High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science

Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera. Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis, P. asiatica, P. borealis, P. borinquensis, P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P. flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii, P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P. mikado, P. nigriventris, P. orientalis, P. rangiferina, P. sipmanii, P. stanleyensis, P. vitikainenii and P. willdenowii; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa; and the following new combination is introduced: P. hymenina var. dissecta. Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza, P. neopolydactyla, P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification. Citation: Magain N, Miadlikowska J, Goffinet B, et al. 2023. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. Persoonia 51: 1-88. doi: 10.3767/persoonia.2023.51.01.

The decision-making threshold and the factors that affect it: A qualitative study of patients' decision-making in knee replacement surgery

BACKGROUND

Osteoarthritis is a significant cause of burden to the ageing population and knee replacement is a common operation for treatment of end-stage disease. We aimed to explore these factors to help understand patients' decision-making, which is critical in informing patient-centred care. These can be used to enhance decision-making and dialogue between clinicians and patients, allowing a more informed choice.

METHODS

The study consisted of two focus groups, in a patient cohort after total knee replacement followed by more in-depth interviews to further test and explore themes from the focus groups, in patients in either the deliberation stage or the decision-making stage.

RESULTS

Using qualitative research methods (iterative thematic analysis) reviewing decision-making and deliberation phases of making informed choices we found nine key themes that emerged from the study groups.

CONCLUSIONS

An awareness of the deliberation phase, the factors that influence it, the stress associated with it, preferred models of care, and the influence of the decision-making threshold will aid useful communication between doctors and patients.

Patients' decision making in total knee arthroplasty: a systematic review of qualitative research

Objectives

A patient-centred approach, usually achieved through shared decision making, has the potential to help improve decision making around knee arthroplasty surgery. However, such an approach requires an understanding of the factors involved in patient decision making. This review’s objective is to systematically examine the qualitative literature surrounding patients’ decision making in knee arthroplasty.

Methods

A systematic literature review using Medline and Embase was conducted to identify qualitative studies that examined patients’ decision making around knee arthroplasty. An aggregated account of what is known about patients’ decision making in knee arthroplasties is provided.

Results

Seven studies with 234 participants in interviews or focus groups are included. Ten themes are replicated across studies, namely: expectations of surgery; coping mechanisms; relationship with clinician; fear; pain; function; psychological implications; social network; previous experience of surgery; and conflict in opinions.

Conclusions

This review is helpful in not only directing future research to areas that are not understood, or require confirmation, but also in highlighting areas that future interventions could address. These include those aimed at delivering information, which are likely to affect the satisfaction rate, demand, and use of knee arthroplasties.

Cite this article: Bone Joint Res 2015;4;163–169.

A systematic review of plate versus intramedullary fixation in the treatment of midshaft clavicle fractures

The best method of fixation for clavicle fractures is not known. The purpose of this review was to examine the evidence comparing plate and intramedullary fixation for midshaft clavicle fractures. A search of MEDLINE in September 2011 identified five papers that compared plate and intramedullary fixation, and fulfilled our eligibility criteria, consisting of; one randomised controlled trial, two quasi-randomised controlled trials, and two retrospective studies. Level of evidence was assessed using the Scottish Intercollegiate Guidelines Network guidance and the Cochrane Bone, Joint and Muscle Trauma Group’s quality assessment tool. No attempt at meta-analysis was made due to the heterogeneity of the study populations and interventions. We found no difference between intramedullary fixation and plate fixation. There was a trend towards a lower complication rate with intramedullary fixation. On the basis of the available evidence, we would advocate both techniques for the treatment of midshaft clavicle fractures.

Effect of cotton padding on the setting properties of plaster slabs

Introduction

Plaster of Paris (PoP) impregnated bandages have been used to maintain the position of bones and joints for over a century. Classically, wool dressing is applied to the limb before the PoP, which can then be moulded to the desired shape. A modification of this practice is to wrap the PoP bandages circumferentially in cotton before wetting and applying to the patient in an attempt to reduce inhalation of plaster dust and reduce mess. However, this may affect the water content of the cast and therefore also its setting properties and strength. This study compared the setting properties of PoP casts when used with and without cotton wrapping.

