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Biomedical subjects

A Botha

Publications and source records attributed to A Botha.

At least 19 recordsLinked to original sources
PubMed2007

Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils.

AIM: To establish a rapid, improved soil environmental DNA extraction and purification protocol. METHODS AND RESULTS: Three different soil DNA isolation and four purification strategies were compared on different soil samples with variable rates of success. Bead beating extraction gave significantly higher DNA yields than microwave-based and liquid nitrogen grinding DNA extraction methods. The inclusion of soil washing prior to cell lysis decreased the amount of purification steps required. Although these soil types differed, polyvinylpolypyrrolidone (PVPP)-sepharose 2B column elution was sufficient for all three samples, yielding DNA pure enough for successful application in molecular studies. One soil sample retained 80% of the initial DNA after successful purification. CONCLUSIONS: Optimization of a purification protocol confirmed that only a combination of previously described methods proved sufficient in yielding pure environmental DNA from humic-rich soils. Total processing time for DNA extraction and subsequent purification from multiple samples was considerably more rapid than the previously described methods. SIGNIFICANCE AND IMPACT OF THE STUDY: This study developed a new optimized soil DNA extraction and purification protocol that is suitable for different environmental sources that are rich in humic acid content.

Bacillus↗
PubMed2006

Microbial exopolymers link predator and prey in a model yeast biofilm system.

Protistan grazing on biofilms is potentially an important conduit enabling energy flow between microbial trophic levels. Contrary to the widely held assumption that protistan feeding primarily involves ingestion of biofilm cells, with negative consequences for the biofilm, this study demonstrated preferential grazing on the noncellular biofilm matrix by a ciliate, with selective ingestion of yeast and bacterial cells of planktonic origin over attached and biofilm-derived planktonic cells. Introducing a ciliate to two biofilm-forming Cryptococcus species, as well as two bacterial species in a model biofilm system, fluorescent probes were applied to determine ingestion of cellular and noncellular biofilm fractions. Fluoromicroscopy, as well as photometric quantification, confirmed that protistan grazing enhanced yeast biofilm metabolism, and an increase in biofilm biomass and viability. We propose that the extracellular polymeric matrix of biofilms may act as an interface regulating interaction between predator and prey, while serving as source of nutrients and energy for protists.

Animals↗
PubMed2006

Neoadjuvant chemotherapy for locally advanced carcinoma of the lower oesophagus and oesophago-gastric junction.

AIMS: To evaluate a single unit's experience with neoadjuvant chemotherapy for treating locally advanced non-metastatic initially resectable and unresectable oesophago-gastric cancer. METHODS: The medical records of all patients with either locally advanced carcinoma of the lower oesophagus or cardia treated with neoadjuvant chemotherapy between August 1999 and January 2003 were reviewed. RESULTS: Sixty-four patients with initially resectable tumours (T2-3 or N+) and 38 patients with initially unresectable tumours (T4 or M1a) received neoadjuvant chemotherapy (83% combination Epirubicin, Cisplatin and 5-Fluorouracil). Symptomatic grade III/IV toxicity was observed in 33% of patients. Chemotherapy was not completed in 20 patients because of death (5.9%) and inadequate tumour response/toxicity (13.7%). Forty-three patients (67.3%) with initially resectable tumours and 19 patients (50%) with initially unresectable tumours underwent surgery. CONCLUSIONS: Chemotherapy in this study was associated with appreciable toxicity. Patients with initially unresectable locally advanced disease can be downstaged with neoadjuvant chemotherapy.

Adenocarcinoma↗
PubMed2005

Response of the microbial community to copper oxychloride in acidic sandy loam soil.

AIMS: Determining the response of different microbial parameters to copper oxychloride in acidic sandy loam soil samples using cultivation-dependent and direct microscopic techniques. METHODS AND RESULTS: Culturable microbial populations were monitored for 245 days in a series of soil microcosms spiked with different copper oxychloride concentrations. Microbial populations responded differently to additional Cu. Protistan numbers and soil metabolic potential decreased. Experiments with more soil samples revealed that metabolic potential was not significantly affected by < or =100 mg kg(-1) additional Cu. However, a negative impact on protista was noted in soil containing only 15 mg kg(-1) EDTA-extractable Cu. The negative impact on protistan numbers was less severe in soils with a higher phosphorous and zinc content. CONCLUSIONS: Bacterial populations responded differently, and protista were most sensitive to elevated Cu levels. Protistan numbers in soil from uncultivated land were higher and seemed to be more sensitive to additional Cu than the numbers of these organisms in soil originating from cultivated land. SIGNIFICANCE AND IMPACT OF THE STUDY: Protistan sensitivity to small increases in Cu levels demonstrates the vulnerability of the soil ecosystem to Cu perturbations, especially when the importance of protista as link in the flow of energy between trophic levels is considered.

