Biology subjects

Soula, M.

Publications and source records attributed to Soula, M..

3 recordsLinked to original sources

bioRxiv2021

MoBiFC: development of a modular bimolecular fluorescence complementation toolkit for the analysis of chloroplast protein-protein interactions.

The bimolecular fluorescence complementation (BiFC) assay has emerged as one of the most popular methods for analysing protein-protein interactions (PPIs) in plant biology. This includes its increasing use as a tool for dissecting the molecular mechanisms of chloroplast function. However, the construction of chloroplast fusion proteins for BiFC can be difficult, and the availability and selection of appropriate controls is not trivial. Furthermore, the challenges of performing BiFC in restricted cellular compartments has not been specifically addressed. Here we describe the development of a flexible modular cloning-based toolkit (MoBiFC) for chloroplast BiFC and proximity labelling using synthetic biology principles. The approach facilitates the cloning process for chloroplast-targeted proteins, allows robust ratiometric quantification, and the toolkit comes with model positive and negative controls. Our study also highlights many potential pitfalls including the choice of fluorescent protein (FP) split, negative controls, cell type, and reference FP. Finally, we provide an example of how users can enrich the toolset by providing functional proximity labelling modules, and we discuss how MoBiFC could be further improved and extended to other compartments of the plant cell.

plant biology↗

bioRxiv2021

Adaptive stimulation of macropinocytosis overcomes aspartate limitation in cancer cells under hypoxia

Stress-adaptive mechanisms enable tumor cells to overcome metabolic constraints in nutrient and oxygen poor tumors. Aspartate is an endogenous metabolic limitation under hypoxic conditions, but the nature of the adaptive mechanisms that contribute to aspartate availability and hypoxic tumor growth are poorly understood. Here, using a combination of metabolomics and CRISPR-based genetic screens, we identify GOT2-catalyzed mitochondrial aspartate synthesis as an essential metabolic dependency for the proliferation of pancreatic tumor cells under hypoxic culture conditions. In contrast, GOT2-catalyzed aspartate synthesis is dispensable for pancreatic tumor formation in vivo. The dependence of pancreatic tumor cells on aspartate synthesis is bypassed in part by a hypoxia-induced potentiation of extracellular protein scavenging via macropinocytosis. This effect is mutant KRas-dependent, and is mediated by hypoxia inducible factor 1 (HIF1A) and its canonical target carbonic anhydrase-9 (CA9) through the cooption of the bicarbonate-macropinocytosis signaling axis. Our findings reveal high plasticity of aspartate metabolism and define an adaptive regulatory role for macropinocytosis by which mutant KRas tumors can overcome nutrient deprivation under hypoxic conditions.

cancer biology↗

bioRxiv2020

Distinct population code for movement kinematics and changes of ongoing movements in human subthalamic nucleus

The subthalamic nucleus (STN) is theorized to globally suppress movement through connections with downstream basal ganglia structures. Current theories are supported by increased STN activity when subjects withhold an uninitiated action plan, but a critical test of these theories requires studying STN responses when an ongoing action is replaced with an alternative. Here, we perform this test using an extended reaching task with instructions to switch movement trajectory mid-action. We show that STN activity decreases during action switches, contrary to prevalent theories. Further, beta oscillations in the local field potential in STN, which are associated with movement inhibition do not show increased power or entraining of neuronal firing during switches. We report an inhomogeneous population neural code in STN, with one sub-population encoding movement kinematics and direction and another encoding unexpected action switches. We suggest an elaborate neural code in STN that contributes to planning actions and changing the plans.

neuroscience↗