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Misrepair mechanism in the development of atherosclerotic plaques

Atherosclerosis is a disease characterized by the development of atherosclerotic plaques (APs) in arterial endothelium. The APs in part of an arterial wall are inhomogeneous on size and on distribution. In order to understand this in-homogeneity, the pathology of APs is analyzed by Misrepair mechanism, a mechanism proposed in our Misrepair-accumulation aging theory. I. In general, development of an AP is a result of repair of injured endothelium. Because of infusion and deposition of lipids beneath endothelial cells, the repair has to be achieved by altered remodeling of local endothelium. Such a repair is a Misrepair. During repair, smooth muscular cells (SMCs) are clustered and collagen fibers are produced to the lesion of endothelium for reconstructing an anchoring structure for endothelial cells and for forming a barrier to isolate the lipids. II. Altered remodeling (Misrepair) makes the local part of endothelium have increased damage-sensitivity and reduced repair-efficiency. Thus, this part of endothelium will have increased risk for injuries, lipid-infusion, and Misrepairs. Focalized accumulation of Misrepairs and focalized deposition of lipids result in development of a plaque. III. By a viscous circle between lipid-infusion and endothelium-Misrepair, growing of an AP is self-accelerating. Namely, once an AP develops, it grows in an increasing rate with time and it does not stop growing. Within part of an arterial wall, older APs grow faster than younger ones. The oldest and the biggest AP is the most threatening one in narrowing local vessel lumen. Therefore, the self-accelerated growing of an AP is a fatal factor in atherosclerosis. In conclusion, development of APs is focalized and self-accelerating, because it is a result of accumulation of Misrepairs of endothelium.

q-bio.TO↗

Cell transformation in tumor-development: a result of accumulation of Misrepairs of DNA through many generations of cells

Development of a tumor is known to be a result of accumulation of DNA changes in somatic cells. However, the processes of how DNA changes are produced and how they accumulate in somatic cells are not clear. DNA changes include two types: point DNA mutations and chromosome changes. However, point DNA mutations (DNA mutations) are the main type of DNA changes that can remain and accumulate in cells. Severe DNA injuries are the causes for DNA mutations. However, Misrepair of DNA is an essential process for transforming a DNA injury into a survivable and inheritable DNA mutation. In somatic cells, Misrepair of DNA is the main source of DNA mutations. Since the surviving chance of a cell by Misrepair of DNA is low, accumulation of DNA mutations can take place only possibly in the cells that can proliferate. Tumors can only develop in the tissues that are regenerable. The accumulation of Misrepairs of DNA needs to proceed in many generations of cells, and cell transformation from a normal cell into a tumor cell is a slow and long process. However, once a cell is transformed especially when it is malignantly transformed, the deficiency of DNA repair and the rapid cell proliferation will accelerate the accumulation of DNA mutations. The process of accumulation of DNA mutations is actually the process of aging of a genome DNA. Repeated cell injuries and repeated cell regenerations are the two preconditions for tumor-development. For cancer prevention, a moderate and flexible living style is advised.

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Tissue fibrosis: a principal proof for the central role of Misrepair in aging

Tissue fibrosis is the phenomenon that a tissue has progressive deposition of collagen fibers with age. Tissue fibrosis is associated with aging of most of our organs, and it is the main pathology in arteriosclerosis, chronic bronchitis/emphysema, and benign prostatic hyperplasia. The causes and characteristics of fibrosis are analyzed with Misrepair mechanism, a mechanism proposed in Misrepair-accumulation aging theory. Tissue fibrosis is known to be a result of repairs of tissue by collagen fibers. A repair with collagen fibers is a manner of "Misrepair". The collagen fibers are used for replacing dead cells or disrupted extracellular matrixes (ECMs) including elastic fibers, myofibers, and basement membrane. The progressive tissue fibrosis with age manifests the essential role of Misrepair in aging, because it reveals three facts: A. a process of Misrepair exists; B. Misrepairs are unavoidable; and C. Misrepairs accumulate. As a result of accumulation of Misrepairs of tissue with collagen fibers, tissue fibrosis is focalized and self-accelerating, appearing as growing of spots of hyaline degeneration. Fibrosis results in stiffness or atrophy of an organ and progressive failure of the organ. In arteriosclerosis, the deposition of collagen fibers in arterial wall is for replacing disrupted elastic fibers or myofibers, however results in hardness of the wall. Wrinkle formation is part of skin fibrosis, and it may be a result of accumulation of collagen fibers of different lengths. Senile hair-loss and hair-whitening are probably consequence of dermal fibrosis. In conclusion, tissue fibrosis is a result of accumulation of Misrepairs of tissue with collagen fibers, and the phenomenon of fibrosis is a powerful proof for the central role of Misrepair in aging.

