Towards an Integrated Ecosystem-Based Bioaccumulation and Metal Speciation Model

Heavy metal bioaccumulation models are important for interpreting water quality data, predicting bioaccumulation in organisms, and investigating the provenance of contaminants. To date they have been predominantly used as single-issue models, under steady-state conditions and in isolation of the biogeochemical processes that control metal bioaccumulation. Models that incorporate these processes would allow a more holistic approach to bioaccumulation modeling and contaminant assessment; however, this has been rarely undertaken, probably because it requires the integration of inter-disciplinary areas. In this study, we have developed such a model that integrates three key multi-disciplinary areas (biological, metal speciation, and bioaccumulation processes) and responds to variations in temporal external and internal forcing. Furthermore, spatial context is provided by developing the model within a simple hydrodynamic box-modeling framework. The calibrated model was able to predict with reasonable accuracy the temporal and spatial trends of soft-tissue copper bioaccumulation in a coastal oyster. This exploratory model was also used to highlight the importance of phytoplankton as an important vector of copper uptake dynamics by an oyster, therefore reinforcing the importance of the integrated approach. Finally, our model provides a framework for greater application beyond this specific example such as in the areas of waterway restoration, which has been shown to be an important area of ecological and environmental research.     

Emerging mechanisms for heavy metal transport in plants

Heavy metal ions such as Cu(2+), Zn(2+), Mn(2+), Fe(2+), Ni(2+) and Co(2+) are essential micronutrients for plant metabolism but when present in excess, these, and non-essential metals such as Cd(2+), Hg(2+) and Pb(2+), can become extremely toxic. Thus mechanisms must exist to satisfy the requirements of cellular metabolism but also to protect cells from toxic effects. The mechanisms deployed in the acquisition of essential heavy metal micronutrients have not been clearly defined although a number of genes have now been identified which encode potential transporters. This review concentrates on three classes of membrane transporters that have been implicated in the transport of heavy metals in a variety of organisms and could serve such a role in plants: the heavy metal (CPx-type) ATPases, the natural resistance-associated macrophage protein (Nramp) family and members of the cation diffusion facilitator (CDF) family. We aim to give an overview of the main features of these transporters in plants in terms of structure, function and regulation drawing on information from studies in a wide variety of organisms.     

Isolation of the exoelectrogenic bacterium Ochrobactrum anthropi YZ-1 by using a U-tube microbial fuel cell

Exoelectrogenic bacteria have potential for many different biotechnology applications due to their ability to transfer electrons outside the cell to insoluble electron acceptors, such as metal oxides or the anodes of microbial fuel cells (MFCs). Very few exoelectrogens have been directly isolated from MFCs, and all of these organisms have been obtained by techniques that potentially restrict the diversity of exoelectrogenic bacteria. A special U-tube-shaped MFC was therefore developed to enrich exoelectrogenic bacteria with isolation based on dilution-to-extinction methods. Using this device, we obtained a pure culture identified as Ochrobactrum anthropi YZ-1 based on 16S rRNA gene sequencing and physiological and biochemical characterization. Strain YZ-1 was unable to respire using hydrous Fe(III) oxide but produced 89 mW/m(2) using acetate as the electron donor in the U-tube MFC. Strain YZ-1 produced current using a wide range of substrates, including acetate, lactate, propionate, butyrate, glucose, sucrose, cellobiose, glycerol, and ethanol. Like another exoelectrogenic bacterium (Pseudomonas aeruginosa), O. anthropi is an opportunistic pathogen, suggesting that electrogenesis should be explored as a characteristic that confers advantages to these types of pathogenic bacteria. Further applications of this new U-tube MFC system should provide a method for obtaining additional exoelectrogenic microorganisms that do not necessarily require metal oxides for cell respiration.     

