Polar lakes may act as ecological islands to aquatic protists

A fundamental question in ecology is whether microorganisms follow the same patterns as multicellular organisms when it comes to population structure and levels of genetic diversity. Enormous population sizes, predominately asexual reproduction and presumably high dispersal because of small body size could have profound implications on their genetic diversity and population structure. Here, we have analysed the population genetic structure in a lake‐dwelling microbial eukaryote (dinoflagellate) and tested the hypothesis that there is population genetic differentiation among nearby lake subpopulations. This dinoflagellate occurs in the marine‐derived saline lakes of the Vestfold Hills, Antarctica, which are ice‐covered most of the year. Clonal strains were isolated from four different lakes and were genotyped using amplified fragment length polymorphism (AFLP). Our results show high genetic differentiation among lake populations despite their close geographic proximity (<9 km). Moreover, genotype diversity was high within populations. Gene flow in this system is clearly limited, either because of physical or biological barriers. Our results discard the null hypothesis that there is free gene flow among protist lake populations. Instead, limnetic protist populations may differentiate genetically, and lakes act as ecological islands even on the microbial scale.     

CORRELATED TROPHIC SPECIALIZATION AND GENETIC DIVERGENCE IN SYMPATRIC LAKE WHITEFISH ECOTYPES (COREGONUS CLUPEAFORMIS): SUPPORT FOR THE ECOLOGICAL SPECIATION HYPOTHESIS

There is ample empirical evidence that phenotypic diversification in an adaptive radiation is the outcome of divergent natural selection related to differential resource use. In contrast, the role of ecological forces in favoring and maintaining reproductive isolation in nature remains poorly understood. If the same forces driving phenotypic divergence are also responsible for speciation, one would predict a correlation between the extent of trophic specialization (reflecting variable intensity of divergent natural selection) and that of reproductive isolation being reached in a given environment. We tested this hypothesis by comparing the extent of morphological and genetic differentiation between sympatric dwarf and normal whitefish ecotypes (Coregonus sp.) from six lakes of the St. John River basin (eastern Canada and northern Maine). Eight meristic variables, 19 morphometric variables, and six microsatellite loci were used to quantify morphological and genetic differentiation, respectively. Dwarf and normal ecotypes in each lake differed primarily by traits related to trophic specialization, but the extent of differentiation varied among lakes. Significant but variable genetic divergence between ecotypes within lakes was also observed. A negative correlation was observed between the extent of gene flow between ecotypes within a lake and that of their morphological differentiation in trophic-related traits. The extent of reproductive isolation reached between dwarf and normal whitefish ecotypes appears to be driven by the potential for occupying distinct trophic niches and, thus, by the same selective forces driving tropic specialization in each lake. These results therefore support the hypothesis of ecological speciation.     

In vitro study of the effects of ELF electric fields on gene expression in human epidermal cells

An acceleration of differentiation, at the expense of proliferation, is observed after exposure of various biological models to low frequency and low amplitude electric and electromagnetic fields. Following these results showing significant modifications, we try to identify the biological mechanism involved at the cell level through microarray screening. For this study, we use epidermis cultures harvested from human abdominoplasty. Two platinum electrodes are used to apply the electric signal. The gene expressions of 38,500 well‐characterized human genes are analyzed using Affymetrix® microarray U133 Plus 2.0 chips. The protocol is repeated on three different patients. After three periods of exposure, a total of 24 chips have been processed. After the application of ELF electric fields, the microarray analysis confirms a modification of the gene expression of epidermis cells. Particularly, four up‐regulated genes (DKK1, TXNRD1, ATF3, and MME) and one down‐regulated gene (MACF1) are involved in the regulation of proliferation and differentiation. Expression of these five genes was also confirmed by real‐time rtPCR in all samples used for microarray analysis. These results corroborate an acceleration of cell differentiation at the expense of cell proliferation. Bioelectromagnetics 32:28–36, 2011. © 2010 Wiley‐Liss, Inc.     

