bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern
Authors: Casamayor Emilio O. , Massana Ramon , Benlloch Susana , Øvreås Lise , Díez Beatriz , Goddard Victoria J. , Gasol Josep M. , Joint Ian , Rodríguez‐Valera Francisco , Pedrós‐Alió Carlos 
Published: March 2003

SummaryMicrobial communities inhabiting a multipond solar saltern were analysed and compared using SSU rRNA polymerase chain reaction (PCR)‐based fingerprintings carried out in parallel by four laboratories. A salinity gradient from seawater (3.7%) to NaCl precipitation (37%) was studied for Bacteria, Archaea and Eukarya, and laboratories applied their own techniques and protocols on the same set of samples. Members of all three domains were retrieved from all salt concentrations. Three fingerprinting techniques were used: denaturing gradient gel electrophoresis (DGGE), ribosomal internal spacer analysis (RISA), and terminal‐restriction fragments length polymorphism (T‐RFLP). In addition, each laboratory used its own biomass collection method and DNA extraction protocols. Prokaryotes were addressed using DGGE and RISA with different ‘domain‐specific’ primers sets. Eukaryotes were analysed by one laboratory using DGGE and T‐RFLP, but targeting the same 18S rDNA site. Fingerprints were compared through cluster analysis and non‐metric multidimensional scaling plots. This exercise allowed fast comparison of microbial assemblages and determined to what extent the picture provided by each laboratory was similar to those of others. Formation of two main, salinity‐based groups of samples in prokaryotes (4–15% and 22–37% salinity) was consistent for all the laboratories. When other clusters appeared, this was a result of the particular technique and the protocol used in each case, but more affected by the primers set used. Eukaryotic microorganisms changed more from pond to pond; 4–5% and 8–37% salinity were but the two main groups detected. Archaea showed the lowest number of bands whereas Eukarya showed the highest number of operational taxonomic units (OTUs) in the initial ponds. Artefacts appeared in the DGGE from ponds with extremely low microbial richness. On the other hand, different 16S rDNA fragments with the same restriction or internal transcribed spacer (ITS) length were the main limitations for T‐RFLP and RISA analyses, respectively, in ponds with the highest OTUs richness. However, although the particular taxonomic composition could vary among protocols, the general structure of the microbial assemblages was maintained.
Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern
Authors: Benlloch Susana , López‐López Arantxa , Casamayor Emilio O. , Øvreås Lise , Goddard Victoria , Daae Frida Lise , Smerdon Gary , Massana Ramón , Joint Ian , Thingstad Frede , Pedrós‐Alió Carlos , Rodríguez‐Valera Francisco 
Published: March 2003

SummaryBacterial and archaeal assemblages have been studied in a multipond solar saltern using a range of microbial ecology techniques by four laboratories simultaneously. These include 16S rDNA sequencing from both denaturing gradient gel electrophoresis (DGGE) and clone libraries, and culturing methods. Water samples from eight ponds were analysed, covering a salinity range from near sea water (4% salt) to saturated sodium chloride (37% salt; ponds called crystallizers). Clone libraries focused on ponds with salinity of 8%, 22% and 32%. Although different cloning strategies were able to retrieve the same type of dominant sequences, there were differing degrees of success with less abundant sequences. Thus, the use of two sets of primers recovered a higher number of phylotypes. Bacterial and archaeal isolates were, however, different from any of the retrieved environmental sequences. For Bacteria, most sequences in the 8% salt pond were related to organisms of marine origin. Thus, representatives of the alpha‐, beta‐, gamma‐ and epsilon‐subdivisions of Proteobacteria, the Cytophaga–Flavobacterium–Bacteroides
group (CFB), high‐G+C Gram‐positive bacteria and cyanobacteria were found. In the
22% salt pond, alpha‐ and gamma‐Proteobacteria, cyanobacteria and CFB were
the only groups found, and most of them were related to specialized halophilic bacteria.
From the 32% salt pond, only CFB were found, and most of the sequences retrieved
clustered with Salinibacter ruber, an extremely halophilic bacterium. A decrease
in the richness of bacterial genera was therefore apparent along the gradient. Archaea
behaved quite similarly. In the lowest salinity ponds, sequences were related to
environmental clones of Marine Archaea Group III (Thermoplasmales relatives)
and to unclassified branches of Euryarchaeaota. In the 8%, 22% and
32% ponds, most of the clones were related to different cultured strains
of Halobacteriaceae. Finally, most sequences from the crystallizers clustered with
the uncultured square archaeon SPhT. Crenarchaeaota were not detected. Despite the
fact that higher prokaryotic richness was apparent in the lower salinity ponds than
in the crystallizers, the diversity index from clone libraries calculated according
to Shannon and Weaver did not show this trend. This was because diversity in the
crystallizers can be considered as ‘microdiversity’, the co‐existence
of several closely related clones of Bacteria (the S. ruber cluster) and Archaea (the SPhT cluster). Regardless of the changes in abundance, both Bacteria and Archaea showed the same pattern; as salinity increased, the number of different clusters decreased, and only one cluster became dominant. Both clusters, however, showed a considerable degree of microdiversity. The meaning of such microdiversity remains to be determined.
Mitigation of avian reproductive tract function by Salmonella enteritidis producing high‐molecular‐mass lipopolysaccharide
Authors: Parker Craig T. , Harmon Barry , Guard‐Petter Jean 
Published: March 2003

