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Water reuse is a growing global reality. In regulating water reuse, viruses have come to the fore as key pathogens due to high shedding rates, low infectious doses, and resilience to traditional wastewater treatments. To demonstrate the high log reductions required by emerging water reuse regulations, cost and practicality necessitate surrogates for viruses for use as challenge organisms in unit process evaluation and monitoring. Bacteriophage surrogates that are mitigated to the same or lesser extent than viruses of concern are routinely used for individual unit process testing. However, the behavior of these surrogates over a multi-barrier treatment train typical of water reuse has not been well-established. Toward this aim, we performed a meta-analysis of log reductions of common bacteriophage surrogates for five treatment processes typical of water reuse treatment trains: advanced oxidation processes, chlorination, membrane filtration, ozonation, and ultraviolet (UV) disinfection. Robust linear regression was applied to identify a range of doses consistent with a given log reduction of bacteriophages and viruses of concern for each treatment process. The results were used to determine relative conservatism of surrogates. We found that no one bacteriophage was a representative or conservative surrogate for viruses of concern across all multi-barrier treatments (encompassing multiple mechanisms of virus mitigation). Rather, a suite of bacteriophage surrogates provides both a representative range of inactivation and information about the effectiveness of individual processes within a treatment train. Based on the abundance of available data and diversity of virus treatability using these five key water reuse treatment processes, bacteriophages MS2, phiX174, and Qbeta were recommended as a core suite of surrogates for virus challenge testing., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier Ltd.)

Studies into the viral fraction of complex microbial communities, like in the mammalian gut, have recently garnered much interest. Yet there is still no standardized protocol for extracting viruses from such samples, and the protocols that exist employ procedures that skew the viral community of the sample one way or another. The first step of the extraction pipeline often consists of the basic filtering of macromolecules and bacteria, yet even this affects the viruses in a strain-specific manner. In this study, we investigate a protocol for viral extraction based on ultrafiltration and how the choice of ultrafilter might influence the extracted viral community. Clinical samples (feces, vaginal swabs, and tracheal suction samples) were spiked with a mock community of known phages (T4, c2, Φ6, Φ29, Φx174, and Φ2972), filtered, and quantified using spot and plaque assays to estimate the loss in recovery. The enveloped Φ6 phage is especially severely affected by the choice of filter, but also tailed phages such as T4 and c2 have a reduced infectivity after ultrafiltration. We conclude that the pore size of ultrafilters may affect the recovery of phages in a strain- and sample-dependent manner, suggesting the need for greater thought when selecting filters for virus extraction.

Phage protein E shuts down cell wall biosynthesis to kill bacteria.

Ubiquitous and abundant in ecosystems and microbiomes, gokushoviruses constitute a Microviridae subfamily, distantly related to bacteriophages ΦX174, α3, and G4. A high-resolution cryo-EM structure of gokushovirus ΦEC6098 was determined, and the atomic model was built de novo . Although gokushoviruses lack external scaffolding and spike proteins, which extensively interact with the ΦX174 capsid protein, the core of the ΦEC6098 coat protein (VP1) displayed a similar structure. There are, however, key differences. At each ΦEC6098 icosahedral 3-fold axis, a long insertion loop formed mushroom-like protrusions, which have been noted in lower-resolution gokushovirus structures. Hydrophobic interfaces at the bottom of these protrusions may confer stability to the capsid shell. In ΦX174, the N-terminus of the capsid protein resides directly atop the 3-fold axes of symmetry; however, the ΦEC6098 N-terminus stretched across the inner surface of the capsid shell, reaching nearly to the 5-fold axis of the neighboring pentamer. Thus, this extended N-terminus interconnected pentamers on the inside of the capsid shell, presumably promoting capsid assembly, a function performed by the ΦX174 external scaffolding protein. There were also key differences between the ΦX174-like DNA-binding J proteins and its ΦEC6098 homologue VP8. As seen with the J proteins, C-terminal VP8 residues were bound into a pocket within the major capsid protein; however, its N-terminal residues were disordered, likely due to flexibility. We show that the combined location and interaction of VP8's C-terminus and a portion of VP1's N-terminus are reminiscent of those seen with the ΦX174 and α3 J proteins. IMPORTANCE There is a dramatic structural and morphogenetic divide within the Microviridae . The well-studied ΦX174-like viruses have prominent spikes at their icosahedral vertices, which are absent in gokushoviruses. Instead, gokushovirus major coat proteins form extensive mushroom-like protrusions at the 3-fold axes of symmetry. In addition, gokushoviruses lack an external scaffolding protein, the more critical of the two ΦX174 assembly proteins, but retain an internal scaffolding protein. The ΦEC6098 virion suggests that key external scaffolding functions are likely performed by coat protein domains unique to gokushoviruses. Thus, within one family, different assembly paths have been taken, demonstrating how a two-scaffolding protein system can evolve into a one-scaffolding protein system, or vice versa.

As part of a viral mitigating strategy for continuous bioprocessing, that utilizes a plug flow reactor (PFR) for continuous viral inactivation (CVI), understanding the minimum residence time as a function of reactor scale and operational conditions is critical. An empirical-based model was utilized to calculate the minimum duration a virus particle experiences within a plug flow reactor as a function of reactor design and operational conditions. This empirical model's calculations were challenged by pulse injecting the bacteriophage ΦX-174 in non-inactivating conditions and monitoring the discharge of the PFR with infectivity assays. The initial proposed empirical model, with the constraint of requiring an operational Dean number of >100, proved to be effective at calculating first breakthrough of ΦX-174 but only for the appropriate Dean number conditions. With the knowledge gained from the first empirical model, a second was generated to eliminate the Dean number constraint. This second modified empirical model proved to be successful at calculating the first breakthrough at all Dean number's tested, however CVI operation at the lower Dean's number will lead to an increased asymmetry (i.e., increased tailing) in the residence time distribution., (© 2021 Wiley Periodicals LLC.)