Differences between karyotypically normal and abnormal human embryonic stem cells

Objectives: To compare different biological characteristics of human embryonic stem cells (HESCs) between those with normal and those with abnormal karyotype. Materials and methods: Culture‐adapted HESCs (chHES‐3) with abnormal karyotype were compared with karyotypically normal cells, with regard to pluripotency and differentiation capacity, ultrastructure, growth characteristics, gene expression profiles and signalling pathways. Results: We found a new abnormal karyotype of HESCs. We observed that chHES‐3 cells with normal and abnormal karyotypes shared similarities in expression markers of pluripotency; however, karyotypically abnormal chHES‐3 cells had a tendency for differentiation towards ectoderm lineages and were easily maintained in suboptimal culturing conditions. Abnormal chHES‐3 cells displayed relatively mature cell organelles compared to normal cells, and karyotypically abnormal chHES‐3 cells had increased survival and population growth. Genes related to cell proliferation and apoptosis were up‐regulated, but genes associated with genetic instability (p53, Rb, BRCA1) were down‐regulated in the karyotypically abnormal cells. Conclusion: Karyotypically abnormal chHES‐3 cells had a more developed capacity for proliferation, resistance to apoptosis and less genetic stability compared to normal chHES‐3 cells and may be an excellent model for studying and characterizing initial stages that determine transition of embryonic stem cells into cancer stem cells.     

Geometry and force control of cell function

Tissue engineering is becoming increasingly ambitious in its efforts to create functional human tissues, and to provide stem cell scientists with culture systems of high biological fidelity. Novel engineering designs are being guided by biological principles, in an attempt to recapitulate more faithfully the complexities of native cellular milieu. Three‐dimensional (3D) scaffolds are being designed to mimic native‐like cell environments and thereby elicit native‐like cell responses. Also, the traditional focus on molecular regulatory factors is shifting towards the combined application of molecular and physical factors. Finally, methods are becoming available for the coordinated presentation of molecular and physical factors in the form of controllable spatial and temporal gradients. Taken together, these recent developments enable the interrogation of cellular behavior within dynamic culture settings designed to mimic some aspects of native tissue development, disease, or regeneration. We discuss here these advanced cell culture environments, with emphasis on the derivation of design principles from the development (the biomimetic paradigm) and the geometry‐force control of cell function (the biophysical regulation paradigm). J. Cell. Biochem. 108: 1047–1058, 2009. © 2009 Wiley‐Liss, Inc.     

Epigenetically facilitated mutational assimilation: epigenetics as a hub within the inclusive evolutionary synthesis

After decades of debate about the existence of non‐genetic inheritance, the focus is now slowly shifting towards dissecting its underlying mechanisms. Here, we propose a new mechanism that, by integrating non‐genetic and genetic inheritance, may help build the long‐sought inclusive vision of evolution. After briefly reviewing the wealth of evidence documenting the existence and ubiquity of non‐genetic inheritance in a table, we review the categories of mechanisms of parent–offspring resemblance that underlie inheritance. We then review several lines of argument for the existence of interactions between non‐genetic and genetic components of inheritance, leading to a discussion of the contrasting timescales of action of non‐genetic and genetic inheritance. This raises the question of how the fidelity of the inheritance system can match the rate of environmental variation. This question is central to understanding the role of different inheritance systems in evolution. We then review and interpret evidence indicating the existence of shifts from inheritance systems with low to higher transmission fidelity. Based on results from different research fields we propose a conceptual hypothesis linking genetic and non‐genetic inheritance systems. According to this hypothesis, over the course of generations, shifts among information systems allow gradual matching between the rate of environmental change and the inheritance fidelity of the corresponding response. A striking conclusion from our review is that documented shifts between types of inherited non‐genetic information converge towards epigenetics (i.e. inclusively heritable molecular variation in gene expression without change in DNA sequence). We then interpret the well‐documented mutagenicity of epigenetic marks as potentially generating a final shift from epigenetic to genetic encoding. This sequence of shifts suggests the existence of a relay in inheritance systems from relatively labile ones to gradually more persistent modes of inheritance, a relay that could constitute a new mechanistic basis for the long‐proposed, but still poorly documented, hypothesis of genetic assimilation. A profound difference between the genocentric and the inclusive vision of heredity revealed by the genetic assimilation relay proposed here lies in the fact that a given form of inheritance can affect the rate of change of other inheritance systems. To explore the consequences of such inter‐connection among inheritance systems, we briefly review published theoretical models to build a model of genetic assimilation focusing on the shift in the engraving of environmentally induced phenotypic variation into the DNA sequence. According to this hypothesis, when environmental change remains stable over a sufficient number of generations, the relay among inheritance systems has the potential to generate a form of genetic assimilation. In this hypothesis, epigenetics appears as a hub by which non‐genetically inherited environmentally induced variation in traits can become genetically encoded over generations, in a form of epigenetically facilitated mutational assimilation. Finally, we illustrate some of the major implications of our hypothetical framework, concerning mutation randomness, the central dogma of molecular biology, concepts of inheritance and the curing of inherited disorders, as well as for the emergence of the inclusive evolutionary synthesis.     

