Biological systems

Motivation: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). Results: To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the Micro-Array Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The * To whom correspondence should be addressed. † The authors wish it to be known that, in their opinion, these two authors should be regarded as joint First Authors. open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. Availability: A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/ SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

Copper, as a heavy metal, is toxic for many biological systems. Thus, the determination of trace amounts of copper in environmental samples is of great importance. In the present work, a new method was developed for the determination of trace amounts of copper in water samples. The method is based on the formation of ternary Cu(II)-CAS-CTAB ion-pair and adsorption of it into a mini-column packed with cotton prior applying inductively coupled plasma optical emission spectrometry (ICP-OES). The experimental parameters that affected the extraction efficiency of the method such as pH, flow rate and volume of the sample solution, concentration of chromazurol S (CAS) and cethyltrimethylammonium bromide (CTAB) as well as type and concentration of eluent were investigated and optimized. The ion-pair (Cu(II)-CAS-CTAB) was quantitatively retained on the cotton under the optimum conditions, then eluted completely using a solution of 25% (v/v) 1-propanol in 0.5 mol L −1 HNO 3 and directly introduced into the nebulizer of the ICP-OES. The detection limit (DL) of the method for copper was 40 ng L −1 (V sample = 100 mL) and the relative standard deviation (R.S.D.) for the determination of copper at 10 g L −1 level was found to be 1.3%. The method was successfully applied to determine the trace amounts of copper in tap water, deep well water, seawater and two different mineral waters, and suitable recoveries were obtained (92-106%).

Recent progress in genomics and experimental biology has brought exponential growth of the biological information available for computational analysis in public genomics databases. However, applying the potentially enormous scientific value of this information to the understanding of biological systems requires computing and data storage technology of an unprecedented scale. The grid, with its aggregated and distributed computational and storage infrastructure, offers an ideal platform for high-throughput bioinformatics analysis. ...

Five principles of skill acquisition are presented based on a review of research on human learning and expertise. Essentially these principles state that practice leads to faster and more efficient uses of knowledge. This enables faster performance and results in less demand on mental resources. In turn these outcomes enable higher level behaviours to be attempted. Ultimately skills are developed through refinement of many component processes. A theory of the mind is proposed that borrows from theories of complex adaptive systems. In this theory, the mind is conceived of as consisting of agents that compete for resources associated with processing information. The nature of this competition is similar to that observed in physical and biological systems in that agents survive or disappear depending on their usefulness. This theory is shown to be capable of explaining the five principles of skill acquisition, without these principles being explicitly built into the theory. Implications for other theories of skill acquisition are considered.

We compared the abilities of Biolog’s GN and ECO plates to distinguish among aerobic and heterotrophic bacterial communities in samples from six aquatic environments. The Biolog system is based on interpreting patterns of sole-carbon substrate utilization indicated by color development in a 96-well microtiter plate. Whether of fresh or saltwater origin, bacterial communities utilized >95% of substrates in both types of plates. Samples from any one environment exhibited similar time courses of average well color development (AWCD) in both GN and ECO plates. Principal component analysis was performed on data sets resulting from combinations of algorithms (AWCD and curve-integration methods) and levels of color development (end-point and set-point approaches). In all cases, the two types of plates demonstrated an equal capacity to discriminate among the heterotrophic expressions of the six microbial communities. Substantial deviation from an anticipated 1:1 correspondence occurred when color development of 25 substrates common to both types of plates was compared. The discrepancies likely are related to the different formulations of low-nutrient media in GN and ECO plates.

Long-term preservation of complex engineered tissues and organs at cryogenic temperatures in the absence of ice has been prevented to date by the difficulty of discovering combinations of cryoprotectants that are both sufficiently nontoxic and sufficiently stable to allow viability to be maintained and ice formation to be avoided during slow cooling to the glass transition temperature and subsequent slow rewarming. A new theory of the origin of non-specific cryoprotectant toxicity was shown to account, in a rabbit renal cortical slice model, for the toxicities of 20 vitrification solutions and to permit the design of new solutions that are dramatically less toxic than previously known solutions for diverse biological systems. Unfertilized mouse ova vitrified with one of the new solutions were successfully fertilized and regained 80% of the absolute control (untreated) rate of development to blastocysts, whereas ova vitrified in VSDP, the best previous solution, developed to blastocysts at a rate only 30% of that of controls. Whole rabbit kidneys perfused at )3°C with another new solution at a concentration of cryoprotectant (8.4 M) that was previously 100% lethal at this temperature exhibited no damage after transplantation and immediate contralateral nephrectomy. It appears that cryoprotectant solutions that are composed to be at the minimum concentrations needed for vitrification at moderate cooling rates are toxic in direct proportion to the average strength of water hydrogen bonding by the polar groups on the permeating cryoprotectants in the solution. Vitrification solutions that are based on minimal perturbation of intracellular water appear to be superior and provide new hope that the successful vitrification of natural organs as well as tissue engineered or clonally produced organ and tissue replacements can be achieved.

