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Unlabelled: Prior research suggests that cold temperatures may stimulate the proliferation of certain antibiotic resistance genes (ARGs) and gene transfer elements during storage of biosolids. This could have important implications on cold weather storage of biosolids, as often required in northern climates until a time suitable for land application. In this study, levels of an integron-associated gene (intI1) and an ARG (sul1) were monitored in biosolids subject to storage at 4, 10 and 20°C. Both intI1 and sul1 were observed to increase during short-term storage (<2 months), but the concentrations returned to background within 4 months. The increases in concentration were more pronounced at lower temperatures than ambient temperatures. Overall, the results suggest that cold stress may induce horizontal gene transfer of integron-associated ARGs and that biosolids storage conditions should be considered prior to land application., Significance and Impact of the Study: Wastewater treatment plants have been identified as the hot spots for the proliferation and dissemination of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) to the environment through discharge of treated effluent to water bodies as well as application of biosolids to land. Identifying critical control points within the treatment process may aid in the development of solutions for the reduction of ARGs and ARB and curbing the spread of antibiotic resistance. This study found increases in ARGs during biosolids storage and identifies changes in operational protocols that could help reduce ARG loading to the environment when biosolids are land-applied., (© 2014 The Society for Applied Microbiology.)

A novel secondary sponge metabolite, peloruside A (peloruside), isolated from the marine sponge Mycale sp. (New Zealand), was tested for its cytotoxic effects on mammalian cells in culture. The macrolide structure of peloruside is similar to that of the protein kinase C (PKC) activator, bryostatin-1 (bryostatin), both containing a pyranose ring adjacent to a gemdimethyl moiety. Peloruside is a potent inhibitor of cell proliferation. Treatment of different mammalian cell lines with peloruside for 48-96 h gave IC50 values ranging from 4 to 15 nM, using the colorimetric 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyl tetrazolium (MTT) cell proliferation assay. Peloruside was shown to be both cytostatic and cytotoxic by trypan blue dye exclusion tests. Peloruside induced apoptosis in a dose-dependent manner in murine (32D) and human (HL-60) myeloid cell lines, revealed by DNA laddering in agarose gels and flow cytometric analysis of annexin-V- and propidium iodide-stained cells. Treatment of HL-60 cells caused vacuolisation, partial substrate adherence, and the appearance of multi-lobed nuclei, suggesting the induction of a differentiation pathway. Vacuolisation was also observed in a human lung cancer cell line (H441). Opening of the pyranose ring of peloruside by sodium borohydride reduction increased the 48 h IC50 value by 26-fold in 32D cells, suggesting a similar active site to that proposed for bryostatin. However, unlike bryostatin, peloruside failed to bind to PKC in HL-60 cells and was unable to synergize with the calcium ionophore, ionomycin, or with interleukin-2, to activate T-lymphocytes in culture. In summary, although structurally similar to bryostatin, peloruside is a potent inhibitor of cell proliferation, has apoptosis-inducing properties and has a unique mode of action independent of PKC.

A precise, sensitive, repeatable and robust reverse-phase liquid chromatographic method has been developed for the control of seven possible impurities of diphenhydramine hydrochloride. The robustness of the method was examined by varying, in turn, each of four mobile-phase parameters (acetonitrile content, buffer salt concentration, ion-pair reagent concentration and pH). The method was linear in the range 0-0.14 mg mL(-1) for diphenhydramine hydrochloride with an acceptable precision and accuracy, and a limit of detection of 0.17 microg mL(-1). Five samples of diphenhydramine hydrochloride from two sources were analysed with the developed liquid chromatographic method.

