Biomedical subjects

J R Saunders

Publications and source records attributed to J R Saunders.

At least 37 records · Page 2Linked to original sources

PubMed2000

Analysis of ammonia-oxidizing bacteria populations in acid forest soil during conditions of moisture limitation.

Ammonia-oxidizer numbers decreased under conditions of moisture limitation in litter, fermentation and humus layers of forest soil in the field, but the extent of regrowth after rehydration varied between layers. Nitrosospira 16S rRNA genes were amplified from all layers, regardless of moisture content or soil pH which varied between 4.1 and 5.2. Nitrosomonas spp. were detected less often, but appeared to exhibit more rapid recovery than the Nitrosospira spp. when drought conditions were relieved by rainfall.

Ammonia↗

PubMed2000

Plasmid transfer between the Bacillus thuringiensis subspecies kurstaki and tenebrionis in laboratory culture and soil and in lepidopteran and coleopteran larvae.

Plasmid transfer between Bacillus thuringiensis subsp. kurstaki HD1 and B. thuringiensis subsp. tenebrionis donor strains and a streptomycin-resistant B. thuringiensis subsp. kurstaki recipient was studied under environmentally relevant laboratory conditions in vitro, in soil, and in insects. Plasmid transfer was detected in vitro at temperatures of 5 to 37 degrees C, at pH 5.9 to 9.0, and at water activities of 0.965 to 0.995, and the highest transfer ratios (up to 10(-1) transconjugant/donor) were detected within 4 h. In contrast, no plasmid transfer was detected in nonsterile soil, and rapid formation of spores by the introduced strains probably contributed most to the lack of plasmid transfer observed. When a B. thuringiensis subsp. kurstaki strain was used as the donor strain, plasmid transfer was detected in killed susceptible lepidopteran insect (Lacanobia oleracea) larvae but not in the nonsusceptible coleopteran insect Phaedon chocleriae. When a B. thuringiensis subsp. tenerbrionis strain was used as the donor strain, no plasmid transfer was detected in either of these insects even when they were killed. These results show that in larger susceptible lepidopteran insects there is a greater opportunity for growth of B. thuringiensis strains, and this finding, combined with decreased competition due to a low initial background bacterial population, can provide suitable conditions for efficient plasmid transfer in the environment.

Animals↗

PubMed1999

Phylogenetic differentiation of two closely related Nitrosomonas spp. That inhabit different sediment environments in an oligotrophic freshwater lake.

The population of ammonia-oxidizing bacteria in a temperate oligotrophic freshwater lake was analyzed by recovering 16S ribosomal DNA (rDNA) from lakewater and sediment samples taken throughout a seasonal cycle. Nitrosospira and Nitrosomonas 16S rRNA genes were amplified in a nested PCR, and the identity of the products was confirmed by oligonucleotide hybridization. Nitrosospira DNA was readily identified in all samples, and nitrosomonad DNA of the Nitrosomonas europaea-Nitrosomonas eutropha lineage was also directly detected, but during the summer months only. Phylogenetic delineation with partial (345 bp) 16S rRNA gene sequences of clones obtained from sediments confirmed the fidelity of the amplified nitrosomonad DNA and identified two sequence clusters closely related to either N. europaea or N. eutropha that were equated with the littoral and profundal sediment sites, respectively. Determination of 701-bp sequences for 16S rDNA clones representing each cluster confirmed this delineation. A PCR-restriction fragment length polymorphism (RFLP) system was developed that enabled identification of clones containing N. europaea and N. eutropha 16S rDNA sequences, including subclasses therein. It proved possible to analyze 16S rDNA amplified directly from sediment samples to determine the relative abundance of each species compared with that of the other. N. europaea and N. eutropha are very closely related, and direct evidence for their presence in lake systems is limited. The correlation of each species with a distinct spatial location in sediment is an unusual example of niche adaptation by two genotypically similar bacteria. Their occurrence and relative distribution can now be routinely monitored in relation to environmental variation by the application of PCR-RFLP analysis.

