Mutant phenotypes for thousands of bacterial genes of unknown function.

One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that have high confidence because they are conserved in other bacteria. By combining these conserved associations with comparative genomics, we identified putative DNA repair proteins; in addition, we propose specific functions for poorly annotated enzymes and transporters and for uncharacterized protein families. Our study demonstrates the scalability of microbial genetics and its utility for improving gene annotations.

Enhanced chlorhexidine skin penetration with 1,8-cineole.

BACKGROUND: Chlorhexidine (CHG) penetrates poorly into skin. The purpose of this study was to compare the depth of CHG skin permeation from solutions containing either 2% (w/v) CHG and 70% (v/v) isopropyl alcohol (IPA) or 2% (w/v) CHG, 70% (v/v) IPA and 2% (v/v) 1,8-cineole. METHODS: An ex-vivo study using Franz diffusion cells was carried out. Full thickness human skin was mounted onto the cells and a CHG solution, with or without 2% (v/v) 1,8-cineole was applied to the skin surface. After twenty-four hours the skin was sectioned horizontally in 100 µm slices to a depth of 2000 µm and the concentration of CHG in each section quantified using high performance liquid chromatography (HPLC). The data were analysed with repeated measures analysis of variance. RESULTS: The concentration of CHG in the skin on average was significantly higher (33.3% [95%, CI 1.5% - 74.9%]) when a CHG solution which contained 1,8-cineole was applied to the skin compared to a CHG solution which did not contain this terpene (P = 0.042). CONCLUSIONS: Enhanced delivery of CHG can be achieved in the presence of 1,8-cineole, which is the major component of eucalyptus oil. This may reduce the numbers of microorganisms located in the deeper layers of the skin which potentially could decrease the risk of surgical site infection.

Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments.

The concentrations of molybdenum (Mo) and 25 other metals were measured in groundwater samples from 80 wells on the Oak Ridge Reservation (ORR) (Oak Ridge, TN), many of which are contaminated with nitrate, as well as uranium and various other metals. The concentrations of nitrate and uranium were in the ranges of 0.1 µM to 230 mM and <0.2 nM to 580 µM, respectively. Almost all metals examined had significantly greater median concentrations in a subset of wells that were highly contaminated with uranium (≥126 nM). They included cadmium, manganese, and cobalt, which were 1,300- to 2,700-fold higher. A notable exception, however, was Mo, which had a lower median concentration in the uranium-contaminated wells. This is significant, because Mo is essential in the dissimilatory nitrate reduction branch of the global nitrogen cycle. It is required at the catalytic site of nitrate reductase, the enzyme that reduces nitrate to nitrite. Moreover, more than 85% of the groundwater samples contained less than 10 nM Mo, whereas concentrations of 10 to 100 nM Mo were required for efficient growth by nitrate reduction for two Pseudomonas strains isolated from ORR wells and by a model denitrifier, Pseudomonas stutzeri RCH2. Higher concentrations of Mo tended to inhibit the growth of these strains due to the accumulation of toxic concentrations of nitrite, and this effect was exacerbated at high nitrate concentrations. The relevance of these results to a Mo-based nitrate removal strategy and the potential community-driving role that Mo plays in contaminated environments are discussed.

Phase II trial of docetaxel, cisplatin and 5FU chemotherapy in locally advanced and metastatic penis cancer (CRUK/09/001).

BACKGROUND: Penis cancer is rare and clinical trial evidence on which to base treatment decisions is limited. Case reports suggest that the combination of docetaxel, cisplatin and 5-flurouracil (TPF) is highly active in this disease. METHODS: Twenty-nine patients with locally advanced or metastatic squamous carcinoma of the penis were recruited into a single-arm phase II trial from nine UK centres. Up to three cycles of chemotherapy were received (docetaxel 75 mg m(-2) day 1, cisplatin 60 mg m(-2) day 1, 5-flurouracil 750 mg m(-2) per day days 1-5, repeated every 3 weeks). Primary outcome was objective response (assessed by RECIST). Fourteen or more responses in 26 evaluable patients were required to confirm a response rate of 60% or higher (Fleming-A'Hern design), warranting further evaluation. Secondary endpoints included toxicity and survival. RESULTS: 10/26 evaluable patients (38.5%, 95% CI: 20.2-59.4) achieved an objective response. Two patients with locally advanced disease achieved radiological complete remission. 65.5% of patients experienced at least one grade 3/4 adverse event. CONCLUSION: Docetaxel, cisplatin and 5FU did not reach the pre-determined threshold for further research and caused significant toxicity. Our results do not support the routine use of TPF. The observed complete responses support further investigation of combination chemotherapy in the neoadjuvant setting.

