PubMed Health⌕ Search

Biomedical subjects

B J Reid

Publications and source records attributed to B J Reid.

At least 19 recordsLinked to original sources
PubMed2007

The influence of a NAPL on the loss and biodegradation of 14C-phenanthrene residues in two dissimilar soils.

This study was carried out to assess the influence of diesel, applied over a log concentration range, on the loss and extractability of phenanthrene (measured as putative 14C-phenanthrene residues) in two different soils. The influence of diesel on the ability of a cyclodextrin based extraction method to predict the microbial bioavailability of 14C-residues was also assessed. An increase in loss of 14C-residues with increasing diesel concentration from 0 to 2000 mg kg-1 was generally observed with time in both soils. It is suggested that this trend is attributable to competitive sorption for soil sorption sites and to a lesser extent to displacement of 14C-residues from soil sorption sites by diesel resulting in greater compound availability and therefore greater loss by degradation via the actions of indigenous microorganisms. However, in the 20000 mg kg-1 diesel treatments of both soils, results indicated a delayed loss. It is suggested that this retarded loss was due to the formation of a discrete NAPL-phase into which 14C-phenanthrene residues partitioned, thereby decreasing their availability and as a consequence their degradation. Furthermore, it is suggested that nutrient limitation may have slowed down degradation rates as diesel concentrations increased. Comparison between cyclodextrin-extractability and microbial mineralisation supported the use of cyclodextrin to assess microbial bioavailability of 14C-residues after 50 d or more ageing up to diesel concentrations of 2000 mg kg-1. However, results suggested that at high diesel concentrations (specifically 20000 mg kg-1) co-extraction of 14C-phenanthrene residues may have occurred as a result of the combined solvation powers of both the cyclodextrin and the diesel. Furthermore, mineralisation of 14C-phenanthrene residues may have been affected by extreme nutrient limitation in this treatment.

Biodegradation, Environmental↗
PubMed2005

Comparison of selected non-exhaustive extraction techniques to assess PAH availability in dissimilar soils.

Recently, it has become apparent that the use of total contaminant concentrations as a measure of potential contaminant exposure to plants or soil organisms is inappropriate and that bioavailability of contaminants is a better measure of potential exposure. In light of this, non-exhaustive extraction techniques are being investigated to assess their appropriateness in determining bioavailability. In this study, phenanthrene extractability using hydroxypropyl-beta-cyclodextrin (HPCD) and desorption kinetics using butan-1-ol (BuOH) were determined in three dissimilar spiked soils. The soils were extracted after 1 d, 40 d and 80 d of soil-compound contact time. The amount of phenanthrene extracted by HPCD was compared to the rapidly desorbed fraction removed by BuOH. Further experiments using the same soils and extraction methods to assess the relative extractability of phenanthrene, pyrene and benzo(a)pyrene were conducted. Overall, the extraction methods used in this study had different extraction efficiencies. Results suggest that as compound hydrophobicity increased, BuOH became a more exhaustive extractant with respect to HPCD, especially for soils with high clay and organic matter content. These results are important as they highlight differences between two contrasting non-exhaustive extraction techniques both of which have been suggested to be appropriate in the assessment of bioavailability.

Chemistry Techniques, Analytical↗
PubMed2002

High-quality RNA and DNA from flow cytometrically sorted human epithelial cells and tissues.

Microarray technologies have made possible comprehensive analyses of nucleic acid sequence and expression. However, the technology to obtain efficiently high-quality RNA and DNA suitable for array analysis from purified populations of neoplastic cells from human tissues has not been well addressed. Microdissection can enrich for populations of cells present in various tumor tissues, but it is not easily automated or performed rapidly, and there are tissues in which cells of interest cannot be readily isolated based on morphologic criteria alone. Here we describe a protocol for efficient RNA and DNA isolation from flow cytometrically purified whole epithelial cells from primary tissue. The aqueous reagent, RNAlater, which preserves RNA, allows immunolabeling and purification of whole epithelial cells by flow sorting without special instrument preparation to reduce RNase activity. We used real-time PCR to determine RNA quality afterflow sorting. High-quality RNA and DNA suitable for expression and genotype analysis can be readily obtained from flow cytometrically purified populations of neoplastic cells from human tissues.