Effect of copper and lead on lipid metabolism in bryophytes and lichens

Bryophytes and lichens have a widespread occurrence and can survive under extreme environmental conditions, such as drought, low temperatures, continuous light or prolonged darkness. It has been shown that lipid metabolism is sensitive to both metal response and metal resistance mechanisms in many organisms, including yeast, Silene cucubalus, and in the marine brown algae Fucus spp. and Ascophyllum nodosum. In the present study, the effects of lead and copper on lipid metabolism have been studied in two moss species, Rhytidiadelphus squarrosus and Dicranum scoparium, and also in the lichen Peltigera horizontalis with a cyanobacterial Nostoc photobiont.     

Evolution of catalytic proteins

Summary It is believed that all present-day organisms descended from a common cellular ancestor. Such a cell must have evolved from more primitive and simpler precursors, but neither their organization nor the route such evolution took are accessible to the molecular techniques available today. We propose a mechanism, based on functional properties of enzymes and the kinetics of growth, which allows us to reconstruct the general course of early enzyme evolution. A precursor cell containing very few multifunctional enzymes with low catalytic activities is shown to lead inevitably to descendants with a large number of differentiated monofunctional enzymes with high turnover numbers. Mutation and natural selection for faster growth are shown to be the only conditions necessary for such a change to have occurred.     

Molding mineral within microporous hydrogels by a polymer-induced liquid-precursor (PILP) process

Natural biominerals often have exquisite morphologies, where the cells exercise a high degree of crystallographic control through secretion of biological macromolecules and regulation of ion transport. One important example is the sea urchin spine. It has recently been shown to be formed through deposition of a transient amorphous calcium carbonate (ACC) precursor phase that later transforms to single-crystalline calcite, ultimately forming an elaborate three-dimensional microporous calcium carbonate structure with interconnected pores. Macromolecules associated with the mineral phase are thought to play a key role in regulating this transformation. The work described here mimics this type of morphological control by "molding" an amorphous calcium carbonate precursor within a porous poly(2-hydroxyethyl methacrylate) (PHEMA) hydrogel that has been prepared as a negative replica from the void space of an urchin spine. Using an acidic biomimetic polymer as a process-directing agent, we show that polyaspartic acid induces amorphous calcium carbonate (ACC) nanoparticles, which have fluidic character and therefore are able to infiltrate the PHEMA hydrogel replica and coalesce into the convoluted morphology that replicates the original microporous structure of the sea urchin spine. By "molding" calcium carbonate into a complex morphology at room temperature, using a precursor process that is induced by a biomimetic acidic macromolecule, the PILP process is a useful in vitro model for examining different aspects of the amorphous-to-crystalline transformation process that is apparently used by a variety of biomineralizing organisms. For example, although we were able to replicate the overall morphology of the spine, it had polycrystalline texture; further studies with this system will focus on controlling the nucleation event, which may help to elucidate how such a convoluted structure can be prepared with single-crystalline texture via an amorphous precursor. Through a better understanding of the mechanisms used by organisms to regulate crystal properties, such biomimetic processes can lead to the synthesis of materials with superior electronic, mechanical, and optical properties.     

Nanoparticles in Biological Hydrogen Production: An Overview

Biological hydrogen (H₂) production enhancement through the use of nanoparticles (NPs) supplement in the media is being recognized as a promising approach. The NPs, including those of metal and metal oxides have shown a significant improvement in the BHP. A number of organisms as pure or mixed cultures can produce H₂ in presence of NPs from pure sugars and biowaste as a feed. However, their H₂ production efficiencies have been found to vary significantly with the type of NPs and their concentration. In this review article, the potential role of NPs in the enhancement of H₂ production has been assessed in dark- and photo-fermentative organisms using sugars and biowaste materials as feed. Further, the integrative approaches for commercial applications of NPs in BHP have been discussed.     

