bluuebunny/crossref_metadata_2025_split huggingface dataset:
The LysR‐type regulator SftR is involved in soil survival and sulphate ester metabolism in Pseudomonas putida
Authors: Kahnert Antje , Mirleau Pascal , Wait Robin , Kertesz Michael A. 
Published: March 2003

SummarySulphate esters make up a large proportion of the available sulphur in agricultural soils, and many pseudomonads can desulphurize a range of aryl‐ and alkylsulphate esters to provide sulphur for growth. After miniTn5 transposon mutagenesis of Pseudomonas putida S‐313, we isolated 19 mutants that were defective in cleavage of the chromogenic sulphate ester 5‐bromo‐4‐chloro‐3‐indoxylsulphate (X‐sulphate). Analysis of these strains revealed that they carried independent insertions in a gene cluster that comprised genes for a sulphate ester/sulphonate transporter (atsRBC) a LysR‐type regulator (sftR), an oxygenolytic alkylsulphatase (atsK), an arylsulphotransferase (astA) and a putative TonB‐dependent receptor (sftP). The SftP protein was localized in the outer membrane, and the arylsulfphotransferase was identified as an intracellular enzyme. Expression of sftR was repressed in the presence of inorganic sulphate, and the sftR gene was required for the expression of atsBC, atsRK and sftP–astA. An sftR mutant was unable to grow with aryl‐ or alkylsulphate esters in laboratory media and showed significantly reduced survival compared with the parent strain during incubation in Danish agricultural and grassland soils. This effect suggests that sulphate esters are an important sulphur source for microbes in aerobic soils and highlights the importance of the microbial population in the soil sulphur cycle.
Development of a novel, bioluminescence‐based, fungal bioassay for toxicity testing
Authors: Weitz Hedda J. , Campbell Colin D. , Killham Ken 
Published: March 2003

SummaryNaturally bioluminescent fungi, Armillaria mellea and Mycena citricolor, were used to develop a novel, bioluminescence‐based bioassay for toxicity testing. Bioassays were carried out to assess the toxicity of 3,5‐dichlorophenol (3,5‐DCP), pentachlorophenol (PCP), copper and zinc. The results suggested that 60 min was a suitable exposure time for the bioassay. Light reduction was observed in response to 3,5‐DCP, PCP and Cu for both A. mellea and M. citricolor, but to Zn only for A. mellea. Armillaria mellea was significantly less sensitive to 3,5‐DCP and PCP than M. citricolor. The EC50 values for A. mellea and M. citricolor were similar to EC50 values for 3,5‐DCP, PCP and Cu (but not Zn) of bioluminescence‐based bacterial biosensors. They were also similar to EC50 values for Cu and Zn of a bioluminescence‐based yeast biosensor. The results highlighted the importance of using both prokaryotic and eukaryotic biosensors. The novel bioassay provides a rapid and sensitive method to assess bioavailability of pollutants as well as a method to determine their toxicity to filamentous fungi. It also expands the range of organisms that can be used for bioluminescence‐based toxicity testing by complementing existing biosensors.
Pseudomonas aeruginosa displays an epidemic population structure
Authors: Pirnay Jean‐Paul , De Vos Daniel , Cochez Christel , Bilocq Florence , Vanderkelen Alain , Zizi Martin , Ghysels Bart , Cornelis Pierre 
Published: March 2003

SummaryBacteria can have population structures ranging from the fully sexual to the highly clonal. Despite numerous studies, the population structure of Pseudomonas aeruginosa is still somewhat contentious. We used a polyphasic approach in order to shed new light on this issue. A data set consisting of three outer membrane (lipo)protein gene sequences (oprI, oprL and oprD), a DNA‐based fingerprint (amplified fragment length polymorphism), serotype and pyoverdine type of 73 P. aeruginosa clinical and environmental isolates, collected across the world, was analysed using biological data analysis software. We observed a clear mosaicism in the results, non‐congruence between results of different typing methods and a microscale mosaic structure in the oprD gene. Hence, in this network, we also observed some clonal complexes characterized by an almost identical data set. The most recent clones exhibited serotypes O1, 6, 11 and 12. No obvious correlation was observed between these dominant clones and habitat or, with the exception of some recent clones, geographical origin. Our results are consistent with, and even clarify, some seemingly contradictory results in earlier epidemiological studies. Therefore, we suggest an epidemic population structure for P. aeruginosa, comparable with that of Neisseria meningitidis, a superficially clonal structure with frequent recombinations, in which occasionally highly successful epidemic clones arise.
Microbial diversity in ikaite tufa columns: an alkaline, cold ecological niche in Greenland
Authors: Stougaard Peter , Jørgensen Flemming , Johnsen Mads G. , Hansen Ole C. 
Published: March 2003