Base Sequence↗
PubMed2001

p16(INK4a) lesions are common, early abnormalities that undergo clonal expansion in Barrett's metaplastic epithelium.

Barrett's esophagus (BE) is the only known precursor to esophageal adenocarcinoma, a cancer of which the incidence has been increasing at an alarming rate in Western countries. p16(INK4a) lesions occur frequently in esophageal adenocarcinomas but their role in neoplastic progression is not well understood. We detected 9p21 loss of heterozygosity, p16 CpG island methylation, and p16 mutations in biopsies from 57%, 61%, and 15%, respectively, of 107 patients with BE. In contrast, no mutations were found in p14(ARF) or p15, and methylation was found in only 4% and 13%, respectively. >85% of Barrett's segments had clones with one (p16+/-) or two (p16-/-) p16 lesions. Both p16+/- and p16-/- clones underwent extensive expansion involving up to 17 cm of esophageal mucosa. The prevalence of established biomarkers in BE, such as 17p (p53) loss of heterozygosity, aneuploidy, and/or increased 4N (tetraploid) populations, increased from 0% to 20% to 44% in patients whose biopsies were p16+/+, p16+/-, and p16-/-, respectively (P < 0.001). Barrett's segment lengths also increased with change in p16 status with a median of 1.5, 6.0, and 8.0 cm for patients with p16+/+, p16+/-, and p16-/- biopsies, respectively (P < 0.001). We conclude that most Barrett's metaplasia contains genetic and/or epigenetic p16 lesions and has the ability to undergo clonal expansion, creating a field in which other abnormalities can arise that can lead to esophageal adenocarcinoma.

Adult↗
PubMed2001

Loss of heterozygosity in childhood de novo acute myelogenous leukemia.

A genome-wide screening for loss of heterozygosity (LOH), a marker for possible involvement of tumor suppressor genes, was conducted in 53 children with de novo acute myelogenous leukemia (AML). A total of 177 highly polymorphic microsatellite repeat markers were used in locus-specific polymerase chain reactions. This comprehensive allelotyping employed flow-sorted cells from diagnostic samples and whole-genome amplification of DNA from small, highly purified samples. Nineteen regions of allelic loss in 17 patients (32%) were detected on chromosome arms 1q, 3q, 5q, 7q (n = 2), 9q (n = 4), 11p (n = 2), 12p (n = 3), 13q (n = 2), 16q, 19q, and Y. The study revealed a degree of allelic loss underestimated by routine cytogenetic analysis, which failed to detect 9 of these LOH events. There was no evidence of LOH by intragenic markers for p53, Nf1, or CBFA2/AML1. Most lymphocytes lacked the deletions, which were detected only in the leukemic myeloid blast population. Analysis of patients' clinical and biologic characteristics indicated that the presence of LOH was associated with a white blood cell count of 20 x 10(9)/L or higher but was not correlated with a shorter overall survival. The relatively low rate of LOH observed in this study compared with findings in solid tumors and in pediatric acute lymphoblastic leukemia and adult AML suggests that tumor suppressor genes are either infrequently involved in the development of pediatric de novo AML or are inactivated by such means as methylation and point mutations. Additional study is needed to determine whether these regions of LOH harbor tumor suppressor genes and whether specific regions of LOH correlate with clinical characteristics. (Blood. 2001;98:1188-1194)

Adolescent↗
PubMed2001

A simple (14)C-respirometric method for assessing microbial catabolic potential and contaminant bioavailability.

This paper describes the validation and application of a simple flask-based (14)C-respirometer system designed to assess mineralisation of (14)C-labelled substrates under defined conditions. Validation of this respirometer system indicated stoichiometric CO(2) trapping up to a maximum of 400 micromol of CO(2) (in a single trap). Polycyclic aromatic hydrocarbon (PAH)-degrading bacteria were used to measure growth-linked biodegradation of [(14)C]naphthalene to (14)CO(2). A (14)C activity balance of 101.7+/-8.9% (n=6), after 74 h incubation time and 10 respirometer-opening events, indicated the suitability of the system for monitoring substrate mineralisation. This respirometric apparatus was then successfully applied to assess: (i) the PAH catabolism of microbes in a field contaminated soil, where naphthalene and phenanthrene were rapidly mineralised and (ii) soil-associated organic contaminant bioavailability, where increased soil-phenanthrene contact time resulted in a reduction in phenanthrene mineralisation in the soil. The described respirometer system differs from existing respirometer systems in that the CO(2) trap can be removed and replaced quickly and easily. The system is efficient, reproducible, adaptable to many situations, easy to construct and simple to use, it therefore affords advantages over existing systems.

