The occurrence of biofilm in an equine experimental wound model of healing by secondary intention

In humans, biofilm is a well-known cause of delayed healing and low-grade inflammation of chronic wounds. In horses, biofilm formation in wounds has been studied to a very limited degree. The objective of this study was thus to investigate the occurrence of biofilm in equine experimental wounds healing by secondary intention. Tissue biopsies from non-contaminated, experimental excisional shoulder and limb wounds were obtained on day 1-2, day 7-10 and day 14-15 post-wounding. Limb wounds were either un-bandaged or bandaged to induce exuberant granulation tissue (EGT) formation and thereby impaired healing. Presence of biofilm in tissue biopsies was assessed by peptide nucleic acid fluorescence in situ hybridization (PNA FISH) and confocal laser scanning microscopy (CLSM). Bandaged limb wounds developed EGT and displayed delayed healing, while shoulder and un-bandaged limb wounds healed normally. Biofilm was detected in limb wounds only. At day 14-15 biofilm was significantly more prevalent in bandaged limb wounds than in un-bandaged limb wounds (P=0.003). Further, bandaged limb wounds had a statistically significant increase in biofilm burden from day 7-10 to day 14-15 (P=0.009). The finding that biofilm was most prevalent in bandaged limb wounds with EGT formation suggests that biofilm may be linked to delayed wound healing in horses, as has been observed in humans. The inability to clear bacteria could be related to hypoxia and low-grade inflammation in the EGT, but the interaction between biofilm forming bacteria and wound healing in horses needs further elucidation.

On-site treatment and landfilling of MSWI air pollution control residues

Air pollution control (APC) residues from municipal solid waste incineration (MSWI) are difficult to landfill due to substantial leaching of trace metals. An on-site pretreatment prior to landfilling of APC-residues was investigated in terms of bench-scale experiments with a semidry APC-residue and a fly ash. The treatment involved mixing of the residues with a ferrous sulphate solution and subsequent oxidation of the suspension. Afterwards, the suspension was spread on a dedicated landfill section and allowed to drain by gravity through the drainage system of the landfill. The wastewater from the process, collected through the drainage system, contained large concentrations of salts (Cl: 14-30 g/l, Na: 4-9 g/l, K: 5-11 g/l, Ca: 2-12 g/l) but low concentrations of trace metals (e.g. Pb: 14-100 microg/l, Cd: <2-7 microg/l). The treated residues left in the landfills were later subject to leaching by simulated rainfall. The leachate contained low concentrations of trace metals (Pb: <120 microg/l, Cd: <2 microg/l, Cr: <485 microg/l). The leachate concentrations from the treated APC-residues were substantially reduced compared to concentrations in leachate from untreated APC-residues. Particularly in the early stages of the leaching, concentrations of trace metals were reduced by up to four orders of magnitude.

Treatment of waste incinerator air-pollution-control residues with FeSO4: concept and product characterisation

This paper describes a new concept for treatment of air pollution-control (APC) residues from waste incineration and characterises the wastewater and stabilised residues generated by the process. The process involves mixing of APC-residues with a ferrous sulphate solution and subsequent oxidation of the suspension (Ferrox-process 1996). The process results in a significant reduction in the leaching of salts and heavy metals from the residue, by washing out most of the salts and by binding the heavy metals in the iron oxides formed. In the laboratory, a semidry gas-cleaning residue and a fly ash were treated by the process. The generated wastewater contained low concentrations of heavy metals (e.g. Pb: 27-39 microg l(-1) and Cd: 2.6-4.6 microg l(-1)), but high concentrations of salts (e.g. Cl, Na, K, and Ca). The treatment process redUced the leaching of Pb from the residues by more than two orders of magnitude at fixed pH as determined by pH-static leaching tests. Likewise, the leaching of Cd, Zn and Cu was significantly reduced. The effect on elements that form oxyanions (e.g. Cr) is marginal and in the current process there is no reduction in the release of Hg.

Charging levels of four tRNA species in Escherichia coli Rel(+) and Rel(-) strains during amino acid starvation: a simple model for the effect of ppGpp on translational accuracy

Escherichia coli strains mutated in the relA gene lack the ability to produce ppGpp during amino acid starvation. One consequence of this deficiency is a tenfold increase in misincorporation at starved codons compared to the wild-type. Previous work had shown that the charging levels of tRNAs were the same in Rel(+) and Rel(-) strains and reduced, at most, two- to fivefold in both strains during starvation. The present reinvestigation of the charging levels of tRNA(2)(Arg), tRNA(1)(Thr), tRNA(1)(Leu) and tRNA(His) during starvation of isogenic Rel(+) and Rel(-) strains showed that starvation reduced charging levels tenfold to 40-fold. This reduction corresponds much better with the decreased rate of protein synthesis during starvation than that reported earlier. The determination of the charging levels of tRNA(2)(Arg) and tRNA(1)(Thr) during starvation were accurate enough to demonstrate that charging levels were at least fivefold lower in the Rel(-) strain compared to the Rel(+) strain. Together with other data from the literature, these new data suggest a simple model in which mis-incorporation increases as the substrate availability decreases and that ppGpp has no direct effect on enhancing translational accuracy at the ribosome.