SummaryHens were infected with a wild‐type Salmonella enteritidis and its wzz mutant, which lacked the ability to make high‐molecular‐mass lipopolysaccharide (LPS), in six experiments paired by dosage and route of exposure. Involution of the reproductive tract occurred in 86% of hens that were injected subcutaneously with 108 cfu of the wild‐type strain, but none did so when injected with the wzz mutant. In spite of the lack of a specific effect on the reproductive tract, infection of hens with the mutant produced more contaminated eggs and heterophilic granulomas in developing ova (yolks) than wild type; thus, overall, the mutant appeared to be more virulent except after intravenous injection. The mutant also decreased shell quality more often than wild type, regardless of dosage or route of infection. These results suggest that egg‐contaminating Salmonella enteritidis that produces high‐molecular‐mass LPS mitigates signs of illness in poultry by altering the response of the avian reproductive tract to infection, but without altering the incidence of egg contamination following bacteraemia. Further research is warranted to determine whether analyses of shell quality might aid in identification of flocks at risk of producing contaminated eggs.
Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia
Authors: Müller Tina Andrea , Werlen Christoph , Spain Jim , Van Der Meer Jan Roelof 
Published: March 2003

SummaryThe genetic structure of two Ralstonia spp., strain JS705 and strain JS745, isolated from the same groundwater aquifer, was characterized with respect to the degradation capacities for toluene and chlorobenzene degradation. Cosmid library construction, cloning, DNA sequencing and mating experiments indicated that the genes for chlorobenzene degradation in strain JS705 were a mosaic of the clc genes, previously described for Pseudomonas sp. strain B13, and a 5 kb fragment identical to strain JS745. The 5 kb fragment identical to both JS705 and JS745 was flanked in JS705 by one complete and one incomplete insertion (IS) element. This suggested involvement of the IS element in mobilizing the genes from JS745 to JS705, although insertional activity of the IS element in its present configuration could not be demonstrated. The complete genetic structure for chlorobenzene degradation in strain JS705 resided on a genomic island very similar to the clc element (Ravatn, R., Studer, S., Springael, D., Zehnder, A.J., van der Meer, J.R. 1998. Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105‐kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. strain B13. J Bacteriol 180: 4360–4369). The unique reconstruction of formation of a metabolic pathway through the activity of IS elements and a genomic island in the chlorobenzene‐degrading strain JS705 demonstrated how pathway evolution can occur under natural conditions in a few ‘steps’.
Sialosyl‐Tn expression in benign and neoplastic proliferative lesions of the colon: of questionable value in predicting dysplasia
Authors: Fogt  , Zimmerman  , Furth  , Deren  , Noffsinger  , Poremba  , Alsaigh  
Published: March 2003