If we are to make advances in the design of information systems for the processing of functional genomic data, we must carefully examine the concepts of gene and function. Therefore, we must consider the biological models that are used to acquire these data from an epistemological point of view. This article introduces three elements of this view: (i) we reviewed the major concepts and the axioms of the systemic paradigm; (ii) we considered their relevance for the modelling of the biological functions within the framework of an intracellular signalling process; (iii) we present an operational input founded on this methodological viewpoint to illustrate the coherence of a theoretical framework and the use of its formalism for the description and the representation of biological activities. This formalism will guide the modelling and the interpretation of molecular interactions in terms of organisational operations producing and transforming the genetic information; thus, providing a better understanding of the complex relationship between the generation, the circulation and the computation of information when biological systems are set up. To cite this article: M. Roux-Rouquié, J.-L. Le Moigne, C. R. Biologies 325 (2002) 419-430. © 2002 Académies des sciences / Éditions scientifiques et médicales Elsevier SAS systemic modelling / epistemology / biological function / knowledge organisation / information system Résumé -Le paradigme systémique et sa pertinence pour la modélisation des fonctions biologiques. Une avancée dans le domaine de la conception des systèmes d'information pour l'exploitation des données de génomique fonctionnelle nécessite une discussion attentive des concepts de gène et de fonction, et donc une réflexion épistémologique sur les modèles biologiques à l'aide desquels sont établis ces systèmes d'information. Dans cet article, nous avons introduit les éléments de cette réflexion suivant trois axes : (i) un axe conceptuel considère les concepts majeurs et les axiomes du paradigme systémique ; (ii) leur pertinence pour la modélisation des fonctions biologiques est examinée dans le cadre d'un processus de signalisation intracellulaire ; (iii) une entrée opératoire, fondée sur cette réflexion méthodologique, illustre la cohérence apportée par un cadre théorique argumenté et l'utilisation de son formalisme pour la description et la représentation des activités biologiques. Ce formalisme conduit à interpréter le traitement des processus moléculaires en termes d'opérations organisationnelles produisant et transformant l'information génétique et à approfondir l'intelligibilité de la génération, de la circulation et du calcul de l'information dans la mise en place des organisations biologiques. Pour citer cet article : M. Roux-Rouquié, J.-L. Le Moigne, C. R. Biologies 325 (2002) 419-430. © 2002 Académies des sciences / Éditions scientifiques et médicales Elsevier SAS modélisation systémique / épistémologie / fonction biologique / organisation des connaissances / système d'information *Correspondence and reprints.

Synthetic biology is an emerging field that strives to build increasingly complex biological networks through the integration of molecular biology and engineering. The growth of the field has been supported by progress in the design and construction of synthetic genetic and protein networks. This has led to the possibility of assembling modular components to attain novel biological functions and tools. In addition, these synthetic networks give rise to insights that facilitate the investigation of interactions and phenomena in naturally-occurring networks. Integration of well-characterized biological components into higher order networks requires computational modeling approaches to rationally construct systems that are directed towards a desired outcome. A computational approach would improve the predictability of the underlying mechanisms that would otherwise be difficult to deduce through experimentation alone. The analysis and interpretation of both qualitative and quantitative ...

Molecular and tissue damage induced by reactive oxygen species is a serious consequence of the production of free radicals in biological systems. Biological markers produced by reactions with hydroxyl radicals are useful indices of free radical processesin vivo.In this respect, hydroxylation of aromatic compounds such as salicylate (2-hydroxybenzoate) has been used extensively as a measure of hydroxyl radical formation. 4-Hydroxybenzoate

insight review articles "For it is simply a fact of observation that the guiding principle in every cell is embodied in a single atomic association existing only in one copy (or sometimes two)-and a fact of observation that it results in producing events which are paragons of orderliness […] the situation is unprecedented, it is unknown anywhere else except in living matter.

