scholarly journals Image based annotation of Chemogenomic Libraries for Phenotypic Screening

2022 ◽  
Author(s):  
Amelie Tjaden ◽  
Apirat Chaikuad ◽  
Eric Kowarz ◽  
Rolf Marschalek ◽  
Stefan Knapp ◽  
...  
Keyword(s):  
Small Molecules ◽  
Cellular Responses ◽  
Chemical Probes ◽  
Cellular Functions ◽  
Single Experiment ◽  
Cell Functions ◽  
Specific Effects ◽  
Apoptosis And Necrosis ◽  
Comprehensive Characterization

Phenotypical screening is a widely used approach in drug discovery for the identification of small molecules with cellular activities. However, functional annotation of identified hits often poses a challenge. The development of small molecules with narrow or exclusive target selectivity such as chemical probes and chemogenomic (CG) libraries, greatly diminishes this challenge, but non-specific effects caused by compound toxicity or interference with basic cellular functions still poses a problem to associate phenotypic readouts with molecular targets. Hence, each compound should ideally be comprehensively characterized regarding its effects on general cell functions. Here, we report an optimized live-cell multiplexed assay that classifies cells based on nuclear morphology, presenting an excellent indicator for cellular responses such as early apoptosis and necrosis. This basic readout in combination with the detection of other general cell damaging activities of small molecules such as changes in cytoskeletal morphology, cell cycle and mitochondrial health provides a comprehensive time-dependent characterization of the effect of small molecules on cellular health in a single experiment. The developed high-content assay offers multi-dimensional comprehensive characterization that can be used to delineate generic effects regarding cell functions and cell viability, allowing an assessment of compound suitability for subsequent detailed phenotypic and mechanistic studies.

scholarly journals Genome-wide analysis of cell-gene interactions

2017 ◽  
Author(s):  
S. Cardinale
Keyword(s):  
Single Gene ◽  
Rna Stability ◽  
Cellular Functions ◽  
Synthetic Genes ◽  
E Coli ◽  
Cell Functions ◽  
Specific Effects ◽  
Genome Wide ◽  
Cell Gene ◽  
Single Gene Deletion

AbstractThe study presents an analysis of how different cellular functions link cell size to the expression of synthetic genes inE. coli. The Size-Expression interaction was mapped with a two-gene genetic probe across 3800 single-gene deletion strains. Through regression analysis, expression-specific effects and gene-specific effects were derived from size effects and generic expression effects, respectively. The entire compendium of cell functions broadly mapped to four systems of distinct primary influence on the Size-Expression map. Specifically, membrane structural components primarily affected size, whereas protein and RNA stability primarily affected gene expression. In addition, major Size-Expression shifts showed no substantial gene-specific effects unless they were mediated by key components of the protein synthesis apparatus.Subject Category:Synthetic Biology

Cell (patho)physiology of magnesium

2007 ◽  
Vol 114 (1) ◽  
pp. 27-35 ◽  
Author(s):  
Federica I. Wolf ◽  
Valentina Trapani
Keyword(s):  
Energy Metabolism ◽  
Dynamic Environment ◽  
Biological Functions ◽  
Cellular Functions ◽  
Intracellular Magnesium ◽  
The Road ◽  
Cell Functions ◽  
Growth Energy

There is an unsettled debate about the role of magnesium as a ‘chronic regulator’ of biological functions, as opposed to the well-known role for calcium as an ‘acute regulator’. New and old findings appear to delineate an increasingly complex and important role for magnesium in many cellular functions. This review summarizes the available evidence for a link between the regulation of intracellular magnesium availability and the control of cell growth, energy metabolism and death, both in healthy and diseased conditions. A comprehensive view is precluded by technical difficulties in tracing magnesium within a multicompartment and dynamic environment like the cell; nevertheless, the last few years has witnessed encouraging progress towards a better characterization of magnesium transport and its storage or mobilization inside the cell. The latest findings pave the road towards a new and deeper appreciation of magnesium homoeostasis and its role in the regulation of essential cell functions.

scholarly journals HDX-MS reveals structural determinants for RORγ hyperactivation by synthetic agonists

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Timothy S Strutzenberg ◽  
Ruben D Garcia-Ordonez ◽  
Scott J Novick ◽  
HaJeung Park ◽  
Mi Ra Chang ◽  
...  
Keyword(s):  
Small Molecules ◽  
Structural Dynamics ◽  
Site Directed Mutagenesis ◽  
Chemical Probes ◽  
Structural Determinants ◽  
X Ray ◽  
Synthetic Ligand ◽  
Hdx Ms

