bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure–function studies of the recombinant protein bioemulsifier AlnA
Authors: Toren Amir , Segal Gil , Ron Eliora Z. , Rosenberg Eugene 
Published: March 2003

Summary Acinetobacter radioresistens KA53 produces an extracellular bioemulsifier,
referred to as alasan. The surface active component of alasan is a 35.77 kDa protein
AlnA. Although AlnA and the Escherichia coli outer membrane protein A (OmpA)
have a high amino acid sequence homology, E. coli OmpA has no emulsifying
activity. Comparison of the amino acid sequences of AlnA and E. coli OmpA
revealed four hydrophobic regions in AlnA that were absent in E. coli OmpA. Deletions and substitutions (with the homologous OmpA sequence) were constructed in each of the four hydrophobic regions of AlnA by site‐directed polymerase chain reaction (PCR) mutagenesis, using the overlap PCR method. Analysis of the emulsifying activities of the mutated AlnA molecules demonstrated that all four hydrophobic regions were necessary for emulsifying activity. However, most of the inactive mutated proteins still adhered avidly to hexadecane. These findings indicate that in addition to binding to hydrocarbons, the protein emulsifier must form a specific structure on the surface of the hydrocarbon that prevents coalescence of oil droplets. This is the first structure–function study of a protein bioemulsifer.
Is bioconvection enhancing bacterial growth in quiescent environments?
Authors: Jánosi Imre M. , Czirók András , Silhavy Dániel , Holczinger András 
Published: March 2003

SummaryBioconvection is an intriguing pattern‐forming phenomenon driven by the swimming activity of various aquatic microorganisms. It is generally assumed that bioconvection has a positive effect on the entire microbial population by carrying oxygen into deep layers of non‐aerated suspensions. In order to examine the presence of such a biological benefit, we analysed the correlation between bioconvective pattern formation and population growth of several Bacillus subtilis and Bacillus licheniformis strains under non‐aerated conditions. Bioconvection is a robust phenomenon, we observed its development in numerous cultures of various strains and growth phases. Nevertheless, evaluation of the data has not revealed detectable positive effects on population growth, questioning the potential biological relevance of bioconvection in natural habitats.
Synchronized expression of ftsZ in natural Prochlorococcus populations of the Red Sea
Authors: Holtzendorff Julia , Marie Dominique , Post Anton F. , Partensky Frédéric , Rivlin Assaf , Hess Wolfgang R. 
Published: March 2003

SummaryThe expression of ftsZ, encoding the initiating protein of the prokaryotic cell division was analysed in natural Prochlorococcus populations in the Gulf of Aqaba, northern Red Sea. During the seasonal Prochlorococcus bloom in September 2000, picoplankton was collected from the deep chlorophyll maximum (DCM) at 2–4 h intervals over 3 consecutive days. Flow cytometric measurements as well as DNA sequence analyses showed that Prochlorococcus was the dominant photosynthetic organism. Cell densities peaked as high as 1.4 × 105 cells ml−1. This DCM population mainly consisted of brightly red fluorescing Prochlorococcus cells, corresponding to low light‐adapted ‘ecotypes’ (sensu Moore et al., 1998, Nature 393: 464–467). Prochlorococcus populations grew in a highly synchronized fashion with DNA replication in the afternoon and cell division during the night. The ftsZ mRNA level reached maximum values within the replication phase between 14.00 and 16.00 hours, and minimum values between 02.00 and 06.00 hours. Thus, the transcriptional regulation of ftsZ could be a major factor triggering the synchronized cell division of Prochlorococcus populations. This is the first application of quantitative reverse transcriptase‐coupled real‐time polymerase chain reaction (PCR) to natural populations of an environmentally relevant marine organism.
Streptomycin‐resistant (rpsL) or rifampicin‐resistant (rpoB) mutation in Pseudomonas putida KH146‐2 confers enhanced tolerance to organic chemicals
Authors: Hosokawa Keiichi , Park Nyun‐Ho , Inaoka Takashi , Itoh Yoshifumi , Ochi Kozo 
Published: March 2003