Barriers to accepting and completing latent tuberculosis infection treatment.

Treatment of Latent Tuberculosis Infection (LTBI) is an important component of any TB control strategy. Acceptance and completion of treatment is poor. We undertook this study to identify barriers to acceptance & completion of treatment. Patients attending TB clinics completed a self-administered survey. Medical notes and electronic pharmacy records were reviewed. 143 surveys were completed. 70 (49%) completed treatment. Patients were less likely to accept treatment (p = 0.01, RR 0.781, CI 0.643-0.950) and less likely to complete treatment (p = 0.01, RR 0.640, CI 0.462-0.885) when concerned about the side effects of LTBI medication. Completion of LTBI treatment is sub-optimal. The major barrier identified was fear about side effects caused by LTBI medications.

Molecular determination of H antigens of Salmonella by use of a microsphere-based liquid array.

Serotyping of Salmonella has been an invaluable subtyping method for epidemiologic studies for more than 70 years. The technical difficulties of serotyping, primarily in antiserum production and quality control, can be overcome with modern molecular methods. We developed a DNA-based assay targeting the genes encoding the flagellar antigens (fliC and fljB) of the Kauffmann-White serotyping scheme. Fifteen H antigens (H:a, -b, -c, -d, -d/j, -e,h, -i, -k, -r, -y, -z, -z(10), -z(29), -z(35), and -z(6)), 5 complex major antigens (H:G, -EN, -Z4, -1, and -L) and 16 complex secondary antigens (H:2, -5, -6, -7, -f, -m/g,m, -m/m,t, -p, -s, -t/m,t, -v, -x, -z(15), -z(24), -z(28), and -z(51)) were targeted in the assay. DNA probes targeting these antigens were designed and evaluated on 500 isolates tested in parallel with traditional serotyping methods. The assay correctly identified 461 (92.2%) isolates based on the 36 antigens detected in the assay. Among the isolates considered correctly identified, 47 (9.4%) were partially serotyped because probes corresponding to some antigens in the strains were not in the assay, and 13 (2.6%) were monophasic or nonmotile strains that possessed flagellar antigen genes that were not expressed but were detected in the assay. The 39 (7.8%) strains that were not correctly identified possessed an antigen that should have been detected by the assay but was not. Apparent false-negative results may be attributed to allelic divergence. The molecular assay provided results that paralleled traditional methods with a much greater throughput, while maintaining the integrity of the Kauffmann-White serotyping scheme, thus providing backwards-compatible epidemiologic data. This assay should greatly enhance the ability of clinical and public health laboratories to serotype Salmonella.

The olfactory bulbectomy disease model: A Re-evaluation.

The olfactory bulbectomized rodent has long been one of the preferred animal models of depression and certain other neuropsychiatric diseases. In fact, it is considered unparalleled, by some, in the search for antidepressant medication and the literature generated about the model is prodigious. We have revisited the "syndrome" of behavioral sequela following bulbectomy choosing ecologically valid tests likely to be underpinned with evolutionarily preserved neural circuits. Our test battery included measurements of activity, intermale aggression, pleasure seeking, stress/fear and non-spatial memory. The emphasis was on the timetable of syndrome emergence, since this has been understudied and bears on the widely held belief that non-olfactory effects dominate. Our results largely agree with previous reports describing the behavioral syndrome in that we document bulbectomized mice as hyperactive, non-aggressive and fearless. However, we did not find deficits in memory as have frequently been reported in previous studies. Notably, our results revealed that some syndrome behaviors-including the hallmark of hyperactivity-appear immediately or soon after surgery. This rapid appearance casts doubt on the widely held view that compensatory reorganization of limbic and prefrontal cortical areas following bulbectomy underlies the syndrome. Rather, hyperactivity, non-aggressiveness, reduced fear and diminished sucrose preference in the olfactory bulbectomized mouse find ready explanations in the loss of smell that is the immediate and irreversible outcome of bulbectomy. Finally, after a critical consideration of the literature and our results, we conclude that the olfactory bulbectomy model lacks the validity and simplicity previously credited to it. Indeed, we deem this lesion unsuitable as a model of most neuropsychiatric diseases since its effects are at least as complex and misunderstood as the disorders it is purported to model.

