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Abstract: We revisit an old Russian paper by V.V. Dynnik, R. Heinrich and E.E. Sel’kov (1980a,b) describing: “A mathematical model of carbohydrate energy metabolism. Interaction between glycolysis, the Krebs cycle and the H-transporting shuttles at varying ATPases load”. We analyse the model mathematically and calculate the control coefficients as a function of ATPase loads. We also evaluate the structure of the metabolic network in terms of elementary flux modes. We show how this model can respond to an ATPase load as well as to the glucose supply. We also show how this simple model can help in understanding the articulation between the major blocks of energetic metabolism, i.e. glycolysis, the Krebs cycle and the H-transporting shuttles. [Copyright &y& Elsevier]

Abstract: Prenatal exposure to low doses (0.25 or 0.5 or 1.0 mg/kg, p.o.) of deltamethrin, a type II pyrethroid insecticide, to pregnant dams from gestation days 5 to 21 (GD5-21) produced dose-dependent alterations in the ontogeny of xenobiotic metabolizing cytochrome P450 (CYP) isoforms in brain and liver of the offsprings. RT-PCR analysis revealed dose-dependent increase in the mRNA expression of cerebral and hepatic CYP1A1, 1A2, 2B1, 2B2, and 2E1 isoenzymes in the offsprings exposed prenatally to deltamethrin. Similar increase in the activity of the marker enzymes of these CYP isoforms has indicated that placental transfer of the pyrethroid, a mixed type of CYP inducer, even at these low doses may be sufficient to induce the CYPs in brain and liver of the offsprings. Our data have further revealed persistence in the increase in expression of xenobiotics metabolizing CYPs up to adulthood in brain and liver of the exposed offsprings, suggesting the potential of deltamethrin to imprint the expression of CYPs in brain and liver of the offsprings following its in utero exposure. Furthermore, though the levels of CYPs were several fold lower in brain, almost equal magnitude of induction in cerebral and hepatic CYPs has further suggested that brain CYPs are responsive to the induction by environmental chemicals. The present data indicating alterations in the expression of xenobiotic metabolizing CYPs during development following prenatal exposure to deltamethrin may be of significance as these CYP enzymes are not only involved in the neurobehavioral toxicity of deltamethrin but have a role in regulating the levels of ligands that modulate growth, differentiation, and neuroendocrine functions. [Copyright &y& Elsevier]

In this paper, we deal with the following coupled chemotaxis-fluid model { n t + u ⋅ ∇ n = Δ n m − ∇ ⋅ ( n ( 1 + n ) − α ∇ c ) + γ n − μ n 2 , c t + u ⋅ ∇ c = Δ c − c + n , u t = Δ u − ∇ π + n ∇ φ , ∇ ⋅ u = 0 in a bounded domain Ω ⊂ R 3 with zero-flux boundary for n , c and no-slip boundary for u . It is shown that for any large initial datum, for any m > 0 , α > 0 , the problem admits a global weak solution, which is uniformly bounded. On the basis of this, the stability of the steady states also be discussed. The study of this paper improve the results in [15] , in which, the global existence and boundedness of weak solutions are established for m > 1 3 , α > 6 5 − m . [ABSTRACT FROM AUTHOR]

Holothuria scabra is one of the most intensively studied holothuroids, or sea cucumbers (Echinodermata: Holothuroidea), having been discussed in the literature since the early 19th century. The species is important for several reasons: (1) it is widely distributed and historically abundant in several shallow soft-bottom habitats throughout the Indo-Pacific, (2) it has a high commercial value on the Asian markets, where it is mainly sold as a dried product (beche-de-mer) and (3) it is the only tropical holothuroid species that can currently be mass-produced in hatcheries. Over 20 years have elapsed since the last comprehensive review on H. scabra published in 2001. Research on H. scabra has continued to accumulate, fuelled by intense commercial exploitation, and further declines in wild stocks over the entire distribution range. This review compiles data from over 950 publications pertaining to the biology, ecology, physiology, biochemical composition, aquaculture, fishery, processing and trade of H. scabra, presenting the most complete synthesis to date, including scientific papers and material published by local institutions and/or in foreign languages. The main goal of this project was to summarize and critically discuss the abundant literature on this species, making it more readily accessible to all stakeholders aiming to conduct fundamental and applied research on H. scabra, or wishing to develop aquaculture, stock enhancement and management programs across its geographic range. [ABSTRACT FROM AUTHOR]

In 1964 Michael Bárány and colleagues published a paper ((M. Bárány, E. Gaetjens, K. Bárány, Karp E. Arch Biochem Biophys 106(1964)280-93. http://10.1016/0003-9861(64)90,189-4)) that has been one of the most cited papers in Archives of Biochemistry and Biophysics. This was followed in 1967 by another most cited paper (M. Bárány. J Gen Physiol 50(1967)197–218. https://doi.org/10.1085/jgp.50.6.197). I have commemorated these achievements as tipping points in the understanding of myosin motors in muscle function. Tipping points are generally defined as a temporal point in which a series of progressive advances (in this case the understanding of the relations between myosin ATP hydrolysis and muscle function) inspire more expansive, wide-ranging, significant changes. I first concisely summarize the background against which the papers came to publication as well as the unimaginable personal challenges faced by Michael and Kate Bárány. A final section summarizes the impact of these publications as key steps in the progression of contemporary understanding of diverse control of myosin ATPase activity with focus on the thick filaments in cardiac homeostasis, disorders, and as targets for therapeutic applications in translational investigations. [ABSTRACT FROM AUTHOR]

Abstract: Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns that constrain network dynamics. This paper contributes to the identification of patterns in the mechanisms that govern network dynamics. The control of nodes in gene regulatory, signaling, and metabolic networks is governed by a variety of biochemical mechanisms, with inputs from other network nodes that act additively or synergistically. This paper focuses on a certain type of logical rule that appears frequently as a regulatory pattern. Within the context of the multistate discrete model paradigm, a rule type is introduced that reduces to the concept of nested canalyzing function in the Boolean network case. It is shown that networks that employ this type of multivalued logic exhibit more robust dynamics than random networks, with few attractors and short limit cycles. It is also shown that the majority of regulatory functions in many published models of gene regulatory and signaling networks are nested canalyzing. [Copyright &y& Elsevier]