Methods

Sixty specimens, compliant with the American Society for Testing and Materials standards for three-point bending tests, were prepared, with thirty wrapped in cotton. All were weighed before and after water immersion, and wrapped around a plastic cylinder to mimic limb application. Bending stiffness and yield strength was measured on a servohydraulic materials testing machine at 2, 6, 12, 24, 48 and 72 hours.

Results

The water content of cotton-wrapped plaster was significantly higher (50%) than that of standard plaster. It had significantly lower strength up to 24 hours and significantly lower stiffness up to 72 hours.

Conclusions

The initial decrease in strength and stiffness of the cast wrapped in cotton may comprise the ability of the backslab to hold the joint or bone in an optimal position. Any modification of the standard plaster slab application technique should allow for the potential adverse effects on the plaster setting properties.

A cross-sectional study of aggression levels in physicians and orthopaedic surgeons: impact on specialty selection and training?

Objectives

To determine if current validated psychometric evaluations could determine a difference in basic behavioural characteristics between surgical and medical specialties.

Design

Cross-sectional study.

Setting

Two district general hospitals and one University teaching hospital in England, UK.

Participants

Internal medicine (16) and trauma and orthopaedic (20) consultants.

Main outcome measures

Aggression levels as assessed by the Buss and Warren questionnaire. The self-administered questionnaire assesses aggression in terms of physical, verbal, anger, hostility, indirect hostility and an overall assessment of aggression.

Results

All participants had aggression scores below the population average. We found a significant difference (P < 0.01) in total level of aggression, with orthopaedic consultants scoring a mean of 61.1 (standard deviation [SD] 9.2) and physicians 51.3 (SD 9.5). When analysis of the five different subtypes of aggression was carried out, orthopaedic surgeons scored significantly higher in terms of verbal aggression (P = 0.005), hostility (P = 0.002) and indirect hostility (P = 0.03).

Conclusion

This study joins a growing evidence base for aspects of behaviour indicative of a given specialty. Aggression is a relatively stable behavioural characteristic from adolescence, and as such this is the first study of its type to suggest that the differences in behavioural characteristics seen between specialties are inherent, rather than learned. It is unclear if the differences observed represent an attraction of that specialty to the personality type or is required for success within the given specialty. Whether this can be used in terms of selection into higher specialty training, or influence training within specialties, requires further work.

First Report of Powdery Mildew Caused by Leveillula taurica on Giant Blazing Star (Mentzelia laevicaulis)

Mentzelia laevicaulis (Dougl. ex Hook.) Torr. & Gray (Loasaceae; common names are giant blazing star and smoothstem blazing star) is widely distributed throughout western North America in sites ranging from lowland deserts to mountainous areas in Canada and the United States. During a plant disease survey in June 2007 in the Owyhee Mountains, Canyon County, Idaho, leaves of M. laevicaulis displaying whitish, mycelial growth were collected from plants growing on stream banks and gravelly road embankments. Diseased leaves exhibited localized, chlorotic discolorations associated with signs of a powdery mildew. Of approximately 20 plants at the site, 50% were infected. White mycelia and conidia were more abundant on the adaxial leaf surfaces than on the abaxial surfaces. Severely diseased leaves were buckled and slightly twisted. By August and through September, sporulation was greatest on mature plants, and lowermost leaves were completely covered with flocculose, dense, white mycelia. Dimorphic conidia were lanceolate or cylindrical and measured (44-) 46 to 67 (-71) × (14-) 14.5 to 20 (-21) μm. DNA was extracted and PCR was used to amplify the internal transcribed spacer (ITS) region as described previously (2), except that primers ITS 5 and P3 (4) were used. The resulting 633-bp sequence (GenBank Accession No. GQ860947) included a 616-bp region identical to a sequence reported previously for Leveillula taurica (Lév.) Arnaud from eastern Washington (GenBank No. AY912077), as well as ITS regions from L. taurica previously reported from Iran (GenBank No. AB048350) (2) and Australia (GenBank No. AF 073351) (2). Based on the ITS sequence, the present fungus grouped within Khodaparast et al. (3) Clade 1 that included L. taurica strains they distinguished from other, superficially similar species of Leveillula. On the basis of morphological and sequence data, the fungus was determined to be L. taurica (1,3). A voucher specimen was deposited in the Mycology Herbarium (WSP) at Washington State University. To our knowledge, this is the first report of a named powdery mildew species from a member of the Loasaceae. The only previous report of a powdery mildew on a loasaceous host was an undetermined Oidium sp. on a species of Mentzelia (1). The discovery of L. taurica on a previously unknown native host species is further evidence that this introduced pathogen is becoming endemic to the Pacific Northwest. Native host species, such as M. laevicaulis, may play a role in the epidemiology of powdery mildew diseases caused by L. taurica on crop and ornamental species in the Pacific Northwest. References: (1) U. Braun. Beih. Nova Hedwigia 89:1, 1987. (2) D. A. Glawe et al. Mycol. Prog. 4:291, 2005. (3) S. A. Khodaparast et al. Mycol. Res. 105:909, 2001. (4) S. Takamatsu and Y. Kano. Mycoscience 42:135, 2001.