ObjectivesTumour‐associated carbohydrate antigen expression patterns have been observed to change during the transformation from benign to dysplastic and malignant cells. Sialosyl‐Tn is an O‐linked mucin‐type tumour‐associated antigen expressed on glycoproteins and is the product of aberrant glycosylation of the Tn glycoprotein, an early precursor of the MN blood group antigen. Sialosyl‐Tn expression has been observed in adenomas and carcinomas of the colon as well as in dysplastic lesions in ulcerative colitis (UC). Sialosyl‐Tn expression has been proposed to be a prognostic marker for the development of dysplasia in UC.Patients and methodsTo evaluate Sialosyl‐Tn expression in benign and malignant proliferative lesions of the colon, and its relevance for prediction of dysplasia, we immunostained cases of adenoma, adenoma with invasive carcinoma, UC with and without dysplasia, hyperplastic polyps, cases of lymphocytic colitis, and cases of acute self‐limited colitis with antibody against Sialosyl‐Tn.ResultsWe found expression of Sialosyl‐Tn in dysplastic lesions in adenomas and UC. We also found expression of Sialosyl‐Tn in epithelium of chronic colitis in virtually all patients with UC, both with dysplasia and without. Sialosyl‐Tn was also present in hyperplastic polyps, and one single case each of lymphocytic colitis and acute self‐limited colitis.ConclusionWe conclude that Sialosyl‐Tn is expressed in dysplastic and malignant epithelial lesions of the colon. Expression of Sialosyl‐Tn in benign proliferative/regenerative lesions in the colon is frequent and is not directly related to the development of dysplasia. Possible mechanisms of Sialosyl‐Tn expression are discussed.
Linear stapled haemorrhoidectomy—an alternative to standard haemorrhoidectomy?
Authors: Abbasakoor  , Nelson  , Patel  , Morgan  , Carr  , Woodward  , Beynon  
Published: March 2003

ObjectiveTo evaluate in a pilot study a new haemorrhoidectomy technique involving the use of a linear stapling device.Patients and methodsTwenty consecutive unselected patients (12 male, eight female; median age 64 years, range 40–81 years) underwent haemorrhoidectomy using the new technique. Fifteen also underwent pre‐ and post‐operative endoanal ultrasound to assess the anal sphincter complex.ResultsThe operation was successfully carried out on all patients. Analgesic requirements were low, with most patients requiring no analgesia or paracetamol only. The majority of patients (n=13) were discharged on the first post‐operative day. Clinically all patients remained fully continent of flatus and faeces after surgery with no recurrence of haemorrhoids. There was no morphologic evidence of internal or external anal sphincter damage in the patients who underwent endoanal ultrasound. There were no re‐admissions of patients immediately after discharge. One late complication involving persistent anal discomfort from retained staples necessitated an operation to have them removed.ConclusionThis study suggests that the use of a linear stapling device for haemorrhoidectomy is safe, being associated with little post‐operative pain, a low complication rate and early discharge. A prospective randomized trial is required to assess this new treatment.
Results of a selective policy for preoperative radiotherapy in rectal cancer surgery
Authors: Gandy  , O’Leary  , Falk  , Roe  
Published: March 2003

ObjectivePreoperative radiotherapy (pRT) for rectal cancer may reduce local recurrence and improve survival. This study was undertaken to assess a selective policy of pRT in rectal cancer. The aim was to determine whether patients likely to have involved circumferential margins (CRM) could be reliably selected for pRT using clinical criteria. We have used CRM and delay in surgery as outcome measures.Patients and methodsSeventy‐nine patients with rectal cancer were assessed for preoperative radiotherapy using clinical criteria.ResultsTwelve of 26 (46%) pRT patients had positive CRM compared with three of 53 (5.6%) who did not receive pRT (P < 0.0001). Using pRT resulted in patients waiting a further 21 days before surgery (pRT 34 days vs no pRT 13 days; P < 0.0001).ConclusionThis policy has been effective in selecting patients most likely to benefit from radiotherapy and has avoided excessive delays prior to surgery. However, almost half of the pRT patients did not have involved CRM. With improved imaging techniques we may be able to refine our selection criteria further.
The cost effectiveness of self‐expanding metal stents in the management of malignant left‐sided large bowel obstruction
Authors: Osman  , Rashid  , Sathananthan  , Parker  
Published: March 2003