Abstract: Is it possible to identify cooked, rather than burnt, bone? Mild heating (≤100°C,1h) – typical of cooking – does not lead to detectable changes in any biochemical parameter of bone yet measured. If it is only possible to detect charred bone, how is it possible to detect cooking in the archaeological record? In a previous paper (, J. Arch. Sci.), we used a Transmission Electron Microscopy (TEM) based approach to investigate changes in the organization of the bone protein, collagen, as it is heated, using bone from heating experiments and short term burials. The work revealed that mineralized collagen, despite requiring aggressive treatment to gelatinise the protein (e.g. 90°C, 240+h), readily accumulates minor damage. We believe that the presence of mineral matrix stabilises the collagen enabling the damage to accumulate, but preventing it from causing immediate gelatinisation. Once the mineral is removed, the damage can be observed using appropriate visualization methods. In this paper the visualization technique was tested in a blind study of bovine bone from the Anglo-Scandinavian site of Coppergate, York. The purpose of the study was to determine if the method could discriminate between bones thought likely, on the basis of zoo-archaeological and spatial evidence, to have been cooked (high meat yield bones from a domestic context) and those which were butchered but unlikely to have been cooked (low yield bones from a butchery site). The results of the TEM analysis identified two clear groups of bones, one set more damaged than the other. This finding was consistent with archaeozoological interpretation, with the exception of one bone from the domestic context, which was not identified as having been cooked. [Copyright &y& Elsevier]

Abstract: Results from the first paper in this series indicated that the “primary” stilbenedisulfonate (PSD) site was not located on the DBDS (4, 4′-dibenzamido-2, 2′-stilbenedisulfonate) transport pathway into magnesium resealed ghosts (MRSG). Rather, transport correlated with DBDS binding to the “second” class of proton-activated binding sites located on the membrane domain of band 3 [Biochem. J. 388 (2005) 343]. Here we report the discovery that reversible binding of extracellular H2DIDS (4, 4′-diisothiocyanatodihydro-2, 2′-stilbenedisulfonate) to the PSD site causes a greater than 5-fold acceleration in the rate of DBDS efflux from pre-loaded MRSG at physiological pH. Pre-labeling all of the PSD sites with H2DIDS inhibited the acceleration effect completely, thus confirming mediation by band 3. Acceleration of DBDS efflux could be mimicked by establishing an externally directed proton gradient (acidic inside, pH 7.4 outside). Under these conditions, addition of extracellular H2DIDS neither accelerated DBDS efflux further nor was proton-induced acceleration inhibited. The results of this paper support the view that the PSD binding site on band 3 is an allosteric regulatory site which is not located on the SD transport pathway. We propose a model where H2DIDS binding to the PSD site modulates activity at the “second” class of sites by raising the pK for transport of DBDS into the physiological pH range. [Copyright &y& Elsevier]

Abstract: In this paper, a generalized JKR model is investigated, in which an elastic cylinder adhesively contacts with an elastic half space and the contact region is assumed to be perfect bonding. An external pulling force is acted on the cylinder in an arbitrary direction. The contact area changes during the pull-off process, which can be predicted using the dynamic Griffith energy balance criterion as the contact edge shifts. Full coupled solution with an oscillatory singularity is obtained and analyzed by numerical calculations. The effect of Dundurs'' parameter on the pull-off process is analyzed, which shows that a nonoscillatory solution can approximate the general one under some conditions, i.e., larger pulling angle ( is the maximum value), smaller or larger nondimensional parameter value of . Relations among the contact half width, the external pulling force and the pulling angle are used to determine the pull-off force and pull-off contact half width explicitly. All the results in the present paper as basic solutions are helpful and applicable for experimenters and engineers. [Copyright &y& Elsevier]

Abstract: Initiation of reverse transcription in retroviruses occurs at a specific point in the viral genome, called the primer-binding site (PBS). The efficiency of reverse transcription initiation is not known. We previously published a paper describing reverse transcription of the retroviral vector S-2PBS containing two PBSs. Reverse transcription of this vector results in a provirus with one of four possible structures, depending, in part, on the PBSs used to initiate reverse transcription. Using Southern blotting analyses of DNA from infected cells, we measured the relative proportions of proviruses with different structures. Although the analysis allowed us to detect multiple initiation events occurring in a single virion, the measurement of frequency of such events was not possible. In this paper, we have built a probability model, which describes the reverse transcription process and predicts the outcomes of different initiation scenarios. By fitting the predicted outcomes to the observed data, we have been able to estimate the initiation efficiency in this system as ∼0.4 initiation per PBS. In addition, we show that even though multiple models of reverse transcription can explain the observed data, all of these models predict approximately the same initiation efficiency. This initiation efficiency is discussed in relation to general replication strategies of retroviruses. [Copyright &y& Elsevier]

Abstract: This paper describes the applicability of in vitro digestion models as a tool for consumer products in (ad hoc) risk assessment. In current risk assessment, oral bioavailability from a specific product is considered to be equal to bioavailability found in toxicity studies in which contaminants are usually ingested via liquids or food matrices. To become bioavailable, contaminants must first be released from the product during the digestion process (i.e. become bioaccessible). Contaminants in consumer products may be less bioaccessible than contaminants in liquid or food. Therefore, the actual risk after oral exposure could be overestimated. This paper describes the applicability of a simple, reliable, fast and relatively inexpensive in vitro method for determining the bioaccessibility of a contaminant from a consumer product. Different models, representing sucking and/or swallowing were developed. The experimental design of each model can be adjusted to the appropriate exposure scenarios as determined by the risk assessor. Several contaminated consumer products were tested in the various models. Although relevant in vivo data are scare, we succeeded to preliminary validate the model for one case. This case showed good correlation and never underestimated the bioavailability. However, validation check needs to be continued. [Copyright &y& Elsevier]

Abstract: We determine conditions under which a random biochemical system is likely to contain a subsystem that is both autocatalytic and able to survive on some ambient ‘food’ source. Such systems have previously been investigated for their relevance to origin-of-life models. In this paper we extend earlier work, by finding precisely the order of catalysation required for the emergence of such self-sustaining autocatalytic networks. This answers questions raised in earlier papers, yet also allows for a more general class of models. We also show that a recently described polynomial-time algorithm for determining whether a catalytic reaction system contains an autocatalytic, self-sustaining subsystem is unlikely to adapt to allow inhibitory catalysation—in this case we show that the associated decision problem is NP-complete. [Copyright &y& Elsevier]