A Randomized Trial of Radical Radiotherapy for the Management of pT1G3 NXM0 Transitional Cell Carcinoma of the Bladder

PURPOSE

We conducted a multicenter randomized trial in the United Kingdom to determine the efficacy of radical radiotherapy in reducing the incidence of progression of pT1G3 transitional cell carcinoma of the bladder to muscle invasive disease and subsequent disease fatality.

MATERIALS AND METHODS

Patients with a new diagnosis of pT1G3 NXM0 transitional cell carcinoma with unifocal disease and no carcinoma in situ (group 1), or with multifocal disease and/or carcinoma in situ (group 2) were eligible for the trial. Patients in group 1 were randomized between observation and radiotherapy to the bladder, and in group 2 between intravesical therapy and radiotherapy.

RESULTS

From September 1991 to February 2003 a total of 210 patients from 37 centers in the United Kingdom were entered into the study. There were 77 patients in group 1 and 133 patients in group 2, and 6 patients were excluded from analysis because they were found to have pT2 disease by the reference pathologist. No evidence of an advantage with radiotherapy was found in terms of progression-free interval (hazard ratio 1.07; 95% CI 0.65, 1.74; p = 0.785), progression-free survival (hazard ratio 1.35; 95% CI 0.92, 1.98; p = 0.133) or overall survival (hazard ratio 1.32; 95% CI 0.86, 2.04; p = 0.193).

CONCLUSIONS

To our knowledge this is the largest randomized trial performed in patients with pT1G3 disease for which 210 patients were recruited during 11 years. There is no evidence that radiotherapy is better than more conservative treatment. The prognosis of this group of patients appears to be poor irrespective of treatment and new treatment strategies need to be investigated.

Amnesic shellfish poison

Amnesic shellfish poisoning (ASP) is caused by consumption of shellfish that have accumulated domoic acid, a neurotoxin produced by some strains of phytoplankton. The neurotoxic properties of domoic acid result in neuronal degeneration and necrosis in specific regions of the hippocampus. A serious outbreak of ASP occurred in Canada in 1987 and involved 150 reported cases, 19 hospitalisations and 4 deaths after consumption of contaminated mussels. Symptoms ranged from gastrointestinal disturbances, to neurotoxic effects such as hallucinations, memory loss and coma. Monitoring programmes are in place in numerous countries worldwide and closures of shellfish harvesting areas occur when domoic acid concentrations exceed regulatory limits. This paper reviews the chemistry, sources, metabolism and toxicology of domoic acid as well as human case reports of ASP and discusses a possible mechanism of toxicity.

The mechanism of DNA repair by uracil-DNA glycosylase: studies using nucleotide analogues

2',4'-Dideoxy-4'-methyleneuridine incorporated into oligodeoxynucleotides forms regular B-DNA duplexes as shown by Tm and CD measurements. Such oligomers are not cleaved by the DNA repair enzyme, UDG, which cleaves the glycosylic bond in dU but not in dT nor in dC nucleosides in single stranded and double stranded DNA. Differential binding of oligomers containing carbadU, 4'-thiodU, and dU residues to wild type and mutant UDG proteins identify an essential role for the furanose 4'-oxygen in recognition and cleavage of dU residues in DNA.