Woody climbers show greater population genetic differentiation than trees: Insights into the link between ecological traits and diversification

The climbing habit is a key innovation in plants: climbing taxa have higher species richness than nonclimbing sister groups. We evaluated the hypothesis that climbing plant species show greater among‐population genetic differentiation than nonclimber species. We compared the among‐population genetic distance in woody climbers (eight species, 30 populations) and trees (seven species, 29 populations) coexisting in nine communities in a temperate rainforest. We also compared within‐population genetic diversity in co‐occurring woody climbers and trees in two communities. Mean genetic distance between populations of climbers was twice that of trees. Isolation by distance (increase in genetic distance with geographic distance) was greater for climbers. Climbers and trees showed similar within‐population genetic diversity. Our longevity estimate suggested that climbers had shorter generation times, while other biological features often associated with diversification (dispersal and pollination syndromes, mating system, size, and metabolic rate) did not show significant differences between groups. We hypothesize that the greater population differentiation in climbers could result from greater evolutionary responses to local selection acting on initially higher within‐population genetic diversity, which could be driven by neutral processes associated with shorter generation times. Increased population genetic differentiation could be incorporated as another line of evidence when testing for key innovations.     

Directional genetic differentiation and relative migration

Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly used to gather this information. One potential caveat is that these measures assume gene flow to be symmetric. However, asymmetric gene flow is common in nature, especially in systems driven by physical processes such as wind or water currents. As information about levels of asymmetric gene flow among populations is essential for the correct interpretation of the distribution of contemporary genetic diversity within species, this should not be overlooked. To obtain information on asymmetric migration patterns from genetic data, complex models based on maximum‐likelihood or Bayesian approaches generally need to be employed, often at great computational cost. Here, a new simpler and more efficient approach for understanding gene flow patterns is presented. This approach allows the estimation of directional components of genetic divergence between pairs of populations at low computational effort, using any of the classical or modern measures of genetic differentiation. These directional measures of genetic differentiation can further be used to calculate directional relative migration and to detect asymmetries in gene flow patterns. This can be done in a user‐friendly web application called divMigrate‐online introduced in this study. Using simulated data sets with known gene flow regimes, we demonstrate that the method is capable of resolving complex migration patterns under a range of study designs.     

Emergentism as a default: Cancer as a problem of tissue organization

During the last fifty years the dominant stance in experimental biology has been reductionism. For the most part, research programs were based on the notion that genes were in ’the driver’s seat’ controlling the developmental program and determining normalcy and disease (genetic reductionism and genetic determinism). Philosophers were the first to realize that the belief that the Mendelian genes were reduced to DNA molecules was questionable. Soon after these pronouncements, experimental data confirmed their misgivings. The optimism of molecular biologists, fueled by early success in tackling relatively simple problems, has now been tempered by the difficulties found when attempting to understand complex biological problems. Here, we analyse experimental data that illustrate the shortcomings of this sort of reductionism. We also examine the prevailing paradigm in cancer research, the somatic mutation theory (SMT), the premises of which are: (i) cancer is derived from a single somatic cell that has accumulated multiple DNA mutations; (ii) the default state of cell proliferation in metazoa is quiescence; and (iii) cancer is a disease of cell proliferation caused by mutations in genes that control proliferation and the cell cycle. We challenge the notion that cancer is a cellular problem caused by mutated genes by assessing data gathered both from within the reductionist paradigm and from an alternative view that regards carcinogenesis as a developmental process gone awry. This alternative view, explored under the name of the tissue organization field theory (TOFT), is based on premises that place cancer in a different hierarchical level of complexity from that proposed by the SMT, namely: (i) carcinogenesis represents a problem of tissue organization comparable to organogenesis, and (ii) proliferation is the default state of all cells. We propose that the organicist view, in which the TOFT is based, is a good starting point from which to explore emergent phenomena. However, new theoretical concepts are needed in order to grapple with the apparent circular causality of complex biological phenomena in development and carcinogenesis.     

Cadherins in the mammary gland and the melanocyte lineage

Cadherins are transmembrane glycoproteins involved in cell-cell adhesion, signalling, proliferation and differentiation. In this review, we have focused upon in vivo cadherin expression and function in two different biological systems, the mammary gland epithelium and the melanocyte lineage. Development of the mammary gland represents a paradigm of in situ epithelial differentiation and the melanocyte lineage of a model of non-epithelial (or mesenchymal) cell differentiation where cells migrate extensively from their site of origin towards the skin compartment. In the mammary epithelium, the predominantly expressed cadherin is E-cadherin, a cell surface molecule that directs morphogenesis and maintenance of the epithelial structure. In the melanocyte lineage, the expression of a number of cadherins is strictly spatiotemporally regulated during development and adult life. The specific functions mediated by this very dynamic cadherin expression are not yet known and their characterisation represents a challenge for the future.     