SummaryIkaite tufa columns from the Ikka Fjord in south‐western Greenland constitute a natural, stable environment at low temperature and with a pH ranging from neutral at the exterior to very alkaline (pH 10.4) at the interior of the column. Phylogenetic analysis of culturable organisms revealed ten different isolates representing three of the major bacterial divisions. Nine of the isolates showed 94–99% similarity to known sequences, whereas one isolate displayed a low degree of similarity (less than 90%) to a Cyclobacterium species. Seven of the isolates were shown to be cold active alkaliphiles, whereas three isolates showed optimal growth at neutral pH. Phylogenetic analysis of DNA isolated directly from the ikaite material demonstrated the presence of a microbial flora more diverse than the culturable isolates. Whereas approximately half of the phylotypes showed 90–99% similarity to known meso‐ or thermophilic alkaliphiles, the rest of the sequences displayed less than 90% similarity when compared to known 16S rRNA gene sequences in databases. Thus, in the present paper, we demonstrate that ikaite columns that host a specialized macroscopic flora and fauna also contain a unique, cold active, alkaliphilic microflora.
Stable augmentation of activated sludge with foreign catabolic genes harboured by an indigenous dominant bacterium
Authors: Watanabe Kazuya , Teramoto Maki , Harayama Shigeaki 
Published: March 2003

Summary Comamonas sp. rN7 is a phenol‐degrading bacterium that represents the dominant catabolic population in activated sludge. The present study examined the utility of this bacterium for establishing foreign catabolic genes in phenol‐digesting activated sludge. The phc genes coding for phenol hydroxylase and its transcriptional regulators of C. testosteroni R5 were integrated into the chromosome of strain rN7. The specific phenol‐oxygenating activity of a resultant transformant designated rN7(R503) was three times higher than the activity of strain rN7, and the phc genes were stably inherited by rN7(R503) grown in a non‐selective laboratory medium. Inoculation of phenol‐acclimatized activated sludge with rN7(R503) resulted in a high phenol‐oxygenating activity and improved resistance to phenol‐shock loading compared to sludge inoculated with either no cells, rN7 or R5. Quantitative competitive polymerase chain reaction (PCR) showed that the phc genes were retained in the rN7(R503)‐inoculated sludge at a density of more than 108 copies per ml of mixed liquor for more than 35 days, whereas those in the R5‐inoculated sludge disappeared rapidly. No transfer of the phc genes to other indigenous populations was apparent in the rN7(R503)‐harbouring sludge. From these results, we concluded that the phenol treatment of the activated sludge was enhanced by the phc genes harboured by the rN7(R503) population. This study suggests a possible bioaugmentation strategy for stably utilizing foreign catabolic genes in natural ecosystems.
Decline in diversity and abundance of endophytic fungi in twigs of Fagus sylvatica L. after experimental long‐term exposure to sodium dodecylbenzene sulphonate (SDBS) aerosol
Authors: Danti Roberto , Sieber Thomas N. , Sanguineti Giovanni , Raddi Paolo , Di Lonardo Vincenzo 
Published: March 2003

