Network development in biological gels: role in lymphatic vessel development

In this paper, we present a model that explains the prepatterning of lymphatic vessel morphology in collagen gels. This model is derived using the theory of two phase rubber material due to Flory and coworkers and it consists of two coupled fourth order partial differential equations describing the evolution of the collagen volume fraction, and the evolution of the proton concentration in a collagen implant; as described in experiments of Boardman and Swartz (Circ. Res. 92, 801–808, 2003). Using linear stability analysis, we find that above a critical level of proton concentration, spatial patterns form due to small perturbations in the initially uniform steady state. Using a long wavelength reduction, we can reduce the two coupled partial differential equations to one fourth order equation that is very similar to the Cahn–Hilliard equation; however, it has more complex nonlinearities and degeneracies. We present the results of numerical simulations and discuss the biological implications of our model

Biological taxonomy and ontology development: scope and limitations

The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast the common usage of a static 'snapshot' hierarchy in ontological representations of taxonomy with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature which taxonomy can only gradually approximate; (2) the evolvability of taxa which means that taxon-defining features may be lost in subordinate members or independently gained across multiple sections of the tree of life; (3) the hybrid approach of defining taxa both in reference to properties (intensional) and members (ostensive) which undermines the individual/class dichotomy sustaining conventional ontologies; (4) the idiosyncratic yet inferentially valuable usage of Linnaean ranks; (5) the indelible and semantically complex 250-year legacy of nomenclatural and taxonomic changes that characterizes the current system; (6) the insufficient taxonomic exploration of large portions of the tree of life; and the need to use a sophisticated terminology for aligning taxonomic entities in order to integrate both (7) single and (8) multiple hierarchies. We briefly such how such integration may proceed based on an initial expert alignment of concept relationship and subsequent use of first-order logic algorithms to maximize consistency, reveal implied relationships, and ultimately merge taxonomies.
 In light of the aforementioned obstacles, we suggest that research along the taxonomy/ontology interface should focus on either strictly nomenclatural entities or specialize in ontology-driven methods for producing alignments between multiple taxonomies. We furthermore suggest that the prospects of developing successful ontologies for taxonomy will largely depend on the ability of the taxonomic expert community to present their phylogenies and classifications in a way that is more compatible with ontological reasoning than concurrent practice. Minimally, this means (1) adopting rigorous standards for linking new core taxonomies to relevant peripheral taxonomies through comprehensive alignments so that their ontological/taxonomic connections are transparent; (2) using lineage-specific ontological standards for phenotype-based accounts of taxa while taking into account the phylogenetic contextuality of phenotypic descriptors; (3) presenting all nomenclatural and taxonomic novelties in an explicit, ontology-compatible format, including intensional and ostensive definitions; and (4) offering comprehensive intensional/ostensive alignments to entities in relevant preceding taxonomies

The Role of Scientific Discovery in the Establishment of the First Biological Weapons Programmes

YesThis report addresses the scientific and technological discoveries in the biological sciences that enabled the early interest in biological warfare to move from hurling infected corpses into enemy cities in ancient times, through use of small cultures of animal pathogens to sabotage enemy livestock in World War I, to the origins of organised military biological weapons (BW) programmes directed at humans, animals, and plants in the inter-war period. It builds on Dando¿s 1999 paper: The Impact of the Development of Modern Biology and Medicine on the Evolution of Offensive Biological Warfare Programs in the Twentieth Century.1 For the historical aspects of biological warfare programmes this report primarily draws from the Stockholm International Peace Research Institute volume: Biological and Toxin Weapons: Research, Development and Use from the Middle Ages to 1945.

"Biological Agriculture in Greece: Constraints and Opportunities for Development"

In the following presentation I will first try to describe the current state of biological agriculture in Greece, and secondly to estimate the constraints and opportunities it faces as an alternative mode of production/consumption in the framework of contemporary EU rural development policies