q-bio.TO↗

An immune system-tumour interactions model with discrete time delay: model analysis and validation

In this article a generalized mathematical model describing the interactions between malignant tumour and immune system with discrete time delay incorporated into the system is considered. Time delay represents the time required to generate an immune response due to the immune system activation by cancer cells. The basic mathematical properties of the considered model, including the global existence, uniqueness, non-negativity of the solutions, the stability of steady sates and the possibility of the existence of the stability switches, are investigated when time delay is treated as a bifurcation parameter. The model is validated with the sets of the experimental data and additional numerical simulations are performed to illustrate, extend, interpret and discuss the analytical results in the context of the tumour progression.

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Misrepair mechanism: a mechanism essential for individual adaptation, species adaptation and species evolution

In Misrepair-accumulation theory, we have proposed a Misrepair mechanism for interpreting aging. However, Misrepair mechanism is also important in biological adaptation. Misrepair is a strategy of repair for increasing the surviving chance of an organism when it suffers from severe injuries. As a surviving strategy, Misrepair mechanism plays also an important role in individual adaptation, species survival, and species differentiation. Firstly, Misrepair of an injury is one of the manners of individual adaptation; and Misrepair mechanism gives an organism a great potential in adapting to changeable and destructive environment. Secondly, Misrepair mechanism is important in maintaining and enlarging the diversity of genome DNAs of a species; and a large diversity of genome DNAs is essential for the adaptation and the differentiation of a species in different environments. On one hand, somatic Misrepairs are essential for maintaining the sufficient number of individuals in a species, which are the vectors of different genome DNAs. On the other hand, Misrepair of DNA is a source of DNA mutations and the DNA Misrepairs in germ cells may contribute to the diversity of genome DNAs in a species. In conclusion, Misrepair mechanism is a mechanism essential for individual adaptation, species adaptation, and species evolution.

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Potential of longevity: hidden in structural complexity

In order to understand the phenomenon of longevity in biological world, the relationship between the potential of longevity and the structural complexity of an organism is analyzed. I. The potential of longevity is the maximum lifespan of an organism if it lives in an ideal environment. The longevity of an organism includes two parts: the time for development (development time) and the time for structure-maintenance (maintenance time). II. The development time of an organism depends on its structural complexity. The maintenance time is related to two factors: the degree of damage-exposure and the potential of functionality for structure-maintenance. The potential of functionality is built in structural complexity. Since both of development time and maintenance time are determined by structural complexity, the potential of longevity of an organism is hidden in structural complexity. III. The individuals of different species have different potentials of longevity because they have different structural complexities. An animal has limited longevity because it has limited structural complexity. Limited structural complexity and limited longevity are essential for the survival of a species. IV. Despite having the same potential of longevity, the individuals of a species can have different lifespans. The lifespan of an individual is more related to the degree of damage-exposure, which is determined by the living environment and the living habit of the individual. In conclusion, the potential of longevity of an organism is hidden in structural complexity, but the real lifespan of an organism is more related to the living environment.

q-bio.TO↗

Premature aging as a consequence of Mis-construction of tissues and organs during body development