In this paper, we are concerned with a system coupling the parabolic–parabolic Keller–Segel system to the viscous incompressible Navier–Stokes equations in spatial dimensions three, and prove the global existence of solutions with small initial data in critical Besov spaces with minimal regularity order by using the elementary paradifferential calculus and a special type of iteration scheme. [ABSTRACT FROM AUTHOR]

In this paper, the carbon nanotubes (CNTs)-deposited Au film photonic crystal fiber (PCF) surface plasmon resonance (SPR) sensor (CNTs/Au-PCF sensor) and CNTs-deposited Ag film PCF SPR sensor (CNTs/Ag-PCF sensor) were developed and utilized to conduct a series of experiments for the refractive index sensing characteristics study of the CNTs-deposited SPR sensors. The PCF, spliced between two sections of multimode fibers (MMFs), was coated with a metal (Au or Ag) film and then deposited with CNTs for further sensing. CNTs coating can enhance the confined electric field intensity surrounding the sensing layer, making the SPR sensor more sensitive to the changes in the ambient medium. Compared with conventional Au film PCF SPR sensor (Au-PCF sensor), the sensitivity of CNTs/Au-PCF sensor increases by 1016.09 nm/RIU. Compared with conventional Ag film PCF SPR sensor (Ag-PCF sensor), the sensitivity of CNTs/Ag-PCF sensor increases by 709.22 nm/RIU. Therefore, we find that CNTs have a more significant effect on the Au-PCF sensor than the Ag-PCF sensor. The experimental measurements results agreed well with the simulation results. Furthermore, CNTs have high surface-to-volume ratio and extremely excellent biocompatibility. Bovine serum albumin (BSA) was employed as the target analyte to evaluate the feasibility of the CNTs/Au-PCF sensor for the detection of biomolecules, and the sensor exhibits higher sensitivity (8.18 nm/(mg/mL)), lower limit of detection (LOD) (2.5 µg/mL), and faster response time (8 s) than the Au-PCF sensor. Such CNTs-deposited SPR sensors with high sensitivities and fast response present highly promising potential for application in the field of biochemistry. [ABSTRACT FROM AUTHOR]

The orderly formation of the avian feather array is a classic example of periodic pattern formation during embryonic development. Various mathematical models have been developed to describe this process, including Turing/activator-inhibitor type reaction-diffusion systems and chemotaxis/mechanical-based models based on cell movement and tissue interactions. In this paper we formulate a mathematical model founded on experimental findings, a set of interactions between the key cellular (dermal and epidermal cell populations) and molecular (fibroblast growth factor, FGF, and bone morphogenetic protein, BMP) players and a medially progressing priming wave that acts as the trigger to initiate patterning. Linear stability analysis is used to show that FGF-mediated chemotaxis of dermal cells is the crucial driver of pattern formation, while perturbations in the form of ubiquitous high BMP expression suppress patterning, consistent with experiments. Numerical simulations demonstrate the capacity of the model to pattern the skin in a spatial-temporal manner analogous to avian feather development. Further, experimental perturbations in the form of bead-displacement experiments are recapitulated and predictions are proposed in the form of blocking mesenchymal cell proliferation. [ABSTRACT FROM AUTHOR]

In this paper, we report the inactivation of copper containing bovine plasma amine oxidase (BPAO) by a series of saturated alkylamines containing halogen atoms at γ-position, which are 1,1,1-trihalo-3-aminopropane, 1,1,1-trifluoro-2-hydroxy-3-aminopropane, 1,1,1-trichloro-2-hydroxy-3-aminopropane, and 1,1,1-trichloro-2-(2-phenethyloxy)-3-aminopropane . The trihalo-2-hydroxypropylamine analogs exhibited a time-dependent inactivation behavior of BPAO, with 1,1,1-trifluoro-2-hydroxy-3-aminopropane as the most efficient inactivator. The incorporation of a OH group at β-position increased inactivation efficiency by 10-fold within the trifluoro analogs, and the incorporation of a phenethyloxy group at β-position exhibited a higher efficiency by 3-fold within the trichloro analogs based on I 75 values. All four compounds were found to be irreversible inactivators for BPAO. [ABSTRACT FROM AUTHOR]

In addition to direct assessment of high energy phosphorus containing metabolite content within tissues, phosphorus magnetic resonance spectroscopy ( 31 P-MRS) provides options to measure phospholipid metabolites and cellular pH, as well as the kinetics of chemical reactions of energy metabolism in vivo. Even though the great potential of 31 P-MR was recognized over 30 years ago, modern MR systems, as well as new, dedicated hardware and measurement techniques provide further opportunities for research of human biochemistry. This paper presents a methodological overview of the 31 P-MR techniques that can be used for basic, physiological, or clinical research of human skeletal muscle and liver in vivo. Practical issues of 31 P-MRS experiments and examples of potential applications are also provided. As signal localization is essential for liver 31 P-MRS and is important for dynamic muscle examinations as well, typical localization strategies for 31 P-MR are also described. [ABSTRACT FROM AUTHOR]

In this study, an extensive characterisation of food waste (FW) was performed with the aim of studying the relation between FW characteristics and FW treatability through an anaerobic digestion process. In addition to the typological composition (paper, meat, fruits, vegetables contents, etc) and the physicochemical characteristics, this study provides an original characterisation of microbial populations present in FW. These intrinsic populations can actively participate to aerobic and anaerobic degradation with the presence of Proteobacteria and Firmicutes species for the bacteria and of Ascomycota phylum for the fungi. However, the characterisation of FW bacterial and fungi community shows to be a challenge because of the biases generated by the non-microbial DNA coming from plant and by the presence of mushrooms in the food. In terms of relations, it was demonstrated that some FW characteristics as the density, the volatile solids and the fibres content vary as a function of the typological composition. No direct relationship was demonstrated between the typological composition and the anaerobic biodegradability. However, the Pearson's matrix results reveal that the anaerobic biodegradation potential of FW was highly related to the total chemical oxygen demand (tCOD), the total solid content (TS), the high weight organic matter molecules soluble in water (SOL W >1.5 kDa) and the C/N ratio content. These relations may help predicting FW behaviour through anaerobic digestion process. Finally, this study also showed that the storage of FW before collection, that could induce pre-biodegradation, seems to impact several biochemical characteristics and could improve the biodegradability of FW. [ABSTRACT FROM AUTHOR]

This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms. [ABSTRACT FROM AUTHOR]