Experimental approaches to identify non-coding RNAs

Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until recent genome-wide searches discovered thousands of these molecules and their genes in a variety of model organisms. Some of these screens were based on biocomputational prediction of ncRNA candidates within entire genomes of model organisms. Alternatively, direct biochemical isolation of expressed ncRNAs from cells, tissues or entire organisms has been shown to be a powerful approach to identify ncRNAs both at the level of individual molecules and at a global scale. In this review, we will survey several such wet-lab strategies, i.e. direct sequencing of ncRNAs, shotgun cloning of small-sized ncRNAs (cDNA libraries), microarray analysis and genomic SELEX to identify novel ncRNAs, and discuss the advantages and limits of these approaches.     

Role of cytosolic factors in the transport of proteins across membranes

In a review article published in 1986 we emphasized that an unfolded conformation is a prerequisite for the transport of precursor proteins across membranes, and that cytosolic factors exist whose function is to maintain what we termed the transport-competent conformation of precursor proteins. Subsequent observations in a number of different in vitro systems related both the competent conformation and the cytosolic factors to the recent observations on the ATP-requirements for protein transport. Here we review the currently available data on such factors, and their ATP-requirements, for prokaryotic as well as eukaryotic organisms. Furthermore, we discuss possible models for their action and relate them to the so-called molecular chaperones. These were originally defined as being involved in the proper folding and assembly of oligomeric protein complexes, but have since been shown in addition to facilitate the transport of proteins across membranes.     

金属结合蛋白基因及其在清除重金属污染中的应用

一些微生物和植物由于对毒性金属具有独特的抗性机制,使得利用它们来清除日益严重的环境污染已发展成为一种十分有效的技术——生物修复。研究表明,不同的金属结合蛋白（如MT 和PC）,在生物忍耐和降解过量重金属毒性机制中起重要作用。愈来愈多的MT 和PC基因被克隆,并已成功地应用于生物遗传转化,这些转基因生物在清除重金属污染方面已显示出潜在的应用价值。 Abstract:Heavy metal pollution has become a global environmental hazard.The use of microorganisms and plants for the decontamination of heavy metals is recognized as a low lost and high efficiency method for cleaning up metal contamination.It shows that various metal-binding proteins such as metallothioneins (MTs) or phytochelatines (PCs) play an important role in defense systems and detoxification to heavy metals in organisms.Many genes of MTs and PCs have been cloned and utilized successfully in genetically modified bacteria and plants for increasing remediation capacity.These transgenic organisms have been displayed a great potential in bioremediation and phytoremediation of heavy metals.     

Ironing out the distribution of [2Fe-2S] motifs in ferrochelatases

Heme, a near ubiquitous cofactor, is synthesized by most organisms. The essential step of insertion of iron into the porphyrin macrocycle is mediated by the enzyme ferrochelatase. Several ferrochelatases have been characterized, and it has been experimentally shown that a fraction of them contain [2Fe-2S] clusters. It has been suggested that all metazoan ferrochelatases have such clusters, but among bacteria, these clusters have been most commonly identified in Actinobacteria and a few other bacteria. Despite this, the function of the [2Fe-2S] cluster remains undefined. With the large number of sequenced genomes currently available, we comprehensively assessed the distribution of putative [2Fe-2S] clusters throughout the ferrochelatase protein family. We discovered that while rare within the bacterial ferrochelatase family, this cluster is prevalent in a subset of phyla. Of note is that genomic data show that the cluster is not common in Actinobacteria, as is currently thought based on the small number of actinobacterial ferrochelatases experimentally examined. With available physiological data for each genome included, we identified a correlation between the presence of the microbial cluster and aerobic metabolism. Additionally, our analysis suggests that Firmicute ferrochelatases are the most ancient and evolutionarily preceded the Alphaproteobacterial precursor to eukaryotic mitochondria. These findings shed light on distribution and evolution of the [2Fe-2S] cluster in ferrochelatases and will aid in determining the function of the cluster in heme synthesis.     

