Bayesian inference of molecular kinetic parameters from astrocyte calcium imaging data.

Model-based Bayesian inference from high-content data obtained on live specimens is a burgeoning field with demonstrated applications to neuroscience. In parallel, computer vision methods for extracting the calcium signaling information from imaging data have advanced in application to neuronal physiology. Here, we are describing in detail a method we have recently developed to study calcium dynamics in astrocytes, which combines computer vision with model-based Bayesian learning to deduce the most likely molecular kinetic parameters underlying the observed calcium activity.

Experimental and computational analyses of calcium dynamics in 22q11.2 deletion model astrocytes.

Methods for deriving mechanistic information from intracellular calcium dynamics have largely been applied to neuronal data despite the knowledge of roles of glial cells in behavior, cognition, and psychiatric disorders. Using calcium imaging, computer vision, and Bayesian kinetic inference (BKI), we analyzed calcium dynamics in primary astrocytes derived from control or Df1/ mice, a model of 22q11.2 deletion (DiGeorge syndrome).

Astrocyte Bioenergetics and Major Psychiatric Disorders.

Ongoing research continues to add new elements to the emerging picture of involvement of astrocyte energy metabolism in the pathophysiology of major psychiatric disorders, including schizophrenia, mood disorders, and addictions. This review outlines what is known about the energy metabolism in astrocytes, the most numerous cell type in the brain, and summarizes the recent work on how specific perturbations of astrocyte bioenergetics may contribute to the neuropsychiatric conditions. The role of astrocyte energy metabolism in mental health and disease is reviewed on the organism, organ, and cell level.

Myosin 1C isoform A is a novel candidate diagnostic marker for prostate cancer.

Early diagnosis of prostate cancer is a challenging issue due to the lack of specific markers. Therefore, a sensitive diagnostic marker that is expressed or upregulated exclusively in prostate cancer cells would facilitate diagnostic procedures and ensure a better outcome. We evaluated the expression of myosin 1C isoform A in 5 prostate cell lines, 41 prostate cancer cases, and 11 benign hyperplasias.

Effect of Palmitic Acid on Exosome-Mediated Secretion and Invasive Motility in Prostate Cancer Cells.

High fat consumption can enhance metastasis and decrease survival in prostate cancer, but the picture remains incomplete on the epidemiological and cell-biological level, impeding progress toward individualized recommendations in the clinic. Recent work has highlighted the role of exosomes secreted by prostate cancer cells in the progression of the disease, particularly in metastatic invasion, and also the utility of targeting these extracellular vesicles for diagnostics, as carriers of disease progression markers. Here, we investigated the question of a potential impact of the chief nutritional saturated fatty acid on the exosome secretion.

Myosins in the Nucleus.

Although originally characterized as a cytoplasmic protein, myosin of various classes also performs key functions in the nucleus. We review the data concerning the nuclear localization, mechanism of entry, and functional interactions of myosin I, II, V, VI, X, XVI, and XVIII. To date, the first-characterized "nuclear myosin I" (or, in the prevailing nomenclature, myosin IC isoform B) remains the best-studied nuclear myosin, although results are rapidly accumulating that illuminate the roles of other myosin classes, and an outline of a unified picture of myosin functions in the nucleus is beginning to emerge.

Effect of polyunsaturated fatty acids on proliferation and survival of prostate cancer cells.

Progression of prostate cancer to lethal forms is marked by emergence of hormone-independent proliferation of the cancer cells. Nutritional and epidemiological studies have indicated that prostate cancer progression is correlated with the consumption of polyunsaturated fatty acids (PUFA). To shed additional light on the cell-level mechanisms of the observed correlation, we compared the sensitivity of hormone-dependent and hormone-independent prostate cancer cells to growth medium supplementation with free PUFAs in a cell proliferation and viability assay.

Specific and reliable detection of Myosin 1C isoform A by RTqPCR in prostate cancer cells.