Prof. Dr. Helmut Sies is a pioneer of “Oxidative Stress”, and has published over 18 papers with the name of “Oxidative Stress” in the title. He has been Editor-in-Chief of the journal “Archives of Biochemistry and Biophysics” for many years, and is a former Editor-in-Chief of the journal “Free Radical Research”. He has clarified our understanding of the causes of chronic developing diseases, and has studied antioxidant factors. In this article, importance of “Oxidative Stress” and our mitochondrial oxidative stress studies; roles of mitochondrial ROS, effects of vitamin E and its homologues in oxidative stress-related diseases, effects of antioxidants in vivo and in vitro , and a mitochondrial superoxide theory for oxidative stress diseases and aging are introduced, and some of our interactions with Helmut are described, congratulating and appreciating his great path. [ABSTRACT FROM AUTHOR]

Mass spectrometry imaging (MSI) is used in an increasing number of biological applications. Typical MSI datasets contain unique, high-resolution mass spectra from tens of thousands of spatial locations, resulting in raw data sizes of tens of gigabytes per sample. In this paper, we review technical progress that is enabling new biological applications and that is driving an increase in the complexity and size of MSI data. Handling such data often requires specialized computational infrastructure, software, and expertise. OpenMSI, our recently described platform, makes it easy to explore and share MSI datasets via the web – even when larger than 50 GB. Here we describe the integration of OpenMSI with IPython notebooks for transparent, sharable, and replicable MSI research. An advantage of this approach is that users do not have to share raw data along with analyses; instead, data is retrieved via OpenMSI's web API. The IPython notebook interface provides a low-barrier entry point for data manipulation that is accessible for scientists without extensive computational training. Via these notebooks, analyses can be easily shared without requiring any data movement. We provide example notebooks for several common MSI analysis types including data normalization, plotting, clustering, and classification, and image registration. [ABSTRACT FROM AUTHOR]

This commentary describes a highly cited paper by Eli Finkelstein, Gerald M. Rosen, and Elmer J. Raukman that appeared in Archives of Biochemistry and Biophysics published in 1980. They reviewed many reports being regularly appearing in the literature describing spin trapping and hydroxyl radicals from various sources and contributed to the development and progress that has been made in oxidative stress research. • Direct detection and identification of short-lived free radical. • Most useful spin trap for the study of oxygen-centered free radical. • Spin trapping of superoxide and hydroxyl radical during oxidative stress. [ABSTRACT FROM AUTHOR]

This paper describes the development of a new bifunctional catalyst system that integrates enzyme and chemical material into a biochemical composite through a stepwise crosslinking approach. The as-prepared biochemical composite not only allows “one-pot” biomass conversion via sequential enzyme-catalyzed hydrolysis of biomass materials to glucose and metal-catalyzed hydrogenation of glucose to sorbitol, but also enables reusability of the catalyst. This design concept facilitates access to fuels and chemicals from the biomass-derived sorbitol and will attract more attention in the foreseeable future. [ABSTRACT FROM AUTHOR]

Cancer invasion, recognised as one of the hallmarks of cancer, is a complex, multiscale phenomenon involving many inter-related genetic, biochemical, cellular and tissue processes at different spatial and temporal scales. Central to invasion is the ability of cancer cells to alter and degrade an extracellular matrix. Combined with abnormal excessive proliferation and migration which is enabled and enhanced by altered cell–cell and cell–matrix adhesion, the cancerous mass can invade the neighbouring tissue. Along with tumour-induced angiogenesis, invasion is a key component of metastatic spread, ultimately leading to the formation of secondary tumours in other parts of the host body. In this paper we explore the spatio-temporal dynamics of a model of cancer invasion, where cell–cell and cell–matrix adhesion is accounted for through non-local interaction terms in a system of partial integro-differential equations. The change of adhesion properties during cancer growth and development is investigated here through time-dependent adhesion characteristics within the cell population as well as those between the cells and the components of the extracellular matrix. Our computational simulation results demonstrate a range of heterogeneous dynamics which are qualitatively similar to the invasive growth patterns observed in a number of different types of cancer, such as tumour infiltrative growth patterns (INF). [ABSTRACT FROM AUTHOR]

The mathematical theory of rigidity of body-bar and body-hinge frameworks provides a useful tool for analyzing the rigidity and flexibility of many articulated structures appearing in engineering, robotics and biochemistry. In this paper we develop a symmetric extension of this theory which permits a rigidity analysis of body-bar and body-hinge structures with point group symmetries. The infinitesimal rigidity of body-bar frameworks can naturally be formulated in the language of the exterior (or Grassmann) algebra. Using this algebraic formulation, we derive symmetry-adapted rigidity matrices to analyze the infinitesimal rigidity of body-bar frameworks with Abelian point group symmetries in an arbitrary dimension. In particular, from the patterns of these new matrices, we derive combinatorial characterizations of infinitesimally rigid body-bar frameworks which are generic with respect to a point group of the form Z / 2Z ×⋯×Z / 2Z. Our characterizations are given in terms of packings of bases of signed-graphic matroids on quotient graphs. Finally, we also extend our methods and results to body-hinge frameworks with Abelian point group symmetries in an arbitrary dimension. [ABSTRACT FROM AUTHOR]

Abstract: Distance-based graph invariants have been of great interest and extensively studied. The classic Wiener index was proposed in biochemistry and defined to be the sum of distances between all pairs of vertices. The sum of distances between all pairs of leaves, named the Gamma index and the terminal Wiener index respectively, was motivated from both biochemistry and phylogenetic reconstruction. The studies of such distance-based graph invariants include, for instance, the “middle part” of a tree, the extremal structures with given constraints, the extremal values of ratios of the distance function at the “middle part” and leaves. In particular, when considering the extremal structures, correlations between the Wiener index and other graph invariants have been discovered and general methods have been developed. Other related graph invariants include the number of subtrees or leaf containing subtrees (corresponding to the “acceptable residue configurations”), subforests, root-containing subtrees (in relation to the antichains in a Hasse diagram with the structure of a rooted tree), to name a few. As has been repeatedly mentioned in earlier works, it is of both mathematical interests and practical importance to generalize the current studies to other distance-based graph invariants. The sum of distances between internal vertices has been considered and many similar results have been obtained. On the other hand, a natural similar concept is the sum of distances between internal vertices and leaves. It has been proposed in different literatures. In this paper we conduct a relatively comprehensive study of this concept, providing results analogous to those of the aforementioned studies. We start with identifying the “middle part” of a tree with respect to the total distance from leaves. Then the extremal ratios with respect to the distance from leaves are examined and the structures achieving the extremal ratios are characterized. Lastly, we provide extremal trees under different constraints that maximize or minimize the sum of all such distances. [Copyright &y& Elsevier]