Cloning, Molecular↗

PubMed1999

Comparison of flagellin genes from clinical and environmental Pseudomonas aeruginosa isolates.

Pseudomonas aeruginosa, an important opportunistic pathogen, was isolated from environmental samples and compared to clinically derived strains. While P. aeruginosa was isolated readily from an experimental mushroom-growing unit, it was found only rarely in other environmental samples. A flagellin gene PCR-restriction fragment length polymorphism analysis of the isolates revealed that environmental and clinical P. aeruginosa strains are not readily distinguishable. The variation in the central regions of the flagellin genes of seven of the isolates was investigated further. The strains used included two strains with type a genes (998 bp), four strains with type b genes (1,258 bp), and one strain, K979, with a novel flagellin gene (2,199 bp). The route by which flagellin gene variation has occurred in P. aeruginosa is discussed.

Agaricales↗

PubMed1998

Gamma probe-directed biopsy of the sentinel node in oral squamous cell carcinoma.

OBJECTIVE: Management of the N0 neck in head and neck squamous cell carcinoma is an important issue for the head and neck surgeon. Experience with radionuclide-labeled colloid injection to identify a sentinel node in malignant melanoma suggests a high level of accuracy for this approach to identify microscopic metastasis when present. We set out to explore the feasibility of using the handheld gamma probe to identify radiolabeled sentinel nodes in oral squamous cell carcinoma. PATIENT POPULATION: Five individuals with N0 necks and accessible oral or oropharyngeal primary sites from a major tertiary referral center. METHODS: Radiolabel with unfiltered technetium Tc 99m sulfur colloid was injected in quadrants around the primary site followed by immediate dynamic lymphoscintigraphy. Open biopsy of the sentinel node was accomplished within 2 hours of injection after extirpation of the primary site. Regional or complete neck dissection was performed after sentinel node biopsy. RESULTS: Sentinel node biopsy accurately identified one or several nodes in 2 cases, including nodes containing metastatic cancer in 1. In the other 3 cases, the radiolabel failed to identify the sentinel node despite the presence of metastatic disease in the nodes at final pathologic study in 2. CONCLUSIONS: Detection and biopsy of the sentinel node are feasible for selected patients with oral head and neck squamous cell carcinoma with N0 necks. There is a potential savings of time, cost, and morbidity with this approach. However, several substantial problems were encountered with the technique in this limited series of patients. Establishing the reliability of lymphoscintigraphy in this setting would require testing in a much larger patient cohort. Our experience suggests that such an investment may not be warranted.

Adult↗

PubMed1997

The genetic basis of head and neck carcinoma.

Research over the past few years has pointed to a genetic basis for numerous cancers. Efforts in this regard are ongoing in squamous carcinoma of the head and neck. Today surgeons and residents in training need to stay up to date on molecular biology and the genetic sequences that are necessary to form a malignancy. In addition, these changes offer diagnosticians and therapists novel ways both to diagnose and treat malignancies. An evolution in molecular genetics, tumor virology, and tumor biology has led to our understanding of how malignancies arise. There are two pathways of cancer production: the activation of an oncogene or the mutation of a tumor suppressor gene. This review discusses the interaction of these genetic changes in the development of squamous carcinoma of the head and neck, their relationship to tobacco and alcohol use, as well as methods to detect the presence of malignancy and novel techniques that may be used to treat malignancies in the future.

Alcohol Drinking↗

PubMed1997

Detection, distribution and probable fate of Escherichia coli O157 from asymptomatic cattle on a dairy farm.