Low 30-day mortality in South African orthopaedic patients undergoing surgery at an academic hospital during the first wave of the COVID-19 pandemic: It was safe to perform orthopaedic procedures at our hospital during the first COVID-19 peak.

BACKGROUND:  Initial local and global evidence suggests that SARS-CoV-2-infected patients who undergo surgery, and those who become infected perioperatively, have an increased mortality risk post surgery. OBJECTIVES: To analyse and describe the 30-day mortality, presurgical COVID-19 status and hospital-acquired SARS-CoV-2 infection rates of patients, both SARS-CoV-2-positive and negative, undergoing orthopaedic surgery at a tertiary academic hospital in South Africa (SA) during the first COVID-19 peak. METHODS: This single-centre, observational, prospective study included patients who underwent orthopaedic procedures from 1 April 2020 (beginning of the COVID-19 case increase in SA) to 31 July 2020 (first COVID-19 peak in SA). All patients were screened for COVID-19 and were confirmed positive if they had a positive laboratory quantitative polymerase chain reaction test for SARS-CoV-2 RNA on a nasopharyngeal or oral swab. Thirty-day mortality, presurgical COVID-19 status and hospital-acquired SARS-CoV-2 infection were assessed. RESULTS:  Overall, a total of 433 operations were performed on 346 patients during the timeframe. Of these patients, 65.9% (n=228) were male and 34.1% (n=118) were female. The mean (standard deviation) age was 42.5 (16.8) years (range 9 - 89). Of the patients, 5 (1.4%) were identified as COVID-19 patients under investigation (PUI) on admission and tested positive for SARS-CoV-2 before surgery, and 1 (0.3%) contracted SARS-CoV-2 perioperatively; all survived 30 days post surgery. Twenty-nine patients were lost to follow-up, and data were missing for 6 patients. The final analysis was performed excluding these 35 patients. Of the 311 patients included in the final 30-day mortality analysis, 303 (97%) had a follow-up observation ≥30 days after the operation. The overall 30-day mortality for these patients was 2.5% (n=8 deaths). None of the recorded deaths were of screened COVID-19 PUI. CONCLUSIONS: We report a low 30-day mortality rate of 2.5% (n=8) for patients undergoing orthopaedic surgery at our hospital during the first COVID-19 peak. None of the deaths were COVID-19 related, and all patients who tested SARS-CoV-2-positive, before or after surgery, survived. Our overall 30-day mortality rate correlates with several other reports of orthopaedic centres analysing over similar timeframes during the first peak of the COVID-19 pandemic. Regarding mortality and SARS-CoV-2 infection risk, we can conclude that with the appropriate measures taken, it was safe to undergo orthopaedic procedures at our hospital during the first peak of the COVID-19 pandemic in SA.

Drastic reduction of orthopaedic services at an urban tertiary hospital in South Africa during COVID-19: Lessons for the future response to the pandemic.

BACKGROUND: The COVID-19 pandemic has impacted on the global surgery landscape. OBJECTIVES: To analyse and describe the initial impact of the COVID-19 pandemic on orthopaedic surgery at Groote Schuur Hospital, a tertiary academic hospital in South Africa. METHODS: The number of orthopaedic surgical cases, emergency theatre patient waiting times, and numbers of outpatient clinic visits, ward admissions, bed occupancies and total inpatient days for January - April 2019 (pre-COVID-19) were compared with the same time frame in 2020 (COVID-19). The COVID-19 timeframe included initiation of a national 'hard lockdown' from 26 March 2020, in preparation for an increasing volume of COVID-19 cases. RESULTS: April 2020, the time of the imposed hard lockdown, was the most affected month, although the number of surgical cases had started to decrease slowly during the 3 preceding months. The total number of surgeries, outpatient visits and ward admissions decreased significantly during April 2020 (55.2%, 69.1% and 60.6%, respectively) compared with April 2019 (p<0.05). Trauma cases were reduced by 40% in April 2020. Overall emergency theatre patient waiting time was 30% lower for April 2020 compared with 2019. CONCLUSIONS: COVID-19 and the associated lockdown has heavily impacted on both orthopaedic inpatient and outpatient services. Lockdown led to a larger reduction in the orthopaedic trauma burden than in international centres, but the overall reduction in surgeries, outpatient visits and hospital admissions was less. This lesser reduction was probably due to local factors, but also to a conscious decision to avoid total collapse of our surgical services.

