bluuebunny/crossref_metadata_2025_split huggingface dataset:
Burkholderia cepacia complex: distribution of genomovars among isolates from the maize rhizosphere in Italy
Authors: Fiore Alessia , Laevens Severine , Bevivino Annamaria , Dalmastri Claudia , Tabacchioni Silvia , Vandamme Peter , Chiarini Luigi 
Published: March 2003

Burkholderia cepacia is a ‘complex’ in which seven genomic species or genomovars have so far been identified. It appears that all seven B. cepacia genomovars are capable of causing infections in vulnerable persons; in particular, the importance of Burkholderia multivorans (genomovar II) and B. cepacia genomovar III among cystic fibrosis isolates, especially epidemic ones, has been emphasized. In order to acquire a better comprehension of the genomovar composition of environmental populations of B. cepacia, 120 strains were isolated from the rhizosphere of maize plants cultivated in fields located in northern, central and southern Italy. The identification of the different genomovars was accomplished by a combination of molecular polymerase chain reaction (PCR)‐based techniques, such as restriction fragment length polymorphism (RFLP) analysis of 16S rDNA (ARDRA), genomovar‐specific PCR tests and RFLP analyses based on polymorphisms in the recA gene whole‐cell protein electrophoresis. ARDRA analysis allowed us to distinguish between all B. cepacia genomovars except B. cepacia genomovar I, B. cepacia genomovar III and Burkholderia ambifaria (genomovar VII). The latter genomovars were differentiated by means of recA PCR tests and RFLP analyses. Among the rhizospheric isolates of B. cepacia, we found only B. cepacia genomovar I, B. cepacia genomovar III, Burkholderia vietnamiensis (genomovar V) and B. ambifaria. B. cepacia genomovars I and III and B. ambifaria were recovered from all three fields, whereas B. vietnamiensis was detected only in the population isolated from the field located in central Italy. Among strains isolated from northern and southern Italy, the most abundant genomovars were B. ambifaria and B. cepacia genomovar III respectively; in contrast, the population isolated in central Italy showed an even distribution of strains among genomovars. These results indicate that it is not possible to differentiate clinical and environmental strains, or pathogenic and non‐pathogenic strains, of the B. cepacia complex simply on the basis of genomovar status, and that the environment may serve as a reservoir for B. cepacia genomovar III infections in vulnerable humans.
Lipopolysaccharide O‐chain microheterogeneity ofSalmonellaserotypes Enteritidis and Typhimurium
Authors: Parker Craig T. , Liebana Ernesto , Henzler David J. , Guard‐Petter Jean 
Published: March 2003

Variability in the lipopolysaccharide (LPS) of the two most prevalentSalmonellaserotypes causing food‐borne salmonellosis was assessed using gas chromatography analysis of neutral sugars from 43Salmonella entericaserovar Enteritidis (S. Enteritidis)and20Salmonella entericaserovar Typhimurium (S. Typhimurium) isolates.Four substantially different types of O‐chain chemotypes were detected using cluster analysis of sugar compositions; these were low‐molecular‐mass (LMM) LPS, glucosylated LMM LPS, high‐molecular‐mass (HMM) LPS and glucosylated HMM LPS. Nineteen out of 20S. Typhimurium isolates yielded glucosylated LMM.In contrast,S. Enteritidis produced a more diverse structure, which varied according to the source and history of the isolate: 45.5% of egg isolates yielded glucosylated HMM LPS; 100% of stored strains lacked glucosylation but retained chain length in some cases; and 83.3% of fresh isolates from the naturally infected house mouseMus musculusproduced glucosylated LMM LPS. A chain length determinant (wzz) mutant ofS. Enteritidis produced a structure similar to that ofS. Typhimurium and was used to define what constituted significant differences in structure using cluster analysis. Fine mapping of theS. Enteritidis chromosome by means of a two‐restriction enzyme‐ribotyping technique suggested that mouse isolates producing glucosylated LMM LPS were closely related to orally invasive strains obtained from eggs, and that stored strains were accumulating genetic changes that correlated with suppression of LPS O‐chain glucosylation. These results suggest that the determination of LPS chemotype is a useful tool for epidemiological monitoring ofS. Enteritidis,which displays an unusual degree of diversity in its LPS O‐chain.
Carbon isotopic fractionations associated with thermophilic bacteria Thermotoga maritima and Persephonella marina
Authors: Zhang Chuanlun L. , Ye Qi , Reysenbach Anna‐Louise , Götz Dorothee , Peacock Aaron , White David C. , Horita Juske , Cole David R. , Fong Jon , Pratt Lisa , Fang Jiasong , Huang Yongsong 
Published: March 2003

