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PubMed2001

Self-organization of a propulsive actin network as an evolutionary process.

The leading edge of motile cells is propelled by polymerization of actin filaments according to a dendritic nucleation/array treadmilling mechanism. However, little attention has been given to the origin and maintenance of the dendritic array. Here we develop and test a population-kinetics model that explains the organization of actin filaments in terms of the reproduction of dendritic units. The life cycle of an actin filament consists of dendritic nucleation on another filament (birth), elongation by addition of actin subunits and, finally, termination of filament growth by capping protein (death). The regularity of branch angle between daughter and mother filaments endows filaments with heredity of their orientation. Fluctuations of branch angle that become fixed in the actin network create errors of orientation (mutations) that may be inherited. In our model, birth and death rates depend on filament orientation, which then becomes a selectable trait. Differential reproduction and elimination of filaments, or natural selection, leads to the evolution of a filament pattern with a characteristic distribution of filament orientations. We develop a procedure based on the Radon transform for quantitatively analyzing actin networks in situ and show that the experimental results are in agreement with the distribution of filament orientations predicted by our model. We conclude that the propulsive actin network can be understood as a self-organizing supramolecular ensemble shaped by the evolution of dendritic lineages through natural selection of their orientation.

Actins↗
PubMed1994

Modulation of cardiac myocyte phenotype in vitro by the composition and orientation of the extracellular matrix.

Cellular phenotype is the result of a dynamic interaction between a cell's intrinsic genetic program and the morphogenetic signals that serve to modulate the extent to which that program is expressed. In the present study we have examined how morphogenetic information might be stored in the extracellular matrix (ECM) and communicated to the neonatal heart cell (NHC) by the cardiac alpha 1 beta 1 integrin molecule. A thin film of type I collagen (T1C) was prepared with a defined orientation. This was achieved by applying T1C to the peripheral edge of a 100 mm culture dish. The T1C was then drawn across the surface of the dish in a continuous stroke with a sterile cell scraper and allowed to polymerize. When NHCs were cultured on this substrate, they spread, as a population, along a common axis in parallel with the gel lattice and expressed an in vivo-like phenotype. Individual NHCs displayed an elongated, rod-like shape and disclosed parallel arrays of myofibrils. These phenotypic characteristics were maintained for at least 4 weeks in primary culture. The evolution of this tissue-like organizational pattern was dependent upon specific interactions between the NHCs and the collagen-based matrix that were mediated by the cardiac alpha 1 beta 1 integrin complex. This conclusion was supported by a variety of experimental results. Altering the tertiary structure of the matrix or blocking the extracellular domains of either the cardiac alpha 1 or beta 1 integrin chain inhibited the expression of the tissue-like pattern of organization. Neither cell-to-cell contact or contractile function were necessary to induce the formation of the rod-like cell shape. However, beating activity was necessary for the assembly of a well-differentiated myofibrillar apparatus. These data suggest that the cardiac alpha 1 beta 1 integrin complex serves to detect and transduce phenotypic information stored within the tertiary structure of the surrounding matrix.

Animals↗
PubMed2000

Sonic hedgehog signaling pathway in vertebrate epithelial appendage morphogenesis: perspectives in development and evolution.

Vertebrate epithelial appendages are elaborate topological transformations of flat epithelia into complex organs that either protrude out of external (integument) and internal (oral cavity, gut) epithelia, or invaginate into the surrounding mesenchyme. Although they have specific structures and diverse functions, most epithelial appendages share similar developmental stages, including induction, morphogenesis, differentiation and cycling. The roles of the SHH pathway are analyzed in exemplary organs including feather, hair, tooth, tongue papilla, lung and foregut. SHH is not essential for induction and differentiation, but is involved heavily in morphogenetic processes including cell proliferation (size regulation), branching morphogenesis, mesenchymal condensation, fate determination (segmentation), polarizing activities and so on. Through differential activation of these processes by SHH in a spatiotemporal-specific fashion, organs of different shape and size are laid down. During evolution, new links of developmental pathways may occur and novel forms of epithelial appendages may emerge, upon which evolutionary selections can act. Sites of major variations have progressed from the body plan to the limb plan to the epithelial appendage plan. With its powerful morphogenetic activities, the SHH pathway would likely continue to play a major role in the evolution of novel epithelial appendages.