Programmed mitophagy is essential for the glycolytic switch during cell differentiation

Retinal ganglion cells (RGCs) are the sole projecting neurons of the retina and their axons form the optic nerve. Here, we show that embryogenesis‐associated mouse RGC differentiation depends on mitophagy, the programmed autophagic clearance of mitochondria. The elimination of mitochondria during RGC differentiation was coupled to a metabolic shift with increased lactate production and elevated expression of glycolytic enzymes at the mRNA level. Pharmacological and genetic inhibition of either mitophagy or glycolysis consistently inhibited RGC differentiation. Local hypoxia triggered expression of the mitophagy regulator BCL2/adenovirus E1B 19‐kDa‐interacting protein 3‐like (BNIP3L, best known as NIX) at peak RGC differentiation. Retinas from NIX‐deficient mice displayed increased mitochondrial mass, reduced expression of glycolytic enzymes and decreased neuronal differentiation. Similarly, we provide evidence that NIX‐dependent mitophagy contributes to mitochondrial elimination during macrophage polarization towards the proinflammatory and more glycolytic M1 phenotype, but not to M2 macrophage differentiation, which primarily relies on oxidative phosphorylation. In summary, developmentally controlled mitophagy promotes a metabolic switch towards glycolysis, which in turn contributes to cellular differentiation in several distinct developmental contexts.     

Emergent Stem Cell Homeostasis in the C.?elegans Germline Is Revealed by Hybrid Modeling

The establishment of homeostasis among cell growth, differentiation, and apoptosis is of key importance for organogenesis. Stem cells respond to temporally and spatially regulated signals by switching from mitotic proliferation to asymmetric cell division and differentiation. Executable computer models of signaling pathways can accurately reproduce a wide range of biological phenomena by reducing detailed chemical kinetics to a discrete, finite form. Moreover, coordinated cell movements and physical cell-cell interactions are required for the formation of three-dimensional structures that are the building blocks of organs. To capture all these aspects, we have developed a hybrid executable/physical model describing stem cell proliferation, differentiation, and homeostasis in the Caenorhabditis elegans germline. Using this hybrid model, we are able to track cell lineages and dynamic cell movements during germ cell differentiation. We further show how apoptosis regulates germ cell homeostasis in the gonad, and propose a role for intercellular pressure in developmental control. Finally, we use the model to demonstrate how an executable model can be developed from the hybrid system, identifying a mechanism that ensures invariance in fate patterns in the presence of instability.     

Stem cell mechanobiology

Stem cells are undifferentiated cells that are capable of proliferation, self‐maintenance and differentiation towards specific cell phenotypes. These processes are controlled by a variety of cues including physicochemical factors associated with the specific mechanical environment in which the cells reside. The control of stem cell biology through mechanical factors remains poorly understood and is the focus of the developing field of mechanobiology. This review provides an insight into the current knowledge of the role of mechanical forces in the induction of differentiation of stem cells. While the details associated with individual studies are complex and typically associated with the stem cell type studied and model system adopted, certain key themes emerge. First, the differentiation process affects the mechanical properties of the cells and of specific subcellular components. Secondly, that stem cells are able to detect and respond to alterations in the stiffness of their surrounding microenvironment via induction of lineage‐specific differentiation. Finally, the application of external mechanical forces to stem cells, transduced through a variety of mechanisms, can initiate and drive differentiation processes. The coalescence of these three key concepts permit the introduction of a new theory for the maintenance of stem cells and alternatively their differentiation via the concept of a stem cell ‘mechano‐niche’, defined as a specific combination of cell mechanical properties, extracellular matrix stiffness and external mechanical cues conducive to the maintenance of the stem cell population. J. Cell. Biochem. 112: 1–9, 2011. © 2010 Wiley‐Liss, Inc.     

Directed Stem Cell Differentiation: The Role of Physical Forces

Abstract

A number of factors contribute to the control of stem cell fate. In particular, the evidence for how physical forces control the stem cell differentiation program is now accruing. In this review, the authors discuss the types of physical forces: mechanical forces, cell shape, extracellular matrix geometry/properties, and cell-cell contacts and morphogenic factors, which evidence suggests play a role in influencing stem cell fate.     