Bacteriological Techniques↗
PubMed2001

Impact of composting strategies on the treatment of soils contaminated with organic pollutants.

Chemical pollution of the environment has become a major source of concern. Studies on degradation of organic compounds have shown that some microorganisms are extremely versatile at catabolizing recalcitrant molecules. By harnessing this catabolic potential, it is possible to bioremediate some chemically contaminated environmental systems. Composting matrices and composts are rich sources of xenobiotic-degrading microorganisms including bacteria, actinomycetes and lignolytic fungi, which can degrade pollutants to innocuous compounds such as carbon dioxide and water. These microorganisms can also biotransform pollutants into less toxic substances and/or lock up pollutants within the organic matrix, thereby reducing pollutant bioavailability. The success or failure of a composting/compost remediation strategy depends however on a number of factors, the most important of which are pollutant bioavailability and biodegradability. This review discusses the interactions of pollutants with soils; look critically at the clean up of soils contaminated with a variety of pollutants using various composting strategies and assess the feasibility of using composting technologies to bioremediate contaminated soil.

Biological Availability↗
PubMed2001

A low-cost fiber-optic instrument to colorimetrically detect patients with Barrett's esophagus for early detection of esophageal adenocarcinoma.

In Barrett's esophagus, the precursor to esophageal adenocarcinoma, the squamocolumnar junction (SCJ) between the normal esophagus and the stomach like mucosa is proximally displaced. Currently it can be detected only by an expensive upper GI endoscopic procedure. We have developed a minimally invasive and easy to operate colorimetric instrument for the low-cost detection of Barrett's esophagus. The instrument is based on a flexible, narrow diameter, fiber-optic probe that performs a colorimetric scan of the esophageal lumen. The instrument was clinically evaluated in 50 subjects. The instrument could identify both symmetric and asymmetric SCJ's. The SCJ locations determined by the colorimetric instrument correlated strongly (R2 = 0.89) with those determined by endoscopy. The instrument identified the SCJ locations accurately (Mean of difference +/- SEM: 0.97 +/- 1.72 cm) and reproducibly (Mean of absolute difference +/- SEM: 1.33 +/- 1.40 cm). The instrument has a 90% sensitivity of identifying patients with Barrett's esophagus, based on the clinical algorithm that if the SCJ is located at a distance less than 37 cm from the teeth, then the subject has Barrett's esophagus, otherwise the subject does not have Barrett's esophagus. In conclusion, the colorimetric instrument has the potential of being a cost-effective way of determining patients likely to have Barrett's esophagus in the population.

Adenocarcinoma↗
PubMed2001

Predictors of progression in Barrett's esophagus II: baseline 17p (p53) loss of heterozygosity identifies a patient subset at increased risk for neoplastic progression.

OBJECTIVES: Most patients with Barrett's esophagus do not progress to cancer, but those who do seem to have markedly increased survival when cancers are detected at an early stage. Most surveillance programs are based on histological assessment of dysplasia, but dysplasia is subject to observer variation and transient diagnoses of dysplasia increase the cost of medical care. We have previously validated flow cytometric increased 4N fractions and aneuploidy as predictors of progression to cancer in Barrett's esophagus. However, multiple somatic genetic lesions develop during neoplastic progression in Barrett's esophagus, and it is likely that a panel of objective biomarkers will be required to manage the cancer risk optimally. METHODS: We prospectively evaluated endoscopic biopsies from 325 patients with Barrett's esophagus, 269 of whom had one or more follow-up endoscopies, by a robust platform for loss of heterozygosity (LOH) analysis, using baseline 17p (p53) LOH as a predictor and increased 4N, aneuploidy, high-grade dysplasia, and esophageal adenocarcinoma as outcomes. RESULTS: The prevalence of 17p (p53) LOH at baseline increased from 6% in negative for dysplasia to 57% in high-grade dysplasia (p < 0.001). Patients with 17p (p53) LOH had increased rates of progression to cancer (relative risk [RR] = 16, p < 0.001), high-grade dysplasia (RR = 3.6, p = 0.02), increased 4N (RR = 6.1, p < 0.001), and aneuploidy (RR = 7.5, p < 0.001). CONCLUSIONS: Patients with 17p (p53) LOH are at increased risk for progression to esophageal adenocarcinoma as well as high-grade dysplasia, increased 4N, and aneuploidy. 17p (p53) LOH is a predictor of progression in Barrett's esophagus that can be combined with a panel of other validated biomarkers for risk assessment as well as intermediate endpoints in prevention trials.