Pyrimidine adducts in cellular DNA arise from modification of the pyrimidine 5,6-double bond by oxidation, reduction or hydration. The biological outcome includes increased mutation rate and potential lethality. A major DNA N:-glycosylase responsible for the excision of modified pyrimidine bases is the base excision repair (BER) glycosylase endonuclease III, for which functional homologs have been identified and characterized in Escherichia coli, yeast and humans. So far, little is known about how hyperthermophilic Archaea cope with such pyrimidine damage. Here we report characterization of an endonuclease III homolog, PaNth, from the hyperthermophilic archaeon Pyrobaculum aerophilum, whose optimal growth temperature is 100 degrees C. The predicted product of 223 amino acids shares significant sequence homology with several [4Fe-4S]-containing DNA N:-glycosylases including E.coli endonuclease III (EcNth). The histidine-tagged recombinant protein was expressed in E.coli and purified. Under optimal conditions of 80-160 mM NaCl and 70 degrees C, PaNth displays DNA glycosylase/ss-lyase activity with the modified pyrimidine base 5,6-dihydrothymine (DHT). This activity is enhanced when DHT is paired with G. Our data, showing the structural and functional similarity between PaNth and EcNth, suggests that BER of modified pyrimidines may be a conserved repair mechanism in Archaea. Conserved amino acid residues are identified for five subfamilies of endonuclease III/UV endonuclease homologs clustered by phylogenetic analysis.

Adenine-DNA glycosylase MutY of Escherichia coli catalyzes the cleavage of adenine when mismatched with 7,8-dihydro-8-oxoguanine (GO), an oxidatively damaged base. The biological outcome is the prevention of C/G-->A/T transversions. The molecular mechanism of base excision repair (BER) of A/GO in mammals is not well understood. In this study we report stimulation of mammalian adenine-DNA glycosylase activity by apurinic/apyrimidinic (AP) endonuclease using murine homolog of MutY (Myh) and human AP endonuclease (Ape1), which shares 94% amino acid identity with its murine homolog Apex. After removal of adenine by the Myh glycosylase activity, intact AP DNA remains due to lack of an efficient Myh AP lyase activity. The study of wild-type Ape1 and its catalytic mutant H309N demonstrates that Ape1 catalytic activity is required for formation of cleaved AP DNA. It also appears that Ape1 stimulates Myh glycosylase activity by increasing formation of the Myh-DNA complex. This stimulation is independent of the catalytic activity of Ape1. Consequently, Ape1 preserves the Myh preference for A/GO over A/G and improves overall glycosylase efficiency. Our study suggests that protein-protein interactions may occur in vivo to achieve efficient BER of A/GO.

We have examined the composition of members of mutator populations of Escherichia coli by employing an extensive set of phenotypic screens that allow us to monitor the function of >700 genes, constituting approximately 15% of the genome. We looked at mismatch repair deficient cells after repeated cycles of single colony isolation on rich medium to generate lineages that are forced through severe bottlenecks, and compared the results to those for wild-type strains. The mutator lineages continued to accumulate mutations rapidly with each increasing cycle of colony isolation. By the end of the 40th cycle, after approximately 1000 generations, most of the lineages had reduced colony size, 4% had died out, 55% had auxotrophic requirements (increasing to 80% after 60 cycles), and 70% had defects in at least one sugar or catabolic pathway. In addition, 33% had a defect in cell motility, and 26% were either temperature-sensitive or cold-sensitive lethals. On the other hand, only 3% of the wild-type lineages had detectable mutations of any type after 40 cycles. By the 60th cycle, the typical mutator cell carried 4-5 inactive genes among the 15% of the genome being monitored, indicating that the average cell carried at least 24-30 inactivated genes distributed throughout the genome. Remarkably, 30% of the lineages had lost the ability to utilize xylose as a carbon source. DNA sequencing revealed that most of the Xyl(-) mutants had a frameshift in a run of eight G's (GGGGGGGG) in the xylB gene, either adding or deleting one -G-. Further analysis indicated that rendering E. coli deficient in mismatch repair unmasks hypermutable sites in certain genes or intergenic regions. Growth curves and competition tests on lineages that passed through 90 cycles of single colony isolation showed that all lineages suffered reduced fitness. We discuss these results in terms of the value of mutators in cellular evolution.