Sunlight-mediated inactivation of microorganisms is a low-cost approach to disinfect drinking water and wastewater. The reactions involved are affected by a wide range of factors, and a lack of knowledge about their relative importance makes it challenging to optimize treatment systems. To characterize the relative importance of environmental conditions, photoreactivity, water quality, and engineering design in the sunlight inactivation of viruses, we modeled the inactivation of three-human adenovirus and two bacteriophages-MS2 and phiX174-in surface waters and waste stabilization ponds by integrating solar irradiance and aquatic photochemistry models under uncertainty. Through global sensitivity analyses, we quantitatively apportioned the variability of predicted sunlight inactivation rate constants to different factors. Most variance was associated with the variability in and interactions among time, location, nonpurgeable organic carbon (NPOC) concentration, and pond depth. The photolysis quantum yield of the virus outweighed the seasonal solar motion in the impact on inactivation rates. Further, comparison of simulated sunlight inactivation efficacy in maturation ponds under different design decisions showed that reducing pond depth can increase the log inactivation at the cost of larger land area, but increasing hydraulic retention time by adding ponds in series yielded greater improvements in inactivation.

Protective clothing manufacturers routinely test their products for resistance to liquid and viral penetration. Several of the test methods specified by the American Society for Testing and Materials (ASTM) and the International Organization for Standardization (ISO) for penetration testing produce binary results (i.e. pass or fail), deliver imprecise pressure regulation, and do not record the location at which penetration events occur. Instead, our approach measures a continuous variable (time of penetration) during a slow and continuous increase of hydrostatic pressure and retains the location of penetration events. Using a fluorescent dye to enhance visual detection, we evaluate temporal and spatial patterns of penetration events. We then compare the time of liquid penetration with the time of penetration of two bacteriophages (Phi-X174 and MS2). For the fabric tested, the mean viral penetration occurred 0.29 minutes earlier than liquid penetration when solved by logistic regression. The breakthrough time of MS2 was not different from the Phi-X174 bacteriophage. The time of liquid penetration was a latent indicator of the time of viral penetration., Competing Interests: The authors have declared that no competing interests exist.

Although microviruses do not possess a visible tail structure, one vertex rearranges after interacting with host lipopolysaccharides. Most examinations of host range, eclipse, and penetration were conducted before this "host-induced" unique vertex was discovered and before DNA sequencing became routine. Consequently, structure-function relationships dictating host range remain undefined. Biochemical and genetic analyses were conducted with two closely related microviruses, α3 and ST-1. Despite ∼90% amino acid identity, the natural host of α3 is Escherichia coli C, whereas ST-1 is a K-12-specific phage. Virions attached and eclipsed to both native and unsusceptible hosts; however, they breached only the native host's cell wall. This suggests that unsusceptible host-phage interactions promote off-pathway reactions that can inactivate viruses without penetration. This phenomenon may have broader ecological implications. To determine which structural proteins conferred host range specificity, chimeric virions were generated by individually interchanging the coat, spike, or DNA pilot proteins. Interchanging the coat protein switched host range. However, host range expansion could be conferred by single point mutations in the coat protein. The expansion phenotype was recessive: genetically mutant progeny from coinfected cells did not display the phenotype. Thus, mutant isolation required populations generated in environments with low multiplicities of infection (MOI), a phenomenon that may have impacted past host range studies in both prokaryotic and eukaryotic systems. The resulting genetic and structural data were consistent enough that host range expansion could be predicted, broadening the classical definition of antireceptors to include interfaces between protein complexes within the capsid. IMPORTANCE To expand host range, viruses must interact with unsusceptible host cell surfaces, which could be detrimental. As observed in this study, virions were inactivated without genome penetration. This may be advantageous to potential new hosts, culling the viral population from which an expanded host range mutant could emerge. When identified, altered host range mutations were recessive. Accordingly, isolation required populations generated in low-MOI environments. However, in laboratory settings, viral propagation includes high-MOI conditions. Typically, infected cultures incubate until all cells produce progeny. Thus, coinfections dominate later replication cycles, masking recessive host range expansion phenotypes. This may have impacted similar studies with other viruses. Last, structural and genetic data could be used to predict site-directed mutant phenotypes, which may broaden the classic antireceptor definition to include interfaces between capsid complexes., (Copyright © 2019 American Society for Microbiology.)

Over four billion people are discharging untreated human excreta into the environment without any prior treatment, causing eutrophication and spreading disease. The most nutrient rich fraction is the urine. Urine can be collected separately and dehydrated in an alkaline bed producing a nutrient rich fertiliser. However, faecal cross-contamination during the collection risks to introduce pathogens to the urine. The objective of this hygiene assessment was to study the inactivation of five microorganisms (Ascaris suum, Enterococcus faecalis, bacteriophages MS2 and ΦX 174 and Salmonella spp) in alkaline dehydrated urine. Fresh human urine was dehydrated in wood ash at 42 °C until the pH decreased to ≤10.5, at which point the saturated ash was inoculated with faeces containing the microorganisms and left open to the air (mimicking stockpiling of the end product) at temperatures of 20 and 42 °C. The bacteria and bacteriophages were inactivated to below the detection limit (100 cfu ml -1 for bacteria; 10 pfu mL -1 for bacteriophages) within four days storage at 20 °C. A. suum inactivation data was fitted to a non-linear regression model, which estimated a required 325 days of storage at 20 °C and 9.2 days at 42 °C to reach a 3 log 10 reduction. However, the urine dehydration in itself achieved a concentration <1 A. suum per 4 g of dehydrated medium which fulfil the WHO guidelines for unrestricted use., (Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The influence of virus type (PRD1 and ΦX174), temperature (flow at 4 and 20°C), a no-flow storage duration (0, 36, 46, and 70 d), and temperature cycling (flow at 20°C and storage at 4°C) on virus transport and fate were investigated in saturated sand-packed columns. The vast majority (84-99.5%) of viruses were irreversibly retained on the sand, even in the presence of deionized water and beef extract at pH = 11. The reversibly retained virus fraction () was small (1.6 × 10 to 0.047) but poses a risk of long-term virus contamination. The value of and associated transport risk was lower at a higher temperature and for increases in the no-flow storage period due to the temperature dependency of the solid phase inactivation. A model that considered advective-dispersive transport, attachment (), detachment (), solid phase inactivation (μ), and liquid phase inactivation (μ) coefficients, and a Langmuirian blocking function provided a good description of the early portion of the breakthrough curve. The removal parameters were found to be in the order of > μ >> μ. Furthermore, μ was an order of magnitude higher than μ for PRD1, whereas μ was two and three orders of magnitude higher than μ for ΦX174 at 4 and 20°C, respectively. Transport modeling with two retention, release, and inactivation sites demonstrated that a small fraction of viruses exhibited a much slower release and solid phase inactivation rate, presumably because variations in the sand and virus surface roughness caused differences in the strength of adhesion. These findings demonstrate the importance of solid phase inactivation, temperature, and storage periods in eliminating virus transport in porous media. This research has potential implications for managed aquifer recharge applications and guidelines to enhance the virus removal by controlling the temperature and aquifer residence time., (Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.)

