Nutrients and Signals

Author: Gianpiero Pescarmona
Date: 14/05/2007


In ecology, a niche (pronounced nich, neesh or nish) is a term describing the relational position of a species or population in its ecosystem. The ecological niche describes how an organism or population responds to the distribution of resources and competitors. This definition applies to any biological system independently of the scale (from social groups to a single cell)

Factors involved in niche definition

Niches types

Different environments can drive cells differentiation (one genome --> many cells)

Stem Cells Niche

stem cells niche

stem cells niche

stem cellsniche hepatocytes

stem cells hair

stem cells niche bone

stem cell migration

Stem-cell populations are established in 'niches' — specific anatomic locations that regulate how they participate in tissue generation, maintenance and repair. The niche saves stem cells from depletion, while protecting the host from over-exuberant stem-cell proliferation. It constitutes a basic unit of tissue physiology, integrating signals that mediate the balanced response of stem cells to the needs of organisms. Yet the niche may also induce pathologies by imposing aberrant function on stem cells or other targets. The interplay between stem cells and their niche creates the dynamic system necessary for sustaining tissues, and for the ultimate design of stem-cell therapeutics.

The stem-cell niche as an entity of action Nature 2007 see figure

The nature of stem cells: state rather than entity 2004

The Stem Cell Niche and breast Cancer 2005 Georgetown University

Bone marrow

The hematopoietic stem cell and its niche: a comparative view 2007

Molecular Characterization of Spontaneous Mesenchymal Stem Cell Transformation 2008

Proteins AA content offers information about AA content in the niche

  • CLoCK protein has been shown to possess histone acetyltransferase activity28, and can acetylate its partner, bmAL1, on lysine 537.
  • The histone deacetylase sirtuin 1 (SIRT1) interacts with CLoCK and can deacetylate lysine 537 of bmAL1 as well as lysine 9 and 14 of histone H3. SIRT1 is expressed in a circadian manner

SIRT1 means glutamine and glutamate and acetylCoA and switch off DNA synthesis

CLoCK means glutamine and bases synthesis and switch on DNA synthesis

Search for the AA % of the 2 proteins. Result

Cell Microenvironments Hold Key To Future Stem Cell Therapies

The ultimate fate of a stem or progenitor cell in a woman's breast -- whether the
cell develops normally or whether it turns cancerous -- may depend upon signals from
multiple microenvironments. New results suggest that modulations of
microenvironmental signals are a promising pathway for future cancer and
regenerative medicine therapies.

No place like home: anatomy and function of the stem cell niche 2008

Cells Heterogeneity

A central challenge of biology is to understand how individual cells process information and respond to perturbations. Much of our knowledge is based on ensemble measurements. However, cell-to-cell differences are always present to some degree in any cell population, and the ensemble behaviors of a population may not represent the behaviors of any individual cell. Here, we discuss examples of when heterogeneity cannot be ignored and describe practical strategies for analyzing and interpreting cellular heterogeneity.
Cellular Heterogeneity: Do Differences Make a Difference? 2010

Figure 1. Ensemble Averages and Heterogeneity(A) Ensemble-averaged measurements can mask information contained in heterogeneity. Behaviors of cells in (i) the tail of a distribution (shaded area) or (ii) a small subpopulation (at right) may differ from the remainder of the population or from the “mean” behavior (dashed line at μ1). (iii) For bimodal cellular behaviors, a population mean may poorly represent the majority of cells. (iv) Multiple measurements may be required to distinguish different patterns of cellular heterogeneity. Correlated (left) or anticorrelated (right) behaviors of cells may be indistinguishable based on single measurements alone (compare histograms at sides of left and right density plots). Axis labels f1 and f2 represent single-cell measurements (e.g., cell size, division time, or expression of a cell surface marker). Dashed lines and triangles indicate population means.(B) Heterogeneity and function: Decompositions of heterogeneity may be tested for functionally important information. (i) Single-cell measurements allow cells (left) to be represented as points in a (high-dimensional) feature space (right). (ii) Cell populations can be partitioned into distinct regions of feature space. This partition may be determined manually or automatically. Illustrated is a decomposition into two subpopulations, S1 and S2; μ represents the population mean. (iii) The values of a functional readout for individual subpopulations and the population mean can be tested for significant differences within a population (left; * indicates significance). Alternatively, different mixtures of heterogeneity observed for populations under different conditions can be tested for correlation with function (middle and right). “Function” refers to the evaluation of a functional readout over a collection of cells, either at the subpopulation or whole-population level (e.g., drug sensitivity).

The construction of 3D-engineered tissues composed of cells and extracellular matrices by hydrogel template approach 2007

The engineered tissue was self-standing and highly dense composite of the cultured cells and collagen produced by the cells. This hydrogel template approach may be useful as a new class of soft-tissue engineering technology to substitute a synthetic polymer scaffold to the ECM scaffold produced from the cultured cells.

Brain neurons niche

Brain diversity evolves via differences in patterning 2010

Divergence among rock-dwellers and sand-dwellers in the relative size of the telencephalon versus the thalamus is correlated with gene expression variation in a regulatory circuit (composed of six3, fezf2, shh, irx1b, and wnt1) known from model organisms to specify anterior-posterior (AP) brain polarity and position the shh-positive signaling boundary zona limitans intrathalamica (ZLI) in the forebrain. To confirm that changes in this coexpression network are sufficient to produce the differences we observe, we manipulated WNT signaling in vivo by treating rock-dwelling cichlid embryos with temporally precise doses of LiCl.

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