Hutchinson-Gilford Progeria syndrome, Werner syndrome, and Cockayne syndrome are three genetic disorders, in which the children have premature aging features. To understand the phenomenon of premature aging, the similarity of aging features in these syndromes to that in normal aging is investigated. Although these three syndromes have different genetic backgrounds, all the patients have abnormal structures of tissues/organs like that in normal aging. Therefore, the abnormality in tissue structure is the common point in premature aging and normal aging. This abnormality links also a defective development and a defective repair, the Misrepair. Defective development is a result of Mis-construction of the structure of tissues and organs as consequence of genetic mutations. Aging is a result of Mis-reconstructions, the Misrepairs, for maintaining the structure of tissues/organs. Construction-reconstruction of the structure of an organism is thus the coupling point of development and aging. Mis- construction and Mis-reconstruction (Misrepair) are the essential processes for the development of aging-like feathers. In conclusion, premature aging is a result of Mis- construction of tissues and organs during body development as consequence of genetic disorders.

q-bio.TO↗

A mathematical insight in the epithelial-mesenchymal-like transition in cancer cells and its effect in the invasion of the extracellular matrix

Current biological knowledge supports the existence of a secondary group of cancer cells within the body of the tumour that exhibits stem cell-like properties. These cells are termed Cancer Stem Cells (CSCs}, and as opposed to the more usual Differentiated Cancer Cells (DCCs), they exhibit higher motility, they are more resilient to therapy, and are able to metastasize to secondary locations within the organism and produce new tumours. The origin of the CSCs is not completely clear; they seem to stem from the DCCs via a transition process related to the Epithelial-Mesenchymal Transition (EMT) that can also be found in normal tissue. In the current work we model and numerically study the transition between these two types of cancer cells, and the resulting "ensemble" invasion of the extracellular matrix. This leads to the derivation and numerical simulation of two systems: an algebraic-elliptic system for the transition and an advection-reaction-diffusion system of Keller-Segel taxis type for the invasion.

q-bio.CB↗

Nonlinear dynamics of the mammalian inner ear

A simple nonlinear transmission-line model of the cochlea with longitudinal coupling is introduced that can reproduce Basilar membrane response and neural tuning in the chinchilla. It is found that the middle ear has little effect on cochlear resonances, and hence conclude that the theory of coherent reflections is not applicable to the model. The model also provides an explanation of the emergence of spontaneous otoacoustic emissions (SOAEs). It is argued that SOAEs arise from Hopf bifurcations of the transmission-line model and not from localized instabilities. The paper shows that emissions can become chaotic, intermittent and fragile to perturbations.

physics.bio-ph↗

Cancer therapeutic potential of combinatorial immuno- and vaso-modulatory interventions

Currently, most of the basic mechanisms governing tumor-immune system interactions, in combination with modulations of tumor-associated vasculature, are far from being completely understood. Here, we propose a mathematical model of vascularized tumor growth, where the main novelty is the modeling of the interplay between functional tumor vasculature and effector cell recruitment dynamics. Parameters are calibrated on the basis of different in vivo immunocompromised Rag1-/- and wild-type (WT) BALB/c murine tumor growth experiments. The model analysis supports that tumor vasculature normalization can be a plausible and effective strategy to treat cancer when combined with appropriate immuno-stimulations. We find that improved levels of functional tumor vasculature, potentially mediated by normalization or stress alleviation strategies, can provide beneficial outcomes in terms of tumor burden reduction and growth control. Normalization of tumor blood vessels opens a therapeutic window of opportunity to augment the antitumor immune responses, as well as to reduce the intratumoral immunosuppression and induced-hypoxia due to vascular abnormalities. The potential success of normalizing tumor-associated vasculature closely depends on the effector cell recruitment dynamics and tumor sizes. Furthermore, an arbitrary increase of initial effector cell concentration does not necessarily imply a better tumor control. We evidence the existence of an optimal concentration range of effector cells for tumor shrinkage. Based on these findings, we suggest a theory-driven therapeutic proposal that optimally combines immuno- and vaso-modulatory interventions.