Intrinsically Disordered Proteins (IDPs) are enriched in charged and polar residues; and, therefore, electrostatic interactions play a predominant role in their dynamics. In order to remain multi-functional and exhibit their characteristic binding promiscuity, they need to retain considerable dynamic flexibility. At the same time, they also need to accommodate a large number of oppositely charged residues, which eventually lead to the formation of salt-bridges, imparting local rigidity. The formation of salt-bridges therefore opposes the desired dynamic flexibility. Hence, there appears to be a meticulous trade-off between the two mechanisms which the current study attempts to unravel. With this objective, we identify and analyze salt-bridges, both as isolated as well as composite ionic bond motifs, in the molecular dynamic trajectories of a set of appropriately chosen IDPs. Time evolved structural properties of these salt-bridges like persistence, associated secondary structural 'order-disorder' transitions, correlated atomic movements, contribution in the overall electrostatic balance of the proteins have been studied in necessary detail. The results suggest that the key to maintain such a trade-off over time is the continuous formation and dissolution of salt-bridges with a wide range of persistence. Also, the continuous dynamic interchange of charged-atom-pairs (coming from a variety of oppositely charged side-chains) in the transient ionic bonds supports a model of dynamic flexibility concomitant with the well characterized stochastic conformational switching in these proteins. The results and conclusions should facilitate the future design of salt-bridges as a mean to further explore the disordered-globular interface in proteins., (Copyright © 2018 Elsevier B.V. All rights reserved.)

In this study, we quantified transport and retention behaviors of a human pathogenic virus (Adenovirus 41, abbreviated as Ad-41) and a model bacteriophage (ϕX174) through metal oxide-removed and goethite-coated sand under saturated flow conditions. Two sets of bench scale column experiments were conducted: transport of each type of viruses alone and co-transport of both viruses. All experiments were conducted at pH 7.5 using 2 mM artificial ground water (AGW) buffer as background solution. Experimental results revealed that goethite-coated sand (i.e., reactive sand) retained much more viruses relative to metal oxide-removed sand (i.e., non-reactive sand), with the difference more pronounced for ϕX174 (effluent concentration decreased by 92.1%) than for Ad-41 (effluent concentration decreased by 59.7%). Interestingly, lower retention of both viruses on goethite-coated sand was observed when they co-existed in the influent. The mutual promotion to the transport of the two viruses may be attributed to attachment site competition and steric hindrance effect (illustrated in the graphical abstract). Mass recovery results revealed that ϕX174 was largely reversibly attached, whereas Ad-41 was mostly irreversibly bound or inactivated. Force measurements using atomic force microscopy (AFM) demonstrated that ϕX174 had doubled affinity to goethite-coated sand compared with Ad-41, consistent with the transport behavior of each type of viruses when they existed alone. As expected, the extended DLVO theory cannot accurately estimate interfacial energy profiles for viruses and reactive sand that have heterogeneous surface properties (i.e., roughness and charge heterogeneity). The results of this study clearly demonstrate that caution must be taken when applying laboratory results, which are generally obtained from experiments employing a single virus species, to predict the mobility and environmental risks in natural systems where multiple agents are present., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Waterborne viruses are increasingly being considered in risk assessment schemes. In general, virus detection by culture methods is time consuming. In contrast, detection by quantitative polymerase chain reaction (qPCR) is more rapid and therefore, more suitable for monitoring. At present, qPCR lacks the essential ability for discriminating between infectious and non-infectious viruses, thus limiting its applicability for monitoring disinfection processes. In this study, a method was developed to quantify UV inactivation by long amplicon (LA)-qPCR. Bacteriophage phiX174 was used as a surrogate for human pathogenic viruses. A qPCR protocol was developed with new sets of primers, resulting in amplicon lengths of 108, 250, 456, 568, 955, 1063, 1544, and 1764 nucleotides. The log reduction of gene copies increased with increasing amplicon length. Additional treatment with the intercalating dye, PMA, had no effect, indicating that the bacteriophage capsids were not damaged by low pressure UV irradiation. A qPCR of nearly the complete genome (approx. 5000 nucleotides) showed similar results to the plaque assay. The log reduction in qPCR correlates with [specific amplicon length x UV dose]. The normalized DNA effect constant can be applied to calculate phiX174 inactivation based on qPCR detection., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Background: To our knowledge, no studies to date demonstrate potential spread of microbes during actual emergency medical service (EMS) activities. Our study introduces a novel approach to identification of contributors to EMS environment contamination and development of infection control strategies, using a bacteriophage surrogate for pathogenic organisms., Methods: Bacteriophage ΦX174 was used to trace cross-contamination and evaluate current disinfection practices and a hydrogen peroxide (H2O2) wipe intervention within emergency response vehicles. Prior to EMS calls, 2 surfaces were seeded with ΦX174. On call completion, EMS vehicle and equipment surfaces were sampled before decontamination, after decontamination per current practices, and after implementation of the intervention., Results: Current decontamination practices did not significantly reduce viral loads on surfaces (P = .3113), but H2O2 wipe intervention did (P = .0065). Bacteriophage spread to 56% (27/48) of sites and was reduced to 54% (26/48) and 40% (19/48) with current decontamination practices and intervention practices, respectively., Conclusion: Results suggest firefighters' hands were the main vehicles of microbial transfer. Current practices were not consistently applied or standardized and minimally reduced prevalence and quantity of microbial contamination on EMS surfaces. Although use of a consistent protocol of H2O2 wipes significantly reduced percent prevalence and concentration of viruses, training and promotion of surface disinfection should be provided., (Published by Elsevier Inc.)