SummaryStable carbon isotopes can provide insight into carbon cycling pathways in natural environments. We examined carbon isotope fractionations associated with a hyperthermophilic fermentative bacterium, Thermotoga maritima, and a thermophilic chemolithoautotrophic bacterium Persephonella marina. In T. maritima, phospholipid fatty acids (PLFA) are slightly enriched in 13C relative to biomass (ɛ = 0.1–0.8‰). However, PLFA and biomass are depleted in 13C relative to the substrate glucose by ~8‰. In P. marina, PLFA are 1.8–14.5‰ enriched in 13C relative to biomass, which suggests that the reversed tricarboxylic acid (TCA) cycle or the 3‐hydroxypropionate pathway may be used for CO2 fixation. This is supported by small fractionation between biomass and CO2 (ɛ = −3.8‰ to −5.0‰), which is similar to fractionations reported for other organisms using similar CO2 fixation pathways. Identification of the exact pathway will require biochemical assay for specific enzymes associated with the reversed TCA cycle or the 3‐hydroxypropionate pathway.
Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila
Authors: López‐García Purificación , Gaill Françoise , Moreira David 
Published: March 2003

SummaryWe carried out a 16S rDNA‐based molecular survey of the prokaryotic diversity associated with the chitin tubes of the giant vent tubeworm Riftia pachyptila (collected at the East Pacific Rise, 9°N and 13°N). Scanning electron microscopy showed dense microbial populations, particularly on the external surface of the middle and upper tube regions, which included very diverse prokaryotic morphotypes. We used archaeal‐ and bacterial‐specific primers for polymerase chain reaction (PCR) amplification, but only bacterial amplicons were obtained. We analysed a total of 87 clones. Most belonged to the ɛ‐Proteobacteria, but also to the δ‐, α‐ and γ‐Proteobacteria. A broad diversity of phylotypes belonging to other bacterial divisions was detected, including Verrucomicrobia, the Cytophaga–Flavobacterium–Bacteroides group and the candidate division OP8. We also retrieved a sequence, R76‐B150, of uncertain phylogenetic affiliation, which could represent a novel candidate division. The sequence of the R. pachyptilaγ‐proteobacterial endosymbiont was not detected. The bacterial diversity found suggests that complex metabolic interactions, particularly based on sulphur chemistry, may be occurring in different microniches of the R. pachyptila tubes.
Factors affecting PCR‐mediated recombination
Authors: Shafikhani Sasha 
Published: March 2003

AbstractIn the past decade, polymerase chain reaction (PCR) has become an important tool for the identification of previously unknown microorganisms and the analysis of environmental microbial diversity. Several studies published during recent years, however, have demonstrated that products obtained after PCR using Taq or Vent DNA polymerases will contain hybrid molecules when several homologous target sequences such as multigene families, alleles, or RNA viruses are co‐amplified. In this report, we examined the recombination frequency and the extent of template switching during PCR using Taq, Pfu and RTth/Vent DNA polymerases. As a test system we constructed a series of plasmids carrying between one and three frame shift mutations in the gene coding for the protease subtilisin or deletions of approximately 100 bp in the lacZα. Highest recombination frequencies were observed when these mutants were co‐amplified with Taq followed by RTth/Vent DNA polymerases. Pfu DNA polymerase displayed no discernable recombination activity under normal PCR conditions. Data also suggest that in vivo repair of heteroduplex DNA molecules in Escherichia coli by a RecA‐independent mechanism, perhaps the mismatch repair, results in the formation of chimeric molecules. Using Bacillus subtilis as the host, however, can significantly diminish non‐PCR RecA‐independent in vivo recombination, owing to the fact that transforming DNA molecules enter B. subtilis as single strands. Combined, these results suggest that using Pfu DNA polymerase for amplification and B. subtilis as the host for transformation may significantly reduce chimera formation.
Diversity of α‐halocarboxylic acid dehalogenases in bacteria isolated from a pristine soil after enrichment and selection on the herbicide 2,2‐dichloropropionic acid (Dalapon)
Authors: Marchesi Julian R. , Weightman Andrew J. 
Published: March 2003

