Liming to remediate Ni contaminated soils with diverse properties and a wide range of Ni concentration

Historic emissions from a Ni refinery at Port Colborne, Ontario, caused Ni contamination of regional soils and raised concerns about potential Ni phytotoxicity. Previous tests revealed that if these soils were made alkaline and fertilized with Mn and other common nutrients as needed to maintain fertility of such alkaline soils, full remediation (prevention of Ni phytotoxicity) would be obtained. This experiment was conducted to test this method of remediation on diverse soils from Port Colborne, and to evaluate chemical extraction tests which would be predictive of plant uptake and potential for Ni phytotoxicity in Ni-contaminated soils. Ten soils with varied levels of Ni contamination and varied soil properties were amended with limestone or nitric acid to raise or lower pH so that a wide pH range could be examined for the soils. For lower Ni organic and mineral soils near the Ontario remediation limit (200 mg/kg), neither crop suffered Ni phytotoxicity at any pH tested. Only when more highly contaminated soils were strongly acidic did Ni phytotoxicity occur. Phytotoxic soils were fully remediated by making soils alkaline even for these Ni-sensitive crop species. Only the most contaminated organic soil remained slightly toxic – but this soil was remarkably contaminated (over 1.1% of Ni). The Sr nitrate extraction method was much more effective in predicting plant Ni concentrations than the DTPA method. This test provides an inexpensive soil extraction result highly predictive of potential for Ni phytotoxicity across soils.     

Design and engineering of E. coli metabolic sensor strains with a wide sensitivity range for glycerate

Microbial biosensors are used to detect the presence of compounds provided externally or produced internally. The latter case is commonly constrained by the need to screen a large library of enzyme or pathway variants to identify those that can efficiently generate the desired compound. To address this limitation, we suggest the use of metabolic sensor strains which can grow only if the relevant compound is present and thus replace screening with direct selection. We used a computational platform to design metabolic sensor strains with varying dependencies on a specific compound. Our method systematically explores combinations of gene deletions and identifies how the growth requirement for a compound changes with the media composition. We demonstrate this approach by constructing a set of E. coli glycerate sensor strains. In each of these strains a different set of enzymes is disrupted such that central metabolism is effectively dissected into multiple segments, each requiring a dedicated carbon source. We find an almost perfect match between the predicted and experimental dependence on glycerate and show that the strains can be used to accurately detect glycerate concentrations across two orders of magnitude. Apart from demonstrating the potential application of metabolic sensor strains, our work reveals key phenomena in central metabolism, including spontaneous degradation of central metabolites and the importance of metabolic sinks for balancing small metabolic networks.     

Fabrication of a glucose sensor based on a novel nanocomposite electrode

The direct electrocatalytic oxidation of glucose in alkaline medium at nanoscale nickel hydroxide modified carbon ionic liquid electrode (CILE) has been investigated. Enzyme free electro-oxidation of glucose have greatly been enhanced at nanoscale Ni(OH)(2) as a result of electrocatalytic effect of Ni(+2)/Ni(+3) redox couple. The sensitivity to glucose was evaluated as 202 microA mM(-1)cm(-2). From 50 microM to 23 mM of glucose can be selectively measured using platelet-like Ni(OH)(2) nanoscale modified CILE with a detection limit of 6 microM (S/N=3). The nanoscale nickel hydroxide modified electrode is relatively insensitive to electroactive interfering species such as ascorbic acid (AA), and uric acid (UA) which are commonly found in blood samples. Long-term stability, high sensitivity and selectivity as well as good reproducibility and high resistivity towards electrode fouling resulted in an ideal inexpensive amperometric glucose biosensor applicable for complex matrices.     

A flexible and wearable glucose sensor based on functional polymers with soft-MEMS techniques

A novel biosensor for glucose measurement using functional polymers was fabricated and tested. The biosensor utilizes the physical and chemical functions of hydrophobic polydimethyl siloxane (PDMS) and hydrophilic 2-methacryloyloxyethyl phosphorylcholine (MPC) copolymerized with dodecyl methacrylate (DMA). The glucose sensor was constructed by immobilizing glucose oxidase (GOD) onto a flexible hydrogen peroxide electrode (Pt working electrode and Ag/AgCl counter/reference electrode). The electrodes were fabricated using microelectromechanical systems (MEMS) techniques onto those functional polymers. The sensor showed novel functions of flexibility and it was stretchable so that the sensor could normally work when it was released after expanding to 120% longer than that of normal length. Also, basic characteristics of the sensor were evaluated. The output current of the hydrogen peroxide electrode was linearly related to the hydrogen peroxide concentration in a range of 0.20-2.50 mmol/l, with a correlation coefficient of 0.998. GOD was then immobilized onto the surface of the sensor using MPC polymer. In this case, the current output of the glucose sensor related to the glucose level over a range of 0.06-2.00 mmol/l, with a correlation coefficient of 0.997. The calibration range includes the reported concentration of tear glucose in normal human subject (0.14 mmol/l).     