High temperature co-treatment of bottom ash and stabilized fly ashes from waste incineration

Bottom ashes from two Danish municipal solid waste incineration plants were heated at 900 degrees C with iron oxide stabilized air pollution control residues at actual mass flow ratios (9:1), simulating a treating method for the residues. The two residues were co-treated, producing one combined stream that may be utilized as a secondary road construction material. Scanning electron microscope analysis and grain size distribution analysis indicated that sintering of the particles did not occur. Batch leaching tests at liquid/solid 10 l/kg at a range of pH-values (6-10) quantified with respect to Cd, Cr and Pb revealed significant positive effects of co-heating the ashes, although Pb showed slightly increased leaching. At a liquid/solid ratio of 10 l/kg the leachate concentrations were still low at pH 7-10 and the release of Pb was, thus, not expected to limit the utilization of the mixed ashes. The process, thus, fixates the metals in the solid residues without altering the leaching properties of the bottom ash too significantly.

The modification of the wobble base of tRNAGlu modulates the translation rate of glutamic acid codons in vivo

In Escherichia coli, uridine in the wobble position of tRNAGlu and tRNALys is modified to mnm5s2U34. This modification is believed to restrict the base-pairing capability, i.e. to prevent misreading of near-cognate codons and reduce the efficiency of cognate codon reading, especially of codons ending in G. We have determined the influence of the 5-methylaminomethyl and the 2-thio modifications of mnm5s2U34 in tRNAGlu on the translation rate of the glutamate codons GAA and GAG in vivo. In wild-type cells, GAG is translated slower (7. 7 codons/second) and GAA faster (18 codons/second) than the average codon (13 codons/second). Surprisingly, tRNAGlu lacking the 5-methylaminomethyl group, thus containing s2U34, translated GAA twofold faster (47 codons/second) and GAG fourfold slower (1.9 codons/second) than fully modified tRNAGlu. In contrast, tRNAGlu that contains mnm5U34 instead of mnm5s2U34 translated GAA fourfold slower (4.5 codons/second) and GAG only 20% slower (6.2 codons/second). Clearly, the 5-methylaminomethyl group of mnm5s2U34 facilitates base-pairing with G while decreasing base-pairing with A, resulting in rates of translation of GAG and GAA that approach that of the average codon. The 2-thio group increases the recognition of GAA and has only a minor effect on the decoding of GAG. Furthermore, the 2-thio group is important for aminoacylation (see the accompanying paper). These data imply that the function of mnm5s2U34 may be different from what has been suggested previously.

Aminoacylation of hypomodified tRNAGlu in vivo

The highly specific interaction of each aminoacyl-tRNA synthetase and its substrate tRNAs constitutes an intriguing problem in protein-RNA recognition. All tRNAs have the same overall three-dimensional structure in order to fit interchangeably into the translational apparatus. Thus, the recognition by aminoacyl-tRNA synthetase must be more or less limited to discrimination between bases at specific positions within the tRNA. The hypermodified nucleotide 5-methylaminomethyl-2-thiouridine (mnm5s2U) present at the wobble position of bacterial tRNAs specific for glutamic acid, lysine and possibly glutamine has been shown to be important in the recognition of these tRNAs by their synthetases in vitro. Here, we have determined the aminoacylation level in vivo of tRNAGlu, tRNALys, and tRNA1GIn in Escherichia coli strains containing undermodified derivatives of mnm5s2U34. Lack of the 5-methylaminomethyl group did not reduce charging levels for any of the three tRNAs. Lack of the s2U34 modification caused a 40% reduction in the charging level of tRNAGlu. Charging of tRNALys and tRNA1Gln were less affected. There was no compensating regulation of expression of glutamyl-tRNA synthetase because the relative synthesis rate was the same in the wild-type and mutant strains. These results indicate that the mnm5U34 modification is not an important recognition element in vivo for the glutamyl-tRNA synthetase. In contrast, lack of the s2U34 modification reduced the efficiency of charging by at least 40%. This is the minimal estimate because the turn-over rate of Glu-tRNAGlu was also reduced in the absence of the 2-thio group. Lack of either modification did not affect mischarging or mistranslation.