Animals↗
PubMed1989

The multicatalytic proteinase (prosome) is ubiquitous from eukaryotes to archaebacteria.

From the thermoacidophilic archaebacterium, Thermoplasma acidophilum, a proteolytically active particle has been isolated which is almost identical in size and shape with the multicatalytic proteinase (prosome) from rat. This result indicates that prosomes have been developed early in evolution and that they possibly serve functions common to all living cells.

Animals↗
PubMed1977

[Current findings on the asymmetric growth of the mullerian tract in female chick embryos].

Shape and orientation of the mesothelial cells were examined in the mullerian ducts of 8, 13 and 15 day female chick embryos with the scanning electron microscope. The observed evolution in the pattern of these cells likely reflects the mechanical conditions to which these organs are subjected during embryonic development: stretching for the left duct, slackening for the right duct. These observations, together with data concerning growth of these organs, suggest that topographical relationships between cells, which in this system result from mechanical factors, play an important role in controlling cell proliferation.

Animals↗
PubMed1995

The sodium pump in the evolution of animal cells.

Plant cells and bacterial cells are surrounded by a massive cellulose wall, which constrains their high internal osmotic pressure (tens of atmospheres). Animal cells, in contrast, are in osmotic equilibrium with their environment, have no restraining surround, can take on a variety of shapes and change these from moment to moment. This osmotic balance is achieved by the action of the energy-consuming sodium pump, one of the P-type ATPase transport protein family, members of which are indeed also found in bacteria. The pump's action brings about a transmembranal electrochemical gradient of sodium ions, harnessed in a range of transport systems that couple the dissipation of this gradient to establishing a gradient of the coupled substrate. The primary role of the sodium pump as a regulator of cell volume has evolved to provide the basis for an enormous variety of physiological functions.

Animals↗
PubMed1993

Human T cells respond to mouse mammary tumor virus-encoded superantigen: V beta restriction and conserved evolutionary features.

Mouse mammary tumor virus (MMTV)-encoded superantigens (SAGs) influence the murine T cell repertoire and stimulate a strong mixed lymphocyte response in vitro. These SAGs are encoded by the open reading frame of the 3' long terminal repeat of MMTV, termed MMTV SAGs. The T cell response to MMTV SAGs is V beta restricted and requires expression of the class II molecules of the major histocompatibility complex (MHC) on the presenting cells. While human T cells respond to bacterial SAGs, it is not known if human T cells or human MHC class II molecules can interact with MMTV SAGs. A fibroblastic cell line expressing the human MHC class II molecule HLA-DR1 and the Mtv-7 sag gene encoding Mls-1 was used to stimulate human T cells. We show here that human T cells efficiently proliferate in response to Mls-1 presented by HLA-DR1. This T cell response was inhibited by mAbs directed against CD4 or MHC class II molecules but not by mAbs specific for CD8 or MHC class I molecules. Moreover, the response to Mls-1 was limited to human T cells expressing a restricted set of T cell receptor V beta chains. Human T cells expressing V beta 12, 13, 14, 15, and 23 were selectively amplified after Mtv-7 sag stimulation. Interestingly, these human V beta s share the highest degree of homology with the mouse V beta s interacting with Mls-1. These results show a strong evolutionary conservation of the structures required for the presentation and the response to retrovirally encoded endogenous SAGs, raising the possibility that similar elements operate in humans to shape the T cell repertoire.

Animals↗
PubMed1998

Chaotic balanced state in a model of cortical circuits.

