Strategies to improve the reliability of a theory: the experiment of bacterial invasion into cultured epithelial cells

An analysis is presented of published methods that have been used by experimenters to justify the reliability of the theory of invasion of microorganisms into cultured cells. The results show that, to demonstrate this invasion, many experimenters used two or more methods that were based on independent technical and theoretical principles, and by doing so improved the reliability of the theory. Subsequently I compare this strategy of ‘multiple derivability’ with other strategies, discussed in the literature in relation to the mesosome, a bacterial organelle that had been detected with the electron microsope, but which appeared later to be an artifact. I propose that different strategies have been applied in this problem, and multiple derivability may have been the decisive one. Finally I discuss the idea that multiple derivability may help to anchor theories in a larger network of theories.     

The parageneses thermodynamic analysis of chemoautotrophic CO2 fixation archaic cycle components, their stability and self-organization in hydrothermal systems

The parageneses physico-chemical analysis based on a method of thermodynamic potentials has been used to study the system of C-H-O organic compounds, which are, in particular, components of biomimetically built primordial cycles of carbon dioxide chemoautotrophic fixation. Thermodynamic data for aqueous organic compounds allowed one to construct the chemical potential diagrams and establish the areas of thermodynamic stability (facies) of components of CO₂ fixation pathways in hydrothermal systems, in particular, a reductive citric cycle (RCC), 3-hydroxypropionate cycle (3-HPC) and acetyl-CoA pathway. An alternative deep source of carbon (hydrocarbons) proved by the data on endogenous emission of hydrocarbons in hydrothermal fields of oceanic ridges was suggested. The system was determined, which combines hydrocarbons, CO₂ and components of RCC, 3-HPC and acetyl-CoA pathway with characteristic parageneses of methane and ethylene with acetate in two-component CH₄-CO₂ and C₂H₄-O₂ subsystems, respectively. The thermodynamic analysis of a redox mode at various pressures and temperatures allowed one to uniquely determine hydrocarbon-organic system able to independently generate acetate and succinate at oxidation of deep hydrothermal hydrocarbon fluids emerging on sea surface. The limits for thermodynamic stability of CO₂ archaic fixation (CAF) components responsible for generation and self-organization in hydrothermal environment was identified. The tentative integrated system of CAF was developed as a combined acetyl-CoA pathway, 3-HPC and RCC containing a succinate-fumarate core, capable of switching electron flow in forward or reverse direction depending on redox potential of geochemical environment that is governed by the (CH)₂(COOH)₂+H₂(CH₂)₂(COOH)₂ reaction. This core is a “redox switch”, which is sensitive to certain conditions of hydrothermal environment and defines electron flow direction. The redox geochemical mode caused by temperature, pressure, composition of a hydrothermal fluid and a mineralogical setting defines stability of CAF cycle components in paragenesis with hydrocarbons and possibility of cycle self-organization.     

The NAD World: A New Systemic Regulatory Network for Metabolism and Aging—Sirt1, Systemic NAD Biosynthesis,and Their Importance

For the past several years, it has been demonstrated that the NAD-dependent protein deacetylase Sirt1 and nicotinamide phosphoribosyltransferase (Nampt)-mediated systemic NAD biosynthesis together play a critical role in the regulation of metabolism and possibly aging in mammals. Based on our recent studies on these two critical components, we have developed a hypothesis of a novel systemic regulatory network, named “NAD World”, for mammalian aging. Conceptually, in the NAD World, systemic NAD biosynthesis mediated by intra- and extracellular Nampt functions as a driver that keeps up the pace of metabolism in multiple tissues/organs, and the NAD-dependent deacetylase Sirt1 serves as a universal mediator that executes metabolic effects in a tissue-dependent manner in response to changes in systemic NAD biosynthesis. This new concept of the NAD World provides important insights into a systemic regulatory mechanism that fundamentally connects metabolism and aging and also conveys the ideas of functional hierarchy and frailty for the regulation of metabolic robustness and aging in mammals.     