ObjectiveSelf‐expanding metal stents have been developed to treat acute left‐sided large bowel obstruction, either for palliation or for bowel decompression prior to subsequent abdominal surgery. The cost effectiveness of stenting vs surgical decompression has been analysed.Patients and methodsBetween April 1997 and April 1998, 16 patients with acute large bowel obstruction were managed by self‐expanding metal stents. This group was compared with 10 unselected patients previously managed by surgical decompression. The cost‐effectiveness of stenting was compared with surgical decompression by analysis of total hospital stay, running costs, and operating theatre/radiology suite utility. This was extended to include stented patients who proceeded to elective anterior resection (n=5) and patients managed by Hartmann’s operation who proceeded to reversal (n=6).ResultsThe results showed significant reduction in the total hospital stay in the stent group, with a mean hospital stay of 2.5 days compared with 13.5 days in the surgical decompression group. There was also a mean net saving of £1760 per stented patient, with a cumulative annual saving of £26 400 on an average of 15 cases stented per year. In patients who proceeded either to post‐stenting anterior resection, or reversal of Hartmann’s operation, the mean hospital stay was 17 days and 23.5 days (including hospital stay for decompression procedure), respectively, with a mean net saving of £685 per stented patient.ConclusionStenting of acute large bowel obstruction is a cost‐effective procedure with a reduction in total hospital stay and expenditure compared with surgical decompression.
Rectovaginal fistulae in Crohn’s disease: a management paradox
Authors: Windsor  , Lunniss  , Khan  , Rumbles  , Williams  , Northover  
Published: March 2003

ObjectiveMuch has been written about the management of rectovaginal fistulae in Crohn’s disease (CD), but there remains little or no consensus on the optimal therapeutic approach. This retrospective case review examined treatment and clinical outcome of women presenting with rectovaginal fistula between 1985 and 1995 in an attempt to clarify treatment guidelines.Patients and methodsA total of 48 case notes was reviewed. Significant symptoms and signs were noted at presentation in 73% and 65% of women, respectively, and fistula classification revealed; three (6%) superficial, 36 (76%) transphincteric, six (12%) suprasphincteric and three (6%) unclassified.ResultsFifteen patients were initially treated conservatively, of whom 73% were eventually rendered asymptomatic and none required proctectomy. Of the remaining 33 fistulae, 12 were treated by laying open or seton insertion, 13 by local repair using transperineal proctotomy or advancement flaps, two by defunctioning alone, and six by proctectomy. Eighty‐three percent of patients undergoing laying open or seton insertion, 77% following local repair and 50% following stoma were eventually rendered asymptomatic. The proctectomy rates were 42%, 15%, and 50% in these three groups, respectively.ConclusionThe results of this study suggest that in the absence of significant symptoms, conservative management provides a good chance of fistula healing without need for proctectomy. However, if symptoms dictate the need for intervention, local repair provides a similar chance of success with a lower ultimate need for proctectomy than laying open or seton. Despite these broad generalities, this study highlights the difficulties we have in advising patients with proctovaginal fistulae in CD.
Evaluation of colonoscopic sized biopsies for microsatellite instability and adenomatous polyposis coli (APC) variants
Authors: Sengupta  , Pearson  , Yiu  , Boulos  
Published: March 2003

ObjectiveKnowledge of certain genetic changes associated with the development of colorectal cancer may influence surgical treatment in the future. Cancers are known to show intratumoural genetic heterogeneity. The aim of this study was to determine whether colonoscopic sized biopsies provide enough tissue to overcome the effects of tumour heterogeneity for the results of genetic analysis to be representative of the tumour as a whole.Patients and methodsUsing colonoscopic biopsy forceps, samples were taken from 30 resected colorectal cancers and investigated for microsatellite instability (MSI) at five loci and changes in the adenomatous polyposis coli gene (APC) by single‐stranded conformational polymorphism analysis. Identical genetic analysis was carried out on larger specimens taken from each of these cancers to determine whether the molecular findings from the large specimen were the same as those from colonoscopic sized biopsies.ResultsThe microsatellite instability and APC status of the colonoscopic sized biopsies and those from larger specimens were completely consistent.ConclusionThese results suggest that colonoscopic sized biopsies are reliable in determining the MSI status and APC variants of individual colorectal cancers.
Improved results in rectal cancer surgery—an effect of specialization?
Authors: Machado  , Goldman  , Järhult  
Published: March 2003

