 promoter to control its native expression in the cell.
Interesting idea but difficult to tune the gene expression from Cdc42. We have currently a strain made by Els which has Bem1 under a galactose inducible promoter.
Write a paper about how the correlation between type of interactions and shared interactors, can be extended to more than one gene deletion. Basically is asking the question, how in a double deleted background, can we identify possible positive, negative and synthetic lethal interactions? with the results of SATAY with strains with multiple mutations.
This is a mindset of constantly looking for correlations among biological properties like gene ontology terms , protein domains, pathways , etc woth genetic interactions. So far when looking at all genes to the shared number of interactors the correlation is not very clear , but there is a tendency for SL to share more interactors and also GO terms.
Test that in order to nrp1 be deleted to improve the overall fitness of the organism, in bem1\(\Delta\)bem3\(\Delta\) background, the hub genes cla4, cdc3 and act1 have to be present. Therefore, I am planning to perform a “short” evolution experiment starting with bem1\(\Delta\)bem3\(\Delta\) background to test the nrp1 deletion in 4 different genetic lines:
bem1\(\Delta\)bem3\(\Delta\)cdc3\(\Delta\)
bem1\(\Delta\)bem3\(\Delta\)act1\(\Delta\)
bem1\(\Delta\)bem3\(\Delta\)cla4\(\Delta\)
This could be tested with SATAY on those triplicates and double mutants , by finding in the double mutants a significant higher reads on nrpi1 locus than in the triplicates where the “hub” genes are deleted.
3.4.3. “Realistic plan” (for 2020) , after 6 months from the GO-NO-GO meeting:#
Write a paper with the results of the mapping of essential/non essential genes from the bem1\(\Delta\) , bem1\(\Delta\)bem3\(\Delta\) and bem1\(\Delta\)bem3\(\Delta\)nrp1\(\Delta\) backgrounds.
Not possible /Not realistic
Write a paper about, how gene expression can influence genetic interactions in bem1\(\Delta\) strains. Specifically, how Cdc42 changes in gene expression can alter the SATAY map of essential and non-essential genes of the Bem1 deleted strain. Or perhaps, engineer a bem1 promoter to control its native expression in the cell.
Not possible /Not realistic
3.5. Outlook for 2021#
My focus in this year will be experimental , I will try to do the biggest number of experiments to get the data from .
I have realized that the data analysis / modelling and the conceptualization tasks are better to perform alone when writing the thesis for example.
3.5.1. Main experiments for 2021#
Strain construction:
\(\Delta bem3\)
\(\Delta bem3\Delta nrp1\)
\(\Delta bem3\Delta bem1\)
\(\Delta bem3\Delta bem1\Delta cla4\) for testing linkage model
\(\Delta bem3\Delta bem1\Delta cdc3\) for testing linkage model
\(\Delta bem3\Delta bem1\Delta act1\) for testing linkage model
SATAY on:
all strains above
Analyse sequencing data
Make the software pipeline FAIR