Ribosomal protein S1 is required for translation of most, if not all, natural mRNAs in Escherichia coli in vivo

We have deleted the chromosomal rpsA gene, encoding ribosomal protein S1, from an Escherichia coli strain carrying a plasmid where rpsA was controlled by the lac promoter and operator. This exogenous source of protein S1 was essential for growth. Thus we have verified the absolute requirement for protein S1. To see if translation of individual mRNAs differed in the requirements for protein S1, we removed the inducer and followed the time-course of the synthesis of several individual proteins and of total RNA, DNA and protein. Growth immediately shifted from being exponential to being linear, with a rate of protein synthesis defined by the pre-existing amount of protein S1. The expression pattern of the individual proteins indicated that the translation of all mRNAs was dependent on protein S1. Unexpectedly, we found that depletion for protein S1 for extended periods introduced a starvation for amino acids. Such starvation was indicated by an increased synthesis of ppGpp and could be reversed by addition of a mixture of all 20 amino acids. Measurements of the peptide chain elongation rate in vivo showed that ribosomes without protein S1 were unable to interfere with the peptide chain elongation rate of the active ribosomes and that, therefore, protein S1 was unable to diffuse from one ribosome to another during translation. We conclude that protein S1-deficient ribosomes are totally inactive in peptide chain elongation on most, if not all, naturally occurring E. coli mRNAs.

High concentrations of ppGpp decrease the RNA chain growth rate. Implications for protein synthesis and translational fidelity during amino acid starvation in Escherichia coli

We show that the RNA chain growth rate on lacZ is reduced by an elevated ppGpp level even in the absence of starvation. Under these conditions the polypeptide chain elongation rate is affected little, if at all. These results lead us to re-examine the role of ppGpp in the reduction of protein synthesis and translational fidelity during amino acid starvation. We find that ppGpp has little or no direct effect on translation rate or fidelity. Rather, the effects of ppGpp on translation are indirectly caused by the fact that ppGpp inhibits mRNA synthesis, making mRNA limiting for translation during amino acid starvation. The reduced level of mRNA thereby reduces the severity of the aminoacyl-tRNA limitation and, in turn, decreases mistranslation. Mistranslation in the starved relA strain therefore results from an increased severity of aminoacyl-tRNA limitation due to the failure of this strain to reduce mRNA levels by increasing the level of ppGpp. Finally, the initial rise of the ppGpp level in the starved stringent strain, followed by a characteristic reduction to a steady poststarved level, can now be explained by the initially high, and then decreasing number of "hungry" codons adjusted through the mRNA pool.

Isolation and characterization of mutants with impaired regulation of rpsA, the gene encoding ribosomal protein S1 of Escherichia coli

In order to select mutants that would help to characterize the post-transcriptional regulation of rpsA, we constructed a strain in which the growth rate on lactose minimal medium is determined by the amount of an rpsA-lacZ' alpha-fragment fusion protein produced, even when this is encoded by a high-copy-number plasmid. In the parental strain, synthesis of the fusion protein is repressed by a wild-type rpsA gene, present on a compatible plasmid. Twenty-eight spontaneous and independent mutants, all of them mapping in the rpsA leader region, were isolated as strains that showed higher growth rates, on lactose medium, due to increased synthesis of the rpsA-lacZ' fusion protein. Among these mutants only three sequence changes were found, mapping 9, 10 and 27 bases upstream of the rpsA start codon. At both the -9 and -10 positions an A to G transition and at -27 a C to G transversion all resulted in a sequence with better complementarity to the 3' end of 16S rRNA. We also isolated two mutations mapping in the plasmid-encoded rpsA structural gene: an ochre nonsense mutation in codon 15 of the rpsA gene and a frameshift mutation, deleting the T residue at position +1186. To facilitate the in vitro assay of alpha-fragment activity we also constructed a strain that overproduces the alpha-acceptor fragment four-fold relative to a strain that is diploid for this lacZ delta M15 allele.

Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes. Expression from reporter genes does not always reflect functional mRNA levels

Induction of beta-galactosidase from high copy-number plasmids was found to reduce the synthesis of other cellular proteins in Escherichia coli. The reduction depends on the protein in question and on the induction level of the beta-galactosidase. It could be observed transiently within one minute after induction and in some cases also during steady-state induction. Our interpretation is that the concentration of the free ribosomal subunits decreases after induction, leading to an increased competition among the individual ribosome binding sites for ribosomes. The immediate reduction in the synthesis individual proteins after induction of beta-galactosidase was used as an assay to measure in vivo the efficiency of a ribosome binding site. These efficiencies were compared to the calculated affinities between the ribosome binding site of specific mRNA species and the 3' end of 16 S RNA. For several mRNAs with similar Shine-Dalgarno sequences, the sensitivity to competition differed twofold. Our results show, that both transiently during induction of lacZ and also at very high steady-state expression levels, the expression from reporter genes, including the lacZ gene itself, does not reflect the levels of the mRNAs in a simple way.