SummaryWe found that certain Str‐, Gen‐ or Rif‐ mutants derived from Pseudomonas putida KH146‐2, which are resistant to streptomycin, gentamicin or rifampicin, respectively, are tolerant to the aromatic compound 4‐hydroxybenzoate (4HBA). The minimum inhibitory concentration (MIC) of 4HBA as the sole carbon source for the wild‐type strain was 1%, whereas the MIC for the mutants was 1.7%. Frequency of 4HBA‐tolerant mutants among spontaneous Str‐, Gen‐ and Rif‐ mutants was 5–15%, 3–5%, and 3% respectively. These 4HBA‐tolerant mutants also tolerated to a variety of organic chemicals such as 3‐hydroxybenzoate, aliphatic and heterocyclic compounds, chlorobenzoates, as well as organic solvents toluene and m‐xylene. The Str mutants had a point mutation in the rpsL gene, which produces the ribosomal protein S12. The Rif mutants were found to have a point mutation in the rpoB gene, which encodes the RNA polymerase β‐subunit. Mutation points in Gen mutants still remain unknown. Str‐, Gen‐ and Rif‐phenotypes occurred in spontaneous 4HBA‐tolerant mutants which had been selected by successively increasing concentrations (from 0.8% to 5%) of 4HBA. Complementation experiments with one of the Str mutants demonstrated a causal relationship between a rpsL mutation (str‐1) and 4HBA tolerance. Uptake experiments using [14C]‐4HBA revealed that apparent ability of 4HBA to be taken up by the membrane transport system was reduced two to threefold in the mutants compared to the wild‐type strain, accounting at least partly for the enhanced tolerance to 4HBA. Our approaches thus could be effective in improvement of tolerance to aromatic compounds of bacteria applicable for bioremediation.
Fluorescence in situ hybridization of 16S rRNA gene clones (Clone‐FISH) for probe validation and screening of clone libraries
Authors: Schramm Andreas , Fuchs Bernhard M. , Nielsen Jeppe L. , Tonolla Mauro , Stahl David A. 
Published: March 2003

SummaryA method is presented for fluorescence in situ hybridization (FISH) of 16S rRNA gene clones targeting in vivo transcribed plasmid inserts (Clone‐FISH). Several different cloning approaches and treatments to generate target‐rRNA in the clones were compared. Highest signal intensities of Clone‐FISH were obtained using plasmids with a T7 RNA polymerase promoter and host cells with an IPTG‐inducible T7 RNA polymerase. Combined IPTG‐induction and chloramphenicol treatment of those clones resulted in FISH signals up to 2.8‐fold higher than signals of FISH with probe EUB338 to cells of Escherichia coli. Probe dissociation curves for three oligonucleotide probes were compared for reference cells containing native (FISH) or cloned (Clone‐FISH) target sequences. Melting behaviour and calculated Td values were virtually identical for clones and cells, providing a format to use 16S rRNA gene clones instead of pure cultures for probe validation and optimization of hybridization conditions. The optimized Clone‐FISH protocol was also used to screen an environmental clone library for insert sequences of interest. In this application format, 13 out of 82 clones examined were identified to contain sulphate‐reducing bacterial rRNA genes. In summary, Clone‐FISH is a simple and fast technique, compatible with a wide variety of cloning vectors and hosts, that should have general utility for probe validation and screening of clone libraries.
Ecology of mixed biofilms subjected daily to a chlorinated alkaline solution: spatial distribution of bacterial species suggests a protective effect of one species to another
Authors: Leriche V. , Briandet R. , Carpentier B. 
Published: March 2003

SummaryThree bacterial strains (Kocuria sp. C714.1, Brevibacterium linens B337.1 and Staphylococcus sciuri CCL101) were grown together on stainless steel and were subjected daily to a commercial alkaline chlorine solution (22 mg l−1 of free chlorine, pH 11) over a period of 4 weeks. After the daily chemical shock, culture madia [1:20 dilution of tryptic soy broth (TSB‐YE/20) or diluted whey] was deposited on the biofilms. The chemical shocks led first to a drop in the culturable population, followed by an increase and finally stabilization at around 106−107 CFU cm−2 by day 11 of the experiment. These changes in the microbial population can be attributed to a decreasing susceptibility to the antimicrobial agent with biofilm age, and to the consumption of free chlorine by biofilm exoproteins. The microbial composition appeared to be linked to the free chlorine concentration that depended on exoprotein production. At the end of the experiment, exoprotein production was greater for biofilms grown in TSBYE/20 than in whey. As a consequence, biofilms grown in whey did not neutralize the chlorine and the dominant strain was the one having the highest resistance to chlorine: K. varians. When biofilm were grown in TSBYE/20, chlorine was neutralized and the dominant strain was the one having the highest growth rate: S. sciuri. The presence of chlorine may also explain the distribution of S. sciuri cells as a ring around Kocuria sp. microcolonies. When chlorine was totally consumed by the biofilm during the chemical shock, S. sciuri was no longer grouped around Kocuria sp. microcolonies but was evenly scattered over the substratum as single cells or in small clusters, as it was before any chemical treatment. These findings strongly suggest protection of S. sciuri by Kocuria sp. microcolonies against the chlorinated solution. This phenomenon, added to the low susceptibility phenotype of the biofilm cells, could at least partly explain the survival of microbial cells in an adverse environment.
Molecular diversity among marine picophytoplankton as revealed by psbA analyses
Authors: Zeidner Gil , Preston Christina M. , Delong Edward F. , Massana Ramon , Post Anton F. , Scanlan David J. , Béjà Oded 
Published: March 2003