Aromatic amines represent one of the most important classes of industrial and environmental chemicals: many of them have been reported to be powerful carcinogens and mutagens, and/or hemotoxicants. Their toxicity has been studied also with quantitative structure-activity relationship (QSAR) methods: these studies are potentially suitable for investigating mechanisms of action and for estimating the toxicity of compounds lacking experimental determinations. In this paper, we first summarized the QSAR models for the rodent carcinogenicity of the aromatic amines. The gradation of potency of the carcinogenic amines depended firstly on their hydrophobicity, and secondly on electronic (reactivity, propensity to be metabolically transformed) and steric properties. On the contrary, the difference between carcinogenic and non-carcinogenic aromatic amines depended mainly on electronic and steric properties. These QSARs can be used directly for estimating the carcinogenicity of aromatic amines. A two-step prediction is possible: (1) estimation of yes/no activity; (2) if the answer from step 1 is yes, then prediction of the degree of potency. The QSARs for rodent carcinogenicity were put in a wider context by comparing them with those for: (a) Salmonella mutagenicity; (b) general toxicity; (c) enzymatic reactions; (d) physical-chemical reactions. This comparative QSAR exercise generated a coherent global picture of the action mechanisms of the aromatic amines. The QSARs for carcinogenicity were similar to those for Salmonella mutagenicity, thus pointing to a similar mechanism of action. On the contrary, the general toxicity QSARs (both in vitro and in vivo systems) were mostly based on hydrophobicity, pointing to an aspecific mechanism of action much simpler than that for carcinogenicity and mutagenicity. The oxidation of the amines (first step in the main metabolic pathway leading to carcinogenic and mutagenic species) had identical QSARs in both enzymatic and physical-chemical systems, thus providing evidence for the link between simple chemical reactions and those in biological systems. The results show that it is possible to generate mechanistically and statistically sound QSAR models for rodent carcinogenicity, and indirectly that the rodent bioassay is a reliable source of good quality data.

Pyocyanin (1-hydroxy-N-methylphenazine) is a cytotoxic pigment secreted by the bacterial species Pseudomonas aeruginosa, which frequently infects the lungs of immunosuppressed patients as well as those with cystic fibrosis. Pyocyanin toxicity results presumably from the ability of the compound to undergo reduction by NAD(P)H and subsequent generation of superoxide and H 2 O 2 directly in the lungs. We report that in the presence of peroxidase mimics, microperoxidase 11, or hemin, pyocyanin undergoes oxidation by H 2 O 2 , as evidenced by loss of the pigment's characteristic absorption spectrum and by EPR detection of a free radical metabolite. The oxidation of pyocyanin is irreversible, suggesting an extensive modification of the pigment's phenazine chromophore. Oxidation of pyocyanin was observed also when exogenous H 2 O 2 was replaced by a H 2 O 2 -generating system consisting of NADH and the pigment itself. That the oxidation involves the phenolate group of pyocyanin was verified by the observation that a related pigment, phenazine methosulfate, which is devoid of this group, does not undergo oxidation by microperoxidase 11/H 2 O 2 . In contrast to intact pyocyanin, oxidized pyocyanin was less efficient in NADH oxidation and stimulation of interleukin-8 release by human alveolar epithelial A549 cells in vitro, suggesting that oxidation of pyocyanin leads to its inactivation. This study demonstrates that pyocyanin may play a dual role in biological systems, first as an oxidant and ROS generator, and second as a substrate for peroxidases, contributing to H 2 O 2 removal. This latter property may cause pyocyanin degradation and inactivation, which may be of considerable biomedical interest. D 2004 Elsevier Inc. All rights reserved.

HO 2 •, usually termed either hydroperoxyl radical or perhydroxyl radical, is the protonated form of superoxide; the protonation/deprotonation equilibrium exhibits a pKa of around 4.8. Consequently, about 0.3% of any superoxide present in the cytosol of a typical cell is in the protonated form. This ratio is rather accurately reflected by the published literature on the two species, as identified by a PubMed search; at the time of writing only 28 articles mention "HO2", "hydroperoxyl" or "perhydroxyl" in their titles, as against 9228 mentioning superoxide. Here it is argued that this correlation is not justifiable: that HO 2 •'s biological and biomedical importance far exceeds the attention it has received. Several key observations of recent years are reviewed that can be explained much more economically when the participation of HO 2 • is postulated. It is suggested that a more widespread appreciation of the possible role of HO 2 • in biological systems would be of considerable benefit to biomedical research.

Synchrony between mechanically separated biological systems is well known. We posed the question: can cells induce synchronous behavior in neighboring cells which are mechanically separated and which cannot communicate via chemical or electrical mechanisms. Caco-2 cell cultures were divided into three groups. "Inducer" cells were exposed to H 2 O 2 . "Detector" cells were placed in separate containers near the inducer cells but were not exposed to H 2 O 2 . Control cells were exposed to fresh media and were kept in a distant laboratory area. Samples were measured for total protein concentration, NFκB activation and structural changes, 10, 30 and 60 min after exposure respectively. Exposing inducer cells to H 2 O 2 resulted in a significant reduction in total protein content (−50%), an increase in nuclear NFκB activation (+38%), and structural damage (56%) compared to controls. There was a similar reduction in total protein content (−48%), increase in the nuclear fraction of NFκB (+ 35%) and structural damage (25%) in detector cells. These findings provide evidence in support of a non-chemical, non-electrical communication. This signaling system possibly plays a role in synchronous, stimulus-appropriate cell responses to noxious stimuli and may explain a number of cellular behaviors that are hard to explain based only on conventional cell signaling systems.

effects of alien species and climate change in the assessment framework, and by the nonlinear doseresponse relationships dominating in biological systems. Attempts to diminish uncertainties in quality assessment have become a new labour-intensive field for researchers.