Animals↗
PubMed2003

Shifts in community composition provide a mechanism for maintenance of activity of soil yeasts in the presence of elevated copper levels.

Soil dilution plates were prepared from different soil samples using a solid synthetic selective medium containing (i). glucose as carbon source, (ii). thymine as nitrogen source, (iii). vitamins, (iv). minerals, and (v). chloramphenicol as antibacterial agent. Using the Diazonium Blue B colour reaction, it was found that both ascomycetous and basidiomycetous yeasts were able to grow on this medium. Subsequently, the medium was used to enumerate yeasts in soil microcosms prepared from four different soil samples, which were experimentally treated with the fungicide copper oxychloride, resulting in copper (Cu) concentrations of up to 1000 ppm. The selective medium supplemented with 32 ppm of Cu was used to enumerate Cu-resistant yeasts in the microcosms. The results showed that the addition of Cu at concentrations >or=approximately 1000 ppm did not have a significant effect on total number of yeasts in the soil. Furthermore, it was found that Cu-resistant yeasts were present in all the soil samples, regardless of the amount of Cu that the soil was challenged with. At the end of the incubation period, yeasts in the microcosms with zero and approximately 1000 ppm of additional Cu were enumerated, isolated, and identified with sequence analyses of the D1/D2 600-650 bp region of the large subunit of ribosomal DNA. Hymenomycetous species dominated in the control soil, while higher numbers of the urediniomycetous species were found in the soil that received Cu. These observations suggest that urediniomycetous yeasts may play an important role in re-establishing overall microbial activity in soils, following perturbations, such as the addition of Cu-based fungicides.

Copper↗
PubMed2002

Possible absence of Helicobacter pylori in the early stages of duodenal ulceration.

BACKGROUND: Helicobacter pylori is thought to be a cause of duodenal ulceration, but there is some evidence that it is found less often in early than in later disease. AIM: To assess the presence of H. pylori in patients undergoing endoscopy for dyspepsia, with respect to their duration of symptoms. DESIGN: Retrospective case note review. METHODS: Patients were categorized as having a history greater or less than 6 months, and as H. pylori-positive or -negative, using biopsy rapid urease, culture and PCR tests. RESULTS: Thirty-two duodenal ulcer patients with a history >6 months were all H. pylori-positive according to the PCR test; the five with a shorter history were H. pylori-negative. No patient H. pylori-negative by PCR was positive by the other tests. DISCUSSION: H. pylori was (at least) less commonly present before 6 months. It is possible that H. pylori, although nearly always present after 6 months, is not present at the onset of the disease. Confirmation of this finding would imply that infection with the organism is not the cause of duodenal ulceration, but a factor producing recurrence and chronicity.

Duodenal Ulcer↗
PubMed2002

Morphological and histochemical observations of the organic components of ostrich eggshell.

The organic component of the avian eggshell can be divided into 3 portions, the shell membranes, the matrix and the cuticle. These have been well characterised in the chicken but little has been published with regard to the ostrich (Struthio camelus). A number of recent studies have indicated that the cause of intra-shell embryonic deaths in the ostrich is similar to intra-shell embryonic deaths that occur in the chicken. These deaths in the chicken are associated with the loss of or damage to the waxy cuticle and other organic components of the eggshell, which is reported to be absent in the ostrich eggshell. In this study, preliminary morphological and histochemical analyses, at the level of the light and electron microscope, have characterised the various organic components of the ostrich eggshell. The results of the histochemical and electron microscopical analyses suggest that there may only be 1 shell membrane in this species, which could play a major role in the limitation of bacterial penetration to the embryonic chamber The shell membrane has a distinct elemental profile as determined by EDS analysis. The matrix is shown to decrease in mesh size from the mammillary layer to the vertical crystal layer. The closer packing of the mesh may indicate the presence of a morphologically discernible termination signal to calcification or the remnants of an evolutionary calcified cuticle. The matrix of the pores may also form a defensive barrier against bacterial invasion, which could be damaged as a result of dipping the eggs before incubation.

Animals↗
PubMed2001

Bioprospecting for novel oxylipins in fungi: the presence of 3-hydroxy oxylipins in Pilobolus.