Background: This was a retrospective review of the long-term results of femorotibial bypass using autologous vein and polytetrafluoroethylene (PTFE) over 24 years., Methods: Some 518 patients who underwent 635 femorotibial bypass grafts were studied. Outcome measures analysed included primary and secondary graft patency, limb salvage rates and death., Results: Overall primary and secondary graft patencies were 62 and 67 per cent respectively at 12 months, and 44 and 48 per cent at 24 months. For vein grafts, the primary and secondary patencies were 63 and 66 per cent at 12 months, and 54 and 56 per cent at 24 months. For PTFE grafts, the primary and secondary patencies were 48 and 54 per cent at 12 months, and 31 and 37 per cent at 24 months. Limb salvage and patient survival rates were 81 and 84 per cent at 12 months, and 73 and 74 per cent at 24 months. Primary and secondary graft patencies for vein were significantly better than for PTFE (P = 0.0001). There was no difference in patency between reversed and in situ grafts., Conclusion: Femorotibial bypass can produce excellent long-term results. Vein remains the conduit of choice but in the absence of vein acceptable results can be achieved with PTFE.

Molecular dynamics simulations were performed on the duplex DNA dodecamers d(CGCGAA TT CGCG): d(CGCGAATTCGCG) and d(GCACGAA TT AAG): d(CTTAATTCGTGC), where TT denotes a cis, syn cyclobutane thymine dimer. The constant temperature and pressure algorithm of the AMBER 4.1 molecular-modeling package was used with explicit water and counterions, periodic boundary conditions and electrostatic interactions evaluated by the particle-mesh Ewald method. Results were analyzed by the CURVES algorithm and its implementation in DIALS and WINDOWS. Calculated distortions of DNA structure by the thymine dimer were qualitatively and quantitatively similar for the two sequences. Despite the enhanced flexibility of the native TpA dinucleotide step, major deviations from the B-DNA values of helicoidal parameters were found only at the Ap and p dinucleotide steps in both sequences. Only the AT base pairs of the two sequences that contain the 5' thymine of the dimers exhibited weakened Watson-Crick hydrogen bonds and anomalous stretching. Hence, we conclude that the pattern of structural perturbations responsible for recognition of cis, syn thymine dimers by repair enzymes is not sensitive to their sequence context.

The hyperthermophilic archaeum, Pyrobaculum aerophilum, grows optimally at 100 degrees C with a doubling time of 180 min. It is a member of the phylogenetically ancient Thermoproteales order, but differs significantly from all other members by its facultatively aerobic metabolism. Due to its simple cultivation requirements and its nearly 100% plating efficiency, it was chosen as a model organism for studying the genome organization of hyperthermophilic ancient archaea. By a G+C content of the DNA of 52 mol%, sequence analysis was easily possible. At least some of the mRNA of P. aerophilum carried poly-A tails facilitating the construction of a cDNA library. 245 sequence tags of a poly-A primed cDNA library and 55 sequence tags from a 1-2 kb Sau3AI-fragment containing genomic library were analyzed and the corresponding amino acid sequences compared with protein sequences from databases. Fourteen percent of the cDNA and >9% of genomic DNA sequence tags revealed significant similarities to proteins in the databases. Matches were obtained to proteins from archaeal, bacterial and eukaryal sources. Some sequences showed greatest similarity to eukaryal rather than to bacterial versions of proteins, other matches were found to proteins which had previously only been found in eukaryotes.

A retrospective investigation was performed to study the benefit obtained from a vein cuff inserted at the distal anastomosis of a primary femoropopliteal bypass graft with polytetrafluoroethylene (PTFE). When PTFE was preferred to vein an attempt was made to assess whether there was subsequent use for the spared vein. A series of 559 primary PTFE bypasses was studied and found to have a cumulative patency rate of 62 per cent at 36 months. Subgroups were also studied for a similar period. In the above-knee position there was no difference in the primary patency rate of PTFE with or without a cuff at 36 months (69 versus 68 per cent, P = 0.89). Below the knee, grafts with a cuff had a better 36-month patency rate than those without (57 versus 29 per cent, P = 0.01). Cuffed PTFE for claudication had a better patency rate than that for threatened limbs at 36 months (68 versus 60 per cent, P = 0.03). Thrombectomy of occluded cuffed PTFE grafts improved the 36-month patency rate from 64 to 74 per cent. The limb salvage rate at 36 months was 97 per cent for claudication and 89 per cent for threatened limbs with cuffed PTFE. Occlusion of cuffed PTFE was associated with preservation of outflow in 91 (51 per cent) of 179 cases, permitting subsequent graft thrombectomy or insertion of a new bypass. Spared vein was rarely used to salvage an occluded PTFE graft, and was associated with poor patency and a high amputation rate. Although this study does not support the use of PTFE for the primary graft, PTFE with a vein cuff interposed at the distal anastomosis is a reasonable substitute when vein is not available.