Adenocarcinoma↗
PubMed2001

Predictors of progression in Barrett's esophagus III: baseline flow cytometric variables.

OBJECTIVES: Barrett's esophagus develops in 5-10% of patients with gastroesophageal reflux disease and predisposes to esophageal adenocarcinoma. We have previously shown that a systematic baseline endoscopic biopsy protocol using flow cytometry with histology identifies subsets of patients with Barrett's esophagus at low and high risk for progression to cancer. In this report, we further examined cytometric variables to better define the characteristics that best enable DNA cytometry to help predict cancer outcome. METHODS: Patients were prospectively evaluated using a systematic endoscopic biopsy protocol, with baseline histological and flow cytometric measurements as predictors and with cancer as the outcome. RESULTS: A receiver operating curve analysis demonstrated that a 4N fraction cut point of 6% was optimal to discriminate cancer risk (relative risk [RR] = 11.7, 95% CI = 6.2-22). The 4N fractions of 6-15% were just as predictive of cancer as were fractions of >15%. We found that only aneuploid DNA contents of >2.7N were predictive of cancer (RR = 9.5, CI = 4.9-18), whereas those patients whose sole abnormality was an aneuploid population with DNA content of < or =2.7 had a low risk for progression. The presence of both 4N fraction of >6% and aneuploid DNA content of >2.7N was highly predictive of cancer (RR = 23, CI = 10-50). S phase was a predictor of cancer risk (RR = 2.3, CI = 1.2-4.4) but was not significant when high-grade dysplasia was accounted for. CONCLUSIONS: Flow cytometry is a useful adjunct to histology in assessing cancer risk in patients with Barrett's esophagus. Careful examination of cytometric variables revealed a better definition of those parameters that are most closely associated with increased cancer risk.

Barrett Esophagus↗
PubMed2001

Biomarkers in Barrett esophagus.

Barrett esophagus is a premalignant condition that may progress to adenocarcinoma. The risk of developing cancer has been estimated to be approximately 1 in 250 patient-years of observation; however, there appear to be subsets of patients at much higher risk. Risk stratification has previously been determined by histological identification of dysplasia. Several new biomarkers are being tested to help clinicians better determine the risk of cancer development. Although none of these biomarkers has been proven in a prospective study to predict the onset of cancer, they have been correlated with cancer development. Most of these are factors that have been associated with cancer development in other organs. These include assessment of cell proliferation, expression of cyclooxygenase 2, growth factors and oncogenes, secretory factors, cell cycle proteins, adhesion molecules, and aneuploidy and other genetic abnormalities. In addition to their role as potential cancer biomarkers, these factors have increasingly been reported as surrogate markers to monitor the effectiveness of conservative treatments for Barrett esophagus. In this article, biological markers are reviewed for their relevance in Barrett esophagus. Although most biological markers need to be evaluated further and, for most, prospective follow-up studies are lacking, at present abnormal ploidy status, P16 and P53 gene abnormalities, or allelic losses are the most extensively documented.

Barrett Esophagus↗
PubMed2000

Effect of segment length on risk for neoplastic progression in patients with Barrett esophagus.

