Identification of source of heavy metal contamination in a site - a case study

Accidental spills and improper disposal of industrial effluent/sludge containing heavy metals onto the open land or into subsurface result in soil and water contamination. Detailed investigations are carried out to identify the source of contamination of heavy metals in an industrial suburb near Bangalore in India. Detailed investigation of ground water and subsurface soil analysis for various heavy metals has been carried out. Ground water samples were collected in the entire area through the cluster of borewells. Subsurface soil samples were collected from near borewells which were found to contain heavy metals. Water samples and soils samples (after acid digestion) were analysed as per APHO-standard method of analysis. While the results of Zn, Ni and Cd showed that they are within allowable limits in the soil, the ground water and soils in the site have concentration of Cr+6 far exceeding the allowable limits (up to 832 mg/kg). Considering the topography of the area, ground water movement and results of chromium concentration in the borewells and subsurface it was possible to identify the origin, zone of contamination and the migration path of Cr+6. The results indicated that the predominant mechanism of migration of Cr+6 is by diffusion.

Investigations of Ramachandran disallowed conformations in protein domain families

In peptide and protein structures, occurrence of (phi,psi.) angles in the disallowed region of the Ramachandran map almost always suggests local regions of error or poor accuracy. However, very rarely genuine disallowed conformations occur as noted in the current study in proteins of known structure available at ultra-high resolution (<= 1.2 (A) over circle). In the current work, extent of conservation of genuine disallowed conformations in homologous proteins of known structures has been analyzed. From a dataset of 124 protein domain families, with structure of at least one constituent member in each family available at a resolution of 1.2 (A) over circle or better, we have analyzed the conservation of 221 disallowed conformations. It is observed that the disallowed conformation is only moderately conservedin protein domain families. In the gross dataset no particular residue type adopting disallowed conformation elicit high conservation of residue type though there are alignment positions in the dataset with complete conservation of both the residue type and the disallowed conformation. Conserved disallowed conformation in protein domain families play biologically significant role in roughly 50% of the cases. The residues with the disallowed conformation or its flanking residues are often located within or around the functional site of the protein. (C) 2013 Elsevier B.V. All rights reserved.

Electronic and Magnetic Properties of Yttrium-doped Silicon Carbide Nanotubes: Density Functional Theory Investigations

The electronic structure of yttrium-doped Silicon Carbide Nanotubes has been theoretically investigated using first principles density functional theory (DFT). Yttrium atom is bonded strongly on the surface of the nanotube with a binding energy of 2.37 eV and prefers to stay on the hollow site at a distance of around 2.25 angstrom from the tube. The semi-conducting nanotube with chirality (4, 4) becomes half mettalic with a magnetic moment of 1.0 mu(B) due to influence of Y atom on the surface. There is strong hybridization between d orbital of Y with p orbital of Si and C causing a charge transfer from d orbital of the Y atom to the tube. The Fermi level is shifted towards higher energy with finite Density of States for only upspin channel making the system half metallic and magnetic which may have application in spintronic devices.

Electrochemical and electron transfer investigations of copper proteins

A study of the pH and temperature dependence of the redox potentials of azurins from five species of bacteria has been performed. The variations in the potentials with pH have been interpreted in terms of electrostatic interactions between the copper site and titrating histidine residues, including the effects of substitutions in the amino acid sequences of the proteins on the electrostatic interactions. A comparison of the observed pH dependences with predictions based on histidine pK_a values known for Pseudomonas aeruginosa (Pae), Alcaligenes denitrificans (Ade), and Alcaligenes faecalis (Afa) azurins indicates that the Pae and Ade redox potentials exhibit pH dependences in line with electrostatic arguments, while Afa azurin exhibits more complex behavior. Redox enthalpies and entropies for four of the azurins at low and high pH values have also been obtained. Based on these results in conjuction with the variable pH experiments, it appears that Bordetella bronchiseptica azurin may undergo a more substantial conformational change with pH than has been observed for other species of azurin.