The nature and origin of the temporal irregularity in the electrical activity of cortical neurons in vivo are not well understood. We consider the hypothesis that this irregularity is due to a balance of excitatory and inhibitory currents into the cortical cells. We study a network model with excitatory and inhibitory populations of simple binary units. The internal feedback is mediated by relatively large synaptic strengths, so that the magnitude of the total excitatory and inhibitory feedback is much larger than the neuronal threshold. The connectivity is random and sparse. The mean number of connections per unit is large, though small compared to the total number of cells in the network. The network also receives a large, temporally regular input from external sources. We present an analytical solution of the mean-field theory of this model, which is exact in the limit of large network size. This theory reveals a new cooperative stationary state of large networks, which we term a balanced state. In this state, a balance between the excitatory and inhibitory inputs emerges dynamically for a wide range of parameters, resulting in a net input whose temporal fluctuations are of the same order as its mean. The internal synaptic inputs act as a strong negative feedback, which linearizes the population responses to the external drive despite the strong nonlinearity of the individual cells. This feedback also greatly stabilizes the system's state and enables it to track a time-dependent input on time scales much shorter than the time constant of a single cell. The spatiotemporal statistics of the balanced state are calculated. It is shown that the autocorrelations decay on a short time scale, yielding an approximate Poissonian temporal statistics. The activity levels of single cells are broadly distributed, and their distribution exhibits a skewed shape with a long power-law tail. The chaotic nature of the balanced state is revealed by showing that the evolution of the microscopic state of the network is extremely sensitive to small deviations in its initial conditions. The balanced state generated by the sparse, strong connections is an asynchronous chaotic state. It is accompanied by weak spatial cross-correlations, the strength of which vanishes in the limit of large network size. This is in contrast to the synchronized chaotic states exhibited by more conventional network models with high connectivity of weak synapses.

Animals↗
PubMedDate not supplied

Flagellar apparatus absolute orientations and the phylogeny of the green algae.

The absolute orientation of the flagellar apparatus in green algal motile cells is a feature of considerable value in studies of green algal systematics and phylogeny. The absolute orientation patterns found in those algae for which this feature is known or can be deduced are reviewed. Counterclockwise absolute orientation occurs in all classes except the Chlorophyceae and is considered primitive, while the clockwise absolute orientation present in most members of the Chlorophyceae is the result of progressive clockwise rotation of components during evolution. Extant intermediates documenting this rotation include Hafniomonas vegetative cells, which show counterclockwise absolute orientation, and Chaetopeltis quadriflagellate zoospores, in which the flagellar apparatus is strictly cruciate except for a slight clockwise offset of the microtubular rootlets. The V-shaped arrangement of the basal bodies in the flagellar apparatus, as well as the presence of proximal sheaths and of two layers of scales on the cell body, further identifies the Chaetopeltis zoospore as a primitive cell type within the Chlorophyceae . Trends towards the exsertion of basal bodies from a flagellar pit, either apically or laterally, the elimination of quadriflagellate cells, and, in the Chlorophyceae , an increasing amount of basal body offset, indicate advancement within the classes. Absolute orientation is conserved during flagellar apparatus replication and development. Events after flagellar apparatus division in the algae studied may be subdivided into component assembly, which is universal and preserves phylogenetically-useful features, and component reorientation, which occurs in relatively few green algae and adapts the flagellar apparatus to specialized functions. From these flagellar apparatus orientation studies, a major reevaluation of evolution within the Chlorophyceae is proposed, with weakly- thalloid algae possessing desmoschisis (e.g. Chaetopeltis ) considered primitive, and most other types, including the Volvocales , considered more advanced. The evolution of wall formation does not preclude the formation of scales in primitive chlorophycean genera. In addition, one or more previously undescribed major lineages may exist within the green algae, including one, the Pleurastrum lineage, whose members possess dorsiventrally -flattened motile cells, counterclockwise absolute orientation of the flagellar apparatus, and a phycoplast at cytokinesis. The Chlorophyceae , the Ulvophyceae , and the Pleurastrum lineage are considered to have a common ancestor that resembled the modern genus Pyramimonas , while the Charophyceae is thought to be of more ancient derivation. Th

Chlorophyta↗
PubMed1999

Controlling septation in fission yeast: finding the middle, and timing it right.

The fission yeast Schizosaccharomyces pombe provides a simple eukaryotic model for the study of cytokinesis. S. pombe cells are rod-shaped, grow mainly by elongation at their tips, and divide by binary fission after forming a centrally placed division septum. Analysis of mutants has begun to shed light upon how septum formation and cytokinesis are regulated both spatially and temporally. Some of the proteins involved in these events have been functionally conserved throughout eukaryotic evolution, suggesting that aspects of this control will be common to all eukaryotic cells.