Evaluation of fingerprint development reagents for biological stain detection

Some latent fingerprint development techniques rely on the reaction with amino acids within the fingerprint and then either change in color or fluoresce to help visualize this fingerprint. Amino acids are the building blocks of proteins and are present in all biological fluid. Thus, these developers should be able to also locate biological stains. In a previous study, ninhydrin was shown to be able to locate biological stains. Two more latent fingerprint developers are introduced as possible universal biological stain detectors: 1,8-diazafluoren-9-one (DFO), and 1,2-indanedione (1,2-IND). Five biological stains were used to test these chemicals: 1:500 diluted blood, saliva, semen, sweat, and urine. A new heating method was also introduced for a more portable application. The hair dryer heating method was optimized for the three chemicals with two traditional oven heating methods: the oven setting at 70oC and the oven setting at 100oC. These chemicals were also examined for their effectiveness on aged samples. Samples aged for three different time intervals were used: 4 weeks, 8 weeks, and 16 weeks. The hair dryer heating method was found to be viable for all three chemicals for each of the biological stains except the 1:500 diluted blood. With the application of the hair dryer for less than 3 minutes, most stains were visible for all three chemicals. 1,2-IND gave slightly different color changes for sweat and the other biological stains. This property can possibly be used to guide subsequent specific body fluids testing. All three chemicals lost their effectiveness as the stain became older. One-month-old stains still gave similar results as fresh stains, but after 2 months, the color became fainter and was barely visible after 4 months. The next stage of this study applied these chemicals as a guide for wearer DNA extraction from worn clothing. Sampling for wearer DNA has mostly been an educated guess with little guidance as to where an abundance of DNA is located. Fingerprint developers can react with amino acids, and cells contain abundant amino acids. Thus, these chemicals may react more to areas with abundant cells. Wearer DNA was extracted from collars of donated shirts before and after the chemical applications to determine the effectiveness of these chemicals as DNA detectors. Of the three collars tested, ninhydrin reacted completely with two of the collars, making any distinction between areas with abundant DNA and areas with no DNA difficult. In addition, the quantitation data of the ninhydrin samples showed no advantage in using ninhydrin as a wearer DNA locator. DFO was shown to have some detrimental effects on the DNA or the DNA extraction and quantitation process. The quantitation data for DFO also showed no advantage in using DFO as a wearer DNA locator. 1,2-IND showed promising results and was the most likely candidate as a wearer DNA locator. All areas that reacted with 1,2-IND produced at least one sample having higher than 0.01 nanograms per microliter of DNA and would be considered viable for DNA profiling

Homesteading the noosphere: The ethics of owning biological information

The idea of homesteading can be extended to the realm of biological entities, to the ownership of information wherein organisms perform artifactual functions as a result of human development. Can the information of biological entities be ethically “homesteaded”: should humans (or businesses) have ownership rights over this information from the basis of mere development and possession, as in Locke’s theory of private property? I offer three non-consequentialist arguments against such homesteading: the information makeup of biological entities is not commonly owned, and thus is not available for homesteading; the value of the individual biological entity extends to the information whereby it is constituted, and includes inalienable rights of an entity over itself and its information; and use of life as an information artifact makes an organism an unending means to an end rather than an end itself. I conclude that the information space of biological entities is not open for homesteading, not liable to private ownership, and should not be available for perpetual exploitation

Porous titanium for biomedical applications : development, characterization and biological evaluation

Metallic biomaterials have so far shown the greatest potential to be the basis of implants for long-term load-bearing orthopedic and dental applications, owing to their excellent mechanical strength when compared to alternative biomaterials, such as polymers and ceramics. Particularly titanium and its alloys are currently receiving much attention because of their biocompatibility, light weight, excellent balance of mechanical properties, corrosion resistance, etc. They are mainly used in implant devices for replacement of failed hard tissue such as artificial hip and knee joints, bone plates and dental implants. In general, failure of joint replacements due to the mechanical failure of materials such as fatigue fracture of the implant seldom occurs. A more common cause of arthroplasty failure is aseptic loosening of the implant that occurs several years after the implant has been in situ and functioning reasonably, due to interfacial instability within host tissues, biomechanical mismatch of Young’s modulus and lacking biological anchorage through tissue ingrowth

Mathematical models in physiology

Computational modelling of biological processes and systems has witnessed a remarkable development in recent years. The search-term (modelling OR modeling) yields over 58000 entries in PubMed, with more than 34000 since the year 2000: thus, almost two-thirds of papers appeared in the last 5–6 years, compared to only about one-third in the preceding 5–6 decades.\ud \ud The development is fuelled both by the continuously improving tools and techniques available for bio-mathematical modelling and by the increasing demand in quantitative assessment of element inter-relations in complex biological systems. This has given rise to a worldwide public domain effort to build a computational framework that provides a comprehensive theoretical representation of integrated biological function—the Physiome.\ud \ud The current and next issues of this journal are devoted to a small sub-set of this initiative and address biocomputation and modelling in physiology, illustrating the breadth and depth of experimental data-based model development in biological research from sub-cellular events to whole organ simulations

Mechanochemical models for generating biological pattern and form in development

The central issue in development is the formation of spatial patterns of cells in the early embryo. The mechanisms which generate these patterns are unknown. Here we describe the new Oster-Murray mechanochemical approach to the problem, the elements of which are experimentally well documented. By way of illustration we derive one of the basic models from first principles and apply it to a variety of problems of current interest and research. We specifically discuss the formation of skin organ patterns, such as feather and scale germs, cartilage condensations in the developing vertebrate limb and finally wound healing