The use of commercial anti-Escherichia coli O157-labelled magnetic beads was investigated to improve detection of E. coli O157 by immunomagnetic separation (IMS) from a range of environments on a dairy farm. Immunomagnetic separation proved effective for separation of target cells from laboratory mixtures and during stress in sterile and non-sterile pond water. The IMS procedure was possible with a range of samples (water, faeces, slurry, grass and soil). Non-specific binding of non-target bacterial cells proved problematic in a number of sample types. However, indigenous E. coli O157 cells were detected from samples with a high faecal load, and only with use of IMS. Data on the probable survival and spread of the organism around the farm environment are also discussed.

Animals↗

PubMed1997

Efficiency of the polymerase chain reaction amplification of the uid gene for detection of Escherichia coli in contaminated water.

Direct detection of Escherichia coli from polluted river water was achieved using polymerase chain reaction (PCR) amplification of the uid gene. Amplification using DNA from environmental samples resulted in non-specific DNA fragments. Specific amplification was achieved through use of the touch-down PCR procedure. Targeting the uidA structural region of the gene gave reproducibly better amplification than targeting the uidR regulatory region. The data demonstrate conditions for optimal specific detection.

Bacteriological Techniques↗

PubMed1997

The flagellin gene as a stable marker for detection of Pseudomonas fluorescens SBW25.

Flagellin gene central regions from 111 isolates of Pseudomonas fluorescens SBW25 obtained from soil during a field release experiment were analysed using a combined PCR/RFLP technique to look for variation. In addition, a 858 bp flagellin gene sequence from the original strain and the last isolate obtained from the release site were compared. There was no variation in flagellin gene sequences indicating that the gene was stable over the period of the release, and that the flagellin gene is a suitable marker for use in the detection of bacteria in release experiments. A comparison of Ps. fluorescens SBW25 flagellin with other sequenced flagellins revealed closest homology to the flagellin of Ps. putida PRS2000.

Base Sequence↗

PubMed1997

Characterization of antibiotic resistance plasmids from Bordetella bronchiseptica.

Of 52 antibiotic-resistant Bordetella bronchiseptica isolates from cats, ten carried plasmids. Only two of these plasmids, pLV1400 and pLV1401, were self-transmissible to Escherichia coli K12; both plasmids encoded resistance to ampicillin, tetracycline, sulphonamides, streptomycin and mercuric chloride, and were of incompatibility group P (IncP). Transferable tetracycline resistance has not been reported in B. bronchiseptica previously. The plasmids were identical in size (c.51 kb), restriction endonuclease digestion pattern and gene sequences (trfA and korA) within the IncP replicon. The trfA and korA sequences differed from those of the archetypal IncP plasmids RP4 and R751. Although the two B. bronchiseptica isolates were from epidemiologically and geographically separated cats, pulsed-field gel electrophoresis of their XbaI- or DraI-digested chromosomal DNA indicated that they were genotypically identical. The plasmid-encoded ampicillin resistance was mediated by a penicillinase of molecular weight 49,000, and pI 8.45 which was inhibited by clavulanate (IC50 = 0.1 mg/L) and tazobactam (IC50 = 0.42 mg/L) but not by parachloromercuribenzoate or EDTA. The high-level tetracycline resistance was mediated by a class C efflux mechanism that has not been described previously in this genus. The presence of transferable multi-drug resistance on a promiscuous plasmid may limit options for therapy of respiratory tract infection in companion and farm animals.

Animals↗

PubMed1997

Surface properties of diarrhoeagenic Escherichia coli isolates.

The surface properties of various Escherichia coli isolates associated with diarrhoeal illness were compared by aqueous partitioning between polyethylene glycol (PEG) and Dextran phases. Two well characterised strains of enteropathogenic E. coli (EPEC) were found to be very hydrophobic, based on the critical polymer concentration. EPEC strain E2348 cured of the EPEC adherence factor (EAF) plasmid had much reduced surface hydrophobicity. Partitioning of a series of diarrhoeagenic E. coli strains demonstrated that the majority of EAF+ EPEC strains were significantly more hydrophobic than EAF- EPEC strains. E. coli strains defined as enteroaggregative on the basis of hybridisation with a specific DNA probe showed much greater heterogeneity in their partitioning behaviour, possibly indicating that the AAF/I pili were not expressed in all strains. The E. coli K-12 strain used as a transformation host for adhesion studies had very low surface hydrophobicity but had a detectable negative charge. No alteration in these properties was observed when transformed with EPEC and recombinant plasmids known to specify adherence to tissue culture cells.

