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The subject of the research is one of the largest World’s mine tailings disposal sites, i.e. Żelazny Most in the Legnica-Głogów Copper Mining District (south-western Poland), where flotation tailings are poured out after copper ore treatment. The protective hydraulic barrier made of 46 vertical drainage wells was characterized and evaluated in view of reduction of major contaminants (Cl, Na, SO4, Ca) migrating from the facility to its foreground. The efficiency of groundwater protection was determined on the basis of a new approach. In applied method the loads of characteristic and commonly recognizable compounds, i.e. salt (NaCl) and gypsum (CaSO4) were calculated, instead their chemical components. The temporal and spatial variability of captured main contaminants loads as well as its causes are discussed. The paper ends with the results of efficiency analyses of the barrier and with respect to the predicted increase in contaminant concentrations in the pulp poured out to the tailings site.

Lambda-like double-stranded (ds) DNA bacteriophage undergo massive conformational changes in their capsid shell during the packaging of their viral genomes. Capsid shells are complex organizations of hundreds of protein subunits [...]

The common laboratory strain of bacteriophage [unkeyable]--[unkeyable] wild type or [unkeyable]PaPa--carries a frameshift mutation relative to Ur-[unkeyable], the original isolate. The Ur-[unkeyable] virions have thin, jointed tail fibers that are absent from [unkeyable] wild type. Two novel proteins of Ur-[unkeyable] constitute the fibers: the product of stf, the gene that is disrupted in [unkeyable] wild type by the frameshift mutation, and the product of gene tfa, a protein that is implicated in facilitating tail fiberassembly. Relative to [unkeyable] wild type, Ur-[unkeyable] has expanded receptor specificity and adsorbs to Escherichia coli cells more rapidly., The tail fibers of the double-stranded DNA bacteriophages are the organelles through which the virus contacts its host in the first steps of the infection process. By forming specific contacts [...]

The present study reports for the first time the occurrence of selected pharmaceuticals and personal care products (PPCPs) in the shallow aquifer underlying the Kraków city. Urban groundwater samples were gathered from 11 wells, which can serve as the emergency water supply wells. Liquid chromatography with tandem mass spectrometry method with the previous pre-concentration of samples using an SPE technique was applied for the determination of the PPCPs selected. There were quantified concentrations of PPCPs from the groups of estrogens (17-α-ethinylestradiol (EE2), 2.6–18.7 ng/L), non-steroidal anti-inflammatory drugs (ketoprofen, 59.5 ng/L in 1 sample), and antimicrobial preservatives used in cosmetic production (methylparaben up to 91.5 ng/L). Triclosan was observed in all analysed water samples in concentrations above the limit of detection. The presence of the PPCPs in the shallow aquifer is an evidence that the sewer network system under the city leaks and then pollutes the urban groundwater. [ABSTRACT FROM AUTHOR]

The long flexible tail tube of bacteriophage lambda connects its capsid to the tail tip. On infection, a DNA ejection signal is passed from the tip, along the tube to the capsid that triggers passage of the DNA down the tube and into the host bacterium. The tail tube is built from repeating units of the major tail protein, gpV, which has two distinctive domains. Its N-terminal domain has the same fold as proteins that form the rigid inner tubes of contractile tail phages, such as T4, and its C-terminal domain adopt an Ig-like fold of unknown function. We determined structures of the lambda tail tube in free tails and in virions before and after DNA ejection using cryoelectron microscopy. Modeling of the density maps reveals how electrostatic interactions and a mobile loop participate in assembly and also impart flexibility to the tube while maintaining its integrity. We also demonstrate how a common protein fold produces rigid tubes in some phages but flexible tubes in others. Image 1 • The flexibility of siphoviridae tails interferes with structure determination. • Tail assembly uses electrostatic interactions and traps dynamic segments. • Tail protein Ig-like domains form ordered filaments around the tail tube. • Tail tubes show little change in structure after DNA injection. • The new model explains how pH and ionic strength effect tail integrity. [ABSTRACT FROM AUTHOR]