SummarySodium dodecylbenzene sulphonate (SDBS) is an anionic synthetic detergent found in polluted sea aerosol and is known for its harmful effects on leaf surface ultrastructure on conifers and broadleaved trees. Four‐year‐old saplings of European beech were sprayed weekly for three consecutive growing seasons with either a 50 mg l−1 solution of SDBS in deionized water or with pure deionized water (control). Two‐ to three‐ year‐old twigs were collected from SDBS‐treated and control plants during the growing season one year after the last treatment to isolate endophytic fungi. The frequency of colonization by endophytic fungi was significantly lower on SDBS‐treated plants (63.8%) than on control plants (85.4%). Multiple colonization of twigs occurred more frequently and diversity of endophyte species was higher in control plants than in SDBS‐treated plants. Thirty‐six fungal species were isolated from 360 twigs. Cladosporium cladosporioides, Coryneum compactum, Phialocephala dimorphospora, and a species each of Mycosphaerella and Phomopsis were the most abundant endophytes with frequencies of colonization of more than 5%. The abundance of the Phomopsis species proved to be significantly reduced by the SDBS treatment. Within the limits of the indoor experimental conditions, the obtained results suggest that long‐term exposure of aerial parts of beech to SDBS can affect the amount and composition of endophytic fungal communities of lignified twigs. Degradation of the leaf epicuticular wax layer and changes of the assimilation capacity and leaf water content (transpiration) of the crowns are presumed to be responsible for the reduction of endophytic fungi detected in twigs of SDBS‐treated plants.
Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01
Authors: Martínez‐Bueno Manuel A. , Tobes Raquel , Rey Manuel , Ramos Juan‐Luis 
Published: March 2003

Summary Pseudomonas putida KT2440 is highly successful in colonizing a variety habitats, including aquatic and edaphic niches. In accordance with this ability and with the need to adapt to changing environmental conditions, P. putida has developed sophisticated mechanisms of transcriptional regulation. We analysed, at the genome level, the repertoire of sigma factors in P. putida KT2440 and identified 24 sigma factors, 19 of which corresponded to the subfamily of extracytoplasmic function (ECF) sigma factors. We detected 13 ECF sigma factors that showed similarity to the Escherichia coli FecI sigma factor, which is involved in iron acquisition. In 11 cases, a fecR‐like gene was found adjacent to the fecI‐like gene and, in 10 cases, a gene encoding an iron receptor lies in the vicinity of the fecI/fecR cluster. This may explain the ability of P. putida KT2440 to grow under low iron availability conditions. Five fecI/fecR/iron receptor gene clusters from P. putida were also identified in the human pathogen Pseudomonas aeruginosa.
Microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16S rRNA‐targeting oligonucleotide probes
Authors: Friedrich Udo , Van Langenhove Herman , Altendorf Karlheinz , Lipski André 
Published: March 2003

SummaryA study was conducted to investigate the microbial community structure, the physicochemical properties, and the relationships between these parameters of a full‐scale industrial biofilter used for waste gas abatement in an animal‐rendering plant. Fluorescencein situhybridization (FISH) was successfully combined with digital image analysis to study the composition of the microbial community. Several new nucleic acid probes were designed and established based on published 16S rDNA sequences and on ones retrieved from the biomass of the biofilter under investigation. Bacterial detection rates varied greatly over time and filterbed depth between 27.2% and 88.1% relative to DAPI counts. Overall, members of theBetaproteobacteriafollowed byActinobacteria,Alphaproteobacteria,Cytophaga‐Flavobacteria,FirmicutesandGammaproteobacteriawere the most abundant groups. Among the groups below phylum level, members of theAlcaligenes/Bordetellalineage were on average the most abundant group accounting for up to 8.5% of DAPI‐stained cells. Whereas the community composition generally showed no vertical gradient, the lower 50 cm of the biofilter proved to be the most active part for the degradation of aldehydes such as 2‐ and 3‐methylbutanal, 2‐methylpropanal, and hexanal. This zone of the filterbed being operated in up‐flow direction degraded about 80% of these compounds. Dimethyldisulphide was the most common reduced sulphur compound. Statistical analysis of microbial versus waste gas parameters generally revealed only weak or non‐significant correlations between the two. Possible explanations for this finding are discussed.
Emergency subtotal colectomy as treatment of choice in obstructing carcinomas of the left colon
Authors: Pérez‐Díaz  , Turégano‐Fuentes  , Calvo‐Serrano  , Tomás‐Palacios J. De , Fuenmayor‐Valera M. L. De , Hernández E. Del Valle , Jiménez F. Muñoz , Quintans‐Rodríguez  
Published: March 2003

