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Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...

q-bio.OT↗

Wobbling of What?

A simple explanation for the symmetry of the genetic code has been suggested. An alternative to the wobble hypothesis has been proposed. The facts revealed in this study offer a new insight into physical mechanisms of the functioning of the genetic code.

physics.bio-ph↗

Hierarchies of Biocomplexity: modeling lifes energetic complexity

In this paper, a model for understanding the effects of selection using systems- level computational approaches is introduced. A number of concepts and principles essential for understanding the motivation for constructing the model will be introduced first. This will be followed by a description of parameters, measurements, and graphical representations used in the model. Four possible outcomes for this model are then introduced and described. In addition, the relationship of relative fitness to selection is described. Finally, the consequences and potential lessons learned from the model are discussed.

q-bio.PE↗

Existence of biological uncertainty principle implies that we can never find 'THE' measure for biological complexity

There are innumerable 'biological complexity measure's. While some patterns emerge from these attempts to represent biological complexity, a single measure to encompass the seemingly countless features of biological systems, still eludes the students of Biology. It is the pursuit of this paper to discuss the feasibility of finding one complete and objective measure for biological complexity. A theoretical construct (the 'Thread-Mesh model') is proposed here to describe biological reality. It segments the entire biological space-time in a series of different biological organizations before modeling the property space of each of these organizations with computational and topological constructs. Acknowledging emergence as a key biological property, it has been proved here that the quest for an objective and all-encompassing biological complexity measure would necessarily end up in failure. Since any study of biological complexity is rooted in the knowledge of biological reality, an expression for possible limit of human knowledge about ontological biological reality, in the form of an uncertainty principle, is proposed here. Two theorems are proposed to model the fundamental limitation, owing to observer dependent nature of description of biological reality. They explain the reasons behind failures to construct a single and complete biological complexity measure. This model finds support in various experimental results and therefore provides a reliable and general way to study biological complexity and biological reality.

q-bio.OT↗

A (possible) mathematical model to describe biological "context-dependence" : case study with protein structure

Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general mathematical construct to model the wide spectrum of context-dependence, eludes the students of biology. An objective and rigorous model, from both 'bottom-up' as well as 'top-down' perspective, is proposed here to serve as the template to describe the various kinds of context-dependence that we encounter in different branches of biology. Interactions between biological contexts was found to be transitive but non-commutative. It is found that a hierarchical nature of dependence amongst the biological contexts models the emergent biological properties efficiently. Reasons for these findings are provided with a general model to describe biological reality. Scheme to algorithmically implement the hierarchic structure of organization of biological contexts was achieved with a construct named 'Context tree'. A 'Context tree' based analysis of context interactions among biophysical factors influencing protein structure was performed.

q-bio.OT↗

Cellular Automata Model of Macroevolution

In this paper I describe a cellular automaton model of a multi-species ecosystem, suitable for the study of emergent properties of macroevolution. Unlike majority of ecological models, the number of coexisting species is not fixed. Starting from one common ancestor they appear by "mutations" of existent species, and then survive or extinct depending on the balance of local ecological interactions. Monte-Carlo numerical simulations show that this model is able to qualitatively reproduce phenomena that have been observed in other models and in nature.

q-bio.PE↗

The genetic code degeneracy and the amino acids chemical composition are connected

We show that our recently published Arithmetic Model of the genetic code based on Godel Encoding is robust against symmetry transformations, specially Rumer s one U > G, A > C, and constitutes a link between the degeneracy structure and the chemical composition of the 20 canonical amino acids. As a result, several remarkable atomic patterns involving hydrogen, carbon, nucleon and atom numbers are derived. This study has no obvious practical application(s) but could, we hope, add some new knowledge concerning the physico-mathematical structrure of the genetic code.

q-bio.OT↗

A new simulation-based model for calculating post-mortem intervals using developmental data for Lucilia sericata (Dipt.: Calliphoridae)