Homology of plasmids with a wide range of hosts

According to blotting hybridization and heteroduplex analysis, plasmids R751, R906 and RP4 of Inc Pi group have continuous regions of homology. These homologous regions were mapped on the R751 and RP4-derived pRP401 deletion mutant DNAs. The plasmid pRP401 (m.w. 21.9 kg) retains the broad host range property and has two regions of intensive homology with other Inc P-1 plasmid DNAs. These regions are localized at 8.2-12.0 kb and 13.9-21.9 kb of the physical map of pRP401 plasmid. Homologous regions of pRP401 DNA include at least the replication genes (oriV, trfA, trfB) as well as genes kilB, korA, korB and probably kilC. The data strongly point out that the broad host range plasmids have the same principle of structural and functional organization.     

Determination of glucose and uric acid with bienzyme colorimetry on microfluidic paper-based analysis devices

An aptamer is an artificial functional oligonucleic acid, which can interact with its target molecule with high affinity and specificity. Enzyme linked aptamer assay (ELAA) is developed to detect cocaine using aptamer fragment/cocaine configuration based on the affinity interaction between aptamer fragments with cocaine. The aptasensor was constructed by cleaving anticocaine aptamer into two fragments: one was assembled on a gold electrode surface, while the other was modified with biotin at 3'-end, which could be further labelled with streptavidin-horseradish peroxidase (SA-HRP). Upon binding with cocaine, the HRP-labelled aptamer fragment/cocaine complex formed on the electrode would increase the reduction current of hydroquinone (HQ) in the presence of H(2)O(2). The sensitivity and the specificity of the proposed electrochemical aptasensor were investigated by differential pulse voltammetry (DPV). The results indicated that the DPV signal change could be used to sensitively detect cocaine with the dynamic range from 0.1 μM to 50 μM and the detection limit down to 20 nM (S/N=3). The proposed aptasensor has the advantages of high sensitivity and low background current. Furthermore, a new configuration for ELAA requiring only a single aptamer sequence is constructed, which can be generalized for detecting different kinds of targets by cleaving the aptamers into two suitable segments.     

Amperometric glucose biosensor with extended concentration range utilizing complexation effect of borate.

Borate buffer strongly decreases amperometric response of a glucose oxidase linked pO2 or H2O2 sensing electrode, extending substantially its linear calibration range. With increasing pH and concentration of the buffer the upper limit for glucose can be varied between 1 and 30 mmol l-1 glucose. The effect of borate ion is explained by the rapid complexation of glucose decreasing the equilibrium concentration of free beta-anomer, the specific substrate of glucose oxidase. The high loading of cross-linked enzyme inside the sensor membrane is necessary for the measurement to ensure an almost constant response factor (delta i per 1 mmol l-1) between pH 5 and 10. Analysis in stirred solution and in a flow-through system has been employed for the measurement of elevated glucose levels in heparinized human blood or plasma samples.     

Thermodynamic analysis of human serum albumin interactions with glucose: insights into the diabetic range of glucose concentration

The interaction of proteins with glucose results in their non-enzymatic glycation and influences their structural and functional properties. Human serum albumin (HSA) interacts with glucose forming glycated HSA. However, the glucose binding sites and the thermodynamic characteristics of the glycated HSA require further delineation. Here, the binding properties of HSA and glucose were studied utilizing fluorescent techniques. HSA was incubated with glucose in the 0-300mM range at 27 or 37 degrees C. The interaction of HSA with glucose showed two sets of binding sites. The first set consists of two sites with positive cooperativity and the second set consists of nine identical non-cooperative sites. The percentage of glycated HSA (gly%) and the moles of glucose bound to moles of HSA (r) were utilized to obtain binding constants and thermodynamic parameters based on the Wyman binding potential. The enthalpy of binding, obtained by van't Hoff relation, presented exothermicity up to 7mM glucose (126mg/dl, normal range) and endothermic propensity at higher glucose concentrations (>7mM, diabetic range). The start of endothermic propensity was consistent with the diabetic range of glucose concentration and indicates unfolding of HSA. The Gibbs free energy and entropy of binding further supports the unfolding of HSA. Therefore, glucose interacts with multiple sites on HSA affecting its biochemical and biophysical properties. This may interfere with HSA normal function contributing to diabetic complications.     