Agglutination Tests↗

PubMed1997

Aerobic bacterial flora of addled raptor eggs in Saskatchewan.

In south-central Saskatchewan, Canada, in 1986, 1987 and 1989, the aerobic bacterial flora was evaluated from 75 unhatched raptor eggs of three species: 42 of the Swainson's hawk (Buteo Swainsoni), 21 of the ferruginous hawk (Buteo regalis), and 12 of the great horned owl (Bubo virginianus). In addled Swainson's hawk eggs, the most common bacterial genera were Enterobacter (18 eggs), Escherichia (12), and Streptococcus (10). Seven great horned owl eggs and six ferruginous hawk eggs also contained Escherichia coli. Salmonella spp. were not isolated. These bacteria were interpreted as secondary contaminants and not the primary cause of reproductive failure.

Animals↗

PubMed1996

Posttranslational modifications of meningococcal pili. Identification of a common trisaccharide substitution on variant pilins of strain C311.

Neisseria meningitidis pili are filamentous protein structures that are essential adhesins in capsulate bacteria. Pili of adhesion variants of meningococcal strain C311 contain glycosyl residues on pilin (PilE), their major structural subunit. Recent studies have shown that a novel O-linked trisaccharide substituent, not previously found as a constituent of glycoproteins, is present within a peptide spanning amino acid residues 50 to 73 of the PilE molecule. The structure was shown to be Gal beta 1-4 Gal alpha 1-3 diacetamidotrideoxyhexose which is directly attached to pilin. Pilins derived from galactose epimerase (galE) mutants lack the digalactosyl moiety, but retain the diacetamidotrideoxyhexose substitution. These studies confirm our previous observations that meningococcal pili are glycosylated and provide the first structural evidence for the presence of covalently linked carbohydrate on pili. We have identified a completely novel protein/carbohydrate linkage on a multimeric protein that is an essential virulence determinant in N. meningitidis.

Amino Acid Sequence↗

PubMed1996

Molecular mechanisms of intramolecular recombination-dependent recircularization of linearized plasmid DNA in Escherichia coli: requirements for the ruvA, ruvB, recG, recF and recR gene products.

Intramolecular recombinogenic recircularization (IRR) of linearized plasmid DNA was used to study mechanistic relationships between recombination functions in Escherichia coli in vivo. Homology requirement for IRR ranges from 1 to 11 bp, and does not exhibit any notable strain to strain variability, with recombination occurring at a large number of possible sites within the plasmid molecule. We show that recF- and recR-deficient strains exhibit greatly reduced IRR efficiency, although neither gene product is totally essential. Mutation of recF and recR does not alter the distribution of recombination sites nor the range of molecules produced during IRR. A recO-deficient strain did not exhibit dramatic reduction in efficiency of IRR, implying that RecF and RecR proteins maintain function during this mechanism in the absence of functional RecO. The main IRR mechanism is ruvA-, ruvB- and recG-dependent and there is a lower efficiency second IRR mechanism operating in ruvA, ruvB and recG mutants. Some evidence suggests that this second mechanism involves functions associated with the replisome.

Bacterial Proteins↗

PubMed1996

Growth and propagation of normal rat intestinal epithelial cells.

A combination of mild proteolytic digestion and selective growth stimulation has been used to isolate and propagate adult rat intestinal epithelial cells with a finite life span. Growth of these cells on a variety of matrices and on mesenchymal cells has resulted in the expression of brush border enzymes including sucrase-isomaltase, aminopeptidase N, and alkaline phosphatase. Examination of the cells at the electron microscopic level has revealed that although these cells express key brush border enzymes, they do not have a fully formed brush border. These findings suggest that the expression of brush border enzymes and structural proteins represent distinct stages of enterocyte differentiation that are under separate transcriptional and temporal control.