With rapid technological advances in network infrastructure, programming languages, compatible component interfaces and so many more areas, today the computational Grid has evolved with the potential of seamless aggregation, integration and interactions. This has made it possible to conceive a new generation of realistic, scientific and engineering simulations of complex physical phenomenon. These applications will symbiotically and opportunistically combine computations, experiments, observations, and real-time data, and will provide important insights into complex phenomena. However, the phenomena being modeled are inherently complex, multi-phased, multi-scaled, dynamic and heterogeneous (in time space and state). Furthermore, their implementations involve multiple researchers with scores of models, hundreds of components and dynamic compositions and interactions between these components. The underlying Grid infrastructure is similarly heterogeneous and dynamic, globally aggregating large numbers of independent computing and communication resources, data stores and sensor networks. The combination of the two results in application development, configuration and management complexities that break current paradigms that are based on passive components and static compositions. In fact, we have reached a level of complexity, heterogeneity, and dynamism that our programming environments and infrastructure are becoming unmanageable/insecure .

a significant relationship was found between soluble P loss in runoff and soil test P. Eghball and Gilley (2001) Soils with high levels of P can contribute to excess P in runoff and found that erosion was the most important factor in subsequently pollute the surface water. Excess P in the soil can be removed from the system by harvesting crops. The objectives of this loss of total and particulate P, whereas runoff amount, study were to evaluate corn (Zea mays L.) P removal effects on tillage, and P source were the important factors influencsoil P reduction, and to evaluate various corn hybrids and soybean ing loss of dissolved and bioavailable P in runoff. The [Glycine max (L.) Merr.] varieties for differences in grain P concentrasoil test P levels in this study did not seem to be high tion and P removal. Soil with varying P levels as a result of annual enough (ranged from 25 to 101 mg kg 1 in the top 5 cm or biennial beef cattle (Bos taurus) feedlot manure or compost applisoil) to ...

Many of the simple mathematical models currently in use often fail to capture important biological factors. Here we extend current models of insect-pathogen interactions to include seasonality in the birth rate. In particular, we consider the SIR model with self-regulation when applied to specific cases-rabbit haemorrhagic disease and fox rabies. In this paper, we briefly summarize the results of the model with a constant time-independent birth rate, a, which we then replace with the time dependent birth rate a(t), to investigate how this effects the dynamics of the host population. We can split parameter space into an area in which the model without seasonality has no oscillations, in which case a simple averaging rule predicts the behaviour. Alternatively, in the area where oscillations to the equilibrium do occur in the non-seasonal model, disease persistence is more complicated and we get more complex dynamical behaviour in this case. We apply resonance techniques to discover the structure of the subharmonic modes of the SIR model with self-regulation. We then look at whether many biological systems are likely to display these ''resonant'' dynamics and find that we would expect them to be widespread.

G-quadruplex secondary structures, which play a structural role in repetitive DNA such as telomeres, may also play a functional role at other genomic locations as targetable regulatory elements which control gene expression. The recent interest in application of quadruplexes in biological systems prompted us to develop a tool for the identification and analysis of quadruplex-forming nucleotide sequences especially in the RNA. Here we present Quadfinder, an online server for prediction and bioinformatics of uni-molecular quadruplex-forming nucleotide sequences. The server is designed to be user-friendly and needs minimal intervention by the user, while providing flexibility of defining the variants of the motif. The server is freely available at URL http://miracle.igib.res.in/quadfinder/.

Physical-chemical processes for the capture and sequestration of CO 2 from fossil fuelfired power plant flue-gases are very expensive. Biological processes for CO 2 utilization involve plant photosynthesis and conversion of the biomass to fuels, with no net CO 2 production. Terrestrial plants cannot utilize flue gas CO 2 directly. Only submerged aquatic plants, particularly microalgae, can utilize CO 2 from power plant flue gases in a practical process. Microalgae have the potential for achieving high productivities and can be converted to gaseous and liquid fuels. A preliminary cost-analysis of such a process is presented that suggests that, if high productivities are achievable, overall costs would compare favorably with alternative physical-chemical processes for flue gas CO 2 capture and sequestration, but would be higher than CO 2 mitigation with terrestrial plants. Microalgae CO 2 utilization systems would be most applicable where land and water (seawater, brackish) resources, not readily utilized by agriculture, are available.

Neuroet is an easy-to-use artificial neural network (NN) package designed to assist with determining relationships among variables in complex ecological and biological systems. The package, which is available for download from the web site http://noble.ce.