The inactivation effects of pressurized CO2 against bacteriophage Qβ and ΦX174 were investigated under the pressure of 0.3-0.9 MPa, initial concentration of 10(7)-10(9) PFU/mL, and temperature of 17.8°C-27.2°C. The optimum conditions were found to be 0.7 MPa and an exposure time of 25 min. Under identical treatment conditions, a greater than 3.3-log reduction in bacteriophage Qβ was achieved by CO2, while a nearly 3.0 log reduction was observed for phage ΦX174. The viricidal effects of N2O (an inactivation gas with similar characteristics to CO2), normal acid (HCl), and CO2 treatment with phosphate buffered saline affirmed the chemical nature of CO2 treatment. The pumping cycle, depressurization rate, and release of intracellular substances caused by CO2 were its viricidal mechanisms. The results indicate that CO2 has the potential for use as a disinfectant without forming disinfection by-products., (Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.)

Objective: To evaluate the protective performance of a positive pressure bio-protective clothing against viral aerosol., Methods: The suspension of indicating virus phage Phi-X174 was made for viral aerosol generating in a hermetic cabin. The diameter of viral aerosol particles were measured with a aerodynamics size analyzer. By adjusting the inner humidity of the cabin, the protective efficiency of the positive pressure bio-protective clothing against viral aerosol in high and low windshield conditions was determined with Andersen six-stage air sampler sampling and plage forming unit (PFU) counting, respectively., Results: The mass median diameter of Phage Phi-X174 aerosol particles was about 0.922 µm and the background concentration is beyond 2 × 10⁴ particles/m³. The protective efficiency of the clothing against phage Phi-X174 aerosol particles was above 99.9% under different test conditions with the range of viral aerosol concentration between 0 - 23 PFU/m³. Airflow (P = 0.84), environment humidity conditions (P = 0.33) and sampling time (P = 0.07) did not affect the protective efficiency statistically., Conclusion: The positive pressure bio-protective clothing provided a relatively high efficiency against phage Phi-X174 aerosol regardless of airflow rate, environment humidity and sampling time.

Developing accurate, scalable algorithms to improve data quality is an important computational challenge associated with recent advances in high-throughput sequencing technology. In this study, a novel error-correction algorithm, called ECHO, is introduced for correcting base-call errors in short-reads, without the need of a reference genome. Unlike most previous methods, ECHO does not require the user to specify parameters of which optimal values are typically unknown a priori. ECHO automatically sets the parameters in the assumed model and estimates error characteristics specific to each sequencing run, while maintaining a running time that is within the range of practical use. ECHO is based on a probabilistic model and is able to assign a quality score to each corrected base. Furthermore, it explicitly models heterozygosity in diploid genomes and provides a reference-free method for detecting bases that originated from heterozygous sites. On both real and simulated data, ECHO is able to improve the accuracy of previous error-correction methods by several folds to an order of magnitude, depending on the sequence coverage depth and the position in the read. The improvement is most pronounced toward the end of the read, where previous methods become noticeably less effective. Using a whole-genome yeast data set, it is demonstrated here that ECHO is capable of coping with nonuniform coverage. Also, it is shown that using ECHO to perform error correction as a preprocessing step considerably facilitates de novo assembly, particularly in the case of low-to-moderate sequence coverage depth.

Bacterial ghosts (BGs) are empty bacterial envelopes generated by expulsion of the bacterial genome and cytoplasmic contents from bacterial cells, and the process is mediated by lysis protein E encoded on bacteriophage PhiX174. BGs represent a new approach in vaccine development and have been applied to a variety of gram-negative bacterial vaccine candidates. In this study, a BG vaccine generated from Salmonella enteritidis (S. enteritidis) strain DH091 was prepared using the highly efficient plasmid, pBV-mE. The efficacy of the BG vaccine was tested using 75 chicks (Gallus gallus) kept under specific pathogen-free (SPF) conditions. A comprehensive evaluation of the immune response, including humoral and cellular immune responses, interferon-γ (IFN-γ) and interleukin-4 (IL-4) production, and histopathology of various tissues, was performed in BG-vaccinated animals subsequently challenged with S. enteritidis. The results were compared with animals that were immunized with the inactivated vaccine. S. enteritidis ghosts not only promoted the generation of high titer antibodies and IFN-γ and IL-4 production but also stimulated a significant increase in CD8(+) and CD4(+) T lymphocytes. In particular, the dramatic increase in CD8(+) T cells indicated that the vaccine was able to induce clearance of intracellular Salmonella. The protective effects of BG vaccination in SPF chicks against 5×10(9) colony forming units of S. enteritidis were a result of the induction of a more effective immune response than that observed with the inactivated vaccine. These findings demonstrate the potential of S. enteritidis ghosts to be used as effective vaccines., (Copyright © 2010 Elsevier GmbH. All rights reserved.)

Among 40 Escherichia coli urine isolates from renal transplant recipients (Galveston, TX, 2003 to 2005), sequence type ST131 (O25:H4) was highly prevalent (representing 35% of isolates overall and 60% of fluoroquinolone-resistant isolates), virulent appearing, antimicrobial resistant (but extended-spectrum-cephalosporin susceptible), and associated with black race. Pulsotypes were diverse; some were linked to other locales. ST131 emerged significantly during the study period. These findings suggest that E. coli ST131 may constitute an important new multidrug-resistant threat to renal transplant recipients.

Fragile X syndrome and other trinucleotide diseases are characterized by an elongation of a repeating DNA triplet. The ensemble-averaged lambda exonuclease digestion rate of different substrates, including one with an elongated FMR1 gene containing 120 CGG repeats, was measured using absorption and fluorescence spectroscopy. By use of magnetic tweezers sequence-dependent digestion rates and pausing was measured for individual lambda exonucleases. Within the triplet repeats a lower average and narrower distribution of rates and a higher frequency of pausing was observed.