Homicide investigations often depend on the determination of a minimum post-mortem interval (PMI$_{min}$) by forensic entomologists. The age of the most developed insect larvae (mostly blow fly larvae) gives reasonably reliable information about the minimum time a person has been dead. Methods such as isomegalen diagrams or ADH calculations can have problems in their reliability, so we established in this study a new growth model to calculate the larval age of \textit{Lucilia sericata} (Meigen 1826). This is based on the actual non-linear development of the blow fly and is designed to include uncertainties, e.g. for temperature values from the crime scene. We used published data for the development of \textit{L. sericata} to estimate non-linear functions describing the temperature dependent behavior of each developmental state. For the new model it is most important to determine the progress within one developmental state as correctly as possible since this affects the accuracy of the PMI estimation by up to 75%. We found that PMI calculations based on one mean temperature value differ by up to 65% from PMIs based on an 12-hourly time temperature profile. Differences of 2\degree C in the estimation of the crime scene temperature result in a deviation in PMI calculation of 15 - 30%.

q-bio.OT↗

On Pattern and Evolution

A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss curvature'K'enters. The model suggests a novel point-like placement for organs such as eyes, antennae, limbs, and wings. In the case of plant patterns, 'leaf' outgrowths from a stem are predicted to be under the control of a yet to be discovered "master regulatiory gene", analogous to the animal case, when various outgrowths from the animal body are generally accompanied by activation of the 'distal-less' (Dll) gene.

q-bio.TO↗

Sparse Approximation of Computational Time Reversal Imaging

Computational time reversal imaging can be used to locate the position of multiple scatterers in a known background medium. Here, we discuss a sparse approximation method for computational time-reversal imaging. The method is formulated entirely in the frequency domain, and besides imaging it can also be used for denoising, and to determine the magnitude of the scattering coefficients in the presence of moderate noise levels.

q-bio.OT↗

Coherent states, fractals and brain waves

I show that a functional representation of self-similarity (as the one occurring in fractals) is provided by squeezed coherent states. In this way, the dissipative model of brain is shown to account for the self-similarity in brain background activity suggested by power-law distributions of power spectral densities of electrocorticograms. I also briefly discuss the action-perception cycle in the dissipative model with reference to intentionality in terms of trajectories in the memory state space.

q-bio.NC↗

Leaf litter decomposition -- Estimates of global variability based on Yasso07 model

Litter decomposition is an important process in the global carbon cycle. It accounts for most of the heterotrophic soil respiration and results in formation of more stable soil organic carbon (SOC) which is the largest terrestrial carbon stock. Litter decomposition may induce remarkable feedbacks to climate change because it is a climate-dependent process. To investigate the global patterns of litter decomposition, we developed a description of this process and tested the validity of this description using a large set of foliar litter mass loss measurements (nearly 10 000 data points derived from approximately 70 000 litter bags). We applied the Markov chain Monte Carlo method to estimate uncertainty in the parameter values and results of our model called Yasso07. The model appeared globally applicable. It estimated the effects of litter type (plant species) and climate on mass loss with little systematic error over the first 10 decomposition years, using only initial litter chemistry, air temperature and precipitation as input variables. Illustrative of the global variability in litter mass loss rates, our example calculations showed that a typical conifer litter had 68% of its initial mass still remaining after two decomposition years in tundra while a deciduous litter had only 15% remaining in the tropics. Uncertainty in these estimates, a direct result of the uncertainty of the parameter values of the model, varied according to the distribution of the litter bag data among climate conditions and ranged from 2% in tundra to 4% in the tropics. This reliability was adequate to use the model and distinguish the effects of even small differences in litter quality or climate conditions on litter decomposition as statistically significant.

q-bio.OT↗

Rapid emergence of co-colonization with community-acquired and hospital-acquired methicillin-resistant Staphylococcus aureus strains in the hospital setting