Members of the nuclear receptor (NR) superfamily regulate both physiological and pathophysiological processes ranging from development and metabolism to inflammation and cancer. Synthetic small molecules targeting NRs are often deployed as therapeutics to correct aberrant NR signaling or as chemical probes to explore the role of the receptor in physiology. Nearly half of NRs do not have specific cognate ligands (termed orphan NRs) and it’s unclear if they possess ligand dependent activities. Here we demonstrate that ligand-dependent action of the orphan RORγ can be defined by selectively disrupting putative endogenous—but not synthetic—ligand binding. Furthermore, the characterization of a library of RORγ modulators reveals that structural dynamics of the receptor assessed by HDX-MS correlate with activity in biochemical and cell-based assays. These findings, corroborated with X-ray co-crystallography and site-directed mutagenesis, collectively reveal the structural determinants of RORγ activation, which is critical for designing RORγ agonists for cancer immunotherapy.

scholarly journals An atlas of the Norway spruce needle seasonal transcriptome

2021 ◽  
Author(s):  
Pushan Bag ◽  
Jenna Lihavainen ◽  
Nicolas Delhomme ◽  
Thomas Riquelme ◽  
Kathryn M Robinson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Norway Spruce ◽  
Cellular Functions ◽  
Developmental Program ◽  
Tentative Model ◽  
Visualization Tools ◽  
Global Transcriptome ◽  
Spruce Needles ◽  
Comprehensive Characterization

Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 to June 30), cell walls, organelles etc. were formed, and this developmental program heavily influenced the transcriptome, explained by over represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July-August), autumn (September-October), winter (November-February) and spring (March-April), where over represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.

Multimode light microscopy and fluorescence-based reagents as tools for the study of chemical and molecular dynamics of living cells and tissues

1992 ◽  
Vol 50 (1) ◽  
pp. 418-419
Author(s):  
D. L. Taylor
Keyword(s):  
Living Cells ◽  
Cellular Level ◽  
Molecular Techniques ◽  
Cellular Functions ◽  
Macromolecular Assemblies ◽  
Cell Functions ◽  
Molecular Events ◽  
Yield Information ◽  
Full Knowledge ◽  
Structural Methods

Cells function through the complex temporal and spatial interplay of ions, metabolites, macromolecules and macromolecular assemblies. Biochemical approaches allow the investigator to define the components and the solution chemical reactions that might be involved in cellular functions. Static structural methods can yield information concerning the 2- and 3-D organization of known and unknown cellular constituents. Genetic and molecular techniques are powerful approaches that can alter specific functions through the manipulation of gene products and thus identify necessary components and sequences of molecular events. However, full knowledge of the mechanism of particular cell functions will require direct measurement of the interplay of cellular constituents. Therefore, there has been a need to develop methods that can yield chemical and molecular information in time and space in living cells, while allowing the integration of information from biochemical, molecular and genetic approaches at the cellular level.

scholarly journals Modulating Tumor Cell Functions by Tunable Nanopatterned Ligand Presentation

Nanomaterials ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 212
Author(s):  
Katharina Amschler ◽  
Michael P. Schön
Keyword(s):  
Extracellular Matrix ◽  
Tumor Cell ◽  
Cell Fate ◽  
Epithelial Mesenchymal Transition ◽  
Model Systems ◽  
Cellular Functions ◽  
Biophysical Parameters ◽  
Ligand Density ◽  
Mesenchymal Transition ◽  
Cell Functions

Cancer comprises a large group of complex diseases which arise from the misrouted interplay of mutated cells with other cells and the extracellular matrix. The extracellular matrix is a highly dynamic structure providing biochemical and biophysical cues that regulate tumor cell behavior. While the relevance of biochemical signals has been appreciated, the complex input of biophysical properties like the variation of ligand density and distribution is a relatively new field in cancer research. Nanotechnology has become a very promising tool to mimic the physiological dimension of biophysical signals and their positive (i.e., growth-promoting) and negative (i.e., anti-tumoral or cytotoxic) effects on cellular functions. Here, we review tumor-associated cellular functions such as proliferation, epithelial-mesenchymal transition (EMT), invasion, and phenotype switch that are regulated by biophysical parameters such as ligand density or substrate elasticity. We also address the question of how such factors exert inhibitory or even toxic effects upon tumor cells. We describe three principles of nanostructured model systems based on block copolymer nanolithography, electron beam lithography, and DNA origami that have contributed to our understanding of how biophysical signals direct cancer cell fate.

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