Examination of outcome following abdominoperineal resection for adenocarcinoma in Oxford.

AIM: Abdominoperineal resection (APR) has been shown to have poor outcomes compared with anterior resection (AR) in the treatment of rectal cancer. We compared APR outcomes with those for low AR. METHOD: Lower third rectal cancers treated at the John Radcliffe Hospital with APR and low AR were examined using a prospectively collected database augmented with review of patient records. For all cases (APR and low AR), a range of patient, cancer and outcome data were collected. A selected group was created on the basis of exclusions. Outcomes for the global and selected APR and low AR groups were compared using the Kaplan-Meier method. CRM+ve and CRM-ve APR cases were compared. RESULTS: Between 1994 and 2003, 70 APR and 93 low AR were performed. After exclusions, 42 APR and 81 low AR remained. Median follow-up was 4.8 years. Five year survival for the APR group was significantly worse than for the low AR group. The APR group showed significantly fewer T0 cancers and significantly more T3 cancers. CRM R1 involvement was significantly higher for the APR group. The CRM+ve APR group contained significantly more later stage cancers, more defective resection specimens, more abscesses and fistulas and was associated with more local recurrence. CONCLUSIONS: These data showed that APR led to worse results than low AR in terms of overall survival and circumferential margin involvement, but that the cancers treated with APR tended to be more locally advanced.

Key Service Improvements After the Introduction of an Integrated Orthogeriatric Service.

INTRODUCTION: Models of orthogeriatric care have been shown to improve functional outcomes for patients after hip fractures and can improve compliance with best practice guidelines for hip fracture care. METHODS: We evaluated improvements to key performance indicators in hip fracture care after implementation of a formal orthogeriatric service. Compliance with Irish Hip Fracture standards of care was reviewed, and additional outcomes such as length of stay, access to rehabilitation, and discharge destination were evaluated. RESULTS: Improvements were observed in all of the hip fracture standards of care. Mean length of stay decreased from 19 to 15.5 days (mean difference 3.5 days; P < .05). A higher proportion of patients were admitted to rehabilitation (16.7% vs 7.9%, P < .05), and this happened in a timelier fashion (17.8 vs 24.8 days, P < .05). We found that less patients required convalescence post-hip fracture. DISCUSSION: A standardized approach to integrated post-hip fracture care with orthogeriatrics has improved standards of care for patients. CONCLUSION: Introduction of orthogeriatric services has resulted in meaningful improvements in clinical outcomes for older people with hip fractures.

Selection for aerobic capacity affects corticosterone, monoamines and wheel-running activity.

A positive genetic relationship between aerobic capacity and voluntary exercise has been suggested from earlier studies of mice selected for increased wheel-running activity. To further investigate the relationship between aerobic capacity and exercise behavior, wheel-running activity was studied in female rats bidirectionally selected for intrinsic aerobic capacity (high capacity runners - HCR; low capacity runners - LCR). Aerobic capacity was measured using a forced treadmill paradigm; the subpopulations of animals used in this experiment exhibited a 471% difference in endurance capacity. Rats were housed individually, with or without access to running wheels. Wheel-running activity was recorded and analyzed from weeks two through seven during an eight-week trial to determine voluntary activity levels. HCR animals exhibited 33% greater total wheel-running distance per day compared to LCR rats (16,838.7+1337.30 m versus 12,665.8+893.88 m), which was due to the HCR rats exhibiting increases in both running speed and duration over LCR rats. Differences in the intermittency of wheel running were also observed. HCR rats engaged in more bouts of running per day than LCR rats, and trended towards running faster, for more time, and for longer distances during bouts of running than LCR rats. Following the running trial, measurement of plasma corticosterone concentration and striatal dopaminergic activity showed differences between HCR and LCR rats, suggesting a divergence of physiological systems that could potentially influence locomotor behaviors in these lines. These results are consistent with earlier work, and suggest an evolutionarily conserved relationship between physiological capacity and behavioral activity of exercise.