The temperature dependence of the redox potential of bovine erythrocyte superoxide dismutase (SOD) has been determined at pH 7.0, with potassium ferricyanide as the mediator. The following thermodynamic parameters have been obtained (T = 25°C): E°' = 403±5 mV vs. NHE, ΔG°' = -9.31 kcal/mol, ΔH°' = -21.4 kcal/mol, ΔS°' = -40.7 eu, ΔS°'_(rc) = -25.1 eu. It is apparent from these results that ΔH°', rather than ΔS°', is the dominant factor in establishing the high redox potential of SOD. The large negative enthalpy of reduction may also reflect the factors which give SOD its high specificity toward reduction and oxidation by superoxide.

Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.

We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.

DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.

While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.

In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.

Final Report of the Phase III Archaeological Investigations at the Dr. Upton Scott House (18AP18), Annapolis, Anne Arundel County, Maryland, 1998-1999

In the summers of 1998 and 1999, the Archaeology in Annapolis project carried out archaeological investigation at the eighteenth century Dr. Upton Scott House site (18AP18)located at 4 Shipwright Street in the historic district of Annapolis, Anne Arundel County, Maryland. The Upton Scott House is significant as one of only a few Georgian houses with remnants of its original plantation-inspired landscape still visible (Graham 1998:147). Investigation was completed in agreement with the owners of the historic property, Mr. and Mrs. Paul Christian, who were interested in determining the condition and arrangement of Dr. Upton Scott’s well-documented pleasure gardens. Betty Cosans’ 1972 Archaeological Feasibility Report, the first real archaeological study of the Upton Scott House site, guided the research design and recovery efforts. Cosans determined that testing and survey in the back and side yards of the Scott property would yield important information on the use and history of the property, including that of Scott’s famous gardens. Excavation units and trenches were placed within three separate areas of backyard activity on the site which included Area One: extant brick stables in the southwest of the property; Area Two: the brick foundations of a small outbuilding located in the northwest area of the site; and Area Three: the area of Scott’s formal gardens. The research design included an interest in recovering evidence of African-American spiritual practice and domestic life at the site. Also of significant importance was an analysis of Scott’s garden beds, concerning the order and layout. Also sought was an understanding of the change in perception and use of the backyard by the various owners of the property.

"It is Quietly Chaotic. It Confuses Time"*: Final Report of Excavations at the Bordley-Randall Site in Annapolis, Maryland, 1993-1995 (18AP50)

*This extract is from Gay P. Crowther's description of the Randall Court pathway (Cowther 1985).

Final Archaeological Investigations at the Maynard-Burgess House (18AP64): An 1850-1980 African-American Household in Annapolis, Maryland

The Maynard-Burgess House was excavated by Archaeology in Annapolis from Fall, 1990 to Summer, 1992. The still-standing house is located at 163 Duke of Gloucester Street in Annapolis' Historic District and is today being restored by Port of Annapolis, Incorporated. Archaeological testing and excavation of the site was developed alongside architectural analyses and archival research as the initial phase of the home's restoration. The Maynard-Burgess House was continuously occupied by two African-American families, the Maynards and the Burgesses, from the 1850s until the late 1980s. The main block of the house was built between 1850 and 1858 by the household of John T. Maynard, a free African American born in 1810,and his wife Maria Spencer Maynard. Maynard descendants lived in the home until it was foreclosed in 1908 and subsequently sold to the family of Willis and Mary Burgess in 1915. Willis had been a boarder in the home in 1880, and his sister Martha Ready had married John and Maria's son John Henry. Burgess descendants lived at the home until its sale in 1990.