Detection of 1,N6-etheno-2'-deoxyadenosine and 3,N4-etheno-2'-deoxycytidine occurring endogenously in DNA

1,N6-Etheno-2'-deoxyadenosine (epsilon dA) and 3,N4-etheno-2'-deoxycytidine (epsilon dC) are DNA adducts formed by a number of genotoxic chemicals, including vinyl chloride. They are also formed endogenously in tissue DNA, probably from a reactive metabolite of lipid peroxidation. Both the qualitative and quantitative detection of endogenous adducts is important in order to place adduct formation by chemicals such as vinyl chloride in the context of this natural background level. Methods with sufficient sensitivity are therefore being developed to measure the natural background of epsilon dA and epsilon dC adducts. We have developed a high-performance liquid chromatography (HPLC)-32P-postlabelling method to measure epsilon dA and epsilon dC at alkylation frequencies of 1 adduct in 10(7)-10(8) nucleotides in 10-microgram samples of DNA. In HPLC-32P-postlabelling analysis of liver DNA from control Wistar rats, epsilon dA and epsilon dC were determined at levels of 1 adduct in 8.1 x 10(7) and 1 adduct in 1.8 x 10(7) nucleotides, respectively. The levels of epsilon dA and epsilon dC measured in liver DNA of animals exposed orally to five daily doses of 50 mg/kg body weight vinyl chloride were found by this method to be 1 adduct in 2.9 x 10(7) and 1 adduct in 1.4 x 10(7) nucleotides, respectively. In contrast, in a direct labelling study, radiolabelled epsilon dA and epsilon dC were not detected in liver DNA of rats exposed for 6 h by nose-only inhalation to [1,2-14C]vinyl chloride at up to 45 ppm v/v. Immunochemical procedures are also being developed for recognizing etheno adducts. Thus, a monoclonal antibody raised to protein conjugates of epsilon dC showed high selectivity in the recognition of this DNA adduct. When the antibody was immobilized on a solid support and used in an immunoenrichment procedure to purify epsilon dC from a large excess of normal nucleotides, one epsilon dC adduct from about 10(8) normal nucleotides could be resolved. Coupling the immunoaffinity enrichment procedure with capillary zone electrophoresis permitted the detection of approximately one epsilon dC adduct in 3 x 10(6) nucleotides.

Formation of deaminated products in styrene oxide reactions with deoxycytidine

The reaction of racemic styrene oxide with deoxycytidine under aqueous conditions was studied. The four principal products isolated were a pair of diastereomeric N(4)-(2-hydroxy-1-phenylethyl)deoxycytidines ( approximately 20% of the products) and a pair of diastereomeric 3-(2-hydroxy-2-phenylethyl)deoxyuridines ( approximately 80% of the products). Reactions with optically active styrene oxides allowed the configurations of the 3-(2-hydroxy-2-phenylethyl)deoxyuridines to be assigned, and these structures were confirmed by an independent synthesis from deoxyuridine. Also, it was possible to tentatively assign the configurations of the N(4)-(2-hydroxy-1-phenylethyl)deoxycytidines that had undergone some racemization during the reaction (the ratio of the retained to inverted configuration of the products was approximately 1:7).

Crystal structure of an octameric RuvA-Holliday junction complex

Holliday junctions occur as intermediates in homologous recombination and DNA repair. In bacteria, resolution of Holliday junctions is accomplished by the RuvABC system, consisting of a junction-specific helicase complex RuvAB, which promotes branch migration, and a junction-specific endonuclease RuvC, which nicks two strands. The crystal structure of a complex between the RuvA protein of M. leprae and a synthetic four-way junction has now been determined. Rather than binding on the open surface of a RuvA tetramer as previously suggested, the DNA is sandwiched between two RuvA tetramers, which form a closed octameric shell, stabilized by a conserved tetramer-tetramer interface. Interactions between the DNA backbone and helix-hairpin-helix motifs from both tetramers suggest a mechanism for strand separation promoted by RuvA.

Structure of a DNA base-excision product resembling a cisplatin inter-strand adduct

Base-excision of a self-complementary oligonucleotide with central G:T mismatches by the G:T/U-specific mismatch DNA glycosylase (MUG), generates an unusual DNA structure which is remarkably similar in conformation to an interstrand DNA adduct of the anti-tumor drug cis-diamminedichloroplatinum. The abasic sugars generated by excision of the mismatched thymines are extruded from the double-helix, and the 'widowed' deoxyguanosines rotate so that their N7 and O6 groups protrude into the minor groove of the duplex and restack in an interleaved intercalative geometry, generating a kink in the helix axis.