PurposeTo assess the morbidity, mortality and function following emergency subtotal colectomy (ESC) with primary anastomosis in obstructing carcinomas of the left colon, to determine whether this technique is warranted as the current treatment of choice for this condition.MethodsRetrospective review of a series of 70 patients with obstructing carcinomas of the left colon who underwent an ESC with primary anastomosis between September 1989 and December 1996. Morbidity, mortality, hospital stay and functional results were analysed, as well as the percentage of patients submitted to this technique.ResultsThe use of ESC has steadily increased at our institution over the last few years, from 22% in 1990 to 84% of all the procedures performed for obstructing carcinomas of the left colon in 1995. The mortality rate of the series was 4.2%. Anastomotic leak rate was 10%, with only three major leaks. A prolonged obstructive ileus was a frequent and distressing complication (26%), and the main determinant of hospital stay. Average daily stool frequency on discharge from hospital was of 2 (range 1–6), with many patients having discontinued anti‐diarrhoeal medications.ConclusionEmergency SC with primary anastomosis has evolved into the treatment of choice for most patients with acutely obstructing malignancies of the left colon at our institution. It can be performed with low mortality, a reasonable morbidity and good functional results.
Medical negligence in coloproctology
Authors: Schofield  
Published: March 2003

There has been a significant increase of litigation in the UK in recent years and for this reason it is appropriate to analyse the reasons for civil litigation. Alleged medical negligence in the colorectal field comes from the activity of general surgeons and gynaecologists as well as colorectal surgeons. This communication deals with problems in the coloproctology area irrespective of the surgeon involved.Two hundred and forty‐five cases are reviewed, consisting of 49 anal problems, 160 abdominal problems with 24 laparoscopic and 12 colonoscopic injuries. Thirty‐two of 49 anal cases had incontinence and these were often difficult to defend, especially the 20 cases due to childbirth injury because of poor documentation. The abdominal problems were due to delay or complications of surgery. The cases based on delay in diagnosis of cancer were often unsuccessful, but the cases of delay in diagnosis of intra‐abdominal infection were difficult to defend. Problems occurring in the operative or early post‐operative period produced allegations which were often justified, but the late complications of surgery were rarely due to poor standard of care.The laparoscopic injuries included bowel perforation, bleeding and major vascular damage which were not recognized at the time. The colonoscopic cases were chiefly due to perforation, which is easily defended provided the endoscopist is experienced and the risk is recorded in the consent.The cases have yielded a number of lessons which are discussed and compared with the American experience. It is concluded that litigation is traumatic to both plaintiff and surgeon and that better ways should be found to resolve complaints of inadequate care.
Anal plug for faecal incontinence
Authors: Norton C. , Kamm M. A. 
Published: March 2003

ObjectiveDespite the availability of pharmacological, behavioural and surgical treatments for faecal incontinence, many patients remain symptomatic. There are few devices designed specifically to cope with this, and perineal pads are inefficient and unacceptable for many patients. This study aimed to evaluate a new device in patients with intractable faecal incontinence.MethodTwo sizes of a purpose‐designed anal plug were evaluated in 20 patients with intractable faecal incontinence for solid or liquid stool. Each plug size was tested for 2 weeks, with patients completing a structured questionnaire after each size.ResultsThe majority [14/20] could not tolerate a plug due to discomfort. Four patients (20%) wished to continue to use a plug on a regular basis after the study, and two others on an occasional basis. However, for this minority who could tolerate a plug, it was highly successful at controlling faecal incontinence. There was no clear preference for the smaller or larger plug. There was no association between comfort in using the plug and anorectal sensitivity as measured by electrophysiological tests. It was not possible to predict which patients would benefit from plug use.ConclusionThe anal plug is effective in controlling faecal incontinence and is well tolerated in a minority of patients. Evaluation quickly reveals whether the patient will find it an effective and acceptable option. This device therefore offers a further management option for patients with faecal incontinence.
Using quality of life scores to help determine treatment: is restoring bowel continuity better than an ostomy?
Authors: Ko C. Y. , Rusin L. C. , Schoetz D. J. , Coller J. A. , Murray J. J. , Roberts P. L. , Moreau L. 
Published: March 2003