Ionizing radiation is responsible for production of double-strand breaks (DSBs) in a DNA structure. In contrast to sparsely ionizing radiation, densely ionizing radiation produces DSBs that are non-randomly distributed along the DNA molecule and can form clusters of various size. The paper discusses minimalistic models that describe observable patterns of fragment length in DNA segments irradiated with heavy ions and applies the formalism to interpret the recent experimental data collected by use of atomic force microscope (AFM).

Although there are powerful drugs against infectious diseases and cancer on the market, delivery systems are needed to decrease serious toxic and noncurative side effects. In order to enhance compliance, several delivery systems such as polymeric micro- and nanoparticles, liposomal systems and erythrocyte ghosts have been developed. Bacterial ghosts representing novel advanced delivery and targeting vehicles suitable for the delivery of hydrophobic or water-soluble drugs, are the main focus of this review. They are useful nonliving carriers, as they can carry different active substances in more than one cellular location separately and simultaneously. Bacterial ghosts combine excellent natural or engineered adhesion properties with versatile carrier functions for drugs, proteins and DNA plasmids or DNA minicircles. The simplicity of both bacterial ghost production and packaging of drugs and/or DNA makes them particularly suitable for the use as a delivery system. Further advantages of bacterial ghost delivery vehicles include high bioavailability and a long shelf life without the need of cold-chain storage due to the possibility to freeze-dry the material.

The DNA binding orientation and dynamic behavior of Cu(II) complexes of 1,4,7-triazacyclononane ([9]aneN(3)), 1, and an acridine conjugate, 2, were investigated by DNA fiber EPR (EPR=electron paramagnetic resonance) spectroscopy. Crystal and molecular structure of 2 were determined by X-ray diffraction. It has been shown that 1 binds to DNA in two different modes at room temperature; one species is rapidly rotating and the other is immobilized randomly on the DNA. The introduction of acridine to [9]aneN(3) fixed the [Cu([9]aneN(3))](2+) moiety of 2 in two different environments on the DNA: the g(mid R:mid R:) axis of one species (g( parallel)=2.26) is aligned perpendicularly to the DNA fiber axis whereas that of the other (g( parallel)=2.24) aligns<90 degrees with the DNA fiber axis. The different DNA binding structures of 1 and 2 are reflected also in their different efficiencies of DNA cleavage; 2 was found to be more effective both in oxidative and hydrolytic cleavage reactions.

The purpose of the present study was to develop a drug delivery model for water soluble drug substances using the bacterial ghost platform technology. Bacterial ghosts are non-denatured bacterial cell envelopes that are produced by the plasmid encoded gene E mediated lysis. We present a novel method to fill and seal bacterial ghosts for the application as a drug delivery system for fluid, non-anchored substances. E. coli ghosts were filled with the reporter substance calcein and sealed by fusion with membrane vesicles. By flow cytometry and fluorescence microscopy it was shown that bacterial ghosts can be filled with calcein, and that the bacterial ghosts can be sealed by restoring the membranes integrity. The adherence and uptake studies showed that almost all murine macrophages and a lower proportion of human colorectal adenocarcinoma cells took up fluorescence labeled bacterial ghosts. Moreover, these cells also took up effectively sealed E. coli ghosts filled with calcein, which then was released within the cells. Therefore, we propose bacterial ghosts as alternative drug delivery and release vehicles for advanced cell targeting.

Objectives: The difference in permeability between one brand of powdered and another of powder-free latex examination gloves was evaluated to determine leak rates., Methods: Thirty-one of each type of glove were tested for each of three different conditions: usage by dental personnel (1) for 15 minutes or longer, (2) for less than 15 minutes, and (3) directly from the manufacturer's packaging (zero usage time). Each glove was evaluated in the fingers and the palm. The phiX-174 viral solution in the glove was allowed to penetrate for 15 minutes. Powder (cornstarch) was subsequently added to 20 powder-free gloves, and 15 of these were pierced with a 30-gauge needle., Results: Powdered gloves showed no leakage rates. Because of this, 30-, 27-, and 25-gauge needles were used to pierce five gloves each. One glove with 27- and 25-gauge needle holes showed leakage. Leakage rates for powder-free gloves: 45.1 percent for more than 15 minutes of use, 25.8 percent for less than 15 minutes of use, and 16.1 percent for zero minutes of use. Two of the 20 pierced and one of the five unpierced powder-free gloves with added cornstarch leaked., Conclusion: Significant differences in leak results between powdered and powder-free gloves suggest further study is needed.

Bacterial ghosts are empty cell envelopes originating from Gram-negative bacteria. They have a natural outer surface make-up which provides them with the original targeting functions of the bacteria they are derived from and are thus able to bind to and/or are taken up by specific cells or tissues of animal, human or plant origin. The extended bacterial ghost system represents a platform technology for creating new qualities in non-living carriers which can be used for the specific targeting of drugs, DNA or other compounds to overcome toxic or non-desired obstacles. Freeze dried bacterial ghosts are stable without the requirement of a cold chain and can be effectively administered orally and aerogenically as drug carriers. The new system is an alternative to liposomes and may have an advantage due to its higher specificity for targeting specific tissues, its easy method of production and its versatility in entrapping and packaging various compounds in different compartments of the carriers.

Preliminary measurements on the production of single- and double-strand breaks in SV40 and phi X174 plasmid DNA by various heavy ions in radioprotective Tris buffer are presented. The dependence of the recorded yields on the LET of the incoming ions is discussed and shown to be comprehensible within the framework of a model based on the X-ray sensitivity of the exposed DNA and the local dose distribution inside the heavy ion track. The question of the influence of the chemical environment is addressed by comparing the measured cross sections to data recorded previously in more radiosensitive TE buffer. The results indicate that also for systems with high scavenging capacity RBE values larger than unity can be achieved with maximum values in the LET range 100-1000 keV micrometers-1.