Searching for the IRA 'disappeared': Ground-penetrating radar investigation of a churchyard burial site, Northern Ireland

A search for the body of a victim of terrorist abduction and murder was made in a graveyard on the periphery of a major conurbation in Northern Ireland. The area is politically sensitive and the case of high profile. This required non-invasive, completely non-destructive and rapid assessment of the scene. A MALA RAMAC ground-penetrating radar system was used to achieve these objectives. Unprocessed and processed 400MHz data shows the presence of a collapse feature above and around a known 1970s burial with no similar collapse above the suspect location. In the saturated, clay-rich sediments of the site, 200MHz data offered no advantage over 400MHz data. Unprocessed 100MHz data shows a series of multiples in the known burial with no similar features in the suspect location. Processed 100MHz lines defined the shape of the collapse around the known burial to 2m depth, together with the geometry of the platform (1m depth) the gravedigger used in the 1970s to construct the site. In addition, processed 100MHz data showed both the dielectric contrast in and internal reflection geometry of the soil imported above the known grave. Thus the sequence, geometry, difference in infill and infill direction of the grave was reconstructed 30 years after burial. The suspect site showed no evidence of shallow or deep inhumation. Subsequently, the missing person������¢���¯���¿���½���¯���¿���½s body was found some distance from this site, vindicating the results and interpretation from ground-penetrating radar. The acquisition, processing, collapse feature and sequence stratigraphic interpretation of the known burial and empty (suspect) burial site may be useful proxies for other, similar investigations. GPR was used to evaluate this site within 3 hours of the survey commencing, using unprocessed data. An additional day of processing established that the suspect body did not reside here, which was counter to police and community intelligence.

Archaeological and Palaeoecological investigations of a Middle Bronze Age settlement at Ballyarnet Lake, Co. Derry

Excavations at Ballyarnet Lake, Co Derry, have identified a Middle Bronze Age settlement site at the margins of the lake. The site is characterised by a palisaded enclosure surrounding a structure containing a hearth. Finds include a large quantity of Cordoned Urn ware, lithics and a faience bead. Palaeoenvironmental studies, including pollen, plant macrofossil and beetle analyses, provide insights into the environmental background of the settlement. The site is considered in terms of the broader context of Middle Bronze Age settlement.

Molecular investigations into vaginal immunization with HIV gp41 antigenic construct H4A in a quick release solid dosage form

A robust vaginal immune response is considered essential for an effective prophylactic vaccine that prevents transmission of HIV and other sexually acquired diseases. Considerable attention has recently focused on the potential of vaginally administered vaccines as a means to induce such local immunity. However, the potential for vaccination at this site remains in doubt as the vaginal mucosa is generally considered to have low immune inductive potential. In the current study, we explored for the first time the use of a quick release, freeze-dried, solid dosage system for practical vaginal administration of a protein antigen. These solid dosage forms overcome the common problem associated with leakage and poor retention of vaginally administered antigen solutions. Mice were immunized vaginally with H4A, an HIV gp41 envelope based recombinant protein, using quick release, freeze-dried solid rods, and the immune responses compared to a control group immunized via subcutaneous H4A injection. Vaginally immunized mice failed to elicit robust immune responses. Our detailed investigations, involving cytokine analysis, the stability of H4A in mouse cervicovaginal lavage, and elucidation of the state of H4A protein in the immediate-release dosage form, revealed that antigen instability in vaginal fluid, the state of the antigen in the dosage form, and the cytokine profile induced are all likely to have contributed to the observed lack of immunogenicity. These are important factors affecting vaginal immunization and provide a rational basis for explaining the typically poor and variable elicitation of immunity at this site, despite the presence of immune responsive cells within the vaginal mucosae. In future mucosal vaccine studies, a more explicit focus on antigen stability in the dosage form and the immune potential of available antigen-responsive cells is recommended. © 2012 Elsevier Ltd. All rights reserved.