Formation of intramolecular cross links by addition of C(5') deoxyribose radicals to the C(8)-N(7) double bond of an attached adenine base was analyzed by ab initio quantum-chemical methods. Conformational preferences that influence the stereospecificity of the reaction were investigated. A good correlation was found between the ratio of experimental yields of R and S stereoisomers of 8,5'-cyclodeoxyadenosine and the relative energy of conformations of the C(5') radical that are precursors to these isomers. Molecular mechanics based on the AMBER force field was used to model the effect of 8,5'-cyclodeoxyadenosine on the conformation of the DNA dodecamer d(CGCGAATTCGCG)2 with the lesion at the A6 position. The R and S stereoisomers of the intrastrand cross link cause comparable levels of DNA distortion with the major conformational changes occurring in backbone torsional angles at the site of the lesion.

Using site-specific mutagenesis in vitro, we have constructed Escherichia coli strains that allow the detection of the inversion of an 800-bp segment in the lac region. The invertible segment is bounded by inverted repeats of either 12 or 23 bp. Inversions occurring at these inverted repeats will restore the Lac+ phenotype. Inversions can be detected at both short homologies at frequencies ranging from 0.5 x 10(-8) to 1 x 10(-7). These events, which have been verified by DNA sequence analysis, are reduced up to 1000-fold in strains deficient for either RecA, RecB or RecC. They are not reduced in strains deficient in the RecF, J pathway. These results show that the RecB,C,D system can mediate rearrangements at short sequence repeats, and probably plays a major role in cellular rearrangements.

We have cloned chromosomal DNA bordering an insert that inactivates mutM. Sequencing of this clone has revealed that the insertion element is located between the promoter and structural gene for formamidopyrimidine-DNA glycosylase (Fapy-DNA glycosylase). An overproducing clone of Fapy-DNA glycosylase complements the original mutM strain that had been isolated after EMS mutagenesis. Thus, we conclude that MutM is actually Fapy-DNA glycosylase. mutM has previously been characterized as a mutator strain that leads specifically to G.C----T.A transversions. This in vivo characterization correlates well with the mutagenic potential of one of the lesions Fapy-DNA glycosylase removes, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-OxodG).

Using site-specific mutagenesis in vitro we constructed a genetic system to detect mutants with altered rates of deletion formation between short repeated sequences in Escherichia coli. After in vivo mutagenesis with chemical mutagens and transposons, the system allowed the identification of mutants with either increased or decreased deletion frequencies. One mutational locus, termed mutR, that results in an increase in deletion formation, was studied in detail. The mutR gene maps at 38.5 min on the E. coli genetic map. Since the precise excision of many transposable elements is also mediated at short repeated sequences, we investigated the effects of the mutant alleles, as well as recA, on precise excision of the transposon Tn9. Neither mutR nor recA affect precise excision of the transposon Tn9, from three different insertions in lacI, whereas these alleles do affect other spontaneous deletions in the same system. These results indicate that deletion events leading to precise excision occur principally via a different pathway than other random spontaneous deletions. It is suggested that, whereas precise excision occurs predominantly via a pathway involving replication enzymes (for instance template strand slippage), deletions on an F'factor are stimulated by recombination enzymes.

The mutY gene of Escherichia coli, which codes for an adenine glycosylase that excises the adenine of a G-A mispair, has been cloned and sequenced. The mutY gene codes for a protein of 350 amino acids (Mr = 39,123) and the clone genetically complements the mutY strain. The protein shows significant sequence homology to E. coli endonuclease III, an enzyme that has previously been shown to have glycosylase activity on damaged base pairs. Sequence analysis suggests that, like endonuclease III, MutY is an iron-sulfur protein with a [4Fe-4S]2+ cluster.