The binuclear zinc(II) complex, [Zn2(HPTP)(CH3COO)]2+ was found highly active to cleave DNA (double-strand super-coiled DNA, pBR322 and phix174) in the presence of hydrogen peroxide. However, no TBARS (2-thiobarbituric acid reactive substance) formation was detected in a solution containing 2-deoxyribose (or 2'-deoxyguanosine, etc); where (HPTP) represents N,N,N'-N'-tetrakis(2-pyridylmethyl)-1,3-diamino-2-propanol. These facts imply that DNA cleavage reaction by the binuclear Zn(II)/H2O2 system should be due to a hydrolytic mechanism, which may be attributed to the enhanced nucleophilicity but depressed electrophilicity of the peroxide ion coordinated to the zinc(II) ion. DFT (density-functional theory) calculations on the peroxide adduct of monomeric zinc(II) have supported the above consideration. Similar DFT calculations on the peroxide adducts of the Al(III) and La(III) compounds have revealed that electrophilicity of the peroxide ion in these compounds is strongly reduced. This gives an important information to elucidate the fact that La3+ can enhance the growth of plants under certain conditions.

Virus retention during ultrafiltration through A/G Technology filter cartridges was investigated to characterize the removal process and validate the degree of virus titre reduction during the filtration of red blood cell haemolysates performed as part of the production of diaspirin crosslinked haemoglobin (DCLHb). When viruses were suspended in phosphate buffered saline solution, retention was greater with larger sized viruses and smaller filter pore size. Virus titre was maintained at starting levels in the filter retentate circuit during the course of filtration, suggesting that the virus removal mechanism is predominantly size exclusion. Evaluation of specific processing variables indicated that the retention of phiX174 virus was increased in the presence of red blood cell haemolysate or at high membrane crossflow rates and transmembrane pressures, while the retention of EMC virus was less sensitive to variations in these parameters. Using these results to design a validation protocol, log reduction values of >7.9 were demonstrated for the retention of human immunodeficiency virus, pseudorabies virus and bovine viral diarrhoea viruses, 7.6 for hepatitis A virus, and 4.2 for porcine parvovirus. It was also shown that the retention of viruses was maintained during repetitive use of the same filter cartridge.

Fenofibrate and ketoprofen (KP) are two drugs of similar structure derived from that of benzophenone. Both are photoallergic and promote cross reactions in patients. However, the cutaneous photosensitizing properties of KP also include phototoxic effects and are more frequently mentioned. To account for this difference in their in vivo properties, their in vitro photosensitizing properties on DNA were compared. First, it was shown that under irradiation at 313 nm, fenofibric acid (FB), the main metabolite of fenofibrate, photosensitized DNA cleavage by a radical mechanism similar to that proposed for KP but with a 50 times lower efficiency. Furthermore, FB did not photosensitize the formation of pyrimidine dimers into DNA in contrast to KP, which did promote this type of DNA damage. Their difference in efficiency as DNA breakers was compared to their relative photochemical reactivity and the quantum yield of FB photolysis was found to be eightfold lower than that of KP. The reactivity of these drugs cannot explain alone the difference in their photosensitizing properties. Other factors such as the magnitude of the ionic character of the photodecarboxylation pathway of these benzophenone-like drugs are considered in the discussion.

A detailed study is presented on the detection of various known point mutations using polymerase chain reaction (PCR) based multi-allele specific amplification (MASA) in conjunction with capillary gel electrophoresis (CGE) separation. The resulting PCR products, corresponding to the individual mutations, are labeled with ethidium bromide during CGE separation, and detected by laser-induced fluorescence. MASA proved to be a novel, fast and cost-effective method for simultaneous analysis of multiple known mutation sites, employing more than one allele specific primers in a single PCR reaction. It results in coexisting amplification of numerous DNA fragments differing in size, which are subsequently separated by CGE. In the present study, several point mutations were analyzed simultaneously by MASA-CGE on the 21-hydroxylase gene of a patient with congenital adrenal hyperplasia.

Electrophoretic velocity and orientation have been used to study the electric-field-induced trapping of supercoiled and relaxed circular DNA (2926 and 5386 bp) in polyacrylamide gels (5% T, 3.3% C) at 7.5-22.5 V/cm, using as controls linear molecules of either the same contour length or the same radius of gyration. The circle-specific trapping is reversible. From the duration of the reverse pulse needed to detrap the molecules, the average trap depth is estimated to be 90 A, which is consistent with the molecular charge and the field strengths needed to keep molecules trapped. Trapped circles exhibit a strong field alignment compared to the linear form, and there is a good correlation between the enhanced field alignment for the circles and the onset of trapping in both constant and pulsed fields. The circles do not exhibit the orientation overshoot response to a field pulse seen with linear DNA, and the rate of orientation growth scales as E(-2+/-0.1) with the field, as opposed to E(-1.1+/-0.1) for the linear form. These results show that the linear form migrates by cyclic reptation, whereas the circles most likely are trapped by impalement on gel fibers. This proposal is supported by very similar velocity and orientation behavior of circular DNA in agarose gels, where impalement has been deemed more likely because of stiffer gel fibers. The trapping efficiency is sensitive to DNA topology, as expected for impalement. In polyacrylamide the supercoiled form (superhelical density sigma = -0.05) has a two- to fourfold lower probability of trapping than the corresponding relaxed species, whereas in agarose gels the supercoiled form is not trapped at all. These results are consistent with existing data on the average holes in the plectonemic supercoiled structures and the fiber thicknesses in the two gel types. On the basis of the topology effect, it is argued that impalement during pulsed-field electrophoresis in polyacrylamide gels may be useful for the separation of more intricate DNA structures such as knots. The results also indicate that linear dichroism on field-aligned molecules can be used to measure the supercoiling angle, if relaxed DNA circles are used as controls for the global degree of orientation.

Ultraviolet light is known to generate crosslinks between the complementary strands of DNA and between DNA and proteins. Here we demonstrate that the UV light also crosslinks DNA duplexes to other DNA duplexes. However, the duplex-to-duplex crosslinks only appear in the presence of about 75% (vol/vol) ethanol plus a millimolar or submillimolar concentration of monovalent or divalent cations, e.g. 2 mM Na+. Methanol or formamide are ineffective. The present observations provide a direct means to detect physical contacts of DNA molecules or their parts, e.g. during recombination. It is remarkable that the solution conditions leading to the duplex-to-duplex UV light-induced crosslink formation are the same as those inducing the B-to-A conformational transition of DNA.