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Development of age spots as a result of accumulation of aged cells in aged skin

Age spots are the brown spots that develop in the skin but change in color and shape with time. To understand the mechanism of development of age spots, characteristics of age spots are analyzed by Misrepair mechanism, a mechanism introduced in Misrepair-accumulation aging theory. An age spot is pathologically a group of aggregated basal cells, which contain lipofuscin bodies. Accumulation of lipofuscin bodies is a sign of aging of a cell. Characteristics of age spots include: inhomogeneity in distribution, growing flatly before becoming protruding, irregularity on shape, inhomogeneity on the color and on the protruding degree of a spot, and softness of a protruding spot. After analyzing these characteristics, we make a hypothesis on the process of development of an age spot. A. Aging of a tissue is the basis for development of age spots. B. A flat spot results from accumulation of lipofuscin containing cells. When an aged cell remains, this cell can accelerate the aging of its neighbor cells by increasing damage sensitivity and reducing repair efficiency of the local tissue. By a viscous circle, more and more neighbor cells become aged and they form a flat spot, which has an irregular shape. C. A protruding spot develops when some of the cells in a flat spot die and release lipofuscin bodies. For the survival of an organism, the un degradable lipofuscin bodies have to be isolated by a capsule made by fibrotic membrane, for maintaining the structural integrity of local epidermis. Successive deaths of lipofuscin containing cells make the capsule include more and more dead substances by layers of fibrotic membrane. In this way, the spot "grows" in three-dimension, resulting in protruding of the spot. In conclusion, development of an age spot is a result of accumulation of aged cells in aged skin.

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Misrepair accumulation theory: a theory for understanding aging, cancer development, longevity, and adaptation

Misrepair accumulation theory is a novel theory in interpreting aging phenomena. With a new concept of Misrepair, this theory reaches a unified understanding of aging: aging of an organism is a result of accumulation of Misrepairs of its structure. Misrepair accumulation theory (MA theory) is distinct and it can improve our understanding of life on several aspects. I. MA theory is fundamentally different from other theories by: A. proposing a generalized concept of Misrepair; B. pointing out the evolutionary advantage of aging mechanism; and C. distinguishing between aging of a cell and aging of a tissue. II. MA theory overcomes the limitations of traditional theories on interpreting the phenomena of tissue fibrosis and cancer development. Tissue fibrosis, as a result of accumulation of Misrepairs with collagen fibers, is a powerful evidence for demonstrating the central role of Misrepairs in aging. Cancer development is a result of accumulation of DNA Misrepairs in somatic cells, which needs to proceed over many generations of cells in a regenerable tissue. III. MA theory improves also our understanding on longevity, premature aging, adaptation, and species evolution. The potential of longevity of an organism is hidden in the complexity of its structure. IV. MA theory suggests that for retarding aging, the most important is to reduce the opportunity of damage-exposure.

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A Report on the Workshop on Biobanking Informatics

The Workshop on Biobanking Informatics in NSW 2013 (WBIN13) was held on Friday, 10 May 2013 at The Wallace Wurth Building in the University of New South Wales. This report summarises the keynotes, presentations and discussions in WBIN13 which discusses current research in the field of Biobanking Informatics in Australia and internationally.

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Efficient monitoring of blood-stage infection in a malaria rodent model by the rotating-crystal magneto-optical method

Global research efforts have been focused on the simultaneous improvement of the efficiency and sensitivity of malaria diagnosis in resource-limited settings and for the active case detection of asymptomatic infections. A recently developed magneto-optical (MO) method allows the high-sensitivity detection of malaria pigment (hemozoin) crystals in blood via their magnetically induced rotational motion. The evaluation of the method using synthetic $β$-hematin crystals and P. falciparum in vitro cultures implies its potential for in-field diagnosis. Here, we study the performance of the method in monitoring the in vivo onset and progression of the blood stage infection using a malaria mouse model. We found that the MO method can detect the first generation of intraerythrocytic parasites at the ring stage 61-66 hours after sporozoite injection demonstrating better sensitivity than light microscopy and flow cytometry. MO measurements performed after treatment of severe P. berghei infections show that the clearance period of hemozoin in mice is approx. 5 days which indicates the feasibility of the detection of later reinfections as well. Being label and reagent-free, cost-effective and rapid, together with the demonstrated sensitivity, we believe that the MO method is a suitable candidate for in-depth clinical evaluation in endemic settings.