The rates of macromolecular chain elongation modulate the initiation frequencies for transcription and translation in Escherichia coli

Here we show that most macromolecular biosynthesis reactions in growing bacteria are sub-saturated with substrate. The experiments should in part test predictions from a previously proposed model (Jensen & Pedersen 1990) which proposed a central role for the rates of the RNA and peptide chain elongation reactions in determining the concentration of initiation competent RNA polymerases and ribosomes and thereby the initiation frequencies for these reactions. We have shown that synthesis of ribosomal RNA and the concentration of ppGpp did not exhibit the normal inverse correlation under balanced growth conditions in batch cultures when the RNA chain elongation rate was limited by substrate supply. The RNA chain elongation rate for the polymerase transcribing lacZ mRNA was directly measured and found to be reduced by two-fold under conditions of high ppGpp levels. In the case of translation, we have shown that the peptide elongation rate varied at different types of codons and even among codons read by the same tRNA species. The faster translated codons probably have the highest cognate tRNA concentration and the highest affinity to the tRNA. Thus, the ribosome may operate close to saturation at some codons and be unsaturated at synonymous codons. Therefore, not only translation of the codons for the seven amino acids, whose biosynthesis is regulated by attenuation, but also a substantial fraction of the other translation reactions may be unsaturated. Recently, we have obtained results which indicate that also many ribosome binding sites are unsaturated with their substrate, i.e. with ribosomes.(ABSTRACT TRUNCATED AT 250 WORDS)

Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate

We have determined the absolute translation rates for four individual codons in Escherichia coli. We used our previously described system for direct measurements of in vivo translation rates using small, in-frame inserts in the lacZ gene. The inserts consisted of multiple synthetic 30 base-pair DNA oligomers with high densities of the four individual codons, GAA (Glu), GAG (Glu), CCG (Pro) and CGA (Arg). Our method is independent of expression level, of mRNA half-life and of transcription rate. Codon GAA was found to be translated with a rate of 21.6 codons/second whereas codon GAG was translated 3.4-fold slower (6.4 codons/s). These two codons are read by the same tRNA species. Codon CCG and CGA are both read by abundant tRNA species but nevertheless we found them to be translated slowly with rates of 5.8 and 4.2 codons/second, respectively. The context of these codons were varied, but we found no significant influence of context on their translation rates and we suggest a mechanism for why context may not affect translation rates. One insert with a low translation rate gave results that most readily can be explained by assuming queue formation of ribosomes on the insert. Such a queue was found to reduce the expression level by approximately 35%. Our experiments allowed us to estimate the average distance between ribosomes and thereby the translation initiation frequency on the wild-type lacZ mRNA. This was found to be one per three seconds.

Cysteine, even in low concentrations, induces transient amino acid starvation in Escherichia coli

Cysteine, in concentrations down to 0.04 micrograms/ml, induces transient amino acid starvation in Escherichia coli growing in minimal medium. The duration depends on the concentration and is 5 min at 2 micrograms of cysteine per ml. At low cysteine concentrations, threonine and isoleucine almost completely abolish the starvation.

Codon usage determines translation rate in Escherichia coli

We wish to determine whether differences in translation rate are correlated with differences in codon usage or with differences in mRNA secondary structure. We therefore inserted a small DNA fragment in the lacZ gene either directly or flanked by a few frame-shifting bases, leaving the reading frame of the lacZ gene unchanged. The fragment was chosen to have "infrequent" codons in one reading frame and "common" codons in the other. The insert in these constructs does not seem to give mRNAs that are able to form extensive secondary structures. The translation time for these modified lacZ mRNAs was measured with a reproducibility better than plus or minus one second. We found that the mRNA with infrequent codons inserted has an approximately three-seconds longer translation time than the one with common codons. In another set of experiments we constructed two almost identical lacZ genes in which the lacZ mRNAs have the potential to generate stem structures with stabilities of about -75 kcal/mol. In this way we could investigate the influence of mRNA structure on translation rate. This type of modified gene was generated in two reading frames with either common or infrequent codons similar to our first experiments. We find that the yield of protein from these mRNAs is reduced, probably due to the action in vivo of an RNase. Nevertheless, the data do not indicate that there is any effect of mRNA secondary structure on translation rate. In contrast, our data persuade us that there is a difference in translation rate between infrequent codons and common codons that is of the order of sixfold.