Pilgrimstad revisited - a multi-proxy reconstruction of Early/Middle Weichselian climate and environment at a key site in central Sweden

The site Pilgrimstad in central Sweden has often been cited as a key locality for discussions of ice-free/ice-covered intervals during the Early and Middle Weichselian. Multi-proxy investigations of a recently excavated section at Pilgrimstad now provide a revised picture of the climatic and environmental development between similar to 80 and 36 ka ago. The combination of sedimentology, geochemistry, OSL and 14C dating, and macrofossil, siliceous microfossil and chironomid analyses shows: (i) a lower succession of glaciofluvial/fluvial, lacustrine and glaciolacustrine sediments; (ii) an upper lacustrine sediment sequence; and (iii) Last Glacial Maximum till cover. Microfossils in the upper lacustrine sediments are initially characteristic for oligo- to mesotrophic lakes, and macrofossils indicate arctic/sub-arctic environments and mean July temperatures > 8 degrees C. These conditions were, however, followed by a return to a low-nutrient lake and a cold and dry climate. The sequence contains several hiatuses, as shown by the often sharp contacts between individual units, which suggests that ice-free intervals alternated with possible ice advances during certain parts of the Early and Middle Weichselian.

Geophysical and hydrogeological characterisation of the impacts of on-site wastewater treatment discharge to groundwater in a poorly productive bedrock acquifer

Contaminants discharging from on-site wastewater treatment systems (OSWTSs) can impact groundwater quality, threatening human health and surface water ecosystems. Risk of negative impacts becomes elevated in areas of extreme vulnerability with high water tables, where thin unsaturated intervals limit vadose zone attenuation. A combined geophysical/hydrogeological investigation into the effects of an OSWTS, located over a poorly productive aquifer (PPA) with thin subsoil cover, aimed to characterise effluent impacts on groundwater. Groundwater, sampled from piezometers down-gradient of the OSWTS percolation area displayed spatially erratic, yet temporally consistent, contaminant distributions. Electrical resistivity tomography identified an area of gross groundwater contamination close to the percolation area and, when combined with seismic refraction and water quality data, indicated that infiltrating effluent reaching the water table discharged to a deeper more permeable zone of weathered shale resting on more competent bedrock. Subsurface structure, defined by geophysics, indicated that elevated chemical and microbiological contaminant levels encountered in groundwater samples collected from piezometers, down-gradient of sampling points with lower contaminant levels, corresponded to those locations where piezometers were screened close to the weathered shale/competent rock interface; those immediately up-gradient were too shallow to intercept this interval, and thus the more impacted zone of the contaminant plume. Intermittent occurrence of faecal indicator bacteria more than 100 m down gradient of the percolation area suggested relatively short travel times. Study findings highlight the utility of geophysics as part of multidisciplinary investigations for OSWTS contaminant plume characterisation, while also demonstrating the capacity of effluent discharging to PPAs to impact groundwater quality at distance. Comparable geophysical responses observed in similar settings across Ireland suggest the phenomena observed in this study are more widespread than previously suspected.

Environmental forensic investigations: The potential use of a novel heavy metal sensor and novel taggants

This chapter presents a novel hand-held instrument capable of real-time in situ detection and identification of heavy metals, along with the potential use of novel taggants in environmental forensic investigations. The proposed system provides the facilities found in a traditional laboratory-based instrument but in a hand held design, without the need for an associated computer. The electrochemical instrument uses anodic stripping voltammetry, which is a precise and sensitive analytical method with excellent limits of detection. The sensors comprise a small disposable plastic strip of screen-printed electrodes rather than the more common glassy carbon disc and gold electrodes. The system is designed for use by a surveyor on site, allowing them to locate hotspots, thus avoiding the expense and time delay of prior laboratory analysis. This is particularly important in environmental forensic analysis when a site may have been released back to the owner and samples could be compromised on return visits. The system can be used in a variety of situations in environmental assessments, the data acquired from which provide a metals fingerprint suitable for input to a database. The proposed novel taggant tracers, based on narrow-band atomic fluorescence, are under development for potential deployment as forensic environmental tracers. The use of discrete fluorescent species in an environmentally stable host has been investigated to replace existing toxic, broadband molecular dye tracers. The narrow band emission signals offer the potential for tracing a large number of signals in the same environment. This will give increased data accuracy and allow multiple source environmental monitoring of environmental parameters.