Background: Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA), a novel strain of MRSA, has recently emerged and rapidly spread in the community. Invasion into the hospital setting with replacement of the hospital-acquired MRSA (HA-MRSA) has also been documented. Co-colonization with both CA-MRSA and HA-MRSA would have important clinical implications given differences in antimicrobial susceptibility profiles and the potential for exchange of genetic information. Methods: A deterministic mathematical model was developed to characterize the transmission dynamics of HA-MRSA and CA-MRSA in the hospital setting and to quantify the emergence of co-colonization with both strains. Results: The model analysis shows that the state of co-colonization becomes endemic over time and that there is no competitive exclusion of either strain. Increasing the length of stay or rate of hospital entry among patients colonized with CA-MRSA leads to a rapid increase in the co-colonized state. Compared to MRSA decolonization strategy, improving hand hygiene compliance has the greatest impact on decreasing the prevalence of HA-MRSA, CA-MRSA and the co-colonized state. Conclusions: The model predicts that with the expanding community reservoir of CA-MRSA, the majority of hospitalized patients will become colonized with both CA-MRSA and HA-MRSA.

q-bio.PE↗

A Molecular Mass Gradient is the Key Parameter of the Genetc Code Organization

The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters used to analyze of the code matrix, the serial numbers of the encoded products and coding elements, ordered by molecular mass. The structural similarity of the amino acid sequences corresponding to two aminoacyl tRNA synthetases classes is found. The code matrix shows how can be organized the so-called second genetic code. The symmetrical pattern of the matrix is supported with the other parameters; it also serves as a basis to construct a 3D model of the genetic code which follows the structure of the simplest Plato solid, tetrahedron. The reasons for this unusual structure of the genetic code remains unclear.

q-bio.OT↗

The structure of human olfactory space

We analyze the psychophysical responses of human observers to an ensemble of monomolecular odorants. Each odorant is characterized by a set of 146 perceptual descriptors obtained from a database of odor character profiles. Each odorant is therefore represented by a point in highly multidimensional sensory space. In this work we study the arrangement of odorants in this perceptual space. We argue that odorants densely sample a two-dimensional curved surface embedded in the multidimensional sensory space. This surface can account for more than half of the variance of the psychophysical data. We also show that only 12 percent of experimental variance cannot be explained by curved surfaces of substantially small dimensionality (<10). We suggest that these curved manifolds represent the relevant spaces sampled by the human olfactory system, thereby providing surrogates for olfactory sensory space. For the case of 2D approximation, we relate the two parameters on the curved surface to the physico-chemical parameters of odorant molecules. We show that one of the dimensions is related to eigenvalues of the molecule connectivity matrix, while the other is correlated with measures of the molecule polarity. We discuss the behavioral significance of these findings.

q-bio.NC↗

Data management in systems biology I - Overview and bibliography

Large systems biology projects can encompass several workgroups often located in different countries. An overview about existing data standards in systems biology and the management, storage, exchange and integration of the generated data in large distributed research projects is given, the pros and cons of the different approaches are illustrated from a practical point of view, the existing software - open source as well as commercial - and the relevant literature is extensively overview, so that the reader should be enabled to decide which data management approach is the best suited for his special needs. An emphasis is laid on the use of workflow systems and of TAB-based formats. The data in this format can be viewed and edited easily using spreadsheet programs which are familiar to the working experimental biologists. The use of workflows for the standardized access to data in either own or publicly available databanks and the standardization of operation procedures is presented. The use of ontologies and semantic web technologies for data management will be discussed in a further paper.

cs.DB↗

A taylor-made arithmetic model of the genetic code and applications

We present a completely new version of our arithmetic model of the standard genetic code and compute in a straightforward manner the exact numeric degeneracies of the five multiplets without any trick for the doublets and the sextets, as we have done previously. We give also some interesting applications.

q-bio.OT↗

Reasons underlying certain tendencies in the data on the frequency of codon usage

The tendencies described in this work were revealed in the course of examination of adenine and uracil distribution in the mRNA encoding sequence. The study also discusses the usage of codons occupied by the amino acid arginine in the table of the universal genetic code. All of the described tendencies are qualitative, so neither sophisticated methods nor cumbersome calculations are necessary to reveal and interpret them.

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