Cell Division↗
PubMed1988

Stereological study of the early ultrastructural differentiation of chick embryo neuroepithelial cells during neurulation.

The neuroectodermal cells of chick embryos have been analyzed during neurulation by stereological and morphometrical ultrastructural methods in an attempt to describe their cytometric evolution. A profound change of cellular form coefficient was observed which is related to the typical process of columnarization of these cells. At stages 7 and 8, the nucleus appeared round in shape, probably due to a loss of pressure of the vitelline inclusions. In this sense, the volume density of these inclusions falls during this period. There was also a significant increase of the nuclear surface density, the significance of which is discussed on the basis of the nucleo-cytoplasmic interchanges and the differentiation process. At the same time, an increase in the number of mitochondria was observed, which is related to the neural folding process. Simultaneously, the amount of rough endoplasmic reticulum increases, presumably related to the remarkable changes of the embryonic extracellular matrix.

Animals↗
PubMed2001

A new look at microbial leaching patterns on sulfide minerals.

Leaching patterns on sulfide minerals were investigated by high-resolution scanning electron microscopy (SEM). Our goal was to evaluate the relative contributions of inorganic surface reactions and reactions localized by attached cells to surface morphology evolution. Experiments utilized pyrite (FeS(2)), marcasite (FeS(2)) and arsenopyrite (FeAsS), and two iron-oxidizing prokaryotes in order to determine the importance of cell type, crystal structure, and mineral dissolution rate in microbially induced pit formation. Pyrite surfaces were reacted with the iron-oxidizing bacterium Acidithiobacillus ferrooxidans (at 25 degrees C), the iron-oxidizing archaeon 'Ferroplasma acidarmanus' (at 37 degrees C), and abiotically in the presence of Fe(3+) ions. In all three experiments, discrete bacillus-sized (1-2 µm) and -shaped (elliptical) pits developed on pyrite surfaces within 1 week of reaction. Results show that attaching cells are not necessary for pit formation on pyrite. Marcasite and arsenopyrite surfaces were reacted with A. ferrooxidans (at 25 degrees C) and 'F. acidarmanus' (at 37 degrees C). Cell-sized and cell-shaped dissolution pits were not observed on marcasite or arsenopyrite at any point during reaction with A. ferrooxidans, or on marcasite surfaces reacted with 'F. acidarmanus'. However, individual 'F. acidarmanus' cells were found within individual shallow (<0.5 µm deep) pits. The size and shape (round rather than elliptical) of the pits conformed closely to the shape of F. acidarmanus (cells) pits on arsenopyrite. We infer these pits to be cell-induced. We attribute the formation of pits readily detectable (by SEM) to the higher reactivity of arsenopyrite compared to pyrite and marcasite under the conditions the experiment was conducted. These pits contributed little to the overall surface topographical evolution, and most likely did not significantly increase surface area during reaction. Our results suggest that overall sulfide mineral dissolution may be dominated by surface reactions with Fe(3+) rather than by reactions at the cell-mineral interface.

Journal Article↗
PubMed1992

Cone visual pigments are present in gecko rod cells.

The Tokay gecko (Gekko gekko), a nocturnal lizard, has two kinds of visual pigments, P467 and P521. In spite of the pure-rod morphology of the photoreceptor cells, the biochemical properties of P521 and P467 resemble those of iodopsin (the chicken red-sensitive cone visual pigment) and rhodopsin, respectively. We have found that the amino acid sequence of P521 deduced from the cDNA was very similar to that of iodopsin. In addition, P467 has the highest homology with the chicken green-sensitive cone visual pigment, although it also has a relatively high homology with rhodopsins. These results give additional strength to the transmutation theory of Walls [Walls, G. L. (1934) Am. J. Ophthalmol. 17, 892-915], who proposed that the rod-shaped photoreceptor cells of lizards have been derived from ancestral cone-like photoreceptors. Apparently amino acid sequences of visual pigments are less changeable than the morphology of the photoreceptor cells in the course of evolution.