This article introduces the finite state projection ͑FSP͒ method for use in the stochastic analysis of chemically reacting systems. One can describe the chemical populations of such systems with probability density vectors that evolve according to a set of linear ordinary differential equations known as the chemical master equation ͑CME͒. Unlike Monte Carlo methods such as the stochastic simulation algorithm ͑SSA͒ or leaping, the FSP directly solves or approximates the solution of the CME. If the CME describes a system that has a finite number of distinct population vectors, the FSP method provides an exact analytical solution. When an infinite or extremely large number of population variations is possible, the state space can be truncated, and the FSP method provides a certificate of accuracy for how closely the truncated space approximation matches the true solution. The proposed FSP algorithm systematically increases the projection space in order to meet prespecified tolerance in the total probability density error. For any system in which a sufficiently accurate FSP exists, the FSP algorithm is shown to converge in a finite number of steps. The FSP is utilized to solve two examples taken from the field of systems biology, and comparisons are made between the FSP, the SSA, and leaping algorithms. In both examples, the FSP outperforms the SSA in terms of accuracy as well as computational efficiency. Furthermore, due to very small molecular counts in these particular examples, the FSP also performs far more effectively than leaping methods.

Biological systems are exceedingly complex. The unraveling of the genome in plants and humans revealed fewer than the anticipated number of genes. Therefore, other processes such as the regulation of gene expression, the action of gene products, and the metabolic networks resulting from catalytic proteins must make fundamental contributions to the remarkable diversity inherent in living systems. Metabolomics is a relatively new approach aimed at improved understanding of these metabolic networks and the subsequent biochemical composition of plants and other biological organisms. Analytical tools within metabolomics including mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy can profile the impact of time, stress, nutritional status, and environmental perturbation on hundreds of metabolites simultaneously resulting in massive, complex data sets. This information, in combination with transcriptomics and proteomics, has the potential to generate a more complete picture of the composition of food and feed products, to optimize crop trait development, and to enhance diet and health. Selected presentations from an American Chemical Society symposium held in March 2005 have been assembled to highlight the emerging application of metabolomics in agriculture.

Mathematical modeling has proven to be valuable in understanding of the complex biological systems dynamics. In the present report we have developed an initial model of the hypothalamic-pituitary-adrenal system self-regulatory activity. A four-dimensional non-linear differential equation model of the hormone secretion was formulated and used to analyze plasma cortisol levels in humans. The aim of this work was to explore in greater detail the role of this system in normal, homeostatic, conditions, since it is the first and unavoidable step in further understanding of the role of this complex neuroendocrine system in pathophysiological conditions. Neither the underlying mechanisms nor the physiological significance of this system are fully understood yet.

Extremely low-frequency electromagnetic fields (ELF-EMF) can effect on biological systems and alters some cell functions like proliferation rate. Therefore, we aimed to attempt the evaluation effect of ELF-EMF on the growth of human adipose derived stem cells (hADSCs). Materials and Methods: ELF-EMF was generated by a system including autotransformer, multi-meter, solenoid coils, teslameter and its probe. We assessed the effect of ELF-EMF with intensity of 0.5 and 1 mT and power line frequency 50 Hz on the survival of hADSCs for 20 and 40 min/day for 7 days by MTT assay. One-way analysis of variance was used to assessment the significant differences in groups. Results: ELF-EMF has maximum effect with intensity of 1 mT for 20 min/day on proliferation of hADSCs. The survival and proliferation effect (PE) in all exposure groups were significantly higher than that in sham groups (P < 0.05) except in group of 1 mT and 40 min/day. Conclusion: Our results show that between 0.5 m and 1 mT ELF-EMF could be enhances survival and PE of hADSCs conserving the duration of exposure.

Skin wound healing is a complex and multiphase process. Despite present therapeutical options such as wound debridement, pressure regulation, application of growth factors, the use of skin equivalents and specific wound dressings, healing of cutaneous wounds costs much time, effort and money. Low-intensity light has been documented as a promising method for various medical problems including wound repair processes. 5,25 Low level laser therapy (LLLT) as a therapeutic method was introduced by Mester and colleagues, who noted beneficial effects of ruby laser on wound healing, resulting in faster closure of refractory and persistent ulcers. Since then several in vitro studies showed the efficiency of LLLT. Helium-neon laser irradiation activates human monocytes and increases the rate of keratinocyte migration and proliferation. Studies with human fibroblasts demonstrated pronounced cell proliferation and migration of fibroblasts, raising the hope that wound closure also in vivo may be accelerated. 12,34 Indeed, LLLT proved to have positive effects in rat skin wound models leading to earlier regression of the inflammatory phase, faster re-epithelialisation and acceleration in maturation phase. LLLT, in some publications also called photostimulation, promoted the tissue repair processes of wounds and increased the quantity of collagen fibres, both in diabetic and non-diabetic rats. 1 Also healing of tendons, nerves and bones can be positively affected by light treatment as shown in several small animal models. 9,27 LLLT at different intensities promoted neovascularisation in damaged Achilles tendons of rats after partial rupture 27 and increased vascularisation and the number of hypertrophic osteoclasts during tibia wound healing in rats. 9 Injury, Int. J. Care Injured xxx (2010) xxx-xxx