Separation and identification of positively charged and neutral nucleoside adducts by capillary electrochromatography-microelectrospray mass spectrometry

Capillary electrochromatography (CEC) is shown to be capable of separating mixtures containing both positively charged and neutral styrene oxide-adenosine adducts. In a study of the mechanism of deamination of positively charged 1-(2-hydroxy-1-phenylethyl) adenosine using 18O-labeled water, possible contamination of the chromatographically purified deamination product, 1-(2-hydroxy-1-phenylethyl) inosine, with the positively charged 1-(2-hydroxy-1-phenylethyl) adenosine was observed. Because the deamination product and the presumed contamination have the same molecular weights and similar structures, CEC-microelectrospray mass spectrometry (CEC-microESI/MS) was used to confirm the presence and identity of the suspected impurity. A trace amount of the positively charged 1-(2-hydroxy-1-phenylethyl) adenosine, which could not be observed by either HPLC-UV or CEC-UV, was detected by CEC-microESI/MS. This discriminatory ability of CEC-microESI/MS is attributed to the fact that positive ion mode ESI-MS is a more sensitive detector for a positively charged compound than a UV detector, and that the combination of electroosmotic and electrophoretic flows and hydrophobic interactions with the stationary phase contributes to the separation of the positively charged compound. As a result, the positively charged compound was observed to elute much earlier and with much sharper peaks than the neutral compounds for which electroosmotic flow is the only "pumping" force for the solvent.

Deamination and Dimroth rearrangement of deoxyadenosine-styrene oxide adducts in DNA

In reactions between styrene oxide and the ring nitrogen at the 1-position of deoxyadenosine, the epoxide is opened at both the alpha- (benzylic) and beta-carbons. The 1-substituted nucleosides formed are unstable and subsequently undergo either Dimroth rearrangement to give N6-substituted deoxyadenosines or deamination to give 1-substituted deoxyinosines. alphaN6-Substituted compounds are also formed from direct reaction at the exocyclic nitrogen. Kinetic experiments revealed that relative rates of deamination of 1-substituted deoxyadenosine-styrene oxides and 1-substituted adenosine-styrene oxides were similar. However, the rate of Dimroth rearrangement in beta1-substituted adenosine-styrene oxides was approximately 2.3-fold greater than that of beta1-substituted deoxyadenosine-styrene oxides and approximately 1.5-fold greater in alpha1-substituted adenosine-styrene oxides relative to alpha1-substituted deoxyadenosine-styrene oxides. Analysis of the products formed from reactions of styrene oxide with [3H]deoxyadenosine and [3H]deoxyadenosine incorporated into native and denatured DNA showed that the double-helical DNA structure reduced the levels of adducts formed 5-fold relative to denatured DNA but did not present a complete barrier to formation of either N6-substituted deoxyadenosine- or 1-substituted deoxyinosine-styrene oxide adducts in native DNA. Additionally, in denatured and native DNA the product distributions were altered in favor of formation of beta1-substituted deoxyinosine-styrene oxide adducts with respect to reactions of the nucleoside. The ratio of retained to inverted configuration of alphaN6-substituted products was higher in DNA than in nucleoside reactions. These experiments indicate that in addition to the N6-position, the ring nitrogen at the 1-position of deoxyadenosine is available, to some extent, for reaction in native DNA. In styrene oxide-DNA reactions, formation of 1-substituted adenines can lead to deaminated products where both Watson-Crick hydrogen-bonding sites are disrupted.

Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions

G:U mismatches resulting from deamination of cytosine are the most common promutagenic lesions occurring in DNA. Uracil is removed in a base-excision repair pathway by uracil DNA-glycosylase (UDG), which excises uracil from both single- and double-stranded DNA. Recently, a biochemically distinct family of DNA repair enzymes has been identified, which excises both uracil and thymine, but only from mispairs with guanine. Crystal structures of the mismatch-specific uracil DNA-glycosylase (MUG) from E. coli, and of a DNA complex, reveal a remarkable structural and functional homology to UDGs despite low sequence identity. Details of the MUG structure explain its thymine DNA-glycosylase activity and the specificity for G:U/T mispairs, which derives from direct recognition of guanine on the complementary strand.