We have used site-directed mutagenesis to alter bases in lacZ near the region encoding essential residues in the active site of beta-galactosidase. The altered sequences generate runs of six or seven identical base pairs which create a frameshift, resulting in a Lac- phenotype. Reversion to Lac+ in each strain can occur only by a specific frameshift at these sequences. Monotonous runs of A's (or of T's on the opposite strand) and G's (or C's) have been constructed, as has an alternating -C-G- sequence. These specific frameshift indicator strains complement a set of six previously described strains which detect each of the base substitutions. We have examined a variety of mutagens and mutators for their ability to cause reversion to Lac+. Surprisingly, frameshifts are well stimulated at many of these runs by ethyl methanesulfonate, N-methyl-N'-nitro-N-nitrosoguanidine and 2-amino-purine, mutagens not widely known to induce frameshifts. A comparison of ethyl methanesulfonate, N-methyl-N'-nitro-N-nitrosoguanidine and 2-aminopurine frameshift specificity with that found with a mutH strain suggests that these mutagens partially or fully saturate or inactivate the methylation-directed mismatch repair system and allow replication errors leading to frameshifts to escape repair. This results in a form of indirect mutagenesis, which can be detected at certain sites.

Forty-nine amino acid substitutions were made at four positions in the Escherichia coli enzyme beta-galactosidase; three of the four targeted amino acids are thought to be part of the active site. Many of the substitutions were made by converting the appropriate codon in lacZ to an amber codon, and using one of 12 suppressor strains to introduce the replacement amino acid. Glu-461 and Tyr-503 were replaced, independently, with 13 amino acids. All 26 of the strains containing mutant enzymes are Lac-. Enzyme activity is reduced to less than 10% of wild type by substitutions at Glu-461 and to less than 1% of wild type by substitutions at Tyr-503. Many of the mutant enzymes have less than 0.1% wild-type activity. His-464 and Met-3 were replaced with 11 and 12 amino acids, respectively. Strains containing any one of these mutant proteins are Lac+. The results support previous evidence that Glu-461 and Tyr-503 are essential for catalysis, and suggest that His-464 is not part of the active site. Site-directed mutagenesis was facilitated by construction of an f1 bacteriophage containing the complete lacZ gene on a single EcoRI fragment.

It has been suggested that the use of an interposition vein cuff for anastomosing PTFE grafts to small calibre arteries confers a haemodynamic advantage. Pulsatile blood flow through a standard anastomosis was compared, in vitro, to that incorporating a vein cuff. 6 mm PTFE was anastomosed end-to-side to 10 pairs of cadaver internal mammary arteries matched for length and internal diameter (median 1.8 mm, range 1.6-2.4). Blood flow was significantly higher through the vein cuff anastomosis than the standard anastomosis (comparison of regression analysis, P less than 0.001) when the arterial diameter was less than 2.0 mm (five pairs). These results suggest that the vein cuff does confer a significant haemodynamic advantage when PTFE is anastomosed to arteries less than 2.0 mm diameter and this may be because the compliant vein cuff allows more distension of the anastomosis thus reducing anastomotic resistance.

Rabbits immunized with autologous renal tubular antigen (Fx1A) developed tubulointerstitial nephritis whereas sheep anti-Fx1A antibody administered i.v. produced glomerulonephritis (GN). This lesion showed heavy granular glomerular deposition of immunoglobulin and subepithelial electron dense deposits, early proteinuria, leucocyte independence and a temporal pattern of quantitated glomerular antibody binding distinct from that reported to occur in passive Heymann's nephritis in rats. Isoelectric focusing followed by immunoblotting of deoxycholate-soluble Fx1A antigens with the heterologous and autologous antibodies, indicated species differences in epitope recognition which could account for dissociation between the two models.

Methods of extraction from pharmaceutical formulations and subsequent determination of benzoic acid and salicylic acid by spectrofluorimetry are described. The recovery of benzoic acid, in the presence of salicylic acid, was 99.3%, with a coefficient of variation of 1.04%, while the recovery of salicylic acid, in the presence of benzoic acid, was 97.7%, with a coefficient of variation of 0-68%.