A long-term lifetime amperometric glucose sensor with a perfluorocarbon polymer coating

We have developed an amperometric glucose sensor whose electrodes are coated with a four-layered membrane: 3-aminopropyltriethoxysilane (gamma-APTES), Nafion, glucose oxidase (GOX), and perfluorocarbon polymer (PFCP). Tests demonstrate the sensor's ability to accurately and successively determine glucose concentrations ranging from 2.8 to 167 mM, over a 66 day period with no increase in response time, while remaining imperviousness to the effects of interference species (2.8 mM ascorbic acid, 0.3 mM uric acid, 0.3 mM p-acetaminophen). Furthermore, tests on diabetic urine samples showed an excellent correlation coefficient of 0.985 (y=1.04x+4.73, n=30) between sensor results and those of Glucose-Dehydrogenase clinical laboratory analyses.     

The ammonia-lyases: enzymes that use a wide range of approaches to catalyze the same type of reaction

Abstract

The paradigm that protein structure determines protein function has been clearly established. What is less clear is whether a specific protein structure is always required to carry out a specific function. Numerous cases are now known where there is no apparent connection between the biological function of a protein and the other members of its structural class, and where functionally related proteins can have quite diverse structures. A set of enzymes with these diverse properties, the ammonia-lyases, will be examined in this review. These are a class of enzymes that catalyze a relatively straightforward deamination reaction. However, the individual enzymes of this class possess a wide variety of different structures, utilize a diverse set of cofactors, and appear to catalyze this related reaction through a range of different mechanisms. This review aims to address a basic question: if there is not a specific protein structure and active site architecture that is both required and sufficient to define a catalyst for a given chemical reaction, then what factor(s) determine the structure and the mechanism that is selected to catalyze a particular reaction?     

A novel unstructured scaffold based on 4EBP1 enables the functional display of a wide range of bioactive peptides

Target validation using protein aptamers enables the characterization of a specific function of a target protein in an environment that resembles native conditions as closely as possible. A major obstacle to the use of this technology has been the generation of bioactive aptamers, which is dependent on the choice of scaffold. Constraining binding peptides within a particular scaffold does not necessarily result in binding aptamers, as suboptimal presentation of peptides can occur. It is therefore understandable that different peptides might require different scaffolds for optimal presentation. In this article, we describe a novel scaffold protein that bypasses the conventional requirement for scaffolds to have known rigid structures and yet successfully presents several peptides that need to adopt a wide range of conformations for binding to their target protein. Using an unstructured protein, 4EBP1, as scaffold, we successfully construct binding aptamers to three different target proteins: Mdm2, proliferating cell nuclear antigen, and cyclin A. The Mdm2-binding aptamer constructed using 4EBP1 as scaffold demonstrates better stability and bioactivity compared to that constructed using thioredoxin as scaffold. This new scaffold protein, which makes it relatively easy to create bioactive aptamers based on known interaction sequences, will greatly facilitate the aptamer approach to target validation.     

A serological study with monoclonal antibodies to an antigen common to a wide range of bacteria

Abstract Three monoclonal antibodies (MCA) against Pseudomonas aeruginosa common antigen (CA) and one MCA against Bordetella pertussis CA were produced. These immunoglobulins were examined by ELISA against extracts of a wide range of Gram-positive and Gram-negative bacteria. No reactions were obtained with Gram-positive organisms. The reaction patterns with Gram-negative organisms were different for each of the monoclonal antibodies and did not follow the accepted taxonomal principles. The results prove that a number of antigen determinants are not shared by CA of different bacteria.     

Amperometric glucose sensor based on coimmobilization of glucose oxidase and Poly(p-phenylenediamine) at a platinum microdisk electrode

A miniaturized glucose biosensor in which glucose oxidase (GOD) and poly(p-phenylenediamine) (poly-PPD) were coimmobilized at the surface of a platinum microdisk electrode was developed and used successfully for amperometric determination of glucose. The performance of sensors prepared at different monomer concentrations and polymerization potentials with different media was investigated in detail. It was found that similarly to poly(o-phenylenediamine) (poly-OPD), (poly-PPD) noticeably eliminated the electrochemical interference of ascorbic acid, uric acid, and l-cysteine. The amperometric response of glucose with the biosensor under optimal conditions exhibited a linear relationship in the range of 5.0 x 10(-5) to 3.0 x 10(-3) M with correlation coefficient 0.9995. According to the Michaelis-Menten equation, the apparent Michaelis constant for glucose and the maximum steady-state current density of the poly-PPD/GOD-modified microelectrode were 3.94 mM and 607.5 microA cm(-2), respectively. The current density of the sensor responding to glucose in the linear range can reach 160 microA cm(-2) mM(-1), which is far greater than that obtained using poly-OPD and poly(phenol) film. In addition, the stability of the sensor was examined over a 2-month period.     

