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Biology subjects

Rost, H.

Publications and source records attributed to Rost, H..

22 records · Page 2Linked to original sources

Cell size homeostasis is maintained by a circuitry involving a CDK4-determined target size that programs the cell size-dependent activation of p38

While molecules that promote the growth of animal cells have been identified, the following question remains: How are growth promoting pathways regulated to specify a characteristic size for each of the different cell types? In 1975, Hartwell and Nurse suggested that in eukaryotes, cell size is determined by size checkpoints - mechanisms that restrict cell cycle progression from cells that are smaller than their target size. Curiously, such checkpoint mechanisms imply a conceptual distinction between a cells actual size and cells target size. In the present study, we materialize this conceptual distinction by describing experimental assays that discriminately quantify a cells target size value. With these assays, we show that a cells size and target size are distinct phenotypes that are subject to different upstream regulators. While mTORC1 promotes growth in cell size, our data suggests that a cells target size value is regulated by other pathways including FGFR3, ROCK2, and CDK4. For example, while rapamycin (an mTORC1 inhibitor) decreases cell size, rapamycin does not change the target size that is required for the G1/S transition. The CDK4/Rb pathway has been previously proposed as a putative regulator of target size. Yet, in lacking experimental means that discriminate perturbations of cell growth from perturbations that reprogram target size, such claims on target size were not validated. To investigate the functions of CDK4 in target size determination, we used genetic and chemical means to dial higher and lower levels of CDK4 activity. These measurements identified functions of CDK4 on target size that are distinct from other G1 CDKs. Using C. elegans, we further demonstrate that these influences of CDK4 on size determination function in vivo. Finally, we propose a model whereby mTORC1, p38, and CDK4 cooperate in a manner that is analogous to the function of a thermostat. While mTORC1 promotes cellular growth as prompted by p38, CDK4 is analogous to the thermostat dial that sets the critical target size associated with cell size homeostasis.

cell biology↗

SmartPeak automates targeted and quantitative metabolomics data processing

SmartPeak is an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of CE-, GC- and LC-MS(/MS) data, and HPLC data for targeted and semi-targeted metabolomics, lipidomics, and fluxomics experiments. HighlightsO_LINovel algorithms for retention time alignment, calibration curve fitting, and peak integration C_LIO_LIEnables reproducibility by reducing operator bias and ensuring high QC/QA C_LIO_LIAutomated pipeline for high throughput targeted and/or quantitative metabolomics, lipidomics, and fluxomics data processing from multiple analytical instruments C_LIO_LIManually curated data set of LC-MS/MS, GC-MS, and HPLC integrated peaks for further algorithm development and benchmarking C_LI

bioinformatics↗

Automated Workflow For Peptide-level Quantitation From DIA/ SWATH-MS Data

Data Independent Acquisition (DIA) is a powerful method to acquire spectra from all ionized precursors of a sample. Considering the complexity of the highly multiplexed spectral data, sophisticated workflows have been developed to obtain peptides quantification. Here we describe an open-source and easy-to-use workflow to obtain a quantitative matrix from multiple DIA runs. This workflow requires as prior information an "assay library", which contains the MS coordinates of peptides. It consists of OpenSWATH, pyProphet and DIAlignR software. For the ease of installation and to isolate operating system related dependency, docker-based containerization is utilized in this workflow.

bioinformatics↗

DrawAlignR: An interactive tool for across run chromatogram alignment visualization

Multi-run alignment is widely used in proteomics to establish analyte correspondence across runs. Generally alignment algorithms return a cumulative score, which may not be easily interpretable for each peptide. Here we present a novel tool, DrawAlignR, to visualize each chromatographic alignment for DIA/SWATH data. Furthermore, we have developed a novel C++ based implementation of raw chromatogram alignment which is 35 times faster than the previously published algorithm. This not only enables users to plot alignment interactively by DrawAlignR, but also allows other software platforms to use the algorithm. DrawAlignR is an open-source web application using R Shiny that can be hosted using the source-code available at https://github.com/Roestlab/DrawAlignR.

bioinformatics↗