Various types of landfills pose a direct threat to groundwater. Polluted groundwater is characterized by significantly reduced electrical resistivity. Geophysical methods -- in particular DC-resistivity methods -- are sensitive to this physical parameter. Applying these methods can allow for a spatial assessment of the groundwater quality near the landfills. The key with that approach is to recognize the geoelectrical structure of an area prior to the existence of a landfill. This information will allow for a geoelectrical background, which would most likely be an image of the natural and uncontaminated study area. Subsequent measurements will be more effective due to the possibility of comparing the current state of the area to the original state. This paper presents an example of such a study. Here, the research area of interest was located in the vicinity of an inactive tailings disposal site. In order to assess the pollution of the groundwater, a vertical electrical sounding method was applied. The results of modern measurements were compared with those from the reinterpretation of the data obtained several decades ago. The selected geoelectrical method proved to be effective, allowing for the determination of the range of contaminated groundwater in regions that were not covered by traditional hydrogeological monitoring by a piezometer network. Repetition of vertical electrical sounding in the future will allow for tracking the displacement of pollution within the aquifer. [ABSTRACT FROM AUTHOR]

Our research aimed to evaluate groundwater pollution risk in the study area in southeastern Poland, that is, in an area where the hydrogeological conditions and land use forms are similar to those of European plains. The authors' own qualitative classifications of the potential impact of major forms of land use on groundwater quality and groundwater pollution risk are proposed. The degree of this risk was assessed as the sum of ratings of intrinsic vulnerability of groundwater to pollution assessed with the original DRASTIC method and ratings of the potential impact of land use. The obtained map of groundwater pollution risk showed that 0.3% of the study area was characterized as being at very high risk, 50% as high, 45% as moderate, and 4.7% as low. In a graphical manner, spatial relationships between selected factors affecting the groundwater pollution risk and the assessed degree of risk are presented. The assessment of groundwater pollution risk employing intrinsic vulnerability of groundwater to pollution and potential impact of land use forms, together with the proposed classification of groundwater pollution risk, made it possible to determine areas of high risk of groundwater pollution in the study area in an effective manner. [ABSTRACT FROM AUTHOR]

The double stranded DNA bacteriophage HK97 provides an advantageous system for investigating the structural basis for protein self-assembly and viral capsid maturation. The solution Raman spectra of Prohead I, Prohead II, and Head II particles are structurally interpreted.

The study focuses on the assessment of surface area thermal activity measured by air thermal photography at the significant geotourism locality of Ema coal tailing dumps. Ema has become a geotourism post-mining landmark associated with black coal mining in Ostrava, the third largest city in the Czech Republic. At the same time, Ostrava is the largest industrial city in the Czech Republic. The study analyses a new approach to assess the surface area thermal activity in coal tailing dumps. A correct analysis of the surface area thermal activity is a fundamental requirement for projects to deal with the clean-up of a dump with thermal activity. Ema has a scientific and geotourism-educational character and it is important to plan solutions to achieve thermal activity stabilization. A 4 year monitoring programme was implemented using a new approach grounded in assessment based on thermal activity area classification (active and inactive), and comparison with a reference point in the dump with the highest temperature without thermal activity during the measurement period. It was this boundary condition that facilitated the correct assessment of the thermal activity surface area and it helped to establish gradual decreases in thermal activity from 0.29 ha (i.e. 0.79% of the total area of the dump) in 2011 to 0.15 ha (i.e. 0.41% of the total area of the dump) in 2014. [ABSTRACT FROM AUTHOR]