Background: Prostate cancer (PC) diagnostics and treatment often present a challenging task due to cancer subtype heterogeneity and differential disease progression in patient subgroups. Hence, the critical issue is finding a reliable and sensitive diagnostic and prognostic PC marker, especially for cases of biopsies with low percentages of cancer cells. Isoform A of myosin 1C was shown to be expressed in PC cells and responsible for their invasive properties, however, its feasibility for diagnostic purposes remains to be elucidated.

Fatty Acids and Calcium Regulation in Prostate Cancer.

Prostate cancer is a widespread malignancy characterized by a comparative ease of primary diagnosis and difficulty in choosing the individualized course of treatment. Management of prostate cancer would benefit from a clearer understanding of the molecular mechanisms behind the transition to the lethal, late-stage forms of the disease, which could potentially yield new biomarkers for differential prognosis and treatment prioritization in addition to possible new therapeutic targets. Epidemiological research has uncovered a significant correlation of prostate cancer incidence and progression with the intake (and often co-intake) of fatty acids and calcium.

Calcium and Nuclear Signaling in Prostate Cancer.

Recently, there have been a number of developments in the fields of calcium and nuclear signaling that point to new avenues for a more effective diagnosis and treatment of prostate cancer. An example is the discovery of new classes of molecules involved in calcium-regulated nuclear import and nuclear calcium signaling, from the G protein-coupled receptor (GPCR) and myosin families. This review surveys the new state of the calcium and nuclear signaling fields with the aim of identifying the unifying themes that hold out promise in the context of the problems presented by prostate cancer.

Myosin isoform expressed in metastatic prostate cancer stimulates cell invasion.

During metastasis, tumor cells migrate out of their original tissue to invade other organs. Secretion of exosomes and metalloproteases is essential for extracellular matrix remodeling, enabling migration through tissue barriers. Metastatic prostate cancer is differentiated by expression of the rare isoform A of the molecular motor myosin IC, however the function of this isoform remained unknown.

Calcium-regulated import of myosin IC into the nucleus.

Myosin IC is a molecular motor involved in intracellular transport, cell motility, and transcription. Its mechanical properties are regulated by calcium via calmodulin binding, and its functions in the nucleus depend on import from the cytoplasm. The import has recently been shown to be mediated by the nuclear localization signal located within the calmodulin-binding domain.

Microtubule appendages mediating T-cell motility and polarity.

Polarization of the centrosome and the Golgi apparatus in the T cell (TC) toward the antigen-presenting cell (APC) is essential for the specificity of the immune response on the cellular level. Previously we reported the existence of thin, long processes on the TC surface, which emanated predominantly from the area next to the Golgi apparatus. They appeared to be involved in the orientation of the TC during the initial phases of its attachment, which preceded the formation of the immunological synapse mediated by lamellipodia.

CFEOM1-associated kinesin KIF21A is a cortical microtubule growth inhibitor.

Mechanisms controlling microtubule dynamics at the cell cortex play a crucial role in cell morphogenesis and neuronal development. Here, we identified kinesin-4 KIF21A as an inhibitor of microtubule growth at the cell cortex. In vitro, KIF21A suppresses microtubule growth and inhibits catastrophes.

Centrobin regulates centrosome function in interphase cells by limiting pericentriolar matrix recruitment.

The amount of pericentriolar matrix at the centrosome is tightly linked to both microtubule nucleation and centriole duplication, although the exact mechanism by which pericentriolar matrix levels are regulated is unclear. Here we show that Centrobin, a centrosomal protein, is involved in regulating these levels. Interphase microtubule arrays in Centrobin-depleted cells are more focused around the centrosome and are less stable than the arrays in control cells.

Equilibria of idealized confined astral microtubules and coupled spindle poles.

Positioning of the mitotic spindle through the interaction of astral microtubules with the cell boundary often determines whether the cell division will be symmetric or asymmetric. This process plays a crucial role in development. In this paper, a numerical model is presented that deals with the force exerted on the spindle by astral microtubules that are bent by virtue of their confinement within the cell boundary.