SummaryFive pure cultures of bacteria (strains DA1–5) able to degrade 2,2‐dichloropropionic acid (22DCPA) were isolated for the first time from pristine bulk soil samples. From 16S rDNA analysis, it was concluded that strains DA2, DA3 and DA4 were members of the Bradyrhizobium subgroup (α‐Proteobacteria), strain DA5 clustered in the Brucella assemblage (α‐Proteobacteria) and strain DA1 clustered in the β‐Proteobacteria. Biochemical and molecular analysis of the dehalogenases from the isolates showed that these enzymes were quite diverse. Several dehalogenases were closely related to group I and II α‐halocarboxylic acid dehalogenases, and partial polymerase chain reaction (PCR) products were obtained from isolates DA1, 2, 3 and 4 using degenerate dehalogenase primers. However, no PCR products were obtained from isolate DA5 using either of the group I or II α‐halocarboxylic acid dehalogenase primers. Isolates DA2 and DA4 contained putative silent dehalogenases. The investigation highlighted the endemic nature of these genes in pristine environments and how diverse these were even from spatially close samples.
Physiological and molecular characterization of anaerobic benzene‐degrading mixed cultures
Authors: Ulrich Ania C. , Edwards Elizabeth A. 
Published: March 2003

SummaryNine distinct anaerobic benzene‐degrading cultures were enriched from sediment samples from four different sites. These cultures used nitrate, sulphate or CO2 as electron acceptors. The shortest doubling times were observed in nitrate‐reducing cultures, although cell yield was lowest in these cultures. The highest substrate concentration utilized and maximum absolute rates of benzene degraded (in µM day−1) were observed in methanogenic cultures. The microbial compositions of a methanogenic and nitrate‐reducing culture were determined from a clone library of 16S rRNA genes. Five Bacterial 16S rRNA sequences, one of which resembled a clone previously found in a sulphate‐reducing, benzene‐degrading culture and four Archaeal 16S rRNA sequences were identified in a methanogenic culture. Four Bacterial and no Archaeal 16S rRNA sequences were identified in a nitrate‐reducing culture. The relative abundance of the four nitrate‐reducing putative species was determined by slot blot hybridization. Two green sulphur bacteria together formed 52% of the clone library, but were found to be less than 4% of the culture by slot blot analysis. One of the cloned 16S rRNA gene sequences comprised 70% of the culture and was phylogenetically 93% similar to both Azoarcus and Dechloromonas species, which have been shown to degrade aromatic compounds, including benzene, under nitrate‐reducing conditions.
Prevalence of faecal incontinence: obstetric and constipation‐related risk factors; a population‐based study
Authors: Lam  , Kennedy  , Chen  , Lubowski  , Talley  
Published: March 2003

Objective Patients suffering from faecal incontinence may be reluctant to seek medical advice and the true prevalence is uncertain. The aim of the study was to determine the prevalence of faecal incontinence and to correlate this with possible risk factors.Subjects and methods A standardized questionnaire was posted to 955 subjects randomly selected from a local Sydney electoral role of 68 821 voters.Results The response rate was 71% (M:F = 259:359). The overall prevalence of faecal incontinence, defined as answering in the affirmative to at least two of three questions which incorporated stool leakage, wearing a pad because of bowel incontinence and frequent incontinence of flatus, was 15% and was more prevalent in men (20%) than women (11%) (P < 0.015). The prevalence of urinary stress incontinence in women was 31%, and similarly 31% for urge incontinence. In men the prevalence of stress and urge urinary incontinence was 4% and 12%, respectively. Overall, there was a significant association between faecal incontinence and a sensation of incomplete rectal evacuation (P < 0.001), obstructed defaecation (P < 0.001), and subjective patient assessment of being constipated (P < 0.001). In women there was a significant association between faecal incontinence and episiotomy (P < 0.01), forceps delivery (P < 0.01), perineal tears (P < 0.01) and hysterectomy (P < 0.049). There was also a strong association between stress urinary incontinence and parity (P < 0.001), episiotomy (P < 0.001), forceps (P < 0.01), perineal tears (P < 0.01) and hysterectomy (P < 0.003). Using logistic regression models, independent risk factors for faecal incontinence were gender (male, odds ratio (OR) = 3.9, 95% confidence interval (CI) = 2.0–7.5), constipation (OR = 27.1, 95% CI = 12.3–59.5), straining (OR = 0.24, 95% CI = 0.1–0.6) and episiotomy (OR = 2.9, 95% CI = 1.4–6.0).Conclusion A higher prevalence of faecal incontinence than previously reported was observed, particularly in males. The prevalence of urinary incontinence was consistent with other studies. Faecal and urinary incontinence are important community health problems in both sexes.
The gelatinases, their activators and inhibitors in the progression of colorectal cancer
Authors: Simpson  , Hemingway  , Crowther  , Goodall  , Thompson  
Published: March 2003