Cellular Systems are defined by cells that have an internal state and local interactions between cells that govern the dynamics of the system. We propose to use a special kind of Cellular Neural Networks (CNNs) which operates in finite iteration discrete-time mode and mimics the processing of visual perception in biological systems for digit recognition. We propose also a solution to another type of pattern recognition problem using a non-standard cellular neural networks called Molecular Graph Networks (MGNs) which offer direct mapping from compound to property of interest such as Physico-Chemical, Toxicity, logP, Inhibitory Activity MGNs translate molecular topology to network topology. We show how to design/train by backpropagation CNNs and MGNs in their discrete-time and finite-iteration versions to perform classification on real-world data sets.

The reverse engineering of metabolic networks from experimental data is traditionally a labor-intensive task requiring a priori systems knowledge. Using a proven model as a test system, we demonstrate an automated method to simplify this process by modifying an existing or related model--suggesting nonlinear terms and structural modifications--or even constructing a new model that agrees with the system&#x27;s time series

Ion channels play a crucial role in the physiology of complex biological systems because of their influence on the electrical equilibrium between the cells and their environment. From an engineering viewpoint, ion chan- nels will be the key components of the design and the production of a new generation of biosensors integrat- ing the selectivity of ion channels with the

Several bacteriological surveys were performed from 1994 to 1996 at different Litopenaeus vannamei hatcheries (in Ecuador) and shrimp farms (in Mexico). Samples were taken from routine productions of healthy and diseased L. vannamei larvae, postlarvae, and their culture environment and from healthy and diseased juveniles and broodstock. In Ecuador, the dominant bacterial flora associated with shrimp larvae showing symptoms of zoea 2 syndrome, mysis mold syndrome, and bolitas syndrome has been determined. Strains were characterized by Biolog metabolic fingerprinting and identified by comparison to a database of 850 Vibrio type and reference strains. A selection of strains was further genotypically fine typed by AFLP. Vibrio alginolyticus is predominantly present in all larval stages and is associated with healthy nauplius and zoea stages. AFLP genetic fingerprinting shows high genetic heterogeneity amongV. alginolyticus strains, and the results suggest that putative probiotic and pat...

I claim that explanations of human behaviour by Edward O. Wilsonand Charles Lumsden are constituted by a religiously functioningmetaphysics: emergent materialism. The constitutive effects areidentified using six criteria, beginning with a metaphorical re-description of dissimilarities between levels of organization interms of the lower level, and consist of conceptual andexplanatory reductions (CER). Wilson and Lumsden practice CER,even though CER is not

NAO is a natural water soluble antioxidant that was isolated and purified from spinach leaves. Using HPLC, NMR, and CMR spectroscopy, the main components were identified as flavonoids and p-coumaric acid derivatives. The NAO was found to be a very effective antioxidant in several in vivo and in vitro biological systems. In the present study, the antioxidant activity of the novel antioxidant glucurinated flavonoid (GF) isolated and characterized from NAO, is compared to well-known antioxidants. In addition, the direct free radical scavenging properties of the purified component GF were studied using the electron spin resonance (ESR) technique. GF and NAO were found to be superior to EGCG and NAC and to the Vitamin E homologue Trolox in inhibiting reactive oxygen species (ROS) formation in the autooxidation system of linoleic acid and in fibroblasts exposed to metal oxidation. GF and NAO were found to inhibit the ESR signal intensity of DMPO-O 2 radical formation during the riboflavin photodynamic reaction. 10 mM GF caused approximately 90% inhibition in the intensity of the ESR signal, while NAO at a concentration of 60 mg/ml caused an inhibition of about 50%. Using the Fenton reaction, GF and NAO were found to inhibit DMPO-OH radical formation. A concentration of 2 mM GF caused a 70% inhibition in the intensity of the DMPO-OH radical ESR signal, while propyl gallate at the same concentration caused only 50% inhibition. Furthermore, both GF and NAO also inhibited the 1 O 2 dependent TEMPO radical generated in the photoradiation TPPS4 system. About 80% inhibition was obtained by 4 mM GF. The results obtained indicate that the natural antioxidants derived from spinach may directly affect the scavenging of ROS and, as a consequence, may be considered as effective sources for combating oxidative damage.

Motion vision (visual odometry, the estimation of camera egomotion) is a well researched field, yet has seen relatively limited use despite strong evidence from biological systems that vision can be extremely valuable for navigation. The limited use of such vision techniques has been attributed to a lack of good algorithms and insufficient computer power, but both of those problems were resolved as long as a decade ago. A gap presently yawns between theory and practice, perhaps due to perceptions of robot vision as less reliable and more complex than other types of sensing. We present an experimental methodology for assessing the realworld precision and reliability of visual odometry techniques in both normal and extreme terrain. This paper evaluates the performance of a mobile robot equipped with a simple vision system in common outdoor and indoor environments, including grass, pavement, ice, and carpet. Our results show that motion vision algorithms can be robust and effective, and suggest a number of directions for further development.