Comparing and identifying matching metabolites, reactions, and compartments in genome-scale reconstructed metabolic networks can be difficult due to inconsistent naming in different networks. In this paper, we propose metabolite and reaction matching techniques for matching metabolites and reactions in a given metabolic network to metabolites and reactions in another metabolic network. We employ a variety of techniques that include approximate string matching, similarity score functions and multi-step filtering techniques, all enhanced by a set of rules based on the underlying metabolic biochemistry. The proposed techniques are evaluated by an empirical study on four pairs of metabolic networks, and significant accuracy gains are achieved using the proposed metabolite and reaction identification techniques. [ABSTRACT FROM AUTHOR]

Biochemical reaction networks tend to exhibit behaviour on more than one timescale and they are inevitably modelled by stiff systems of ordinary differential equations. Singular perturbation is a well-established method for approximating stiff systems at a given timescale. Standard applications of singular perturbation partition the state variable into fast and slow modules and assume a quasi-steady state behaviour in the fast module. In biochemical reaction networks, many reactants may take part in both fast and slow reactions; it is not necessarily the case that the reactants themselves are fast or slow. Transformations of the state space are often required in order to create fast and slow modules, which thus no longer model the original species concentrations. This paper introduces a layered decomposition, which is a natural choice when reaction speeds are separated in scale. The new framework ensures that model reduction can be carried out without seeking state space transformations, and that the effect of the fast dynamics on the slow timescale can be described directly in terms of the original species. [ABSTRACT FROM AUTHOR]

Abstract: Most adults affected with hereditary hemochromatosis are homozygous for a single point mutation of HFE (p.Cys282Tyr). Apart from the compound heterozygous state for the p.Cys282Tyr mutant and the widespread p.His63Asp variant allele, other rare HFE mutations can be found in trans and may have clinical impact. In the present report we describe the structural and functional consequences of a new mutation, namely the p.Arg226Gly which was inherited in trans with the p.Cys282Tyr allele in a patient affected with a mild iron overload. Because the R226G substitution is located in the vicinity of the normal Cys225S–S282Cys disulfide bond we initially investigated the structure of the variant by molecular dynamics techniques in order to estimate the effect of the mutation on the global structure of HFE domain α3. We found that the solvation free energy, hydrophobicity and formation of salt bridges are slightly modified with the global secondary structure of the α3 domain being conserved. In a previous paper, we demonstrated that the Q283P substitution leads to the loss of the normal Cys225S–S282Cys disulfide bridge. Similar to the Q283P substitution, the R226G substitution does not substitute a residue directly involved in the formation of the disulfide bridge. However, unlike the p.Gln283Pro variant which destroyed the normal disulfide bridge, the R226G mutation does not affect the normal Cys225S–S282Cys bridge. Furthermore based on cell line studies we clearly show that the mutation does not prevent cell surface localization, β2-microglobulin association and binding to transferrin receptor 1. This new compound heterozygous phenotype is very close to those of the C282Y/H63D compound heterozygous patients who display the biochemical hemochromatosis phenotype but with lower body iron stores than C282Y homozygotes. Our results do not exclude unknown genetic and/or metabolic factors that may act synergistically to increase the ferritin level. [Copyright &y& Elsevier]

Abstract: A class of theoretical models seeks to explain rhythmic single cell data by postulating that they are generated by intrinsic noise in biochemical systems whose deterministic models exhibit only damped oscillations. The main features of such noise-induced oscillations are quantified by the power spectrum which measures the dependence of the oscillatory signal's power with frequency. In this paper we derive an approximate closed-form expression for the power spectrum of any monostable biochemical system close to a Hopf bifurcation, where noise-induced oscillations are most pronounced. Unlike the commonly used linear noise approximation which is valid in the macroscopic limit of large volumes, our theory is valid over a wide range of volumes and hence affords a more suitable description of single cell noise-induced oscillations. Our theory predicts that the spectra have three universal features: (i) a dominant peak at some frequency, (ii) a smaller peak at twice the frequency of the dominant peak and (iii) a peak at zero frequency. Of these, the linear noise approximation predicts only the first feature while the remaining two stem from the combination of intrinsic noise and nonlinearity in the law of mass action. The theoretical expressions are shown to accurately match the power spectra determined from stochastic simulations of mitotic and circadian oscillators. Furthermore it is shown how recently acquired single cell rhythmic fibroblast data displays all the features predicted by our theory and that the experimental spectrum is well described by our theory but not by the conventional linear noise approximation. [Copyright &y& Elsevier]

Abstract: The increased production of urban sewage sludge requires alternative methods for final disposal. A very promising choice is the use of sewage sludge as a fertilizer in agriculture, since it is rich in organic matter, macro and micronutrients. However, urban sewage sludge may contain toxic substances that may cause deleterious effects on the biota, water and soil, and consequently on humans. There is a lack of studies evaluating how safe the consumption of food cultivated in soils containing urban sewage sludge is. Thus, the aim of this paper was to evaluate biochemical and redox parameters in rats fed with corn produced in a soil treated with urban sewage sludge for a long term. For these experiments, maize plants were grown in soil amended with sewage sludge (rates of 5, 10 and 20t/ha) or not (control). Four different diets were prepared with the corn grains produced in the field experiment, and rats were fed with these diets for 1, 2, 4, 8 and 12 weeks. Biochemical parameters (glucose, total cholesterol and fractions, triglycerides, aspartate aminotransferase and alanine aminotransferase) as well the redox state biomarkers such as reduced glutathione (GSH), malondialdehyde (MDA), catalase, glutathione peroxidase and butyrylcholinesterase (BuChE) were assessed. Our results show no differences in the biomarkers over 1 or 2 weeks. However, at 4 weeks BuChE activity was inhibited in rats fed with corn grown in soil amended with sewage sludge (5, 10 and 20t/ha), while MDA levels increased. Furthermore, prolonged exposure to corn cultivated in the highest amount per hectare of sewage sludge (8 and 12 weeks) was associated with an increase in MDA levels and a decrease in GSH levels, respectively. Our findings add new evidence of the risks of consuming food grown with urban sewage sludge. However, considering that the amount and type of toxic substances present in urban sewage sludge varies considerably among different sampling areas, further studies are needed to evaluate sludge samples collected from different sources and/or undergoing different types of treatment. [Copyright &y& Elsevier]