BackgroudThe matrix metalloproteinases (MMPs) are a family of proteolytic enzymes which are reported to play an important role in the invasion and metastasis of a number of human cancers. The gelatinase subfamily has substrate specificity for type IV collagen, the principal component of human epithelial basement membrane. They are over‐expressed in colorectal tumour tissues. The relatively recent discovery of a family of membrane‐associated MMPs, some of which function as activators of MMP‐2, represents an important development relevant to this field.MethodsA literature review was performed on the PubMed and Medline databases for English language publications relating to the gelatinases and their activators and inhibitors in colorectal cancer.ResultsThere is evidence to support the up‐regulation and involvement of the gelatinases in the progression of colorectal cancer. The active MMP‐2 species appears particularly closely related to the malignant phenotype. There has been little published on the role of the recently discovered membrane‐associated MMPs in colorectal cancer. Studies in other cancers suggest these may play an important role in the activation of MMP‐2 in vivo.ConclusionGelatinases play an important role in the progression of colorectal cancer. More work is required to understand the mechanisms underlying the up‐regulation of gelatinolytic activity in these tumours. Such work could lead to the development of novel new therapies for the improved treatment of this disease in future years.
Ureteric injuries during colorectal surgery: strategies for prevention
Authors: Kutiyanawala  , Scott  , Jameson  
Published: March 2003

BackgroundInjuries to the ureter are a known complication of pelvic surgery and well described during gynaecological procedures. There is however little published recent literature on ureteric injuries during surgery for rectal and sigmoid pathology.Patients and methodsAll patients undergoing pelvic colorectal surgery over a 4‐year period were identified from data prospectively gathered for the purposes of audit and iatrogenic ureteric injuries identified. This information was cross‐checked with data entered in the pathology computer.ResultsFive patients had identified ureteric injuries. An incidence of 1.9% compares favourably with other published series. There was increased morbidity in this group with loss of kidney in one patient, a consequence of the ureteric trauma.ConclusionPreoperative imaging of the ureter, ureteric catheterization in selected cases and careful meticulous surgical technique will help prevent damage to the ureters intra‐operatively.
Topical Nifedipine® for conservative treatment of acute haemorrhoidal thrombosis
Authors: Perrotti  , Antropoli  , Noschese  , Bartone  , Mo De Stefano  , Pacifico  , Maffettone  , Antropoli  
Published: March 2003

ObjectiveThe aim of this prospective, randomized trial was to test the efficacy of the local application of Nifedipine gel® in healing acute thrombosed haemorrhoids by relaxing the internal anal sphincter.Patients and methodsNinety patients who gave written informed consent were recruited; they received a clinical examination, anoscopy and a questionnaire to evaluate symptoms, pain and concurrent use of analgesics. Patients treated with Nifedipine (n=46) received topical 0.3% Nifedipine and 1.5% lidocaine gel every 12 h for 2 weeks. The control group, consisting of 44 patients, received topical 1.5% lidocaine and 1% hydrocortisone acetate gel during therapy.ResultsThe results were as follows: relief of pain in 84.7% in Nifedipine group as opposed to 50% of controls after 7 days of therapy (P < 0.01); oral analgesics were used by 8.6% of patients in the Nifedipine group as opposed to 54.5% of the control group (P < 0.01); resolution of thrombosed haemorrhoids occurred after 14 days of therapy in 91.3% of the Nifedipine‐treated patients, as opposed to 45.4% of the controls (P < 0.01). No systemic side effects or significant anorectal bleeding were observed in patients treated with Nifedipine.ConclusionOur study clearly demonstrates that the use of Nifedipine, which at present is for treatment of cardiovascular disorders, should be extended to the conservative treatment of acute thrombosed haemorrhoids, using a topical application.
Anorectal physiological testing before and after a successful sphincter repair: a prospective study
Authors: Ooi  , Tjandra  , Tang  , Dwyer  , Carey  
Published: March 2003