Biological processes and methods have been influencing science and technology for many decades. The ideas of feedback and control processes Norbert Wiener used in his cybernetics were based on observation of these phenomena in biological systems. Artificial intelligence and intelligent systems have been fundamentally interested in the phenomenology of living systems, namely perception, decision-making, action, and learning. Natural systems exhibit many properties that form fundamentals for a number of nature inspired applications – dynamics, flexibility, robustness, self-organisation, simplicity of basic elements, and decentralization. This paper reviews examples of nature inspired software applications focused on optimization problems, mostly drawing inspiration from collective behaviour of social colonies.

Time-resolved flash photography was used to investigate the dynamics of shock waves and cavitation bubbles generated by picosecond optical breakdown in bovine corneal tissue and water. A picosecond NdYLF laser was employed. A rapid decay of the shock waves was observed in both materials, with similar temporal characteristics, indicating that water serves as a good model for shock wave studies. In contrast, differences in the cavitation bubble dynamics were found between cornea and water, which are related to differences in the mechanical and thermal properties of the two media, suggesting that water should not be used to model cavitation dynamics in cornea. The experimental results also suggest that the efficiency of intrastromal ablation may be increased by using short pulses and moderate pulse energies in order to avoid the creation of large cavitation bubbles. The experiment indicates that the optimum laser repetition rate for intrastromal ablation is between 1 and 5 kHz.

The recognition that nutrients have the ability to interact and modulate molecular mechanisms underlying an organism's physiological functions has prompted a revolution in the field of nutrition. Performing population-scaled epidemiological studies in the absence of genetic knowledge may result in erroneous scientific conclusions and misinformed nutritional recommendations. To circumvent such issues and more comprehensively probe the relationship between genes and diet, the field of nutrition has begun to capitalize on both the technologies and supporting analytical software brought forth in the post-genomic era. The creation of nutrigenomics and nutrigenetics, two fields with distinct approaches to elucidate the interaction between diet and genes but with a common ultimate goal to optimize health through the personalization of diet, provide powerful approaches to unravel the complex relationship between nutritional molecules, genetic polymorphisms, and the biological system as a whole. Reluctance to embrace these new fields exists primarily due to the fear that producing overwhelming quantities of biological data within the confines of a single study will submerge the original query; however, the current review aims to position nutrigenomics and nutrigenetics as the emerging faces of nutrition that, when considered with more classical approaches, will provide the necessary stepping stones to achieve the ambitious goal of optimizing an individual's health via nutritional intervention.-Mutch, D. M., Wahli, W., Williamson, G. Nutrigenomics and nutrigenetics: the emerging faces of nutrition. FASEB J. 19, 1602-1616 (2005)

Fatty acids play important roles in biological systems and the newborns fatty acids requirements are covered only by the milk. It is of particular interest to qualify the content of the fatty acids in the milk. This study was performed to determine the levels of some fatty acids in the infant formulas and also to describe a method without derivatization for the fatty acids analysis and applying it to the control of infant formulas. Free fatty acids were produced by adding isopropanol- KOH to milk fat extract and heating it to saponify and acidify by H2SO4. Free fatty acids were extracted and were quantified by capillary gas chromatography on a fused silica column (AT-1000) and flame ionization detector. The average experimental values of lauric, palmitic, stearic and linoleic fatty acids contents of twenty infant formulas were 6.47, 16.52, 2.11 and 14.56 g/100g, respectively. The obtained experimental values of lauric and linoleic fatty acids contents of twenty infant formulas were ...

Reactive oxygen species (ROS) play important roles in the defense mechanism against infection and in the pathogenesis of various diseases. Although chemical properties of ROS generated by leukocytes have been studied extensively, methods available for their analysis are not sufficiently sensitive. We found that 8-amino-5-chloro-7-phenylpyrido[3,4-d]pyridazine-1,4-(2H,3H)dione (L-012) reacted with various types of ROS generated by activated neutrophils in human blood and oral cavity, and from peritoneal cavity of the rat, and developed strong chemiluminescence (CHL). Under physiological conditions, opsonized zymosan-dependent CHL intensity of L-012 in human blood and rat peritoneal neutrophils was about 100 and 10 times higher than that of luminol and luciferin analog MCLA, respectively. Phorbol ester-activated CHL of oral neutrophils was also higher with L-012 than that with luminol and MCLA. The presence of either superoxide dismutase, catalase, uric acid, deferoxamine, or azide decreased CHL intensity of L-012 by 52, 57, 57, 63, and 91%, respectively. Kinetic analysis revealed that L-012 developed CHL predominantly by reacting with hydroxyl radical and hypochlorite. Thus, highly sensitive L-012 permits studies on ROS generation by complex biological systems, such as leukocytes, and on the role of ROS in the pathogenesis of various diseases.