Abstract: Hairpin completion is an operation on formal languages that has been inspired by hairpin formation in DNA biochemistry and by DNA computing. In this paper we investigate the one- and two-sided hairpin completion of regular languages. We solve an open problem from the literature by showing that the regularity problem for hairpin completions is decidable. Actually, we show that the problem is decidable in polynomial time if the input is specified by DFAs. Furthermore, we prove that the hairpin completion of regular languages is an unambiguous linear context-free language. Beforehand, it was known only that it is linear context-free. Unambiguity is a strong additional property because it allows to compute the growth function or the topological entropy. In particular, we can compare the growth of the hairpin completion with the growth of the defining regular languages. We show that the growth of the hairpin completion is exponential if and only if the growth of the underlying languages is exponential. Even if both growth functions are exponential, they can be as far apart as for the hairpin completion and for the defining regular languages. However, if the hairpin completion is still regular, then the hairpin completion and its underlying language have essentially the same growth and same topological entropy. [Copyright &y& Elsevier]

Abstract: Biological systems are typically modelled by nonlinear differential equations. In an effort to produce high fidelity representations of the underlying phenomena, these models are usually of high dimension and involve multiple temporal and spatial scales. However, this complexity and associated stiffness makes numerical simulation difficult and mathematical analysis impossible. In order to understand the functionality of these systems, these models are usually approximated by lower dimensional descriptions. These can be analysed and simulated more easily, and the reduced description also simplifies the parameter space of the model. This model reduction inevitably introduces error: the accuracy of the conclusions one makes about the system, based on reduced models, depends heavily on the error introduced in the reduction process. In this paper we propose a method to calculate the error associated with a model reduction algorithm, using ideas from dynamical systems. We first define an error system, whose output is the error between observables of the original and reduced systems. We then use convex optimisation techniques in order to find approximations to the error as a function of the initial conditions. In particular, we use the Sum of Squares decomposition of polynomials in order to compute an upper bound on the worst-case error between the original and reduced systems. We give biological examples to illustrate the theory, which leads us to a discussion about how these techniques can be used to model-reduce large, structured models typical of systems biology. [Copyright &y& Elsevier]

Abstract: For more than a century the simple single-substrate enzyme kinetics model and related Henri-Michaelis–Menten (HMM) rate equation have been thoroughly explored in various directions. In the present paper we are concerned with a possible generalization of this rate equation recently proposed by F. Kargi (BBRC 382 (2009) 157–159), which is assumed to be valid both in the case that the total substrate or enzyme is in excess and the quasi-steady-state is achieved. We demonstrate that this generalization is grossly inadequate and propose another generalization based on application of the quasi-steady-state condition and conservation equations for both enzyme and substrate. The standard HMM equation is derived by (a) assuming the quasi-steady-state condition, (b) applying the conservation equation only for the enzyme, and (c) assuming that the substrate concentration at quasi-steady-state can be approximated by the total substrate concentration [S]0. In our formula the rate is already expressed through [S]0, and we only assume that when quasi-steady-state is achieved the amount of product formed is negligible compared to [S]0. Numerical simulations show that our formula is generally more accurate than the HMM formula and also can provide a good approximation when the enzyme is in excess, which is not the case for the HMM formula. We show that the HMM formula can be derived from our expression by further assuming that the total enzyme concentration is negligible compared to [S]0. [Copyright &y& Elsevier]

Abstract: Due to almost identical chemical properties of C-terminal and side-chain carboxylic groups, selective C-terminal derivatization has been difficult. Although oxazolone-based C-terminal derivatization is the only selective C-terminal modification available, it has not been used widely because of its low derivatization efficiency. In this paper, an improved oxazolone chemistry for incorporation of Br signature to C-terminus is reported. MS/MS analysis of the brominated peptides led to a series of y ions with Br signature, facilitating de novo C-terminal sequencing. [Copyright &y& Elsevier]

Abstract: Deterministic descriptions of three biochemical reaction channels formerly considered by Bratsun et al. (2005) are studied. These descriptions are based on the mass action law and for the simple protein production with delayed degradation differ from that proposed by Bratsun et al. An explicit solution to this model is calculated. For the model of reaction with negative feedback and delayed production, global stability of a unique positive steady state is proved. According to the models of these two reaction channels considered in the present paper there cannot appear delayed induced oscillations. For the model of reaction with negative feedback, dimerisation and delayed protein production, local stability for a unique positive steady state is shown for some range of parameters. It is also proved that for some range of parameters the destabilisation due to the increasing delay can occur and delayed induced oscillations may appear. [Copyright &y& Elsevier]

Abstract: Why the genetic code has a fixed length? Protein information is transferred by coding each amino acid using codons whose length equals 3 for all amino acids. Hence the most probable and the least probable amino acid get a codeword with an equal length. Moreover, the distributions of amino acids found in nature are not uniform and therefore the efficiency of such codes is sub-optimal. The origins of these apparently non-efficient codes are yet unclear. In this paper we propose an a priori argument for the energy efficiency of such codes resulting from their reversibility, in contrast to their time inefficiency. Such codes are reversible in the sense that a primitive processor, reading three letters in each step, can always reverse its operation, undoing its process. We examine the codes for the distributions of amino acids that exist in nature and show that they could not be both time efficient and reversible. We investigate a family of Zipf-type distributions and present their efficient (non-fixed length) prefix code, their graphs, and the condition for their reversibility. We prove that for a large family of such distributions, if the code is time efficient, it could not be reversible. In other words, if pre-biotic processes demand reversibility, the protein code could not be time efficient. The benefits of reversibility are clear: reversible processes are adiabatic, namely, they dissipate a very small amount of energy. Such processes must be done slowly enough; therefore time efficiency is non-important. It is reasonable to assume that early biochemical complexes were more prone towards energy efficiency, where forward and backward processes were almost symmetrical. [Copyright &y& Elsevier]