Alkaline Phosphatase↗

PubMed1996

Expression of Aeromonas caviae bla genes in Escherichia coli.

An isolate of Aeromonas caviae 035 carried a 55.5 kb self-transferable plasmid. Transfer of the plasmid to Escherichia coli K12 resulted in the expression of a TEM-like beta-lactamase that was not expressed in parental A. caviae. The bla gene sequence was detectable by DNA hybridization and PCR amplification of the plasmid when extracted from parental A. caviae or from E. coli K12 transconjugants. Sequence analysis of the bla genes revealed in each case an 858 bp open reading frame, differing from the TEM-1 sequence by five nucleotide substitutions. Only one of these resulted in amino acid substitution (at position 162 serine-->arginine). The sequence most closely resembles that of TEM-12.

Aeromonas↗

PubMed1996

Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis.

The presence of methanogenic bacteria was assessed in peat and soil cores taken from upland moors. The sampling area was largely covered by blanket bog peat together with small areas of red-brown limestone and peaty gley. A 30-cm-deep core of each soil type was taken, and DNA was extracted from 5-cm transverse sections. Purified DNA was subjected to PCR amplification with primers IAf and 1100Ar, which specifically amplify 1.1 kb of the archaeal 16S rRNA gene, and ME1 and ME2, which were designed to amplify a 0.75-kb region of the alpha-subunit gene for methyl coenzyme M reductase (MCR). Amplification with both primer pairs was obtained only with DNA extracted from the two deepest sections of the blanket bog peat core. This is consistent with the notion that anaerobiosis is required for activity and survival of the methanogen population. PCR products from both amplifications were cloned, and the resulting transformants were screened with specific oligonucleotide probes internal to the MCR or archaeal 16S rRNA PCR product. Plasmid DNA was extracted from probe-positive clones of both types and the insert was sequenced. The DNA sequences of 8 MCR clones were identical, as were those of 16 of the 17 16S rRNA clones. One clone showed marked variation from the remainder in specific regions of the sequence. From a comparison of these two different 16S rRNA sequences, an oligonucleotide was synthesized that was 100% homologous to a sequence region of the first 16 clones but had six mismatches with the variant. This probe was used to screen primary populations of PCR clones, and all of those that were probe negative were checked for the presence of inserts, which were then sequenced. By using this strategy, further novel methanogen 16S rRNA variants were identified and analyzed. The sequences recovered from the peat formed two clusters on the end of long branches within the methanogen radiation that are distinct from each other. These cannot be placed directly with sequences from any cultured taxa for which sequence information is available.

Base Sequence↗

PubMed1995

Effects of concanavalin A and pokeweed lectins on microvillar membrane proteins during the organ culture of rabbit intestinal mucosa.

The effects of pokeweed lectin (PWL) and concanavalin A (Con A) on microvillar membrane (MVM) proteins during the organ culture of rabbit ileal explants for 24 hours were compared with the known effects of enteropathogenic Escherichia coli (EPEC). PWL resulted in the accelerated release of brush border enzymes into the culture medium, accompanied by decreased tissue activities and an increase in the total activity present in the tissue and culture medium. Con A had less effect on the release and tissue activities of brush border enzymes and the total activity was not increased. Sucrose density gradient centrifugation of the culture medium showed that MVM enzymes were predominantly particulate, consistent with their release as vesicles. Centrifugation of ileal explants showed that PWL, but not Con A, resulted in a decrease in the modal density of the brush border which was consistent with a lower glycoprotein-to-lipid ratio. These findings suggest that PWL, in common with EPEC, may cause the disruption and vesiculation of microvilli and the compensatory stimulation of MVM protein synthesis.

Animals↗