We have characterized a DNA binding protein (DBNP-B) from the thermoacidophilic archaeon Sulfolobus acidocaldarius with respect to its interaction with single and double stranded DNA. The protein in solution exists predominantly as dimer as indicated by cross linking studies. Binding of DBNP-B to etheno DNA and poly (dA) resulted in fluorescence enhancement and hyperchromicity respectively. Ethidium bromide intercalated into DNA was completely displaced by DBNP-B. DNase I digestion of dsDNA was increased at subsaturating concentration of the protein and was inhibited at higher concentrations. These results and electron microscopy indicate that the protein forms different types of novel complexes with DNA at different protein to DNA ratios.

Universal precautions mandate the use of examination and surgical gloves to protect the health professional from contact with the HIV virus. The purpose of this paper is to provide a review of the literature on the barrier properties of examination and surgical gloves measured by water leakage and viral penetration. The literature data indicate that glove composition, glove manufacturer, glove design (examination vs. surgical), and mechanical manipulation had considerable influence on glove performance when tested for leakage and viral penetration. In general, latex gloves were found to be superior to vinyl gloves as barriers to water leakage and viral penetration.

The purpose of this study was to determine whether glove hydration influenced bacteriophage penetration. Using an electronic glove hole-detection device, one brand of latex glove was identified that hydrated rapidly (3.25 min +/- 0.71 min), while another brand was selected that resisted hydration (120 min +/- 0 min). Using a standard bacteriophage penetration model, the amount of bacteriophage penetration in both the rapidly hydrating gloves and the gloves that resisted hydration was extremely small and did not differ significantly from each other.

Initiation of Escherichia coli DNA synthesis primed by homologous recombination is believed to require the phiX174-type primosome, a mobile priming apparatus assembled without the initiator protein DnaA. We show that this primosome plays an essential role in bacteriophage Mu DNA replication by transposition. Upon promoting transfer of Mu ends to target DNA, the Mu transpososome undergoes transition to a pre-replisome that permits initiation of DNA synthesis only in the presence of primosome assembly proteins PriA, DnaT, DnaB and DnaC. These assembly proteins promote the engagement of primase and DNA polymerase III holoenzyme, initiating semi-discontinuous replication preferentially at the Mu left end. The results indicate that these proteins play a crucial role in promoting replisome assembly on a recombination intermediate.

The co-purification of the U1snRNP particle with a high-molecular-weight human homologous pairing activity has been observed consistently. Using human autoimmune sera directed against various snRNPs, it has been found that autoantibody binding to antigenic determinants specifically associated with the U1snRNP particle inhibits the formation of paired DNA molecules by the human homologous pairing activity. Immunoprecipitation of U1snRNP with anti-(U1)RNP autoantibodies significantly reduced the homologous pairing activity in these fractions. NaDodSO4-PAGE analysis of immunoprecipitated samples has revealed their content to be mostly composed of anti-(U1)RNP precipitable material. Taken together, these results suggest that some biochemical reactions in the process of homologous pairing promoted by high-molecular-weight complex are dependent upon U1snRNP components. It is postulated that the U1snRNP may be associated with the recombination complex in human cells.

The RepA protein of plasmid pC194 initiates and terminates rolling circle replication. At initiation, it forms a 5'-phosphotyrosyl DNA link, whereas at termination, a glutamate residue directs hydrolytic cleavage of the newly synthesized origin, and the resulting 3'-hydroxyl group undergoes transesterification with the phosphotyrosine link. The protein is thus released from DNA, and the termination is uncoupled from reinitiation of replication. Replacement of the glutamate with tyrosine in RepA altered this mechanism, so that termination occurred by two successive transesterifications and became coupled to reinitiation. This result suggests that various enzymes involved in DNA cleavage and rejoining may have similar mechanistic and evolutionary roots.

Replacement of lysine 72 in RecA protein with arginine produces a mutant protein that binds but does not hydrolyze ATP. The protein nevertheless promotes DNA strand exchange (Rehrauer, W. M., and Kowalczykowski, S. C. (1993) J. Biol. Chem. 268, 1292-1297). With RecA K72R protein, the formation of the hybrid DNA product of strand exchange is greatly affected by the concentration of Mg2+ in ways that reflect the concentration of a Mg.dATP complex. When Mg2+ is present at concentrations just sufficient to form the Mg.dATP complex, substantial generation of completed product hybrid DNAs over 7 kilobase pairs in length is observed (albeit slowly). Higher levels of Mg2+ are required for optimal uptake of substrate duplex DNA into the nucleoprotein filament, indicating that the formation of joint molecules is facilitated by Mg2+ levels that inhibit the subsequent migration of a DNA branch. We also show that the strand exchange reaction promoted by RecA K72R, regardless of the Mg2+ concentration, is bidirectional and incapable of bypassing structural barriers in the DNA or accommodating four DNA strands. The reaction exhibits the same limitations as that promoted by wild type RecA protein in the presence of adenosine 5'-O-(3-thio)triphosphate. The Mg2+ effects, the limitations of RecA-mediated DNA strand exchange in the absence of ATP hydrolysis, and unusual DNA structures observed by electron microscopy in some experiments, are interpreted in the context of a model in which a fast phase of DNA strand exchange produces a discontinuous three-stranded DNA pairing intermediate, followed by a slow phase in which the discontinuities are resolved. The mutant protein also facilitates the autocatalytic cleavage of the LexA repressor, but at a reduced rate.

RecA protein promotes a limited DNA strand exchange reaction, without ATP hydrolysis, that typically results in formation of short (1-2 kilobase pairs) regions of hybrid DNA. This nascent hybrid DNA is extended in a reaction that can be coupled to ATP hydrolysis. When ATP is hydrolyzed, the extension phase is progressive and its rate is 380 +/- 20 bp min-1 at 37 degrees C. A single RecA nucleoprotein filament can participate in multiple DNA strand exchange reactions concurrently (involving duplex DNA fragments that are homologous to different segments of the DNA within a nucleoprotein filament), with no effect on the observed rate of ATP hydrolysis. The ATP hydrolytic and hybrid DNA extension activities exhibit a dependence on temperature between 25 and 45 degrees C that is, within experimental error, identical. This provides new evidence that the two processes are coupled. Arrhenius activation energies derived from the work are 13.3 +/- 1.1 kcal mole-1 for DNA strand exchange, and 14.4 +/- 1.4 kcal mole-1 for ATP hydrolysis during strand exchange. The rate of branch movement in the extension phase (base pair min-1) is related to the kcat for ATP hydrolysis during strand exchange (min-1) by a factor equivalent to 18 bp throughout the temperature range examined. The 18-base pair factor conforms to a quantitative prediction derived from a model in which ATP hydrolysis is coupled to a facilitated rotation of the DNA substrates. RecA filaments possess an intrinsic capacity for DNA strand exchange, mediated by binding energy rather than ATP hydrolysis, that is augmented by an ATP-dependent molecular motor.