Abstract: Regulatory relations between biological molecules constitute complex network systems and realize diverse biological functions through the dynamics of molecular activities. However, we currently have very little understanding of the relationship between the structure of a regulatory network and its dynamical properties. In this paper we introduce a new method, named “linkage logic” to analyze the dynamics of network systems. By this method, we can restrict possible steady states of a given complex network system from the knowledge of regulatory linkages alone. The regulatory linkage simply specifies the list of variables that affect the dynamics of each variable. We formalize two aspects of the linkage logic: the “Principle of Compatibility” determines the upper limit of the diversity of possible steady states of the dynamics realized by a given network; the “Principle of Dependency” determines the possible combinations of states of the system. By combining these two aspects, (i) for a given network, we can identify a cluster of nodes that gives an alternative representation of the steady states of the whole system, (ii) we can reduce a given complex network into a simpler one without loss of the ability to generate the diversity of steady states, (iii) we can examine the consistency between the structure of network and observed set of steady states, and (iv) sometimes we can predict unknown states or unknown regulations from an observed set of steady states alone. We illustrate the method by several applications to an experimentally determined regulatory network for biological functions. [ABSTRACT FROM AUTHOR]

Abstract: The primary obstacle to de novo protein structure prediction is conformational sampling: the native state generally has lower free energy than nonnative structures but is exceedingly difficult to locate. Structure predictions with atomic level accuracy have been made for small proteins using the Rosetta structure prediction method, but for larger and more complex proteins, the native state is virtually never sampled, and it has been unclear how much of an increase in computing power would be required to successfully predict the structures of such proteins. In this paper, we develop an approach to determining how much computer power is required to accurately predict the structure of a protein, based on a reformulation of the conformational search problem as a combinatorial sampling problem in a discrete feature space. We find that conformational sampling for many proteins is limited by critical “linchpin” features, often the backbone torsion angles of individual residues, which are sampled very rarely in unbiased trajectories and, when constrained, dramatically increase the sampling of the native state. These critical features frequently occur in less regular and likely strained regions of proteins that contribute to protein function. In a number of proteins, the linchpin features are in regions found experimentally to form late in folding, suggesting a correspondence between folding in silico and in reality. [Copyright &y& Elsevier]

Abstract: We consider the chemotaxis system in a smooth bounded domain , where and g generalizes the logistic function with , and . A concept of very weak solutions is introduced, and global existence of such solutions for any nonnegative initial data is proved under the assumption that . Moreover, boundedness properties of the constructed solutions are studied. Inter alia, it is shown that if b is sufficiently large and has small norm in for some then the solution is globally bounded. Finally, in the case that additionally holds, a bounded set in can be found which eventually attracts very weak solutions emanating from arbitrary initial data. The paper closes with numerical experiments that illustrate some of the theoretically established results. [Copyright &y& Elsevier]

Abstract: A novel class of isotope-coded affinity tag is proposed possessing a fluorescent feature, referred to as fluorescent isotope-coded affinity tag (FCAT), to provide a new tool for quantitative proteomics. The label is designed to bind cysteine containing proteins or peptides. The FCAT reagent comprises four functional elements: a specific chemical reactivity group toward sulfhydryl groups; a linker that can incorporate the stable isotopes; a hydroxymethylbenzoic residue (base labile group) to cleave off a large part of the label before MS analysis; and a fluorescent tag for absolute quantification. The fluorescent part of the tag is also planned to be utilized to isolate the FCAT-labeled peptides via antibody based pull-down method. In this paper, we report on the solid phase organic synthesis of the light isotope containing FCAT molecule. The new labeling reagent showed good reactivity with model cysteine containing peptides. The fluorophore group was also effectively cleaved off from the labeled products to accommodate easier MS based analysis. [Copyright &y& Elsevier]

Abstract: In this paper, a DSC and Raman study of hydrated multilamellar DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) and DMPE (1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine) liposomes in presence of increasing amounts of DDT is reported. The observed changes denote that DDT molecules interact with both phospholipids and that the interaction mainly involves the external part of the bilayer since the deep penetration into the hydrophobic core is prevented by the setting up of polar interactions between the three aliphatic C–Cl bonds of the trichloro group of DDT and the –N+(CH3)3 of DMPC or the –NH3 + groups of DMPE molecules. This behaviour was particularly evidenced in presence of DMPE, as the insertion of DDT molecules into the central part of the bilayer seems to be completely excluded. Moreover, in DMPE liposomes the overall structure of the bilayer changes to a well defined and structured ‘phase II’ in presence of even small DDT amounts. [Copyright &y& Elsevier]

Abstract: We develop the theory of biphasic somatic growth in fish using models based on the distinction between pre- and post-maturation growth and an explicit description of energy allocation within a growing season. We define a ‘generic biphasic’ (GB) model that assumes post-maturation growth has a von Bertalanffy (vB) form. For this model we derive an explicit expression for the gonad weight/somatic weight ratio (g) which may either remain fixed or vary with size. Optimal biphasic models are then developed with reproductive strategies that maximise lifetime reproductive output. We consider two optimal growth models. In the first (fixed g optimal), gonad weight is constrained to be proportional to somatic weight. In the second (variable g optimal) model, allocation to reproduction is unconstrained and g increases with size. For the first of these two models, adult growth in a scaled measure of length has the exact vB form. When there are no constraints on allocation, growth is vB to a very good approximation. In both models, pre-maturation growth is linear. In a companion paper we use growth data from lake trout (Salvelinus namaycush) to test the bioenergetics assumptions used to develop these models, and demonstrate that they have advantages over the vB model, both in quality of fit, and in the information contained in the fitted parameters. [Copyright &y& Elsevier]

Abstract: The standard mathematical model for stepwise “slow-binding” enzyme inhibition assumes that the initial enzyme–inhibitor complex is always at equilibrium with the free component species and . This assumption implies that the dissociation rate constant is infinitely higher than the isomerization rate constant for . This paper presents a more general mathematical treatment, under the steady state approximation rather than the usual rapid-equilibrium approximation, whereby the two rate constants for the disappearance of are allowed to be comparable in magnitude. Experimentally relevant illustrative examples include discrimination between a single-step and a two-step mechanism for slow-binding inhibition kinetics. [Copyright &y& Elsevier]