BACKGROUND: The increased risk for esophageal adenocarcinoma associated with long-segment (> or =3 cm) Barrett esophagus is well recognized. Recent studies suggest that short-segment (<3 cm) Barrett esophagus is substantially more common; however, the risk for neoplastic progression in patients with this disorder is largely unknown. OBJECTIVE: To examine the relation between segment length and risk for aneuploidy and esophageal adenocarcinoma in patients with Barrett esophagus. DESIGN: Prospective cohort study. SETTING: University medical center in Seattle, Washington. PATIENTS: 309 patients with Barrett esophagus. MEASUREMENTS: Patients were monitored for progression to aneuploidy and adenocarcinoma by repeated endoscopy with biopsy for an average of 3.8 years. Cox proportional hazards analysis was used to calculate adjusted relative risks and 95% Cls. RESULTS: After adjustment for histologic diagnosis at study entry, segment length was not related to risk for cancer in the full cohort (P > 0.2 for trend). When patients with high-grade dysplasia at baseline were excluded, however, a nonsignificant trend was observed; based on a linear model, a 5-cm difference in segment length was associated with a 1.7-fold (95% CI, 0.8-fold to 3.8-fold) increase in cancer risk. Among all eligible patients, a 5-cm difference in segment length was associated with a small increase in the risk for aneuploidy (relative risk, 1.4 [CI, 1.0 to 2.1]; P = 0.06 for trend). A similar trend was observed among patients without high-grade dysplasia at baseline. CONCLUSIONS: The risk for esophageal adenocarcinoma in patients with short-segment Barrett esophagus was not substantially lower than that in patients with longer segments. Although our results suggest a small increase in risk for neoplastic progression with increasing segment length, additional follow-up is needed to determine whether the patterns of risk occurred by chance or represent true differences. Until more data are available, the frequency of endoscopic surveillance should be selected without regard to segment length.

Adenocarcinoma↗
PubMed2000

Impact of electrical cable insulating oil on the mineralisation of [1-(14)C]glucose in soil.

Subsurface high voltage electric cables are commonly insulated using dodecylbenzene in combination with mineral oil. This work assessed the impact of increasing concentrations of cable insulating oil (0-10% dry weight) on soil microbial respiration as determined by mineralisation of [1-(14)C]glucose (11 microg C g(-1) soil). Acute impact was assessed from 0 days to 21 days, and chronic impact was assessed after 300 days. This study found that cable insulating oil increased respiratory activity of soil microflora. The extent of impact was found to depend on both oil concentration and the length of oil-soil contact time. Following acute exposure (21-days oil-soil contact time), it was found that oil concentrations up to 1% promoted a significant (P<0.05) increase in the extent of [1-(14)C]glucose mineralisation to (14)CO(2) relative to the control. In contrast, higher concentrations of cable insulating oil (5% and 10%) promoted no significant (P0.05) increase in the extent of [1-(14)C]glucose mineralisation to (14)CO(2) relative to the control. Following chronic exposure (300-days oil-soil contact time), the extent of mineralisation was greater at all oil concentrations applied relative to the control. For oil concentrations up to and including 1%, there was a decrease in the extent of elevation in mineralisation relative to the values after 21-days exposure. At higher oil concentrations, namely 5% and 10%, the extent of elevation in mineralisation was comparable with that after 21-days oil-soil contact time. We suggest that the increase in mineralisation of glucose indicates that cable insulating oil is a readily available carbon source to the carbon-limited soil microflora.

Bacteria↗
PubMed2000

Bioavailability of persistent organic pollutants in soils and sediments--a perspective on mechanisms, consequences and assessment.

It has been observed that as soil-pollutant contact time increases, pollutant bioavailability and extractability decreases. This phenomenon has been termed 'ageing'. Decreased chemical extractability with increased soil-chemical contact time is evident where both 'harsh' techniques, e.g. dichloromethane Soxhlet extraction, and 'non-exhaustive' techniques, e.g. butanol shake extraction, have been used. It has also been observed that the amount of chemical extracted by these techniques varies considerably over time. Similarly, decreases in bioavailability with increased soil-pollutant contact time have been described in bacterial, earthworm and other organism studies. From these investigations, it has been shown that the fraction of pollutant determined to be bioavailable can vary between organisms. Thus, there is an immediate definition problem, what is bioavailability? Additionally, if bioavailability is to be assessed by a chemical means, which organisms should (or can) be mimicked by the extraction procedure? This review provides a background to the processes inherent to ageing, a discussion of its consequences on bioavailability and ends with some reflections on the appropriateness of chemical extraction techniques to mimic bioavailability

Journal Article↗
PubMed2000

Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays.