Direct measurement of the substrate preference of uracil-DNA glycosylase

Site-directed mutants of the herpes simplex virus type 1 uracil-DNA glycosylase lacking catalytic activity have been used to probe the substrate recognition of this highly conserved and ubiquitous class of DNA-repair enzyme utilizing surface plasmon resonance. The residues aspartic acid-88 and histidine-210, implicated in the catalytic mechanism of the enzyme (Savva, R., McAuley-Hecht, K., Brown, T., and Pearl, L. (1995) Nature 373, 487-493; Slupphaug, G., Mol, C. D., Kavli, B., Arvai, A. S., Krokan, H. E. and Tainer, J. A. (1996) Nature 384, 87-92) were separately mutated to asparagine to allow investigations of substrate recognition in the absence of catalysis. The mutants were shown to be correctly folded and to lack catalytic activity. Binding to single- and double-stranded oligonucleotides, with or without uracil, was monitored by real-time biomolecular interaction analysis using surface plasmon resonance. Both mutants exhibited comparable rates of binding and dissociation on the same uracil-containing substrates. Interaction with single-stranded uracil-DNA was found to be stronger than with double-stranded uracil-DNA, and the binding to Gua:Ura mismatches was significantly stronger than that to Ade:Ura base pairs suggesting that the stability of the base pair determines the efficiency of interaction. Also, there was negligible interaction between the mutants and single- or double-stranded DNA lacking uracil, or with DNA containing abasic sites. These results suggest that it is uracil in the DNA, rather than DNA itself, that is recognized by the uracil-DNA glycosylases.

RNase E, the major player in mRNA degradation, is down-regulated in Escherichia coli during a transient growth retardation (diauxic lag)

The endoribonuclease RNase E plays a major part in mRNA degradation in Escherichia coli in addition to its role in processing rRNA. RNase E is encoded by an essential gene, rne, also known as ams and hmp, which is autoregulated post-transcriptionally. Here we report a transient decrease in the steady state level of the full-length rne transcript and a corresponding decline in the amount of the protein and enzymatic activity. During this period an mRNA fragment, lacking an intact 5' end, accumulates. This down-regulation of RNase E occurs under aerobic growth conditions in rich medium during a short diauxic lag in mid-exponential phase; it most likely reflects an exhaustion of a not yet identified medium compound which is followed by switching on a new metabolic pathway. During this lag, the levels of bulk protein are maintained. Our results suggest that a transient drop in the intracellular RNase E level is a means of cells to retard mRNA turnover in a period of adjustment to medium utilization. Furthermore, the here described regulation of the rne transcript and its cognate gene product seems to occur by an RNase E-independent mechanism responsive to changes in growth conditions.

Aralkylation of guanosine with para-substituted styrene oxides

To probe mechanisms of nucleoside aralkylation, product distributions and product stereochemistries were determined in reactions of optically active p-methyl- and p-bromostyrene oxide with guanosine. The proportion of 7-, N2-, and O6-substituted guanosine products was approximately 0.32:0.62:0.06 in neutral, aqueous reactions with the (R)-p-methylstyrene oxide and approximately 0.85: 0.09:0.04 in reactions with the (R)-p-bromostyrene oxide. The exocyclic positions opened the epoxide at the alpha-carbon. Epoxide ring opening by the nitrogen at the 7-position showed little preference for the alpha- or beta-carbons in reactions with p-methylstyrene oxide. However, the p-bromostyrene oxide favored reaction at the beta-carbon almost 4-fold over reaction at the alpha-carbon. Almost total inversion of stereochemistry was found to occur in reactions at the 7-position. In contrast, the ratio of inversion to retention of configuration in N2- and O6-substituted products was approximately 2:1 and approximately 1:1 for reactions with the p-methylstyrene oxide and approximately 6:1 and approximately 3:1 for reactions with p-bromostyrene oxide, respectively. These experiments suggest that an SN2 mechanism is in effect with reactions at the 7-position, whereas substrates of an increasingly ionic nature are involved in reactions at the N2- and O6-positions, respectively.

Investigation of hydrolytic deamination of 1-(2-hydroxy-1-phenylethyl)adenosine

The ring nitrogen of adenosine reacts at both the alpha- (benzylic) and beta-carbons of styrene oxide to form 1-substituted products. The 1-(2-hydroxy-1-phenylethyl)adenosines formed by oxirane ring opening at the alpha-position are prone to an unusually facile hydrolytic deamination. By conducting hydrolysis reactions in [18O]water and analyzing the reaction products by electrospray mass spectrometry, we find that deamination occurs by direct attack of water at the 6-position of the adenine ring system with displacement of the exocyclic amino group.