A mitochondrial model for premature ageing of somatically cloned mammals

Cloned sheep have recently been discovered to have an unexpectedly advanced biological age. We propose that the explanation is a simple consequence of inheritance of acquired, free radical-induced cellular damage with somatic mitochondria that contribute to the mitochondrial population of cloned cells but not to zygotes produced by fertilization in normal sexual reproduction. Each increment of ageing in cloning experiments is therefore predicted to be maternally inherited. The hypothesis suggests practical ways of decreasing the effect. The hypothesis is itself a prediction of the recent proposal that mitochondria of the female germ line function primarily as genetic templates.     

Membrane deformation under local pH gradient: mimicking mitochondrial cristae dynamics

Mitochondria are cell substructures (organelles) critical for cell life, because biological fuel production, the ATP synthesis by oxidative phosphorylation, occurs in them driven by acidity (pH) gradients. Mitochondria play a key role as well in the cell death and in various fatigue and exercise intolerance syndromes. It is clear now that mitochondria present an astonishing variety of inner membrane morphologies, dynamically correlated with their functional state, coupled with the rate of the ATP synthesis, and characteristic for normal as well as for pathological cases. Our work offers some original insights into the factors that determine the dynamical tubular structures of the inner membrane cristae. We show the possibility to induce, by localized proton flow, a macroscopic cristae-like shape remodeling of an only-lipid membrane. We designed a minimal membrane system (GUV) and experimentally showed that the directional modulation of local pH gradient at membrane level of cardiolipin-containing vesicles induces dynamic cristae-like membrane invaginations. We propose a mechanism and theoretical model to explain the observed tubular membrane morphology and suggest the underlying role of cardiolipin. Our results support the hypothesis of localized bioenergetic transduction and contribute to showing the inherent capacity of cristae morphology to become self-maintaining and to optimize the ATP synthesis.     

Heterogeneous phenotype of human glioblastoma: In vitro study

Glioblastomas (GBMs) are the most lethal primary brain tumours. Increasing evidence shows that brain tumours contain the population of stem cells, so‐called cancer stem cells (CSCs). Stem cell marker CD133 was reported to identify CSC population in GBM. Further studies have indicated that CD133 negative cells exhibiting similar properties and are able to initiate the tumour, self‐renew and undergo multilineage differentiation. GBM is a highly heterogeneous tumour and may contain different stem cell populations with different functional properties. We characterized five GBM cell lines, established from surgical samples, according to the marker expression, proliferation and differentiation potential. CD133 positive cell lines showed increased proliferation rate in neurosphere condition and marked differentiation potential towards neuronal lineages. Whereas two cell lines low‐expressing CD133 marker showed mesenchymal properties in vitro, that is high proliferation rate in serum condition and differentiation in mesenchymal cell types. Further, we compared therapy resistance capacity of GBM cell lines treated with hydroxyurea. Our results suggest that CSC concept is more complex than it was believed before, and CD133 could not define entire stem cell population within GBM. At least two different subtypes of GBM CSCs exist, which may have different biological characteristics and imply different therapeutic strategies. Copyright © 2013 John Wiley & Sons, Ltd.     

Demographic and population‐genetic tests provide mixed support for the abundant centre hypothesis in the endemic plant Leavenworthia stylosa

The abundant centre hypothesis (ACH) assumes that population abundance, population size, density and per‐capita reproductive output should peak at the centre of a species' geographic range and decline towards the periphery. Increased isolation among and decreased reproductive output within edge populations should reduce within‐population genetic diversity and increase genetic differentiation among edge relative to central populations. The ACH also predicts asymmetrical gene flow, with net movement of migrants from the centre to edges. We evaluated these ecological assumptions and population‐genetic predictions in the endemic flowering plant Leavenworthia stylosa. Although populations were more spatially isolated near range edges, the geographic centre was surrounded by and not coincident with areas of peak population abundance, and plant density increased towards range edges. Per‐capita seed number was not associated with distance to the range centre, but seed number/m² increased near range edges. In support of ACH predictions, allelic diversity at 12 microsatellite loci declined with distance from the range centre, and pairwise F_ST values were higher between edge populations than between central populations. Coalescent analyses confirmed that gene flow was most infrequent between edge populations, but there was not an asymmetric pattern of gene flow predicted by the ACH. This study shows that among‐population demographic variability largely did not support the ACH, while patterns of genetic diversity, differentiation and gene flow were generally consistent with its predictions. Such mixed support has frequently been observed in tests of the ACH and raises concerns regarding the generality of this hypothesis for species range limits.