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Principles Of Fluorescence Spectroscopy

Naming and necessity

Phosphoinositides (PIs) make up only a small fraction of cellular phospholipids, yet they control almost all aspects of a cell's life and death. These lipids gained tremendous research interest as plasma membrane signaling molecules when discovered in the 1970s and 1980s. Research in the last 15 years has added a wide range of biological processes regulated by PIs, turning these lipids into one of the most universal signaling entities in eukaryotic cells. PIs control organelle biology by regulating vesicular trafficking, but they also modulate lipid distribution and metabolism via their close relationship with lipid transfer proteins. PIs regulate ion channels, pumps, and transporters and control both endocytic and exocytic processes. The nuclear phosphoinositides have grown from being an epiphenomenon to a research area of its own. As expected from such pleiotropic regulators, derangements of phosphoinositide metabolism are responsible for a number of human diseases ranging from rare genetic disorders to the most common ones such as cancer, obesity, and diabetes. Moreover, it is increasingly evident that a number of infectious agents hijack the PI regulatory systems of host cells for their intracellular movements, replication, and assembly. As a result, PI converting enzymes began to be noticed by pharmaceutical companies as potential therapeutic targets. This review is an attempt to give an overview of this enormous research field focusing on major developments in diverse areas of basic science linked to cellular physiology and disease.

Phosphoinositides: Tiny Lipids With Giant Impact on Cell Regulation

Nociception is the process whereby primary afferent nerve fibers of the somatosensory system detect noxious stimuli. Pungent irritants from pepper, mint, and mustard plants have served as powerful pharmacological tools for identifying molecules and mechanisms underlying this initial step of pain sensation. These natural products have revealed three members of the transient receptor potential (TRP) ion channel family—TRPV1, TRPM8, and TRPA1—as molecular detectors of thermal and chemical stimuli that activate sensory neurons to produce acute or persistent pain. Analysis of TRP channel function and expression has validated the existence of nociceptors as a specialized group of somatosensory neurons devoted to the detection of noxious stimuli. These studies are also providing insight into the coding logic of nociception and how specification of nociceptor subtypes underlies behavioral discrimination of noxious thermal, chemical, and mechanical stimuli. Biophysical and pharmacological characterization of these...

TRP Channels and Pain

We report the engineering of mScarlet, a truly monomeric red fluorescent protein with record brightness, quantum yield (70%) and fluorescence lifetime (3.9 ns). We developed mScarlet starting with a consensus synthetic template and using improved spectroscopic screening techniques; mScarlet's crystal structure reveals a planar and rigidified chromophore. mScarlet outperforms existing red fluorescent proteins as a fusion tag, and it is especially useful as a Forster resonance energy transfer (FRET) acceptor in ratiometric imaging.

mScarlet: a bright monomeric red fluorescent protein for cellular imaging

Reporting of the actual data in graphs and plots increases transparency and enables independent evaluation. On the other hand, data summaries are often used in graphs because they aid interpretation. To democratize state-of-the-art data visualization of raw data with a selection of statistical summaries, a freely available, open-source web app was written using R/shiny that uses the ggplot2 package for generating plots. Users can to choose how to display the data and which of the data summaries to add. In addition, the 95% confidence intervals (95CIs) can be added for visual inferences. By adjusting the visibility of the layers, the visualization of the raw data and their summaries can be tuned for optimal presentation and interpretation. The app is dubbed PlotsOfData and is available at https://huygens.science.uva.nl/PlotsOfData/.

/pdf/plotsofdata-a-web-app-for-visualizing-data-together-with-2nxmpo6w87.pdf

PlotsOfData—A web app for visualizing data together with their summaries

Chemotaxis is the result of a refined interplay among various intracellular molecules that process spatial and temporal information. Here we present a modular scheme of the complex interactions between the front and the back of cells that allows them to navigate. First, at the front of the cell, activated Rho-type GTPases induce actin polymerization and pseudopod formation. Second, phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P3) is produced in a patch at the leading edge, where it binds pleckstrin-homology-domain-containing proteins, which enhance actin polymerization and translocation of the pseudopod. Third, in Dictyostelium amoebae, a cyclic-GMP-signalling cascade has been identified that regulates myosin filament formation in the posterior of the cell, thereby inhibiting the formation of lateral pseudopodia that could misdirect the cell.

/pdf/chemotaxis-signalling-modules-join-hands-at-front-and-tail-2q3zj4o6v5.pdf

Chemotaxis: signalling modules join hands at front and tail.

http://web.mit.edu/biophysics/sbio/PDFs/postma.pdf

A Diffusion–Translocation Model for Gradient Sensing by Chemotactic Cells

http://www.martenpostma.nl/docs/Huang2010.pdf

Marten Postma

Papers

mScarlet: a bright monomeric red fluorescent protein for cellular imaging

PlotsOfData—A web app for visualizing data together with their summaries

Chemotaxis: signalling modules join hands at front and tail.

A Diffusion–Translocation Model for Gradient Sensing by Chemotactic Cells

Activation of TRP channels by protons and phosphoinositide depletion in Drosophila photoreceptors.