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Contact: a.t.molines@gmail.com 

ATMscience

My interests

Microtubule Network Organisation, dynamic, and bundling.

Since my Ph.D. in plant cell biology, I'm fascinated by how a network of microtubules, which are dynamic filaments, is organized and how this organization is maintained or adapted over time.
Microtubules are long and rigid filaments. Their length (1 – 10 μm) and their persistence length (≈ 1mm) exceeding the size of most cells, microtubules are often bent (inside cells). A cell is a crowded dynamic 3D environment inside which the microtubule network is constantly dynamic, microtubule bending comes from motor activity and/or encounter with obstacles such as microtubules, organelles or the cell edge. How are those constraints, imposed by the cytoplasm and the cell shape/volume, impacting the organization of the microtubule network?

Several studies have addressed these questions showing, for example, that microtubule network organization participate in cell shape but also that the cell shape feedbacks on the microtubule network organization (Hamant and Traas, 2009 – Minc, Bratman et al., 2009 –  Terenna et al., 2008 – Dixit and Cyr, 2004 – Eren et al., 2010).
Lateral interactions between microtubules usually organized them into bundles. Bundling is a more challenging parameter to assess because of the size of a single microtubule that is below the limit of resolution of conventional microscopes. However, some pioneer studies have started to address the effect of microtubule bundling on microtubule dynamic instability and microtubule network organization. (Portran et al., 2013 – Shaw and Lucas, 2011 – Stoppin-Mellet et al., 2013 – Komis et al., 2014).

Microtubule network reorganization upon blue light treatment in Arabidopsis thaliana epidermal hypocotyl cell.
Lindeboom et al., 2013, Science.

To go further in vivo, we need to build new analysis processes and new tools. We have to be able to quantitatively describe the organization of a network, the 3D environment (i.e. the cell shape and the cytoplasm density) and the microtubules intrinsic properties (dynamic instability and mechanical properties) and also to accurately modify these quantities in order to follow their respective impact on microtubule network organization and behavior.
For these obvious reasons, this topic needs the collaborations of cell biologists, biochemists, and physicists.

During my Ph.D. (PDFI2BC, Ph.D. supervisor: F. Coquelle) I participated in the description of the function of a microtubule-associated protein (EB1) on microtubule network organization, microtubule bundling, and microtubule dynamics in Arabidopsis thaliana using super-resolution microscopy and image analysis (Molines et al., 2018).

Cytoplasm density, cellular content.
 

More recently, during my postdoc, I became fascinated by the cytoplasm. The cytoplasm is a very crowded environment that behaves more as a viscoelastic or a poroelastic material than like a true liquid because of the very high concentration of proteins (200-400mg.ml), RNA and other molecules it contains. A correct and comprehensive description of the cytoplasm is still lacking.  Is it homogenous or heterogeneous? Some studies suggest that the cytoplasm could be constituted of regions of different composition, each possibly specialized in one or multiple functions.

Is the crowding/density/viscosity of the cytoplasm monitored by the cell or are those quantities "side effects" of the metabolism?

Model of the Bacterial Cytoplasm.
McGuffee and Elcock, 2010, PLoS Comput Biol 

Various stresses can change cell volume or affect anabolism, thus modifying the concentration/crowding/density of the cytoplasm. In prokaryotic organisms, this can change cytoplasm properties and turn it into a gel-like or glass-like material. In a eukaryotic cell, how does that change cytoplasm properties? And then, how does that affect metabolism or cytoskeleton dynamics?
Then, a related question that is particularly interesting to me is how are cells adapting to it? A yeast cell will first shrink after an osmotic upshift but then the cell will recover its volume (Atligan et al., 2015). The recovery of the volume should restore the cytoplasm crowding/density to its normal level. The restoration of the volume can take several tens of minutes, how is the cell doing during this time? Is the change in the cytoplasm concentration affecting cellular processes? How? Is the cell only adapting its volume or also compensating for the increased concentration in the cytoplasm by degrading some of its own constituents?

The cytoplasm is not homogenous throughout the cell volume, some places are more dense/crowded, some contains specific enzymes and metabolic pathways. How is that heterogeneity generated? How does it change during cell cycle?

All these questions interrogate what we know of the cell biochemistry and biophysical properties. To understand and describe how a cell work in its globality, we need to be able to describe how the inside of the cell behaves, how it is organized and, how this organization can affect cellular processes.

As a postdoc (Fred Chang Lab, UCSF) I’m currently studying the effect of a change in cytoplasm density/crowding in yeast and mammalian cells on cytoskeleton dynamics.

 

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