System-level design of bacterial cell cycle control

Understanding of the cell cycle control logic in Caulobacter has progressed to the point where we now have an integrated view of the operation of an entire bacterial cell cycle system functioning as a state machine. Oscillating levels of a few temporally-controlled master regulator proteins in a cyclical circuit drive cell cycle progression. To a striking degree, the cell cycle regulation is a whole cell phenomenon. Phospho-signaling proteins and proteases dynamically deployed to specific locations on the cell wall are vital. An essential phospho-signaling system integral to the cell cycle circuitry is central to accomplishing asymmetric cell division.     

Generation model of positional values as cell operation during the development of multicellular organisms

Many conventional models have used the positional information hypothesis to explain each elementary process of morphogenesis during the development of multicellular organisms. Their models assume that the steady concentration patterns of morphogens formed in an extracellular environment have an important property of positional information, so-called “robustness”. However, recent experiments reported that a steady morphogen pattern, the concentration gradient of the Bicoid protein, during early Drosophila embryonic development is not robust for embryo-to-embryo variability. These reports encourage a reconsideration of a long-standing problem in systematic cell differentiation: what is the entity of positional information for cells? And, what is the origin of the robust boundary of gene expression? To address these problems at a cellular level, in this article we pay attention to the re-generative phenomena that show another important property of positional information, “size invariance”. In view of regenerative phenomena, we propose a new mathematical model to describe the generation mechanism of a spatial pattern of positional values. In this model, the positional values are defined as the values into which differentiable cells transform a spatial pattern providing positional information. The model is mathematically described as an associative algebra composed of various terms, each of which is the multiplication of some fundamental operators under the assumption that the operators are derived from the remarkable properties of cell differentiation on an amputation surface in regenerative phenomena. We apply this model to the concentration pattern of the Bicoid protein during the anterior-posterior axis formation in Drosophila, and consider the conditions needed to establish the robust boundary of the expression of the hunchback gene.     

FogBank: a single cell segmentation across multiple cell lines and image modalities

Background

Many cell lines currently used in medical research, such as cancer cells or stem cells, grow in confluent sheets or colonies. The biology of individual cells provide valuable information, thus the separation of touching cells in these microscopy images is critical for counting, identification and measurement of individual cells. Over-segmentation of single cells continues to be a major problem for methods based on morphological watershed due to the high level of noise in microscopy cell images. There is a need for a new segmentation method that is robust over a wide variety of biological images and can accurately separate individual cells even in challenging datasets such as confluent sheets or colonies.

Results

We present a new automated segmentation method called FogBank that accurately separates cells when confluent and touching each other. This technique is successfully applied to phase contrast, bright field, fluorescence microscopy and binary images. The method is based on morphological watershed principles with two new features to improve accuracy and minimize over-segmentation.First, FogBank uses histogram binning to quantize pixel intensities which minimizes the image noise that causes over-segmentation. Second, FogBank uses a geodesic distance mask derived from raw images to detect the shapes of individual cells, in contrast to the more linear cell edges that other watershed-like algorithms produce.We evaluated the segmentation accuracy against manually segmented datasets using two metrics. FogBank achieved segmentation accuracy on the order of 0.75 (1 being a perfect match). We compared our method with other available segmentation techniques in term of achieved performance over the reference data sets. FogBank outperformed all related algorithms. The accuracy has also been visually verified on data sets with 14 cell lines across 3 imaging modalities leading to 876 segmentation evaluation images.

Conclusions

FogBank produces single cell segmentation from confluent cell sheets with high accuracy. It can be applied to microscopy images of multiple cell lines and a variety of imaging modalities. The code for the segmentation method is available as open-source and includes a Graphical User Interface for user friendly execution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0431-x) contains supplementary material, which is available to authorized users.     

Does a quorum sensing mechanism direct the behavior of immune cells?

Quorum sensing is a decision-making process used by decentralized groups such as colonies of bacteria to trigger a coordinated behavior. The existence of decentralized coordinated behavior has also been suggested in the immune system. In this paper, we explore the possibility for quorum sensing mechanisms in the immune response. Cytokines are good candidates as inducer of quorum sensing effects on migration, proliferation and differentiation of immune cells. The existence of a quorum sensing mechanism should be explored experimentally. It may provide new perspectives into immune responses and could lead to new therapeutic strategies.