Most human cancers are characterized by genomic instability, the accumulation of multiple genetic alterations and allelic imbalance throughout the genome. Loss of heterozygosity (LOH) is a common form of allelic imbalance and the detection of LOH has been used to identify genomic regions that harbor tumor suppressor genes and to characterize tumor stages and progression. Here we describe the use of high-density oligonucleotide arrays for genome-wide scans for LOH and allelic imbalance in human tumors. The arrays contain redundant sets of probes for 600 genetic loci that are distributed across all human chromosomes. The arrays were used to detect allelic imbalance in two types of human tumors, and a subset of the results was confirmed using conventional gel-based methods. We also tested the ability to study heterogeneous cell populations and found that allelic imbalance can be detected in the presence of a substantial background of normal cells. The detection of LOH and other chromosomal changes using large numbers of single nucleotide polymorphism (SNP) markers should enable identification of patterns of allelic imbalance with potential prognostic and diagnostic utility.

Adenocarcinoma↗
PubMed2000

Safety of a systematic endoscopic biopsy protocol in patients with Barrett's esophagus.

OBJECTIVE: Widespread implementation of rigorous, systematic endoscopic biopsy protocols for patients with Barrett's esophagus may be hindered by concerns about their safety. This report describes the safety experience of a large series of patients with gastroesophageal reflux disease and Barrett's esophagus who underwent such procedures. METHODS: Patients in the Seattle Barrett's Esophagus Project undergo biopsy surveillance in a research-based clinical setting, using large channel endoscopes and "jumbo" biopsy forceps. After visual inspection, multiple biopsies are obtained from lesions and at 1- to 2-cm intervals throughout the Barrett's esophageal segment. RESULTS: From 1983 to 1997, 1,458 consecutive endoscopies were performed on 705 patients and 50,833 biopsies (average, 35; maximum, 120 per procedure) were taken. Procedures lasted from 15 to 90 min during which one to two biopsies were obtained per minute. Eleven patients experienced 18 significant adverse events, five of which led to overnight hospitalizations: two for bleeding attributed to concomitant esophageal stricture dilation; two for cardiac dysrhythmias; and one for respiratory arrest. Events managed in outpatient settings included chest pain during seven endoscopies (all accounted for by two patients), chest or epigastric pain developing after five endoscopies, and one tonsillar abrasion. All patients recovered completely, and no deaths, perforations, aspiration, or esophageal stricturing resulted from the procedures. CONCLUSIONS: A rigorous, systematic endoscopic biopsy protocol in patients with Barrett's esophagus does not produce esophageal perforation or bleeding when performed by an experienced team of physicians, nurses, and technicians.

Barrett Esophagus↗
PubMed2000

Predictors of progression to cancer in Barrett's esophagus: baseline histology and flow cytometry identify low- and high-risk patient subsets.

OBJECTIVE: Barrett's esophagus develops in 5-20% of patients with gastroesophageal reflux disease and predisposes to esophageal adenocarcinoma. The value of endoscopic biopsy surveillance is questioned because most patients do not develop cancer. Furthermore, observer variation in histological diagnosis makes validation of surveillance guidelines difficult because varying histological interpretations may lead to different estimated rates of progression. Thus, objective biomarkers need to be validated for use with histology to stratify patients according to their risk for progression to cancer. METHODS: We prospectively evaluated patients using a systematic endoscopic biopsy protocol with baseline histological and flow cytometric abnormalities as predictors and cancer as the outcome. RESULTS: Among patients with negative, indefinite, or low-grade dysplasia, those with neither aneuploidy nor increased 4N fractions had a 0% 5-yr cumulative cancer incidence compared with 28% for those with either aneuploidy or increased 4N. Patients with baseline increased 4N, aneuploidy, and high-grade dysplasia had 5-yr cancer incidences of 56%, 43%, and 59%, respectively. Aneuploidy, increased 4N, or HGD were detected at baseline in all 35 patients who developed cancer within 5 yr. CONCLUSIONS: A systematic baseline endoscopic biopsy protocol using histology and flow cytometry identifies subsets of patients with Barrett's esophagus at low and high risk for progression to cancer. Patients whose baseline biopsies are negative, indefinite, or low-grade displasia without increased 4N or aneuploidy may have surveillance deferred for up to 5 yr. Patients with cytometric abnormalities merit more frequent surveillance, and management of high-grade dysplasia can be individualized.

Adult↗