ObjectiveIn colorectal surgery, evaluation of heath‐related quality of life (HRQL) has been relatively minimal when compared to other medical specialties. Would the performance of such HRQL evaluations change our decision‐making in patient care? In familial adenomatous polyposis (FAP), procedures that restore bowel continuity (i.e. Ileorectal anastomosis or ileal pouch anal anastomosis) are routinely preferred to ileostomy because of the perceived, but unproven, better HRQL. This study evaluates FAP patients who underwent prophylactic colectomy with either permanent ileostomy or ‘restored bowel continuity’ reconstruction. The functional outcomes of both groups are reported, and the HRQL assessments are compared.MethodsAll FAP patients who underwent (procto) colectomy resection with reconstruction, either restored bowel continuity (BC) or permanent ileostomy (OST), between 1980 and 1998 were studied. Functional data were obtained by questionnaire and medical record review. HRQL was assessed by 2 validated instruments – the SF‐36 Physical and Mental Health Summary Scales and the SF‐36 Health Survey – which measure physical summary (PSF) and mental summary functioning (MSF) as well as eight separate health quality dimensions including health perception (HP), physical (PF) and social functioning (SF), physical (PR) and emotional role limitations (ER), mental health (MH), bodily pain (BP), and energy level (E).ResultsResults were obtained in 54 patients; bowel continuity (44), ileostomy (10). Mean patient age was 39 years, mean follow up time was 10.5 years. Mean patient age at operation was 28 years. Functional results for BC included number of bowel movements/day (6.7), leakage (30%), having to wear a pad (11%), perianal skin problems (25%), food avoidance (68%), and inability to distinguish gas (27%). Functional results for OST were routinely excellent. Results of the HRQL surveys reveal no significant differences for BC vs OST (HP: 67 ± 28 vs 79 ± 39; PF: 91 ± 14 vs 90 ± 17; SF: 86 ± 23 vs 97 ± 5; PR: 79 ± 34 vs 83 ± 40; ER: 86 ± 28 vs 88 ± 27; MH: 77 ± 19 vs 82 ± 14; BP: 78 ± 24 vs 71 ± 32; E 60 ± 21 vs 58 ± 18, respectively).ConclusionAlthough the perceived quality of life for ileostomy patients is generally worse than the ‘restored bowel continuity’ group, the measured HRQL is the same for both groups. These results suggest that a permanent ileostomy should be included as a viable and appropriate first line treatment option for FAP patients after resection. This study also suggests that HRQL should play a greater role in the evaluation of care and treatment in colorectal surgery.
A prospective study to assess the implementation of a fast‐track system to meet the two‐week target for colorectal cancer in Somerset
Authors: Davies R. J. , Ewings P. , Welbourn R. , Collins C. , Kennedy R. , Royle C. 
Published: March 2003

ObjectiveThis prospective study assesses the introduction of a fast‐track referral system for patients with suspected colorectal cancer.Patients and methodsThe referral system was initiated in Yeovil District Hospital and Taunton and Somerset Hospital using six screening criteria to select high‐risk patients. Data on all high‐risk patients from 1 November 1999 to 30 April 2000 was recorded prospectively. Patients with proven colorectal cancer diagnosed between 1 November 1998 and 30 April 1999 have been identified for comparison.ResultsThere were 158 new cases of colorectal cancer in total (111 elective, 47 emergency). 59 cases of colorectal cancer were diagnosed from 433 fast‐track referrals (53% of total elective cases). Median time from referral to diagnosis in the fast‐track group was 11 days vs. 32.5 days for nonfast‐track elective patients (P < 0.001). Median time from referral to diagnosis for all elective cases was 17 days vs. 38.5 days for patients presenting one year earlier (P < 0.001). 75% of fast‐track patients were diagnosed with colorectal cancer within two weeks, compared with 17% of nonfast‐track elective patients (P < 0.001). The proportion of emergency admissions was reduced from 40% to 30% (P=0.07) following the introduction of this system.ConclusionData from the first six months reveal that over half of the elective cases of colorectal cancer were diagnosed within the fast‐track system. The median time from referral to diagnosis in these patients was within two weeks and there has been a significant reduction in the time to diagnosis associated with the introduction of this service.