Spatio-temporal nested patterns in macroinvertebrate assemblages across a pond network with a wide hydroperiod range

Nestedness has been widely used to measure the structure of biological communities and occurs when species-poor sites contain subsets of species-rich ones. Here, we examine nested patterns across the macroinvertebrate assemblages of 91 ponds in Doñana National Park, Spain, and explore temporal variation of nestedness and species richness in 19 temporary ponds over 2 years with differing rainfall. Macroinvertebrate assemblages were significantly nested; both pond spatial arrangement and environmental variation being important in driving nested patterns. Despite the nested structure observed, a number of taxa and ponds deviate from this pattern (termed idiosyncratic), by occurring more frequently than expected in species-poor sites, or having assemblages dominated by species largely absent from species-rich sites. Aquatic adults of winged insects, capable of dispersal, were more highly nested than non-dispersing taxa and life-history stages. Idiosyncratic taxa were found in ponds spanning a wide range of hydroperiods, although nestedness was higher in more permanent waterbodies. Monthly sampling demonstrated a gradual increase of species richness and nestedness from pond filling to April–May, when the most temporary ponds started to dry. Although the degree of nestedness of individual pond assemblages varied from month to month, the overall degree of nestedness in the two study years was practically identical despite marked differences in hydroperiod. Our results suggest that differential colonization and environmental variation are key processes driving the nested structure of Doñana ponds, that macroinvertebrate assemblages change in a predictable manner each year in response to cycles of pond wetting and drying, and that connectivity and environmental variability maintain biodiversity in pond networks.     

A novel vector allowing the expression of genes in a wide range of gram-negative bacteria

The construction and use of a novel vector allowing the expression of genes in a wide range of Gram-negative bacteria is described. The vector utilizes the regulatory region from IS50. The 70-bp promoter region was isolated from one of the terminal inverted repeats of Tn5 by creating EcoRI and Sa/I or PstI restriction sites by in vitro mutagenesis. This 70-bp region was shown to direct the expression of cat and lacZ genes in different bacterial genera including Alcaligenes, Enterobacter cloacae, Klebsiella pneumoniae, Pseudomonas stutzeri, Pseudomonas fluorescens, and Serratia marcescens. Different strains containing the cat gene behind the regulatory elements of IS50 were able to tolerate high concentrations (300 micrograms/ml) of chloramphenicol in the medium. The 70-bp promoter region was cloned into a broad-host-range plasmid behind multiple cloning sites to create pAV10, which has unique restriction sites for BamHI, KpnI, SstI, and XbaI. Genes cloned into pAV10 can be expressed in a variety of Gram-negative bacteria.     

A method for eluting DNA in a wide range of molecular weights from agarose gels

We have developed a simple and rapid method for recovering DNAs of a wide range of molecular weights from agarose gels. A DNA-containing gel slice is placed on a Parafilm sheet in the center of a circular (positive) electrode and covered with a drop of buffer, while a linear (negative) electrode is placed on the top of the gel and driven about 1 mm into the gel itself. When a continuous current is applied, the DNA migrates into the buffer toward the circular electrode. We have obtained almost total recovery of DNAs up to 10 kb in size. Our method may also be used, under appropriate conditions, for higher molecular weight DNAs. The yield and all the biological assays performed on the DNAs obtained by our method recommend it for routine laboratory use.     

Plasmid pBS195 with a wide range of hosts, isolated from lactobacilli

The nonconjugative 4.4 kb plasmid pBS195 has been found in Lactobacillus sp. 195 strain resistant to kanamycin and streptomycin. The plasmid pBS195 determining the resistance to kanamycin has a broad host range. It is inherited by the Gram-positive microorganisms (Bacillus subtilis) as well as by Escherichia coli cells, has the cleavage sites for the restriction endonucleases BamHI, EcoRI, HindIII, PstI, KpnI. The restriction map of the plasmid for these enzymes is constructed. The broad host range, efficiently expressed marker, the presence of the unique restriction sites, small size make the plasmid pBS195 promising for the genetic engineering research.