The 90-nm-diameter capsid of coliphage T5 is organized with T = 13 icosahedral geometry and encloses a double-stranded DNA genome that measures 121 kbp. Its assembly follows a path similar to that of phage HK97 but yielding a larger structure that includes 775 subunits of the major head protein, 12 subunits of the portal protein and 120 subunits of the decoration protein. As for phage HK97, T5 encodes the scaffold function as an N-terminal extension (-domain) to the major head protein that is cleaved by the maturation protease after assembly of the initial prohead I form and prior to DNA packaging and capsid expansion. Although the major head protein alone is sufficient to assemble capsid-like particles, the yield is poor and includes many deformed structures. Here we explore the role of both the portal and the protease in capsid assembly by generating constructs that include the major head protein and a combination of protease (wild type or an inactive mutant) and portal proteins and overexpressing them in Escherichia coli. Our results show that the inactive protease mutant acts to trigger assembly of the major head protein, probably through binding to the Δ-domain, while the portal protein regulates assembly into the correct T = 13 geometry. A cryo-electron microscopy reconstruction of prohead I including inactivated protease reveals density projecting from the prohead interior surface toward its center that is compatible with the -domain, as well as additional internal density that we assign as the inactivated protease. These results reveal complexity in T5 beyond that of the HK97 system. [ABSTRACT FROM AUTHOR]

Copyright of Archives of Mining Sciences is the property of Polish Academy of Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This paper assesses the groundwater resources for hydraulic fracturing of gas shales in the Lublin Basin in 2030. Such evaluations are useful for gas concession holders who plan the magnitude and schedule of gas production. In order to determine the disposable groundwater resources, a water management balance model was developed. The data from the balance and forecast of groundwater resources for 2030 in the Vistula River Basin were used as basic input data. The model accounts for the following specific factors determining the quantity of water resources in prospective gas exploitation areas: reduced groundwater recharge due to climate changes, unregistered water usage by individual households, demand for water associated with shale gas mining development, and the rate of water utilization for fracturing or returned to hydrological circulation. The extent to which these factors will affect the resources available in 2030 is uncertain. The study therefore analysed two environmental scenarios - a moderately rigorous and a rigorous one - assuming major climate change effects and a radical increase in the demand for water. Disposable water resources were determined for 12 separate balance zones in accordance with groundwater bodies (GWB) or their subsections located in the research area. This prediction refers to groundwater resources without stratigraphic division into aquifers. Depending on the zone, the resources will range from 1,072,735 to 79,458,310 m3/year for Scenario I, and from 733,285 to 49,103,085 m3/year for Scenario II. Gas concession holders are interested in relative values of resources expressed per area unit which, depending on the zone, will range from 10,132 to 32,300m3/(year·km2) for Scenario I, and from 5,212 to 24,200m3/(year·km2) for Scenario II. The analysis of the balance model reveals that the prediction for guaranteed groundwater resources in the balance zones of the Lublin Basin area in the year 2030 is large; thus development of shale gas mining should not negatively affect the quantity of water in this region. [ABSTRACT FROM AUTHOR]

Copyright of Archives of Mining Sciences is the property of Polish Academy of Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract: Tailed double-stranded DNA bacteriophages and herpesviruses build capsids by co-assembling a major capsid protein with an internal scaffolding protein that then exits from the assembled structure either intact or after digestion in situ by a protease. In bacteriophage HK97, the 102-residue N-terminal delta domain of the major capsid protein is also removed by proteolysis after assembly and appears to perform the scaffolding function. We describe the HK97 protease that carries out these maturation cleavages. Insertion mutations at seven sites in the protease gene produced mutant proteins that assemble into proheads, and those in the N-terminal two-thirds were enzymatically inactive. Plasmid-expressed protease was rapidly cleaved in vivo but was stabilized by co-expression with the delta domain. Purified protease was found to be active during the assembly of proheads in vitro. Heterologous fusions to the intact protease or to C-terminal fragments targeted fusion proteins into proheads. We confirm that the catalytic activity resides in the N-terminal two-thirds of the protease polypeptide and suggest that the C-terminal one-fifth of the protein contains a capsid targeting signal. The implications of this arrangement are compared to capsid targeting systems in other phages, herpesviruses, and encapsulins. [Copyright &y& Elsevier]