From heavy metal‐binders to biosensors: Ciliate metallothioneins discussed

Metallothioneins (MTs) are ubiquitous proteins with the capacity to bind heavy metal ions (mainly Cd, Zn or Cu), and they have been found in animals, plants, eukaryotic and prokaryotic micro‐organisms. We have carried out a comparative analysis of ciliate MTs (Tetrahymena species) to well‐known MTs from other organisms, discussing their exclusive features, such as the presence of aromatic amino acid residues and almost exclusive cysteine clusters (CCC) present in cadmium‐binding metallothioneins (CdMTs), higher heavy metal‐MT stoichiometry values, and a strictly conserved modular–submodular structure. Based on this last feature and an extensive gene duplication, we propose a possible model for the evolutionary history of T. thermophila MTs. We also suggest possible functions for these MTs from consideration of their differential gene expressions and discuss the potential use of these proteins and/or their gene promoters for designing molecular or whole‐cell biosensors for a fast detection of heavy metals in diverse polluted ecosystems.     

Multiple mechanisms controlling carbon metabolism in bacteria

Catabolite repression is a universal phenomenon, found in virtually all living organisms. These organisms range from the simplest bacteria to higher fungi, plants, and animals. A mechanism involving cyclic AMP and its receptor protein (CRP) in Escherichia coli was established years ago, and this mechanism has been assumed by many to serve as the prototype for catabolite repression in all organisms. However, recent studies have shown that this mechanism is restricted to enteric bacteria and their close relatives. Cyclic AMP-independent mechanisms of catabolite repression occur in other bacteria, yeast, plants, and even E. coli. In fact, single-celled organisms such as E. coli, Bacillus subtilis, and Saccharomyces cerevisiae exhibit multiple mechanisms of catabolite repression, and most of these are cyclic AMP-independent. The mechanistic features of the best of such characterized processes are briefly reviewed, and references are provided that will allow the reader to delve more deeply into these subjects.     

Progress in Studies of Plant Homologs of Mitogen-Activated Protein (MAP) Kinase and Potential Upstream Components in Kinase Cascades

Mitogen-activated protein (MAP) kinase cascades were originally identified as protein phosphorylation systems that control the division and the growth of yeast and animal cells. Such cascades consist of MAP kinases, MAP-kinase kinases, and MAP-kinase-kinase kinases. In addition, these organisms have been also shown to have structurally related but functionally different MAP kinase cascades, which are involved in various cellular processes such as a response to osmotic stress and apoptosis. Plants also have been shown to have a number of members of each kinase family. Although physiological and genetic functions of most plant members have yet to be established, some of members have been shown to be responsible for the cellular transmission of signals generated by wounding or a mechanical stress, which predicts that MAP kinase cascades may function in a variety of physiological processes in the plant cells. In the present review, we summarize recent progresses of researches on plant members of each kinase family as well as those of analyses of the cascades in other organisms.     

Hydrolysis of carbohydrates in roach (Rutilus rutilus (L.)) at different levels of mercury accumulation

It has been shown that chronic exposure to dietary mercury results in the intensive accumulation of this metal in roach yearlings. The concentrations of accumulated mercury in their organisms were proportional to the amount of metal added to water of experimental tanks. Increased Hg content in the organisms (0.05–0.16 mg/kg) of developing juvenile roaches decreases the activity of digestive carbohydrases and the affinity of enzymes to substrate with subsequent retardation of rates of initial stages of digestion. The accumulation of mercury in the organism is accompanied by an increase in the body length and weight in the exposed fish compared to the control. The possible mechanisms responsible for such an increase in fish with high Hg body burdens, and with a simultaneous decrease in carbohydrate metabolism rate, are discussed in the paper.     