Roles for Gcn5p and Ada2p in transcription and nucleotide excision repair at the Saccharomyces cerevisiae MET16 gene.

Chromatin structure, transcription and repair of cyclobutane pyrimidine dimers at the MET16 gene of wild type, gcn5Delta and ada2Delta Saccharomyces cerevisiae cells were studied under repressing or derepressing conditions. These two components of the SAGA/ADA chromatin remodelling complexes are expendable for the basal transcription of MET16 but are mandatory for its full transcription induction. Despite their influence on transcription neither protein induces major changes in MET16 chromatin structure, but some minor ones occur. Repair at the coding region of the transcribed strand is faster than repair at non-transcribed regions in all strains and either growth condition. Moreover, the more MET16 is transcribed the faster the repair. The data show that by changing the transcription extent the rate of repair at each DNA strand is altered in a different way, confirming that repair at this locus is strongly modulated by its chromatin structure and transcription level. Deletion of GCN5 or ADA2 reduces repair at MET16. The results are discussed in light of the current understanding of Gcn5p and Ada2p functions, and they are the first to report a role for Ada2p in the nucleotide excision repair of the regulatory and transcribed regions of a gene.

Clinical and laboratory investigations of the outbreaks of foot-and-mouth disease in southern England in 2007.

A case of foot-and-mouth disease (fmd) on a cattle farm in Normandy, Surrey, was confirmed on Friday August 3, 2007, the first case in the uk since 2001. The infection was detected nearby on a second farm on August 6. On September 12, fmd was confirmed on a farm approximately 20 km from Normandy in Egham, and this was followed by cases on five more farms in that area in the next three weeks. The majority of the infected farms consisted of multiple beef cattle holdings in semi-urban areas. In total, 1578 animals were culled on the infected farms, and fmd virus infection was confirmed in 278 of them by the detection of viral antigen, genome or antibodies to the virus, or by clinical signs. This paper describes the findings from animal inspections on the infected farms, including the estimated ages of the fmd lesions and the numbers of animals infected. It also summarises the test results from samples taken for investigation, including the detection of preclinically viraemic animals by using real-time reverse transcriptase-pcr.

Clinically relevant fatigue in cancer outpatients: the Edinburgh Cancer Centre symptom study.

BACKGROUND: Fatigue is associated with cancer and its treatment but we know little about how many and which patients suffer fatigue of clinical severity. We aimed to determine the prevalence of clinically relevant fatigue (CRF) and its associations in outpatients with various cancer diagnoses. PATIENTS AND METHODS: A survey of outpatients with colorectal, breast, gynaecological, genitourinary, sarcoma, melanoma and miscellaneous tumours at a regional cancer centre. Patients completed the European Organisation for Research and Treatment of Cancer (EORTC) fatigue subscale and the Hospital Anxiety and Depression Scale (HADS). These self-report data were linked to demographic and clinical variables. Data were available on 2867 outpatients. RESULTS: The prevalence of CRF (EORTC fatigue subscale > or =40) was 32% (95% confidence interval 31-34%). The variables independently associated with CRF were primary cancer site, having disease present, type of cancer treatment and emotional distress (total HADS score > or =15). Emotional distress had the strongest association with fatigue but half the cases of CRF were not distressed. CONCLUSION: CRF is common in cancer outpatients and is associated with type of disease and treatment, as well as with emotional distress. The association between CRF and emotional distress is strong but they are not equivalent conditions.

Assessing radiation-associated mutational risk to the germline: repetitive DNA sequences as mutational targets and biomarkers.

This review assesses recent data on mutational risk to the germline after radiation exposure obtained by molecular analysis of tandemly repeated DNA loci (TRDLs): minisatellites in humans and expanded simple tandem repeats in mice. Some studies, particularly those including exposure to internal emitters, indicate that TRDL mutation can be used as a marker of human radiation exposure; most human studies, however, are negative. Although mouse studies have suggested that TRDL mutation analysis may be more widely applicable in biomonitoring, there are important differences between the structure of mouse and human TRDLs. Mutational mechanisms probably differ between the two species, and so care should be taken in predicting effects in humans from mouse data. In mice and humans, TRDL mutations are largely untargeted with only limited evidence of dose dependence. Transgenerational mutation has been observed in mice but not in humans, but the mechanisms driving such mutation transmission are unknown. Some minisatellite variants are associated with human diseases and may affect gene transcription, but causal relationships have not yet been established. It is concluded that at present the TRDL mutation data do not warrant a dramatic revision of germline or cancer risk estimates for radiation.

