High-Throughput Measurement of Single-Fission Yeast Cell Volume Using Fluorescence Exclusion.

Cell volume is a critical parameter for the biology of living species and has an impact on virtually all cellular functions. In Schizosaccharomyces pombe, the regulation of cell size has been the focus of intense investigation, and mechanisms that couple size control with cell cycle progression have been identified. In fission yeast, cell length at division is generally used as a proxy for determining cell size.

Extended Methods for 2D Confinement.

Physical confinement in microfluidic devices has become a common technique to induce and study cell migration in a large range of cell types. Confined migration was previously understudied due to the limitations of 2D migration assays but has emerged as an important mode of migration in the past decade. Furthermore, confinement improves the quality of the imaging and simplifies the analysis of trajectories by confining migration to the plane of acquisition.

Fluorescence exclusion - a rapid, accurate and powerful method for measuring yeast cell volume.

Cells exist in an astonishing range of volumes across and within species. However, our understanding of cell size control remains limited, owing in large part to the challenges associated with accurate determination of cell volume. Much of our comprehension of size regulation derives from yeast models, but even for these morphologically stereotypical cells, assessment of cell volume has mostly relied on proxies and extrapolations from two-dimensional measurements.

A mechano-osmotic feedback couples cell volume to the rate of cell deformation.

Mechanics has been a central focus of physical biology in the past decade. In comparison, how cells manage their size is less understood. Here, we show that a parameter central to both the physics and the physiology of the cell, its volume, depends on a mechano-osmotic coupling.

Volume growth in animal cells is cell cycle dependent and shows additive fluctuations.

The way proliferating animal cells coordinate the growth of their mass, volume, and other relevant size parameters is a long-standing question in biology. Studies focusing on cell mass have identified patterns of mass growth as a function of time and cell cycle phase, but little is known about volume growth. To address this question, we improved our fluorescence exclusion method of volume measurement (FXm) and obtained 1700 single-cell volume growth trajectories of HeLa cells.

Profilin and formin constitute a pacemaker system for robust actin filament growth.

The actin cytoskeleton drives many essential biological processes, from cell morphogenesis to motility. Assembly of functional actin networks requires control over the speed at which actin filaments grow. How this can be achieved at the high and variable levels of soluble actin subunits found in cells is unclear.

Mathematical Justification of Expression-Based Pathway Activation Scoring (PAS).

Although modeling of activation kinetics for various cell signaling pathways has reached a high grade of sophistication and thoroughness, most such kinetic models still remain of rather limited practical value for biomedicine. Nevertheless, recent advancements have been made in application of signaling pathway science for real needs of prescription of the most effective drugs for individual patients. The methods for such prescription evaluate the degree of pathological changes in the signaling machinery based on two types of data: first, on the results of high-throughput gene expression profiling, and second, on the molecular pathway graphs that reflect interactions between the pathway members.

Fluorescence eXclusion Measurement of volume in live cells.

Volume is a basic physical property of cells; however, it has been poorly investigated in cell biology so far, mostly because it is difficult to measure it precisely. Recently, large efforts were made to experimentally measure mammalian cell size and used mass, density, or volume as proxies for cell size. Here, we describe a method enabling cell volume measurements for single living cells.

In search for geroprotectors: in silico screening and in vitro validation of signalome-level mimetics of young healthy state.

Populations in developed nations throughout the world are rapidly aging, and the search for geroprotectors, or anti-aging interventions, has never been more important. Yet while hundreds of geroprotectors have extended lifespan in animal models, none have yet been approved for widespread use in humans. GeroScope is a computational tool that can aid prediction of novel geroprotectors from existing human gene expression data.

Vimentin is involved in regulation of mitochondrial motility and membrane potential by Rac1.

In this study we show that binding of mitochondria to vimentin intermediate filaments (VIF) is regulated by GTPase Rac1. The activation of Rac1 leads to a redoubling of mitochondrial motility in murine fibroblasts. Using double-mutants Rac1(G12V, F37L) and Rac1(G12V, Y40H) that are capable to activate different effectors of Rac1, we show that mitochondrial movements are regulated through PAK1 kinase.

Combinatorial high-throughput experimental and bioinformatic approach identifies molecular pathways linked with the sensitivity to anticancer target drugs.

Effective choice of anticancer drugs is important problem of modern medicine. We developed a method termed OncoFinder for the analysis of new type of biomarkers reflecting activation of intracellular signaling and metabolic molecular pathways. These biomarkers may be linked with the sensitivity to anticancer drugs.

[Modern opportunities and prospects for studying pathogenesis, diagnosing and treating hereditary optic neuropathies].

Objective: To evaluate modern opportunities and prospects for studying pathogenesis and improving diagnostics and treatment of hereditary optic neuropathies (HON).

Material And Methods: The article presents summarized data on the pathogenesis, diagnostics, and treatment of HON based on modern methods of assessment.

Results: The results of long-term worldwide studies and those performed in the Research Institute of Eye Diseases in collaboration with several other institutions are presented.

Signaling pathways activation profiles make better markers of cancer than expression of individual genes.

Identification of reliable and accurate molecular markers remains one of the major challenges of contemporary biomedicine. We developed a new bioinformatic technique termed OncoFinder that for the first time enables to quantatively measure activation of intracellular signaling pathways basing on transcriptomic data. Signaling pathways regulate all major cellular events in health and disease.

Oncofinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data.

We propose a new biomathematical method, OncoFinder, for both quantitative and qualitative analysis of the intracellular signaling pathway activation (SPA). This method is universal and may be used for the analysis of any physiological, stress, malignancy and other perturbed conditions at the molecular level. In contrast to the other existing techniques for aggregation and generalization of the gene expression data for individual samples, we suggest to distinguish the positive/activator and negative/repressor role of every gene product in each pathway.

The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis.

The diversity of the installed sequencing and microarray equipment make it increasingly difficult to compare and analyze the gene expression datasets obtained using the different methods. Many applications requiring high-quality and low error rates cannot make use of available data using traditional analytical approaches. Recently, we proposed a new concept of signalome-wide analysis of functional changes in the intracellular pathways termed OncoFinder, a bioinformatic tool for quantitative estimation of the signaling pathway activation (SPA).