ObjectiveThe surgeon‐ and hospital‐related variability in outcome after surgery for rectal cancer has been much debated. This study comprises a 6‐year period of rectal cancer treatment at a single surgical Institution, where substantial changes in the treatment strategy of rectal cancer were implemented.Patients and methodsProspective and retrospective analysis of complications, stoma frequency, local recurrence rate and survival in 252 patients operated on for rectal cancer before (1990–1992) and after (1994–1996) the creation of a specialized rectal cancer team.ResultsSpecialization led to a significant decrease both in the need of permanent stomas (52% before vs 33% after specialization; P=0.02) and in the frequency of local recurrence (18% vs 3%; P=0.002). No increase in the frequency of post‐operative complications, re‐operations or, specifically, pelvic sepsis could be detected in the later period, although more extensive surgery was used and the anastomotic level decreased from 8 to 4 cm (P < 0.001). Cancer‐specific survival at 2 years after operation was significantly higher in patients operated in 1994–1996 than in those operated 1990–1992 (P=0.006).ConclusionConcentrating the care of patients with rectal cancer to a specialized team seems to improve quality and outcome.
Utility of appropriate peritonitis grading in the surgical management of perforated sigmoid diverticulitis
Authors: Thaler K. , Neumann F. , Gerö A. , Kreuzer W. 
Published: March 2003

ObjectiveWe evaluated the prognostic validity of preoperative risk scores in the surgical management of patients with diverticular perforation and diffuse peritonitis.Patients and methodsFrom 1988 to 1998, 82 patients, mean age 72 ± 15 years, underwent urgent surgery for perforated diverticulitis with generalized peritonitis. They were operated either with the Hartmann technique or with resection and primary anastomosis. ASA Classification and Mannheimer Peritonitis Index (MPI) were documented as risk scores at time of surgery and used as guidelines to decide for one of both procedures.ResultsA Hartmann resection (HA) was performed in 62 patients (76%) and resection with primary anastomosis (PA) in 20 (24%). Seventy‐one percent of patients in the HA group corresponded to ASA IV/V, compared with 35% in the group with primary anastomosis (P < 0.001). Patients with Hartmann resection had also a higher MPI (23 ± 8) vs those with primary anastomosis (18 ± 7; P < 0.004). However, differences between the HA group and the PA group due to post‐operative morbidity (21% vs 35%) and mortality (35% vs 20%) did not reach statistical significance. Nevertheless, multivariate analysis of the whole series revealed a significant relationship between MPI and mortality (P < 0.0043), independent of ASA class, age and operative procedure.ConclusionPatients assigned to Hartmann procedure had more co‐morbidities and more advanced peritonitis as assessed by increased ASA and higher MPI. The Mannheimer Peritonitis Index proved to be an independent prognostic index in estimating mortality with respect to peritonitis extension and septic status of the patient.
Consensus statement of definitions for anorectal physiology and rectal cancer*
Authors: Lowry A. C. , Simmang C. L. , Boulos P. , Farmer K. C. , Finan P. J. , Hyman N. , Killingback M. , Lubowski D. Z. , Moore R. , Penfold C. , Savoca P. , Stitz R. , Tjandra J. J. 
Published: March 2003

Introduction from the Editor An international working party co‐ordinated by Dr Ann Lowry, University of Minnesota, was charged with the task of producing definitions of terms applicable to anorectal physiology and rectal cancer. The consensus achieved is published below and will simultaneously appear in Diseases of Colon and Rectum and in the Australian New Zealand Journal of Surgery. It is essential that there is uniformity in descriptions and it is hoped that the Statement will be generally adopted and become standard terminology.