Efficiency of organelle capture by microtubules as a function of centrosome nucleation capacity: general theory and the special case of polyspermia.

Transport of organelles along microtubules is essential for the cell metabolism and morphogenesis. The presented analysis derives the probability that an organelle of a given size comes in contact with the microtubule aster. The question is asked how this measure of functionality of the microtubule aster is controlled by the centrosome.

Systems biomechanics of centrosome positioning: A conserved complexity.

Positioning of centrosomes within cells determines the directionality of cell division, as well as directionality of cellular activities in the interphase. This brief review focuses on similarities (and differences) of centrosome positioning during early divisions in the Caenorhabditis embryo and during the interaction of T lymphocytes with other cells in the course of immune response. In the study of the two phenomena, a synergy of experimentation and numerical mechanical analysis has recently been achieved.

Introduction: a practical guide to the systems approach in biology.

This essay provides an informal review of the modern systems-centric biological methodology for the practical researcher. The systems approach is defined, and a generic recipe for employing it in biomedical research is offered. General caveats are discussed that pertain to biological complexity, to explanation in molecular terms, and to bottom-up investigation.

Deterministic mechanical model of T-killer cell polarization reproduces the wandering of aim between simultaneously engaged targets.

T-killer cells of the immune system eliminate virus-infected and tumorous cells through direct cell-cell interactions. Reorientation of the killing apparatus inside the T cell to the T-cell interface with the target cell ensures specificity of the immune response. The killing apparatus can also oscillate next to the cell-cell interface.

An experimental and computational study of effects of microtubule stabilization on T-cell polarity.

T-killer cells eliminate infected and cancerous cells with precision by positioning their centrosome near the interface (immunological synapse) with the target cell. The mechanism of centrosome positioning has remained controversial, in particular the role of microtubule dynamics in it. We re-examined the issue in the experimental model of Jurkat cells presented with a T cell receptor-binding artificial substrate, which permits controlled stimulation and reproducible measurements.

Retractile processes in T lymphocyte orientation on a stimulatory substrate: morphology and dynamics.

T cells of the immune system target infected and tumor cells in crowded tissues with high precision by coming into direct contact with the intended target and orienting the intracellular Golgi apparatus and the associated organelles to the area of the cell-cell contact. The mechanism of this orientation remains largely unknown. To further elucidate it we used three-dimensional microscopy of living T cells presented with an artificial substrate mimicking the target cell surface.

Rab6 regulates transport and targeting of exocytotic carriers.

Constitutive exocytosis delivers newly synthesized proteins, lipids, and other molecules from the Golgi apparatus to the cell surface. This process is mediated by vesicles, which bud off the trans-Golgi network, move along cytoskeletal filaments, and fuse with the plasma membrane. Here, we show that the small GTPase Rab6 marks exocytotic vesicles and, together with the microtubule plus-end-directed motor kinesin-1, stimulates their processive microtubule-based transport to the cell periphery.

A model for the interplay of receptor recycling and receptor-mediated contact in T cells.

Orientation of organelles inside T cells (TC) toward antigen-presenting cells (APC) ensures that the immune response is properly directed, but the orientation mechanisms remain largely unknown. Structural dynamics of TC are coupled to dynamics of T-cell receptor (TCR), which recognizes antigen on the APC surface. Engagement of the TCR triggers its internalization followed by delayed polarized recycling to the plasma membrane through the submembrane recycling compartment (RC), which organelle shares intracellular location with the TC effector apparatus.

Contribution of whole-cell optimization via cell body rolling to polarization of T cells.

Directed secretion of cytotoxins or cytokines by T cells during immune response depends on migration of the centrosome in the T cell to the interface with the target cell. The mechanism of the centrosome translocation has been elusive. The presented computational analysis demonstrates that the centrosome should be positioned at the interface if the T cell attempts simultaneously (a) to minimize its surface area, (b) to maximize the interface area, (c) to maintain the cell volume and (d) to straighten the microtubules.