HomeBiologyBSDB Gurdon Studentship Report – Zhikai Li

BSDB Gurdon Studentship Report – Zhikai Li

Quickly after beginning the primary 12 months of medical college, I had ambitions of enterprise substantial scientific analysis in future since biomedical analysis and scientific observe complement one another, however little concept concerning the nature of scientific analysis. On my seek for a venture, I got here throughout the Gallop lab on the Gurdon Institute and was capable of attend an interview with the lab the place I offered a paper. I used to be then provisionally accepted as a summer season pupil, and after a profitable utility for a BSDB Studentship, the venture was given the go forward.

The Gallop lab investigates actin signalling with emphasis on filopodia, concerning their macroscopic behaviour, molecular dynamics, and lipid composition. Actin biology had been talked about in our first 12 months programs however not explored additional. I used to be subsequently wanting to analysis a comparatively novel space for myself, and after dialogue with Dr Gallop we selected a venture which might cater to each the labs and my pursuits.

The venture would use embryos from the African clawed frog, Xenopus laevis, to review filopodia. The lab had just lately found heterogeneity of actin regulatory molecules at filopodial ideas, noting that filopodial extension and retraction charges in Drosophila myotubes forming myotendinous junctions observe an outlined mathematical relationship, the Laplace distribution (Dobramysl et al. (2021)).

The distribution highlights how the poorly understood and apparently random biochemical processes in filopodia are nonetheless ruled by some underlying order. The theoretical framework for our present understanding of filopodia dynamics, is that actin polymerisation is occurs on the ideas, with fixed retrograde stream and actin depolymerisation occurring on the filopodium base (Mallavarapu and Mitchison, 1999). Due to this fact, a query my venture sought to reply was whether or not different filopodia and actin incorporation on the ideas additionally observe Laplace distributions of their dynamics. To reply this, I used forefront mesendoderm (LEM) cells, remoted from stage 10.25 Xenopus gastrula and allowed to unfold on a fibronectin matrix due to their accessibility and quick incubation time. Moreover, the big cells on the 2-cell stage permit ease of injecting labelled membrane marker RNA (GAP-RFP) and labelled actin (with Atto-488). Any variations between the macroscopic behaviour of filopodia in cells in vivo in contrast ex vivo might present perception into elements driving the filopodia behaviour.

If filopodia extension/retraction charges in Xenopus LEM cells match a Laplace distribution, an additional analysis query can be whether or not actin depolymerisation solely happens on the filopodia base or if there could also be actin depolymerisation on the filopodia ideas too. Any findings can account for variations within the charges of filopodia extension and retraction.

TIRF (Whole Inner Reflection Fluorescence) microscopy can be used to picture filopodia. The membrane marker permits visualisation of the filopodia define, and timelapses can then be analysed to trace many filopodia over time utilizing a plugin known as ‘Filopodyan’ written in Fiji and R (Urbancic et al, 2017), producing graphs displaying the distribution of filopodia extension and retraction charges. The labelled actin permits for photobleaching to reply the second analysis query, by monitoring a stripe of photobleached actin.

The beginning of the venture largely concerned studying strategies. I discovered find out how to fertilise, deal with, and inject embryos, take explants, and use the microscope. Due to the intricate nature of injecting embryos and taking explants, growing these abilities had been pleasurable however took time. I discovered explant-taking with eyebrow knives and hair-loops particularly enjoyable, reinforcing my want to decide on hands-on surgical specialties in future. In direction of the tip of the venture, I used to be happy to see the development in my aptitude for injecting embryos and taking explants.

The primary experiment was in week 2, but it surely was discovered that the explants weren’t focused sufficient, and quite a lot of vegetal endoderm continued within the MaTek dishes used for imaging. There was additionally no actin fluorescence, so we hypothesised injecting GAP-RFP and labelled actin in separate needles, quite than a single, may permit actin to be launched efficiently. The second experiment was certainly extra profitable, as LEM cells with filopodia may very well be seen with some examples in Fig. 1 under.

Fig. 1 – LEM cell with good filopodia, particularly within the enlarged body. Actin sign was weaker than membrane marker sign.

Additional experiments centered on bettering the actin sign depth for extra correct filopodia segmentation in ImageJ. We tried switching wavelengths to make use of actin conjugated with a purple dye (Alexa-568) and growing the Atto-488 actin focus, the latter of which proved extra profitable. Getting correct and exact explants was additionally tough, nonetheless refining the explant approach with assist from Dr Gallop and my day-to-day supervisor, Julia Mason, improved the yield of LEM cells.

LEM cells had many cellular filopodia on the vanguard, nonetheless except for segmentation issues as a result of low actin sign, overlapping filopodia had been additionally inaccurately segmented by Filopodyan. Just a few cells from the ultimate runs may very well be analysed absolutely in ImageJ, producing tables which had been fed into the Filopodyan script in R and producing graphs that approximated a Laplace distribution of filopodia extension and retraction charges.

Lastly, to deal with the venture particularly, the script needed to be rewritten to plot a logarithmic scatter plot as a substitute of a histogram. The very best match traces nonetheless want integrating into the script, and this together with perfecting the experimental process might kind the idea for one more quick venture to complete my work on the Laplace distribution and reply the second a part of the analysis query on actin dynamics.

Total the venture has been invaluable, not solely in growing arduous abilities like working with primary bench tools, manipulating embryos and imaging, but in addition in highlighting the unpredictable nature of scientific analysis. Finishing this venture has higher ready me for future analysis alternatives, which I shall be in search of, in addition to allowed me to fulfill glorious colleagues which have been of nice assist, for which I categorical my deepest gratitude.


Dobramysl U, Jarsch IK, Inoue Y, Shimo H, Richier B, Gadsby JR, Mason J, Szałapak A, Ioannou PS, Correia GP, Walrant A, Butler R, Hannezo E, Simons BD, Gallop JL. Stochastic combos of actin regulatory proteins are ample to drive filopodia formation. J Cell Biol. 2021 Apr 5;220(4):e202003052.
Mallavarapu A, Mitchison T. Regulated actin cytoskeleton meeting at filopodium ideas controls their extension and retraction. J Cell Biol. 1999 Sep 6;146(5):1097-106.
Urbančič V, Butler R, Richier B, Peter M, Mason J, Livesey FJ, Holt CE, Gallop JL. Filopodyan: An open-source pipeline for the evaluation of filopodia. J Cell Biol. 2017 Oct 2;216(10):3405-3422.

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