ObjectiveAnorectal physiological testing often yields contradictory results in patients with faecal incontinence. This prospective study aims to determine if there are any discriminatory changes in anorectal physiological testing after a successful sphincter repair for sphincter defects.Patients and methodsFrom 1995 to 1998, 20 consecutive females who underwent a successful overlapping sphincter repair for sphincter defect were evaluated by anorectal manometry and neurophysiologic testing before and 2–4 months after surgery. The sphincter defect was diagnosed preoperatively by clinical and endosonographic examination, confirmed at surgery. The severity of faecal incontinence was evaluated using the Cleveland Clinic Continence Score (0–20): 0 being perfect continence, and 20 being complete incontinence.ResultsOf 20 consecutive patients who were improved following direct sphincter repair, 12 had significant improvement with a median score of 3 (range 1–6), while eight had mild improvement with a median score of 9 (range 7–12). There was a significant improvement in the mean resting anal canal pressure (80 vs 50 mmHg; P=0.016), maximum squeeze anal canal pressure (120 vs 80 mmHg; P=0.0002) and functional anal canal length (3 vs 2 cm; P=0.0069) post‐operatively, with significant improvement in faecal continence following sphincter repair. However, a mild improvement in faecal continence was not associated with any significant changes in the mean resting anal canal pressure (50 vs 40 mmHg; P=0.089), maximum squeeze anal canal pressures (100 vs 100 mmHg; P=0.19) or functional anal canal length (2 vs 2 cm; P=0.47).ConclusionMarked improvement of faecal continence after overlapping sphincter repair is reflected by a marked increase in the mean resting anal canal pressure, maximum squeeze anal canal pressures and functional anal canal length.
Stapled mucosectomy for acute thrombosed circumferentially prolapsed piles: a prospective randomized comparison with conventional haemorrhoidectomy
Authors: Brown S. R. , Ballan K. , Ho E. , Ho Fams Y. H. , Seow‐Choen F. 
Published: March 2003

ObjectiveStapled mucosectomy has been developed as an alternative to conventional haemorrhoidectomy for the elective treatment of haemorrhoids, but has not been assessed in the emergency setting. The aim of this study was to compare this technique with a conventional procedure for acute thrombosed circumferential prolapsed haemorrhoids.Patients and methodsA prospective randomized comparison of conventional Milligan‐Morgan haemorrhoidectomy and stapled mucosectomy was carried out on 35 consecutive patients presenting with acute thrombosed circumferential prolapsed haemorrhoids. Operative data, postoperative stay, pain assessment and persistent symptoms were compared at discharge and at 2 week and 6 week review. Additionally at 6 week review the time to return to work was recorded and an endoanal ultrasound was carried out.ResultsThirty patients were randomized and followed up for six weeks. Although postoperative stay and in‐hospital analgesia were the same, patients from the stapled group reported significantly more pain at discharge. However, by 2 weeks the conventional group reported significantly higher pain scores particularly on passing stool. By this stage over half the stapled group patients reported no pain at all. More patients in the conventional group complained of persistent symptoms of pain, bleeding and discharge at 2 week and 6 week review with 20% requiring readmission compared with none in the stapled group. The median return to work was significantly shorter for the stapled group (14 days vs 28 days, P < 0.05). Although all patients claimed to be continent, two patients from each group had ultrasonic evidence of internal sphincter damage.ConclusionStapled mucosectomy for acute thrombosed circumferential piles is feasible and may result in less pain, a more rapid resolution of symptoms and an earlier return to work compared with a conventional procedure.