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Joachim Goedhart

Publications and source records attributed to Joachim Goedhart.

2 recordsLinked to original sources

Calculation of a distribution free estimate of effect size and confidence intervals using VBA/Excel

Reporting effect sizes aids the transparent presentation and independent interpretation of scientific data. However, calculation and reporting of effect sizes for data obtained in basic research is rare. A standardized effect size was reported by Norman Cliff, known as Cliff's delta. It has several advantageous features, as (i) it makes no assumption on the shape of the underlying distribution, (ii) it works well for small to moderate samples (n>10), (iii) it is easy to calculate, and (iv) its basis is readily understood by non statisticians. Here, a VBA macro, implemented in Excel, is presented. The macro takes two independent samples as input and calculates Cliff's delta with 95% confidence intervals. The macro will reduce the barrier for calculating the effect size and can be a valuable tool for research and teaching.

Preprint

Palmitoylation of the oncogenic RhoGEF TGAT is dispensable for membrane affinity and consequent activation of RhoA

Rho guanine exchange factors (RhoGEFs) control many aspects of the cellular cytoskeleton, and thereby regulate and control processes such as cell migration, cell adhesion and proliferation. TGAT is a splice variant of the RhoGEF Trio, with oncogenic potential. Whether the subcellular location of TGAT is critical for its activity is unknown. Confocal microscopy of fluorescent protein tagged TGAT revealed co-localization with a Golgi marker. Because plasma membrane localized RhoGEFs are particularly effective at activating RhoA, plasma membrane localization of TGAT was studied. In order to quantitatively measure plasma membrane association we developed a novel, highly sensitive image analysis method. The method requires a cytoplasmic marker and a plasma membrane marker, which are co-imaged with the tagged protein of interest. Linear unmixing is performed to determine the plasma membrane and cytoplasmic component in the fluorescence signal of protein of interest. The analysis revealed that wild-type TGAT is partially co-localized with the plasma membrane. Strikingly, cysteine TGAT-mutants lacking one or more palmitoylation sites in the C-tail, still showed membrane association. In contrast, a truncated variant, lacking the last 15 amino acids, TGAT{Delta}15, lost membrane association. The functional role of membrane localization was determined by measuring TGAT activity in single cells with a RhoA FRET-sensor and F-actin levels. Mutants of TGAT that still maintained membrane association showed similar activity as wild-type TGAT. In contrast, the activity was abrogated for the cytoplasmic TGAT{Delta}15 variant. Synthetic recruitment of TGAT{Delta}15 to membranes confirmed that TGAT effectively activates RhoA at the plasma membrane. Together, these results show that membrane association of TGAT is critical for its activity, but that palmitoylation is dispensable.

Cell Biology