Molecular basis of active copper resistance mechanisms in Gram-negative bacteria

Copper is a metallic element that is crucial for cell metabolism; however, in extended concentrations, it is toxic for all living organisms. The dual nature of copper has forced organisms, including bacteria, to keep a tight hold on cellular copper content. This challenge has led to the evolution of complex mechanisms that on one hand enable them to deliver the essential element and on the other to protect cells against its toxicity. Such mechanisms have been found in both eukaryotic and prokaryotic cells. In bacteria a number of different systems such as extra- and intracellular sequestration, enzymatic detoxification, and metal removal from the cell enabling them to survive in the presence of high concentration of copper have been identified. Gram-negative bacteria, due to their additional compartment, need to deal with both cytoplasmic and periplasmic copper. Therefore, these bacteria have evolved intricate and precisely regulated systems which interact with each other. In this review the active mechanisms of copper resistance at their molecular level are discussed.     

Update of microbial genome programs for bacteria and archaea

Since the Haemophilus influenzae genome sequence was completed in 1995, 172 other prokaryotic genomes have been completely sequenced, while 508 projects are underway. Besides pathogens, organisms important in several other fields, such as biotechnology and bioremediation, have also been sequenced. Institutions choose the organisms they wish to sequence according to the importance that these species represent to them, the availability of the microbes, and based on the similarity of a species of interest with others that have been sequenced previously. Improvements in sequencing techniques and in associated methodologies have been achieved; however, scientists need to continue working on the development of this field. In Brazil, a multicentered, centrally coordinated and research-focused network was adopted and successfully used for the sequencing of several important organisms. We analyzed the current status of microbial genomes, the trends for criteria used to choose new sequencing projects, the future of microbial sequencing, and the Brazilian genome network.     

Effects of Metal Mixtures on Aquatic Biota: A Review of Observations and Methods

A brief review of the historical development of metal mixture interaction analyses is presented. The two major classifications of mixture models are outlined, the “Concentration Addition” and the “Response Addition” approaches. Within these two categories, a number of graphical, mathematical and statistical methods have been used, such as the toxic unit approach, relative potencies, toxicity equivalence factors, and dose-response relationships that have been described using several methods such as probit, logit, and regression analyses. A database was generated to evaluate the frequency of occurrence of less than additive, strictly additive, and more than additive responses to metal mixture effects reported in the literature. The three responses occurred at 43, 27, and 29%, respectively. The database is available electronically from the lead author. The research required to determine the most appropriate methods to quantify the effects of metal mixtures in an ecological risk assessment (ERA) framework is discussed. Until this research is completed, ERAs should use existing models such as the toxic unit or the effects addition approach. Bioaccumulation measurements by organisms for which the accumulation to response relationship is known would also be a useful complement.     

The effect of process parameters on the Liquid Flame Spray generated titania nanoparticles

Nanoparticles have become important in many applications. It is essential to be able to control the particle size because the properties of nanoparticles change dramatically with particle size. An efficient way to generate nanoparticles is via aerosol processes. In this study we used Liquid Flame Spray consisting of liquid precursor droplets sprayed into a high-speed hydrogen/oxygen flame where they evaporate, vapours react and nucleate to form titania nanoparticles. Using flame methods, also dopants and sensitizers can easily be introduced in order to, e.g. improve the photocatalytic activity of the nanomaterial. To obtain a practical guideline in order to tailor the final nanoparticle size in the process, we have systematically studied the effects of different process parameters on the particle size of titania. Titania is used, e.g. as a photocatalyst, and then both particle size and crystal structure are important when looking at the efficiency. In this work, the generated nanoparticle size has been measured by aerosol instrumentation and the particle morphology has been verified with transmission electron microscopy. In Liquid Flame Spray method, there are several adjustable parameters such as precursor feed rate into the flame; concentration of the precursor; precursor material itself as well as solvent used in the precursor; mass flow of combustion gases and also the mechanical design of the torch used. We used metal organic based titanium precursors in alcohol solvents, predominantly ethanol and 2-propanol. Large differences in particle production between the precursors were found. Differences could also be seen for various solvents. As for precursor feed in the flame, the more mass is introduced the larger the nanoparticles are, i.e. precursor concentration and precursor feed rate have an impact on particle size. A similar phenomenon can be discovered for the combustion gas flow rates. Torch design also plays an important role in controlling the particle size.