SummaryPhotosynthetic microorganisms play a crucial role in the marine environment. In vast areas of the oceans, marine primary productivity is performed by cells smaller than 2–3 µm (picoplankton). Here, we report on molecular analyses of the conserved photosynthetic psbA gene (coding for protein D1 of photosystem II reaction centre) as a diversity indicator of naturally occurring marine oxygenic picophytoplankton. The psbA genes proved to be good indicators of the presence of a wide variety of photosynthetic marine microbial groups, including new cyanobacterial groups and eukaryotic algae (prasinophytes). Furthermore, using environmental bacterial artificial chromosome (BAC) libraries, we were able to correlate psbA genes with small subunit rRNAs and, therefore, to confirm their phylogenetic affiliation.
Is there a role for the colorectal team in the management of acute severe third‐degree vaginal tears?
Authors: Cook  , Keane  , Mortensen  
Published: March 2003

ObjectiveThe repair of sphincter injuries following vaginal delivery is often inadequate. The purpose of this study was to assess the short‐term impact of involving a colorectal team in the management of patients with complicated acute severe third‐degree tears.Patients and methodsOver a 1‐year period, four women (age 29–31 years) with acute severe third‐degree tears extending into the anal canal or rectum were referred to the colorectal unit for repair of the injury. The internal anal sphincter (IAS) was identified and imbricated. A nerve stimulator was used to help identify the external anal sphincter (EAS) which was repaired using an overlapping technique. The women were reassessed at 3 months with anal manometry, pudendal nerve latencies and anal ultrasound. Further clinical assessment was performed at 1 year.ResultsAnal ultrasound revealed intact EAS repairs in all four women, although the IAS was thinned anteriorly in two. Resting anal pressures were slightly low (range 40–56 cmH2O) but satisfactory squeeze pressures were obtained in all four women (range 78–100 cmH2O). Pudendal nerve latencies were normal in three and prolonged on one side in the fourth woman. At 1 year, three were continent to solids, liquids and flatus, incontinence score=0, but one had occasional urgency. The fourth experienced occasional liquid seepage and frequent incontinence to flatus likely to represent IAS dysfunction (incontinence score=7).ConclusionSatisfactory short‐term results may be achieved following repair of acute severe third‐degree tears and a nerve stimulator is important in identifying viable EAS to be used in repair. An integrated approach involving the experience of the colorectal team and anorectal physiology permits planning of future deliveries and may improve the long‐term outcome.
Rectal cancer recurrence: factors and mechanisms
Authors: Heriot  , Kumar  
Published: March 2003

ObjectiveThere have been significant developments in treatment for rectal carcinoma, both in surgical and adjuvant therapy. They may however have associated morbidity and hence individualized therapy for rectal cancer is desirable, to optimize treatment but avoid over‐treatment for cases where the risk of recurrence is low.Materials and methodsA literature review was undertaken of the reported incidence of recurrence of rectal carcinoma following curative surgery, factors which predispose to recurrence and proposed mechanisms for recurrence, and the evidence for each critically evaluated.ResultsThe incidence of local recurrence of rectal carcinoma following curative resection ranges from 2.6% to 32%, with an average of 15%. Tumour stage is the strongest predictor of tumour recurrence. Upstaging using molecular biology may predict increased risk of recurrence but is not yet proven. Histological factors including differentiation and vascular invasion increase recurrence but are imprecise. Tumour microvascular density and vascular endothelial growth factor (VEGF) levels may be predictive but need refinement. Adequate resection margins are important but recurrence may occur despite this. Tumour cell spillage and distant dissemination may be a mechanism for tumour recurrence following curative resection, but further research is required before this could be applied clinically.ConclusionRecurrence of rectal cancer remains a significant problem following ‘curative’ surgery. Multiple factors may influence recurrence risk, though currently however only tumour stage and histological resection margins have demonstrated sufficient importance for management decisions to be made upon them.
Comparison of prognosis in cancer of the colon and rectum
Authors: Hall  , Finan  , Brown  , Ai‐Jaberi  , Tsang  
Published: March 2003

