Comparative Genomics of Non-Model Invertebrates

Blog post: COVID-19 impact on IGNITE ESR projects

The global pandemic has been an unfortunate consequence of the COVID-19 outbreak, which affected numerous sectors of our everyday life. Now, a few months after it all began, the IGNITE PhD students share how the pandemic and the resulting lockdown affected their work and life. Fortunately, although being restricted from laboratory access, the majority of the students’ work has not been severely affected. By utilising numerous means of virtual communication, such as online meetings, the progress of the projects has not been seriously deprived and the productive work could largely continue. 

ESR Project 1: The global COVID-19 pandemic caused the LMU to shut down and restrict the office use to only one person at a time. I continued working from home. My progress was not affected because all of the work I have to do now is computational. I was lucky to end most of the experiments that required lab use just before the outbreak. The lab kept having regular meetings with my supervisor and the group, and we also held some journal clubs via Zoom LMU platform. Currently, I continue to work on phylogenomics together with the genomics project and in parallel help ESR 2, Ramon Rivera to work on a genome assembly project. Unfortunately, secondments and conferences are now in different formats if they happen at all. Those are important parts of IGNITEs training objectives and I am concerned about missing them during this period. 

ESR Project 2: Due to the COVID-19 pandemic, my project was also affected. I was doing my secondment at EMBL Heidelberg when the lockdown started. All the experiments could not be finished and we could not perform any sequencing. However, during this time I fostered new collaborations with ESR1 (Ksenia Juravel) and other colleagues from my research group at LMU, and external collaborators. We meet via video conferencing and we stay in contact to help each other. In the upcoming months, I am hoping I can finish my secondments and continue with this part of the project.

ESR Project 3: During the global COVID-19 pandemic the CIIMAR and the Faculty shut down. My sampling trip to Cape Verde (in May) and secondments in Belgium and Galway (June and July) were postponed until an unknown date. Although I was able to communicate with my colleagues and supervisors via email and Zoom, I am not able to continue my work due to the lack of data. I am now making a new plan for my PhD project and hopefully it will be back to normal soon.

IGNITE ESRs and other young researchers from their labs united in spreading awareness and motivation in response to the global COVID-19 pandemic.

ESR Project 4: Due to the fact that EMBL Heidelberg shut down quite early for any lab work, from that moment on wet lab work was not possible any more. Unfortunately, my project largely depends on proteomics data, which I am still missing. Large proteomics experiments require careful preparation, which were not possible any more. Therefore - still missing most of the data to work with - during the lockdown I mostly conceptualized the theoretical background of the project and went through a lot of literature concerning the latter. In addition, I tried to prepare for an online Porto meeting by testing different software for phylogenetic reconstruction. Since EMBL opened with restrictions again in July, I’ve been back as often as possible and as much the regulations allowed it. Due to the pandemic, I had to reschedule secondments and due to missing data, I won’t be able to present at the conference “Mechanisms in Evolution and Ecology” at EMBL.

ESR Project 5: Since the beginning of lockdown, I have been working from home, which is not problematic in my case as I work in bioinformatics and the WiFi is better. We communicated with coworkers and my PI via videoconferences. I was going to supervise an intern and we were able to maintain this internship with github and videoconferences. I was lucky to complete my last secondment in February, where I generated crucial data for my project. I was able to make great progress on several projects and I deposited a preprint as first author. I attended the virtual conference JOBIM2020 where I gave a talk and received an award for the best talk. I was also lucky to have a surprise Zoom birthday party with my coworkers and IGNITE members. 

ESR Project 6: As with most of my colleagues the pandemic had also affected my project. The Faculty has been closed for several months hence I could not perform any wet lab work. This resulted in a severe delay regarding sequencing data acquisition. Luckily I had a dataset I could work on during the lockdown but it had its own limitations. The output of this analysis is at the moment validated in the lab. Also I missed out on meetings and conferences which I would’ve attended this year (IGNITE meeting in Portugal, Euro Evo Devo conference got postponed). 

ESR Project 7: I was fortunate to have acquired a lot of next generation sequencing data prior to the lockdown. This has given me plenty of computational work to pursue while I have been working from home. Apart from that I have primarily been writing a manuscript for future publication which has also largely been unaffected by the lockdown. Genome sequencing of additional organisms has been somewhat delayed, but I am confident that this can be accomplished later in 2020. The biggest setback the lockdown has had is delaying the planned workshops and secondments I was supposed to attend this year. Overall the lockdown has caused small but manageable obstacles to my project.

ESR Project 9: COVID-19 has had limited effect on my work. A paper was delayed until next year due to the pandemic, but no work was lost. Communication with labmates has been primarily through skype and slack, but also the occasional in person meeting at the office. The offices are now open in a limited capacity, which allows for in person interaction with my coworkers. In total, everything is nominal for my PhD.

ESR Project 10: During the global COVID-19 pandemic, my work has been affected to varying degrees, First, two workshops in May (one is organized by ourselves in Portugal, another is ‘Computational Molecular Evolution’ in Greece) and one secondment in July had to be canceled or postponed. Second, my sampling trip to Greenland to collect Limacina helicina in June was also canceled and that will be a big problem for my further research, since we already tried two times with the old sample and couldn’t get enough high molecular weight DNA which is needed for subsequent genome sequencing. We urgently need to get fresh and well-preserved new samples and now we are keeping contact with people who are on /will have a sampling trip in Barents Sea, Seward and Antarctic, and hopefully get some samples from them. Third, my data analyzing work was shortly influenced during the maintenance of LRZ, but as it returned to normal, the computational work became the same as before.

ESR Project 11: During the global COVID-19 pandemic, the institute shut down. Hence, I was working from home. Since all of my work is computational, it did not affect my progress on my project. I communicated with my colleagues every week, via GoToMeeting and the Inria visioconference. I also attended the JOBIM2020 virtual conference, where I presented my work through a poster. Now, the institute is open and I can continue my work at the office, which makes the collaborations with colleagues easier. However, before the global COVID-19 pandemic, I was doing my secondment in Belgium (that was supposed to last the whole month of March). I managed to do the first two weeks of the secondment, but then in mid-March, I had to go back to France. There is now a lack of perspective regarding the secondments and the conferences, due to the COVID-19 pandemic. 

ESR Project 12: During the global COVID-19 pandemic the university shut down and I continued working from home. My progress was not affected because all of my work is computational. We kept having regular meetings with my supervisor and the group, and we also held some journal clubs and a quiz night via Zoom. We also managed to release a preprint in biorXiv. Finally, I had arranged to attend the SMBE2020 conference in Canada but it was cancelled, and a Virtual Phylogenomics Symposium was held instead where I presented my work.

ESR Project 15: During the global COVID-19 pandemic the whole company started working from home. Since my project does not involve any lab or field work, I was able to continue my work regardless of this change. I communicated with my colleagues and other collaborators via Skype and GoToMeeting every week which helped us finish a project we had started before the pandemic and even start a new one. We are now back in the office which feels like a relief because communication is easier and it’s nice to see everyone in person.

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