Amino Acid Sequence↗
PubMed1999

Analysis of heavy and light chain pairings indicates that receptor editing shapes the human antibody repertoire.

In the bone marrow, diversity in the primary antibody repertoire is created by the combinatorial rearrangement of different gene segments and by the association of different heavy and light chains. During the secondary response in the germinal centres, antibodies are diversified by somatic mutation and possibly by further rearrangements, or "receptor editing". Here, we have analysed the pairings of heavy and light chain variable domains (VH and VL) in 365 human IgG+ B cells from peripheral blood, and established that these pairings are largely random. The repertoire is dominated by a limited number of pairings of segments and folds. Among these pairings we identified two identical mutated heavy chains in combination with two different mutated light chains (one kappa and one lambda). This shows that receptor editing occurs in the human periphery and that the same antibody lineage can be subjected to both receptor editing and somatic hypermutation. This suggests that receptor editing may be used together with somatic mutation for the affinity maturation of antibodies. We also propose that receptor editing has shaped variable gene segment use and the evolution of V gene families.

Amino Acid Sequence↗
PubMed1997

Mitochondrial and nuclear genes present conflicting portraits of human origins.

Human mitochondrial DNA (mtDNA) sequences reveal an abundance of polymorphic sites in which the frequencies of the segregating bases are very different. A typical polymorphism involves one base at low frequency and the other base at high frequency. In contrast, nuclear gene data sets tend to show an excess of polymorphisms in which both segregating bases are at intermediate frequencies. A new statistical test of this difference finds significant differences between mtDNA and nuclear gene data sets reported in the literature. However, differences in the polymorphism patterns could be caused by different sample origins for the different data sets. To examine the mtDNA-nuclear difference more closely, DNA sequences were generated from a portion of the X-linked pyruvate dehydrogenase E1 alpha subunit (PDHA1) locus and from a portion of mitochondrial control region I (CRI) from each of eight individuals, four from sub-Saharan Africa. The two genes revealed a significant difference in the site frequency distribution of polymorphic sites. PDHA1 revealed an excess of intermediate-frequency polymorphisms, while CRI showed an excess of sites with the low-high frequency pattern. The discrepancy suggests that mitochondrial variation has been shaped by natural selection, and may not be ideal for some questions on human origins.

Cell Nucleus↗
PubMed2026

Competing subclones and fitness diversity shape tumor evolution across cancer types.

MOTIVATION: Intratumor heterogeneity arises from ongoing somatic evolution and complicates cancer diagnosis, prognosis, and treatment. Reconstructing evolutionary dynamics typically requires spatiotemporal samples, which are often unavailable in clinical settings. Computational approaches that can infer tumor evolutionary history from single-timepoint bulk sequencing data remain limited. RESULTS: We present estimating evolutionary events through single-timepoint sequencing (TEATIME), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric-fitness diversity-which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types. AVAILABILITY AND IMPLEMENTATION: R implementation of TEATIME is available on GitHub (https://github.com/liliulab/TEATIME) and Zenodo (https://zenodo.org/records/17422174).

Neoplasms↗
PubMed2001

Bringing gene order into bacterial shape.

A different arrangement of a cluster of genes involved in division and cell-wall synthesis separates bacilli from other bacteria in a phylogenetic analysis. We conclude that the relationships between these genes are not random and might reflect significant events in the evolution of the coupling between growth and division in bacteria.

Bacteria↗
PubMed1997

Alzheimer's disease: transiently developing dendritic changes in pyramidal cells of sector CA1 of the Ammon's horn.

In the course of Alzheimer's disease, specific CA1 pyramidal cells develop dendritic changes, which can only be observed transiently. Distal segments of the apical dendrite running through the stratum lacunosum-moleculare show spindle-shaped dilations filled with abnormal tau protein. The alteration eventually leads to amputation of the changed segment. The damage first appears at stage II in the evolution of the neurofibrillary changes [5], is best developed at stage III, and vanishes from the tissue at stage IV. It is usually not observed in stages V and VI (fully developed Alzheimer's disease).

Adult↗