ObjectiveTo determine whether there is a difference in prognosis between colon and rectal cancer.Patients and methodsA prospective audit was conducted of a cohort of consecutive patients presenting to a single colorectal surgeon over an 8‐year period, in a teaching hospital colorectal unit. There were 492 patients, 274 with colon cancer and 218 with rectal cancer, followed up to death or for a median of 43 months. Resection of all macroscopic disease was performed where possible by performing, if necessary, en bloc excision of local disease in continuity with adjacent involved structures. There was total mesorectal excision for middle and lower third rectal cancers. The main outcome measures were local recurrence, any recurrence, and survival.ResultsFive year survival excluding non‐colorectal cancer deaths was 80% for colon cancer and 70% for rectal cancer after curative excision when all stages were grouped together (logrank P=0.25). Survival curves for Dukes’ A and B cancers at each site were the same. Dukes’ C rectal cancers recurred locally more frequently than colon cancers, but there was no significant difference in survival.ConclusionWith appropriate radical surgery, survival after curative resection of rectal cancer can be as favourable as for colon cancer. Patients with Dukes’ C cancers of the rectum are more at risk of local recurrence and this group should be the focus of efforts to improve outcome further.
Emergency admission with colorectal cancer: its relationship to primary health care organization
Authors: Oldale  , McKenna  , Waddecar  , Scott  
Published: March 2003

ObjectiveTo determine if associations exist between emergency admission with colorectal cancer and patient demographics and features of primary health care organization.Patients and methodsBetween 1992 and 1997 a prospective study of 485 consecutive colorectal cancer admissions to the Hope Hospital Colorectal Cancer Database (HCCD) was performed. Details of patient gender, age, marital status, postcode and general practitioner (GP) code were recorded at admission. The Jarman (UPA) score was derived from each patient’s postcode. The GP code was used to identify from the local health authority lists for each patient, the number of GPs in the referring practice, the fund‐holding status of practice and the presence or absence of a GP trainer in the practice.ResultsNeither patient gender nor Jarman (UPA) score was associated with emergency admission. Patient age >75 years (P=0.05) and patient (single/divorced/widowed) marital status (P=0.07) were associated with emergency admission. There was no association between the number of GPs, the fund‐holding or training status of the referring practice and patient referral as an emergency with colorectal cancer.ConclusionEmergency admission with colorectal cancer is not associated with present aspects of primary health care organization—specifically number of GPs in practice, fund‐holding or training.
Abnormal hepatic perfusion index predicts recurrence of colorectal carcinoma
Authors: Sarela A. I. , Gallagher H. J. , Macadam R. C. A. , O’Riordain D. S. , Parkin A. , Guillou P. J. 
Published: March 2003

ObjectiveThe hepatic perfusion index (HPI) is a ratio of the gradient of hepatic arterial to total hepatic blood flow. This study correlated HPI with histopathological indicators of prognosis and disease‐free survival following curative resection of colorectal cancer.Patients and methodsHPI was measured preoperatively by dynamic hepatic scintigraphy in 37 patients with a primary colorectal cancer and no evidence of distant metastases who underwent a curative resection.ResultsAbnormally elevated HPI were detected in 49% of patients and were significantly more frequent in association with locally advanced tumours (T3 and T4) in comparison with early tumours (T1 and T2; 59% vs 20%, respectively; P=0.04). There was no association between abnormal HPI and presence of lymph node metastases or degree of tumour differentiation. The 18‐month disease‐free survival rate of patients with abnormal HPI was significantly shorter than that of patients with normal HPI (53% vs 100%, respectively; P=0.01), and this was independent of the T category.ConclusionHPI predicts the risk of recurrent colorectal carcinoma, and this measurement should be included in the panel of prognostic markers in future clinical trials.
Results of anterior levatorplasty for rectocele
Authors: Lamah M. , Ho J. , Leicester R. J. 
Published: March 2003