physics.bio-ph↗

The Universality of Cancer

Cancer has been characterized as a constellation of hundreds of diseases differing in underlying mutations and depending on cellular environments. Carcinogenesis as a stochastic physical process has been studied for over sixty years, but there is no accepted standard model. We show that the hazard rates of all cancers are characterized by a simple dynamic stochastic process on a half-line, with a universal linear restoring force balancing a universal simple Brownian motion starting from a universal initial distribution. Only a critical radius defining the transition from normal to tumorigenic genomes distinguishes between different cancer types when time is measured in cell--cycle units. Reparametrizing to chronological time units introduces two additional parameters: the onset of cellular senescence with age and the time interval over which this cessation in replication takes place. This universality implies that there may exist a finite separation between normal cells and tumorigenic cells in all tissue types that may be a viable target for both early detection and preventive therapy.

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Cell bystander effect induced by radiofrequency electromagnetic fields and magnetic nanoparticles

Induced effects by direct exposure to ionizing radiation (IR) are a central issue in many fields like radiation protection, clinic diagnosis and oncological therapies. Direct irradiation at certain doses induce cell death, but similar effects can also occur in cells no directly exposed to IR, a mechanism known as bystander effect. Non-IR (radiofrequency waves) can induce the death of cells loaded with MNPs in a focused oncological therapy known as magnetic hyperthermia. Indirect mechanisms are also able to induce the death of unloaded MNPs cells. Using in vitro cell models, we found that colocalization of the MNPs at the lysosomes and the non-increase of the temperature induces bystander effect under non-IR. Our results provide a landscape in which bystander effects are a more general mechanism, up to now only observed and clinically used in the field of radiotherapy.

q-bio.SC↗

Multiscale modelling of intestinal crypt organization and carcinogenesis

Colorectal cancers are the third most common type of cancer. They originate from intestinal crypts, glands that descend from the intestinal lumen into the underlying connective tissue. Normal crypts are thought to exist in a dynamic equilibrium where the rate of cell production at the base of a crypt is matched by that of loss at the top. Understanding how genetic alterations accumulate and proceed to disrupt this dynamic equilibrium is fundamental to understanding the origins of colorectal cancer. Colorectal cancer emerges from the interaction of biological processes that span several spatial scales, from mutations that cause inappropriate intracellular responses to changes at the cell/tissue level, such as uncontrolled proliferation and altered motility and adhesion. Multiscale mathematical modelling can provide insight into the spatiotemporal organisation of such a complex, highly regulated and dynamic system. Moreover, the aforementioned challenges are inherent to the multiscale modelling of biological tissue more generally. In this review we describe the mathematical approaches that have been applied to investigate multiscale aspects of crypt behaviour, highlighting a number of model predictions that have since been validated experimentally. We also discuss some of the key mathematical and computational challenges associated with the multiscale modelling approach. We conclude by discussing recent efforts to derive coarse-grained descriptions of such models, which may offer one way of reducing the computational cost of simulation by leveraging well-established tools of mathematical analysis to address key problems in multiscale modelling.

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Commentary: The nature of cancer research

Cancer research reflects an implicit conflict. On the one hand, there is an overwhelming desire to control the disease. We all wish that. On the other hand, we would like to understand why cancer follows so many clearly defined yet puzzling patterns. Why is there such regularity in the rates of progression? Why do different tissues vary so much? There should, of course, be no conflict between control and understanding. But the history of cancer research seems to say that those different goals remain oddly estranged. Peto's 1977 article locates the seeds of this conflict most clearly. He describes what is still the most powerful theoretical perspective for analyzing the causes of cancer. He presents many key unsolved puzzles within that context. He also says why most cancer researchers are not interested in these fundamental issues. The subsequent decades of research grew around this rift, blindly, in the way that research disciplines often grow. Let us revisit Peto, almost 40 years ago. We can learn much about the current nature of cancer research.

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