Excision repair at the level of the nucleotide in the upstream control region, the coding sequence and in the region where transcription terminates of the Saccharomyces cerevisiae MFA2 gene and the role of RAD26.

RAD26, the yeast homologue of human CSB, has an essential role in transcription-coupled repair (TCR). We have mapped the requisite of Rad26 for nucleotide excision repair (NER) within the different regions of the yeast Saccharomyces cerevisiae MFA2 gene at nucleotide resolution. Our results show that Rad26 is dispensable for enhanced NER in both the MFA2 upstream promoter, except in the TATA box region, and for enhanced NER in both strands of the active gene at a site close to the transcription termination region. As expected, it is not needed for repair of regions downstream of where transcription terminates. However, it is required for TCR in the transcription initiation and elongation regions. Our data support the hypothesis that Rad26 is required for the interchange between holo-TFIIH and a putative repairosome containing core TFIIH and other NER proteins. Close to the end of transcription, hotspots for the repair of CPDs in both the transcribed strand and the non-transcribed strand occur. This enhanced repair is independent of Rad26. Hence, TFIIH may take a form favourable for forming a repairosome without Rad26 assistance; here the organisation of the DNA during the termination of transcription may facilitate access of a repair complex to enable enhanced repair of both strands.

The mapping of nucleosomes and regulatory protein binding sites at the Saccharomyces cerevisiae MFA2 gene: a high resolution approach.

We have developed an end-labelling approach to map the positions of nucleosomes and protein binding sites at nucleotide resolution by footprinting micrococcal nuclease (MNase)-sensitive sites. Using this approach we determined that the MFA2 gene and its upstream control regions have four positioned nucleosomes when transcription is repressed in mating type alpha cells and that the nucleosomes lose their positioning when the gene became transcriptionally active in mating type a cells. We also detected MNase-hypersensitive sites in the alpha2 operator region of MFA2 in alpha cells but not in a cells. These probably result from the change in the local DNA conformation due to protein(s) binding in this region that governs MFA2 transcription.

Excision repair of nitrogen mustard-DNA adducts in Saccharomyces cerevisiae.

The bifunctional alkylating anticancer drug nitrogen mustard forms a variety of DNA lesions, including monoadducts and intrastrand and interstrand crosslinks. Although it is known that nucleotide excision repair (NER) is important in processing these adducts, the role of the other principal excision repair pathway, base excision repair (BER) is less well defined. Using isogenic Saccharomyces cerevisiae strains disrupted for a variety of NER and BER genes we have examined the relative importance of the two pathways in the repair of nitrogen mustard adducts. As expected, NER defective cells (rad4 and rad14 strains) are extremely sensitive to the drug. One of the BER mutants, a 3-methyladenine glycosylase defective (mag1) strain also shows significant hypersensitivity. Using a rad4/mag1 double mutant it is shown that the two excision repair pathways are epistatic to each other for nitrogen mustard sensitivity. Furthermore, both rad14 and mag1 disruptants show elevated levels of nitrogen mustard-induced forward mutation. Measurements of repair rates of nitrogen mustard N-alkylpurine adducts in the highly transcribed RPB2 gene demonstrate defects in the processing of mono-adducts in rad4, rad14 and mag1 strains. However, there are differences in the kinetics of adduct removal in the NER mutants compared to the mag1 strain. In the mag1 strain significant repair occurs within 1 h with evidence of enhanced repair on the transcribed strand. Adducts however accumulate at later times in this strain. In contrast, in the NER mutants repair is only evident at times greater than 1 h. In a mag1/rad4 double mutant damage accumulates with no evidence of repair. Comparison of the rates of repair in this gene with those in a different genomic region indicate that the contributions of NER and BER to the repair of nitrogen mustard adducts may not be the same genome wide.