Retarded RNA turnover in Escherichia coli: a means of maintaining gene expression during anaerobiosis

In this study, we extend earlier observations on the influence of growth rate on mRNA stability and rRNA processing in Escherichia coli during continuous culture, to the effect of anaerobiosis. During slow anaerobic growth (generation time 700 min) both ompA and bla mRNA had a prolonged half-life compared to that during slow aerobic growth and the processing of 9S RNA was even more profoundly retarded, which indicated a general slowing of mRNA turnover. The latter was confirmed by a nearly fourfold increase in the functional half-life of bulk mRNA. In spite of this difference in stability, steady state levels of RNA, as judged by those of the ompA and 9S transcripts, were the same in aerobic and anaerobic cells at a given growth rate. Furthermore, we found that RNA synthesis during anaerobiosis was a fraction of that observed during slow aerobic growth and it is proposed that this offsets the general increase in mRNA stability. Our data therefore suggest that a constant level of RNA is maintained by matching the rate of decay to the level of RNA synthesis.

Evidence for a new ribonucleotide reductase in anaerobic E. coli

E. coli conditional iron-containing ribonucleotide reductase (Fe-RR) mutant and wild type strains grew anaerobically under conditions when Fe-RR was absent or inhibited. Furthermore, a B12-independent, hydroxyurea-resistant RR activity, unaffected by monoclonal antibodies against either subunit B1 or B2 of Fe-RR, was partially purified from anaerobically grown mutant and wild-type E. coli. These findings indicate that E. coli has a second RR representative of a new class of RRs and that this is the first report where both in vivo and in vitro evidence is presented. It is probable that other facultative anaerobes also have two different RRs such that an optimal supply of deoxyribonucleotides is maintained under all growth conditions.

Production and characterization of monoclonal antibodies against the two subunits proteins B1 and B2 of Escherichia coli ribonucleotide reductase

Ribonucleotide reductase from Escherichia coli consists of two nonidentical subunits, named protein B1 (170 000) and protein B2 (87 000). We purified and characterized five monoclonal antibodies against B1 and three against B2 from hybridomas obtained by fusion of spleen cells from immunized mice and the myeloma cell line P3-X63Ag8. All are of the IgG1 class with a high affinity for the antigen with dissociation constants in the nanomolar range. Four of the anti-B1 monoclonals and all three anti-B2 monoclonals neutralize reductase activity while one anti-B1 monoclonal binds tightly to B1 without affecting its activity. Fab fragments prepared from three anti-B1 monoclonals had similar dissociation constants. The anti-B1 monoclonals interacted with separate epitopes while two of the anti-B2 monoclonals appeared to react with the same epitope. In the case of B1, various allosteric states of the protein induced by binding of effectors had no apparent effect on the interaction with monoclonals, nor did their binding prevent subsequent binding of effectors. With B2, binding of monoclonals did not affect the typical electron paramagnetic resonance spectrum of the protein and thus did not involve either the tyrosyl free radical or the iron center of B2. All neutralizing antibodies interfered with the interaction between the two subunits, explaining their effect on enzyme activity, since active ribonucleotide reductase consists of a B1-B2 complex.

Enzymic modification of a tyrosine residue to a stable free radical in ribonucleotide reductase

Protein B2, a subunit of ribonucleotide reductase from Escherichia coli, contains in its active form a tyrosyl free radical as part of the polypeptide chain and a dimeric iron center that stabilizes the radical. The enzyme depends on this radical for its catalytic activity. Treatment with hydroxyurea scavenges the radical without disturbing the iron center and, thereby, results in an inactive form of the subunit, B2/HU. A second inactive form, apoB2, lacking both the radical and the iron center, is obtained by treatment of B2 with 8-hydroxyquinoline. Here we describe an enzyme activity in extracts from E. coli that transforms the catalytically inactive B2/HU form into the active B2 subunit by regeneration of the tyrosyl radical. This reaction requires the presence of oxygen, dithiothreitol, and Mg2+ and does not proceed through apoB2. Under anaerobic conditions, we obtained evidence for a second activity in the bacterial extract that destroys the free radical and transforms B2 into B2/HU. We suggest that this novel type of protein modification is functionally related to the synthesis of deoxyribonucleotides and DNA.