Abstract. Invariance is a necessary feature of a visual system able to recognize real objects in all their possible appearance. It is also the processing step most problematic to understand in biological systems, and most difficult to simulate in computational models. This work investigates the possibility to achieve viewpoint invariance without adopting any explicit theorical solution to the problem, but simply by exposing a hierarchical architecture of self-organizing artificial cortical maps to series of images under various viewpoints. 1

Metabolomics is a post genomic research field concerned with developing methods for analysis of low molecular weight compounds in biological systems, such as cells, organs or organisms. Analyzing metabolic differences between unperturbed and perturbed systems, such as healthy volunteers and patients with a disease, can lead to insights into the underlying pathology. In metabolomics analysis, large amounts of data are routinely produced in order to characterize samples. The use of multivariate data analysis techniques and chemometrics is a commonly used strategy for obtaining reliable results. Metabolomics have been applied in different fields such as disease diagnosis, toxicology, plant science and pharmaceutical and environmental research. In this review we take a closer look at the chemometric methods used and the available results within the field of disease diagnosis. We will first present some current strategies for performing metabolomics studies, especially regarding disease diagnosis. The main focus will be on data analysis strategies and validation of multivariate models, since there are many pitfalls in this regard. Further, we highlight the most interesting metabolomics publications and discuss these in detail; additional studies are mentioned as a reference for the interested reader. A general trend is an increased focus on biological interpretation rather than merely the ability to classify samples. In the conclusions, the general trends and some recommendations for improving metabolomics data analysis are provided.

Functionality of biological and inorganic systems ranging from nonvolatile computer memories and microelectromechanical systems to electromotor proteins and cellular membranes is ultimately based on the intricate coupling between electrical and mechanical ...

Contaminated sites represent new ecological niches where historical pollution has originated an unusual microbial biodiversity. The knowledge of these microorganisms contributes to the discovery of new pathways and metabolic networks and may offer potential solutions for damaged areas. In the present work seven microbial consortia have been isolated from an abandoned mine of blend and galena (Ingurtosu, Italy) through a selection for resistance to zinc (tested up to 40 mM in solution). All the consortia were able to accumulate zinc and the best accumulator, named Ing5, has been studied for the following characteristics: resistance and accumulation of Zn, Cd, Hg, bioaccumulation mechanisms of Zn, and influence of Zn and Cd on the metabolic profile. The results indicate that the consortium Ing5 bears resistance systems for Cd and Hg as well as Zn and that, for some of the 5 isolates belonging to Ing5, the resistance thresholds are higher in consortium than in pure culture. The prevalent mechanism for zinc accumulation can be reasonably considered to be metabolism-dependent, inducible and regulated by metal concentrations. The study on the metabolic profile, carried out by the Biolog system, shows that Zn exerts a very low influence on the metabolic profile and that this influence can also be positive; Cd has a stronger negative influence but that, despite this, the consortium is able to maintain a wide metabolic potential in the presence of heavy metals. These features of Ing5 make it a good candidate for biotechnological applications and for further investigation of the degradation of organic pollutants in the presence of metals.

Microbial functional diversity in four soils sampled in the vicinity of Wanda Glacier, Antarctic Peninsula, was determined using Biolog EcoPlates at 5°C and 25°C. Comparisons of the patterns of substrate utilization and the diversity index showed differences in community composition, reflecting the heterogeneous distribution of microorganisms in this environment. Differences in microbial diversity may be related to soil chemical properties. Higher incubation temperature influenced the overall microbial diversity, reducing richness due to the selection of psychrotrophic microorganisms. To our knowledge, this is the first study with microbial communities from Wanda Glacier and contributes to understanding the microbial diversity of Antarctic environments.

The polarity of biological mediums controls a host of physiological processes such as digestion, signaling, transportation, metabolism, and excretion. With the recent widespread use of near-infrared (NIR) fluorescent dyes for biological imaging of cells and living organisms, reporting medium polarity with these dyes would provide invaluable functional information in addition to conventional optical imaging parameters. Here, we report a new approach to determine polarities of macro-and microsystems for in vitro and potential in vivo applications using NIR polymethine molecular probes. Unlike the poor solvatochromic response of NIR dyes in solvents with diverse polarity, their fluorescence lifetimes are highly sensitive, increasing by a factor of up to 8 on moving from polar to nonpolar mediums. We also established a correlation between fluorescence lifetime and solvent orientation polarizability and developed a lifetime polarity index for determining the polarity of complex systems, including micelles and albumin binding sites. Because of the importance of medium polarity in molecular, cellular, and biochemical processes and the significance of reduced autofluorescence and deep tissue penetration of light in the NIR region, the findings reported herein represent an important advance toward using NIR molecular probes to measure the polarity of complex biological systems in vitro and in vivo.