Abstract: Functioning as an “address tag” that directs nascent proteins to their proper cellular and extracellular locations, signal peptides have become a crucial tool in finding new drugs or reprogramming cells for gene therapy. To effectively and timely use such a tool, however, the first important thing is to develop an automated method for rapidly and accurately identifying the signal peptide for a given nascent protein. With the avalanche of new protein sequences generated in the post-genomic era, the challenge has become even more urgent and critical. In this paper, we have developed a novel method for predicting signal peptide sequences and their cleavage sites in human, plant, animal, eukaryotic, Gram-positive, and Gram-negative protein sequences, respectively. The new predictor is called Signal-3L that consists of three prediction engines working, respectively, for the following three progressively deepening layers: (1) identifying a query protein as secretory or non-secretory by an ensemble classifier formed by fusing many individual OET-KNN (optimized evidence-theoretic K nearest neighbor) classifiers operated in various dimensions of PseAA (pseudo amino acid) composition spaces; (2) selecting a set of candidates for the possible signal peptide cleavage sites of a query secretory protein by a subsite-coupled discrimination algorithm; (3) determining the final cleavage site by fusing the global sequence alignment outcome for each of the aforementioned candidates through a voting system. Signal-3L is featured by high success prediction rates with short computational time, and hence is particularly useful for the analysis of large-scale datasets. Signal-3L is freely available as a web-server at http://chou.med.harvard.edu/bioinf/Signal-3L/ or http://202.120.37.186/bioinf/Signal-3L, where, to further support the demand of the related areas, the signal peptides identified by Signal-3L for all the protein entries in Swiss-Prot databank that do not have signal peptide annotations or are annotated with uncertain terms but are classified by Signal-3L as secretory proteins are provided in a downloadable file. The large-scale file is prepared with Microsoft Excel and named “Tab-Signal-3L.xls”, and will be updated once a year to include new protein entries and reflect the continuous development of Signal-3L. [Copyright &y& Elsevier]

Abstract: Urocortin (UCN) and corticotropin-releasing factor (CRF) are members of CRF family. Though CRF is mainly distributed in central nervous system (CNS), UCN has been reported to play biologically diverse roles in several systems such as cardiovascular, respiratory, digestive, reproductive, stress, immunologic system, etc. UCN and CRF bind to two known receptors, CRFR1 and CRFR2, to function. Both CRF receptors are distributed in CNS and periphery tissues, and their expression in cancer tissues has been reported. Now there are many documents indicating UCN/CRF play an important role in the regulation of carcinogenesis. There is also evidence indicating UCN/CRF have anticancer effects via CRFRs. This paper will review the effects of CRF family in cancers. [Copyright &y& Elsevier]

Bioavailability considerations are one of the tools for a proper assignment of sites potentially and actually at risk as it allows assessing both the extent (hazard) and probability (risk) of adverse effects. In this paper, bioavailability considerations are linked to physico-chemical methods available for assessing metal fractions in soils. The focus of the overview is on empirical methods for extraction of metals from soils as a surrogate for the metal-, species-and soil-type-dependent bioavailable and bioaccessible metal pools. This cumulates in a generalized flow chart for monitoring of metals in soils. In support of the general monitoring strategy, examples are given of successful applications of analytical methods for predicting metal uptake by plants and animals, for assessing the origin of metals in soils, as well as the leaching potential of soils and the extent of soil contamination. It is concluded that a large arrays of chemical assessment methodologies for metal speciation in solid and liquid soil phases are available. As most assessment methodologies are operationally defined instead of being functionally defined, examples of mechanistically based monitoring approaches of bioavailability are still scarce. The value of the methods for measuring bioavailability can be significantly improved when the species, metal, and soil specific aspects of bioavailability are more accurately taken into account in the design of chemical simulation methodologies. [Copyright &y& Elsevier]

Abstract: Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach, i.e. by using available biomolecules. This type of synthetic approach has so far been only partially successful, and appropriate models of the synthetic protocell cycle might be needed to guide future experiments. In this paper, we present a simple biochemically and physically feasible model of cell replication involving a discrete semi-permeable vesicle with an internal minimal metabolism involving two reactive centers. It is shown that such a system can effectively undergo a whole cell replication cycle. The model can be used as a basic framework to model whole protocell dynamics including more complex sets of reactions. The possible implementation of our design in future synthetic protocells is outlined. [Copyright &y& Elsevier]

Abstract: Environmental dispersion and transformation of mercury discharged from gold mining operations has been investigated in field and laboratory studies in order to provide better understanding of the degree of mercury (Hg) pollution and bioavailability in the Lake Victoria goldfields (LVGF) ecosystems. This paper reviews results already published elsewhere and presents additional data on Hg dynamics in the LVGF. Studies conducted at the Mugusu and Rwamagaza artisanal mines indicated different degrees of Hg contamination and dispersion in environmental matrices. Mercury concentration in contaminated river sediments near the Mugusu mine varied from 6.0 to 0.5mg/kg on a dry weight basis. The highest Hg contamination levels (165–232mg/kg) were associated with mine tailings at the Rwamagaza mine. Mercury concentrations in fish representing different dietary habits on the southwestern shore of Lake Victoria at the Nungwe Bay were very low (2–35μg/kg) and thought to represent background levels. These and other results suggested that the use of Hg in gold extraction in the LVGF has not caused high Hg levels in lake fish. The study of Hg in lichens showed Parmelia lichen to be an effective bioindicator for atmospheric Hg contamination due to Hg emissions from gold-amalgam firing and purification operations. The Hg levels in the lichens around the Mugusu mine ranged from 3.1 to 0.1μg/g; the highest levels were recorded in the lichens sampled close to gold-amalgam processing sites. The regional background level in the Parmelia lichen was 0.05–0.10μg/g, with a mean level of 0.07μg/g. Studies of Hg transformation in the mine tailings revealed unexpectedly high methylmercury (MeHg) levels in the tailings (629–710ng/g), which indicated that oxidation and methylation of metallic Hg in the tailings occurred at significant levels under tropical conditions. Re-equilibration of the tailings with freshwater (FW) indicated the MeHg was firmly bound in the tailings and therefore very little MeHg was released to the water column (0.2–1.5ng/L). The methylation of Hg in tropical loamy clay soil contaminated with HgCl2 (5mgHg/kg) yielded MeHg concentrations of 11 and 14ng/g when inundated with seawater and FW, respectively, for 4 weeks. Little MeHg was transferred from the soil to the equilibrated water (⩽0.4ng/L). Atmospheric exposure of the soil pre-inundated with FW resulted in net degradation of MeHg during the 1st week of exposure, followed by net production and accumulation of MeHg in the soil (up to 15.5ng/g) during atmospheric desiccation. Mercury uptake by fish from the Hg0-contaminated aquatic sediment–tailings system in the aquarium experiment was found to be low, suggesting the low availability of MeHg for bioaccumulation in the system. These and other results provide useful insights into Hg transformation, mobility and bioavailability in tropical aquatic systems affected by Hg pollution from gold mining operations. [Copyright &y& Elsevier]