Abstract: Encapsidation of duplex DNA by bacteriophages represents an extreme case of genome condensation, reaching near-crystalline concentrations of DNA. The HK97 system is well suited to study this phenomenon in view of the detailed knowledge of its capsid structure. To characterize the interactions involved, we combined calorimetry with cryo-electron microscopy and native gel electrophoresis. We found that, as in other phages, HK97 DNA is organized in coaxially wound nested shells. When DNA-filled capsids (heads) are scanned in buffer containing 1 mM Mg2+, DNA melting and capsid denaturation both contribute to the complex thermal profile between 82 °C and 96 °C. In other conditions (absence of Mg2+ and lower ionic strength), DNA melting shifts to lower temperatures and the two events are resolved. Heads release their DNA at temperatures well below the onset of DNA melting or capsid denaturation. We suggest that, on heating, the internal pressure increases, causing the DNA to exit—probably via the portal vertex–while the capsid, although largely intact, sustains local damage that leads to an earlier onset of thermal denaturation. Heads differ structurally from empty capsids in the curvature of their protein shell, a change attributable to outwards pressure exerted by the DNA. We propose that this transition is sensed by the portal that is embedded in the capsid wall, whereupon the structure of the portal and its interactions with terminase, the packaging enzyme, are altered, thus signaling that packaging is at or approaching completion. [Copyright &y& Elsevier]

HK97 Prohead H is an early intermediate in the maturation of HK97, a T = 7 dsDNA-tailed bacteriophage related to bacteriophage λ. Previously, selected capsid-protein genes of HK97 were expressed in Escherichia coli and spontaneously assembled to form an icosahedral capsid that followed a maturation pathway closely similar to the authentic virion. The crystal structure of the mature HK97 capsid (Head II) made in this way was reported at 3.5 Å resolution, Additional high-resolution structures of intermediates are needed to understand the maturation mechanism. The crystal structure of expressed Prohead II will elucidate the early steps of HK97 assembly. Crystals of the Prohead II mutant W336F were grown in 0.1 M HEPES pH 7.5, 0.2 M CaCI[SUB2] and 2-3% PEG 4000 at a Pinhead II concentration of 16.5 mg ml[SUB-1]. It was not possible to grow high-quality crystals of wild-type Prohead II. Diffraction was observed to 5 Å resolution from these crystals on beamline 14BM-C at the Advanced Photon Source and data were collected to 5.5 Å with a completeness of 77%. The space group was P2[SUB1],3, with unit-cell parameter a = 707.0 Å and four particles in the unit cell. The particles are on the body diagonals of the cubic cell, with icosahedral threefold axes coincident with crystallographic threefold axes. Self rotation function and locked-rotation function analysis determined the particle orientation and a one-dimensional R-factor search along the body diagonal indicated that the particle centers were close to (1/4, 1/4. 1/4) and symmetry-related positions. Molecular-replacement averaging and phase extension are under way. [ABSTRACT FROM AUTHOR]

Reports on the characterization of the electrophoretic and biochemical properties of complexes between chaperonin GroEL and the capsid protein of bacteriophage HK97. Origin of the band shift in native gel electrophoresis caused by gp5 binding; Mechanism of interaction between GroEL and its substrate polypeptides.

Presents a study of the common laboratory strain of bacteriophage lambda--lambda wild type or lambdaPaPa--that carries a frameshift mutation relative to Ur-lambda, the original isolate. Ur-lambda's expanded receptor specificity relative to lambda wild type; More.

Studies the molecular structures of bacteriophage HK97 capsid shells. Discussion on protein chainmail; Functions; Implications of capsid assembly and structure; Details on protein catenation.

probe the virion structure of bacteriophage ϕ29 by asymmetric reconstructions of cryo-electron microscopy images, visualizing subunit conformations, protein-DNA interactions, and a novel twist of dsDNA that may aid in retention of the genome prior to ejection. [Copyright &y& Elsevier]