ObjectiveTransanal and transvaginal repair of rectocele have been advocated in the treatment of rectocele, with mixed results. The aim of this study was to assess our experience using anterior levatorplasty in the surgical management of rectocele.Patients and methodsSixty of 90 women who had undergone anterior levatorplasty for rectocele over a seven year period were traced, and 44 (33 with rectocele only and 11 with rectocele and faecal incontinence) responded to a standardized questionnaire 6 months to 7 years (mean 3.5 years) after anterior levatorplasty. Results were expressed in general and specific improvement of symptoms and were classified as excellent, good, fair, or poor. The effects on social activities, sexual function, and employment were also assessed.ResultsGeneral satisfaction with the operation was rated as good or excellent in 27 of 33 (82%) and 18 of 24 (75%) patients with rectocele only at 2 and 3.2 years follow‐up, respectively, and in 7 of 11 (64%) and 5 of 11 (45%) patients with rectocele and faecal incontinence at 2 and 4 years follow‐up, respectively. 31 (70%) and 34 (77%) of all patients reported an improvement in sensation and the ability to defaecate, respectively. An improvement in social activities, sexual satisfaction and employment was noted in 10 of 21 (48%), 10 of 23 (43%), and 7 of 12 (58%) patients, respectively.ConclusionAnterior levatorplasty provides good short and long‐term symptomatic improvement in patients with rectocele and avoids complications associated with rectal or vaginal approaches.
Evaluation of the role of pre‐operative magnetic resonance imaging in the management of rectal cancer
Authors: Botterill I. D. , Blunt D. M. , Quirke P. , Sebag‐Montefiore D. , Sagar P. M. , Finan P. J. , Chalmers A. G. 
Published: March 2003

ObjectivesThis study assesses the ability of body coil magnetic resonance imaging (MRI) to pre‐operatively stage mural penetration, nodal status and circumferential resection margin (CRM) involvement of rectal cancer.Patients and methodsBetween 1995 and 1997, MRI using a body coil was performed in consecutive patients with primary rectal carcinomas. Group A: 67 patients underwent surgery without long course neo‐adjuvant therapy. Predicted tumour stage was compared to the histology of the specimen. Group B: 21 patients with MRI evidence of advanced disease, underwent long course neo‐adjuvant therapy followed by repeat MRI prior to surgery. The second scan assessed response to treatment and likelihood of CRM involvement at subsequent surgery.ResultsGroup A: Accuracy of pre‐operative staging was: ‘T’ stage – 54%, ‘N’ stage – 77%, involvement of CRM by tumour – 97%. Group B: After long course neo‐adjuvant therapy the second MRI scan was 95% accurate in predicting CRM involvement by tumour.ConclusionIn this study pre‐operative rectal cancer staging with MRI and a body coil lacks accuracy in predicting mural penetration and nodal involvement. Body coil MRI can accurately predict the potential for CRM involvement. This technique may help determine which patients require long course neo‐adjuvant therapy.
Minimally invasive surgery for ileo–colic Crohn's disease
Authors: Motson R. W. , Kadirkamanathan S. S. , Gallegos N. 
Published: March 2003

ObjectivePatients requiring surgery for Crohn's disease are likely to undergo further surgery due to recurrent disease. A prospective study of laparoscopic‐assisted surgery for ileo‐colic Crohn's disease is reported.MethodForty‐one patients (26 female; median age 35 years) with ileo‐colic Crohn's disease, without evidence of either fistula or abscess formation underwent laparoscopic‐assisted surgery. All had medical therapy, including steroids, but had failed to respond or relapsed. Sixteen patients (39%) had previous surgery for Crohn's disease and 26 (63.4%) had previous abdominal surgery. Laparoscopic procedures (n=42) included ileocaecal/ileocolic resection (n=39), small bowel resection (n=1) and strictureplasty (n=2).ResultsThe median operating time was 90 min (range 60–180). There were 6 conversions (14.6%). Of the 35 patients whose operation was completed laparoscopically, the median postoperative stay was 5 days (3–9) and the median time to full activity was 20 days (7–49). No major complications or death were recorded. The median follow up (34 out of 35) after surgery is 15.3 months (1–55). Twenty‐four patients remain symptom free and 4 have minimal symptoms with no clinical or radiological evidence of recurrence of Crohn's disease. Six have however, developed recurrence requiring medical (n=5) and surgical (n=1) treatment.ConclusionLaparoscopic‐assisted surgery for Crohn's disease is feasible. It has the advantage of minimizing hospital stay and promoting early recovery in a group of patients who are likely to have further surgery due to the nature of the disease.