The Escherichia coli RecA protein has served as a model for understanding protein-catalyzed homologous recombination, both in vitro and in vivo. Although RecA proteins have now been sequenced from over 60 different bacteria, almost all of our structural knowledge about RecA has come from studies of the E. coli protein. We have used electron microscopy and image analysis to examine three different structures formed by the RecA protein from the thermophilic bacterium Thermus aquaticus. This protein has previously been shown to catalyze an in vitro strand exchange reaction at an optimal temperature of about 60 degrees C. We show that the active filament formed by the T. aquaticus RecA on DNA in the presence of a nucleotide cofactor is extremely similar to the filament formed by the E. coli protein, including the extension of DNA to a 5.1-A rise per base pair within this filament. This parameter appears highly conserved through evolution, as it has been observed for the eukaryotic RecA analogs as well. We have also characterized bundles of filaments formed by the T. aquaticus RecA in the absence of both DNA and nucleotide cofactor, as well as hexameric rings of the protein formed under all conditions examined. The bundles display a very large plasticity of mass within the RecA filament, as well as showing a polymorphism in filament-filament contacts that may be important to understanding mutations that affect surface residues on the RecA filament.

In this paper we explore the feasibility of using DNA molecules as a biophysical radiation dosimeter. Supercoiled phi X174 bacteriophage DNA molecules were irradiated with different gamma radiation doses. The strand breakage produced by ionizing radiation within supercoiled double-stranded DNA molecules (RFI) yields relaxed circular DNA molecules (RFII) and linear DNA molecules (RFIII) as a result of single-strand breaks and double-strand breaks, respectively. The irradiated samples were subjected to electrophoresis on agarose gels to separate the three forms. A proprietary fluorescent dye was used to detect DNA bands within the gel, which was photographed under UV transillumination. The negative was scanned with a computerized imaging densitometric system for DNA band quantitation. The relative fractions of the three molecular forms are dose dependent, and can be modeled mathematically with five parameters. The values of the parameters were determined by optimizing the fit of the model to the data, using a nonlinear regression procedure of a commercial statistical analysis package. Once the parameters of DNA breakage have been determined, absorbed dose can be measured by this technique, which we have termed supercoil relaxation dosimetry. The average accuracy of dose determination for our system over the range of 1-40 Gy was about 5%. Supercoil relaxation dosimetry may be well suited to certain difficult dosimetric problems.

The influence of the nature of ligands on the efficiency of ruthenium complexes for photosensitizing DNA cleavage was investigated. Ru(bipy)2dppz2+ and Ru(bpz)2dppz2+ were selected as DNA breakers on the basis of their high affinity for DNA due to the presence of a dppz ligand which can partially intercalate in the major groove of DNA. Their photosensitizing properties were compared to those of Ru(bipy)3(2+), a complex which binds to DNA with a far lower constant. Upon irradiation, these complexes promoted the formation of single strand breaks in supercoiled phi X 174 DNA. Unexpectedly, Ru(bipy)2dppz2+ was found to be less efficient than Ru(bipy)3(2+) whatever the dye concentration or the [base pair]/[Ru] molar ratio r. Scavenging experiments have shown that the oxidative DNA cleavage induced by Ru(bipy)2dppz2+ mainly results from a Type II mechanism. The behavior of Ru(bipy)2dppz2+ was different: this compound was clearly more efficient than Ru(bipy)3(2+) as DNA breaker and its efficiency was not modified by the presence of oxygen or by addition of scavengers of reactive oxygen species. In this case, a mechanism involving electron transfer between the excited state of the ruthenium complex and the guanine residue was proposed in agreement emission lifetime measurements. The change in mechanism observed between Ru(bipy)2dppz2+ and Ru (bipy)2dppz2+ results from an increase of the reduction potential of the ruthenium complexes in the excited state, which appears to be the main factor controlling the efficiency.

The RAD51 gene of Saccharomyces cerevisiae is required for genetic recombination and DNA double-strand break repair. Here it is demonstrated that RAD51 protein pairs circular viral single-stranded DNA from phi X 174 or M13 with its respective homologous linear double-stranded form. The product of synapsis between these DNA partners is further processed by RAD51 to yield nicked circular duplex DNA, which indicates that RAD51 can catalyze strand exchange. The pairing and strand exchange reaction requires adenosine triphosphate, a result consistent with the presence of a DNA-dependent adenosine triphosphatase activity in RAD51 protein. Thus, RAD51 is a eukaryotic recombination protein that can catalyze the strand exchange reaction.

Xeroderma pigmentosum (XP), a genetically heterogeneous human disease, results from a defect in nucleotide excision repair of ultraviolet-damaged DNA. XP patients are extremely sensitive to sunlight and suffer from a high incidence of skin cancers. Cell fusion studies have identified seven XP complementation groups, A-G. Group D is of particular interest as mutations in this gene can also cause Cockayne's syndrome and trichothiodystrophy. The XPD gene was initially named ERCC2 (excision repair cross complementing) as it was cloned using human DNA to complement the ultraviolet sensitivity of a rodent cell line. We have purified the XPD protein to near homogeneity and show that it possesses single-stranded DNA-dependent ATPase and DNA helicase activities. We tested whether XPD can substitute for its yeast counterpart RAD3, which is essential for excision repair and for cell viability. Expression of the XPD gene in Saccharomyces cerevisiae can complement the lethality defect of a mutation in the RAD3 gene, suggesting that XPD is an essential gene in humans.