Abstract: The G-loop is a 10-residue glycine-rich loop that protrudes from the surface of the mature bacteriophage HK97 capsid at the C-terminal end of the long backbone helix of major capsid protein subunits. The G-loop is essential for assembly, is conserved in related capsid and encapsulin proteins, and plays its role during HK97 capsid assembly by making crucial contacts between the hill-like hexamers and pentamers in precursor proheads. These contacts are not preserved in the flattened capsomers of the mature capsid. Aspartate 231 in each of the ~400 G-loops interacts with lysine 178 of the E-loop (extended loop) of a subunit on an adjacent capsomer. Mutations disrupting this interaction prevented correct assembly and, in some cases, induced abnormal assembly into tubes, or small, incomplete capsids. Assembly remained defective when D231 and K178 were replaced with larger charged residues or when their positions were exchanged. Second-site suppressors of lethal mutants containing substitution D231L replaced the ionic interaction with new interactions between neutral and hydrophobic residues of about the same size: D231L/K178V, D231L/K178I, and D231L/K178N. We conclude that it is not the charge but the size and shape of the side chains of residues 178 and 231 that are important. These two residues control the geometry of contacts between the E-loop and the G-loop, which apparently must be precisely spaced and oriented for correct assembly to occur. We present a model for how the G-loop could control HK97 assembly and identify G-loop-like protrusions in other capsid proteins that may play analogous roles. [Copyright &y& Elsevier]

Abstract: Bacteriophage λ makes two proteins with overlapping amino acid sequences that are essential for tail assembly. These two proteins, gpG and gpGT, are related by a programmed translational frameshift that is conserved among diverse phages and functions in λ to ensure that gpG and the frameshift product gpGT are made in a molar ratio of approximately 30:1. Although both proteins are required and must be present in the correct ratio for assembly of functional tails, neither is present in mature tails. During λ tail assembly, major tail protein gpV polymerizes to form a long tube whose length is controlled by the tape measure protein gpH. We show that the “G” domains of gpG and gpGT bind to all or parts of tail length tape measure protein gpH and that the “T” domain of gpGT binds to major tail shaft subunit gpV, and present a model for how gpG and gpGT chaperone gpH and direct the polymerization of gpV to form a tail of the correct length. [Copyright &y& Elsevier]

Abstract: In bacteriophage λ, the overlapping open reading frames G and T are expressed by a programmed translational frameshift similar to that of the gag-pol genes of many retroviruses to produce the proteins gpG and gpGT. An analogous frameshift is widely conserved among other dsDNA tailed phages in their corresponding “G” and “GT” tail genes even in the absence of detectable sequence homology. The longer protein gpGT is known to be essential for tail assembly, but the requirement for the shorter gpG remained unclear because mutations in gene G affect both proteins. A plasmid system that can direct the efficient synthesis of tails was created and used to show that gpG and gpGT are both essential for correct tail assembly. Phage complementation assays under conditions where levels of plasmid-expressed gpG or gpGT could be altered independently revealed that the correct molar ratio of these two related proteins, normally determined by the efficiency of the frameshift, is also crucial for efficient assembly of functional tails. Finally, the physical connection between the G and T domains of gpGT, a consequence of the frameshift mechanism of protein expression, appears to be important for efficient tail assembly. [Copyright &y& Elsevier]

A programmed translational frameshift similar to frameshifts in retroviral gag-pol genes and bacterial insertion elements was found to be strongly conserved in tail assembly genes of dsDNA phages and to be independent of sequence similarities. In bacteriophage λ, this frameshift controls production of two proteins with overlapping sequences, gpG and gpGT, that are required for tail assembly. We developed bioinformatic approaches to identify analogous -1 frameshifting sites and experimentally confirmed our predictions for five additional phages. Clear evidence was also found for an unusual but analogous -2 frameshift in phage Mu. Frameshifting sites could be identified for most phages with contractile or noncontractile tails whose length is controlled by a tape measure protein. Phages from a broad spectrum of hosts spanning Eubacteria and Archaea appear to conserve this frameshift as a fundamental component of their tail assembly mechanisms, supporting the idea that their tail genes share a common, distant ancestry. [Copyright &y& Elsevier]