As previously found in various members of the Mucorales, 3-hydroxy oxylipins in Mucor genevensis are associated with the sporangia, i.e. mainly the columella structure and between aggregating sporangiospores. To determine if this phenomenon is also true in distantly related members, the mucoralean fungus Pilobolus was examined. This fungus is characterized by relatively large sub sporangial-columella structures which actively eject sporangia in a sticky liquid for attachment onto herbage surrounding its growth medium--in this case horse dung. Strikingly, this fungus produced a novel oxylipin i.e. a 3-hydroxy monounsaturated fatty acid, possibly a nonenoic acid, which is mainly associated with the sub sporangial-columella structure and aggregating sporangiospores. The specificity of the antibody against 3-hydroxy oxylipins used in immunofluorescence mapping of the mucoralean fungi, was further confirmed in the yeast, Saccharomycopsis malanga which produces 3-hydroxy palmitate in crystal form. These crystals occur between aggregating yeast cells. On the basis of the available data, we hypothesize that 3-hydroxy oxylipins probably function as adhesives, attaching fungal cells to each other or to other surfaces through entropic based hydrophobic forces and/or hydrogen bonds.

Fatty Acids, Unsaturated↗
PubMed2000

A novel oxylipin-associated 'ghosting' phenomenon in yeast flocculation.

Research on the distribution of oxylipins (3-hydroxy fatty acids) in flocculant strains of the yeast Saccharomyces cerevisiae led to the uncovering of a novel 'ghosting' phenomenon observed during assumed lectin-mediated aggregation. We found that intracellular oxylipin-containing osmiophilic layers migrate through yeast cell walls in a 'ghostlike' fashion without visually affecting the cell wall structure or the layers. This migration resulted in the binding of these layers to cell walls of adjacent cells. Consequently, 'ghosting' seems a prerequisite for flocculation to occur. However, 'ghosting' alone may not be sufficient to ensure flocculation.

Cell Wall↗
PubMed2000

Mapping the distribution of 3-hydroxylipins in the Mucorales using immunofluorescence microscopy.

The distribution of endogenous 3-hydroxylipins (3-OH oxylipins) in representatives of the Mucorales was mapped using immunofluorescence microscopy. Strains of each of the following genera were examined: Absidia, Actinomucor, Cunninghamella, Mortierella (subgenus Micromucor), Mortierella (subgenus Mortierella), Mucor and Rhizomucor. Immunofluorescence microscopy was carried out using an antibody that was raised against 3R-hydroxy-5Z,8Z, 11 Z, 14Z-eicosatetraenoic acid (3R-HETE), which cross-reacts with other 3-OH oxylipins. Subsequently, the occurrence and distribution of the antibody on the various reproductive stages of each fungus was noted. In Absidia, Actinomucor, Mortierella (subgenus Micromucor), Mucor and Rhizomucor, 3-OH oxylipins were found to be associated with the columellae and/or wall of the sporangium. In the representative of Cunninghamella, the 3-OH oxylipins were associated with the single-spored sporangiola. No 3-OH oxylipins were detected in the strains representing Mortierella (subgenus Mortierella).

Fatty Acids↗
PubMed1999

An isolation procedure for arachidonic acid producing Mortierella species.

Malt extract agar and an incubation temperature of 5 degrees C were used to selectively isolate representatives of the genus Mortierella from soil. Fungi in a soil sample from mountain grassland able to grow under these conditions, amounted to a total of 2640 colony forming units per gram soil. Circa 94% of the total fungal isolates represented Mortierella subgenus Mortierella. The rest of the colony-forming units consisted of Mucor isolates (6.0%) and higher fungi (1.5%). All the Mortierella isolates produced arachidonic acid.

Arachidonic Acid↗
PubMed1998

Oxylipin formation in fungi: biotransformation of arachidonic acid to 3-hydroxy-5,8-tetradecadienoic acid by Mucor genevensis.

The soil fungus Mucor genevensis was shown to convert exogenous arachidonic acid to the oxylipin 3-hydroxy-5Z,8Z-tetradecadienoic acid (3-HTDE) as determined by gas chromatography/mass spectrometry. This metabolite was only found in the aqueous supernatant together with free linoleic acid, but not in the final fungal biomass. In contrast, the corresponding primary arachidonic acid metabolite (3R)-hydroxy-(5Z,8Z,11Z,14Z)-eicosatetraenoic acid (3-HETE), which has been earlier shown to be produced by the yeast Dipodascopsis uninucleata, could not be detected. These observations may be plausibly explained by a retroconversion by M. genevensis of arachidonic acid to linoleic acid before the latter is metabolised to 3-HTDE.

Arachidonic Acid↗
PubMed1998

Helicobacter pylori: the mouth, stomach, and gut axis.

The aim of this study was to identify the natural reservoir and route of transmission of Helicobacter pylori infection. Two hundred eight (208) dyspeptic patients (114 males, 94 females; peak age of cohort, 50-59.9) were recruited. Specimens were collected from saliva, supra- and subgingival dental plaque, tongue scrapings, and oropharyngeal swabs. At subsequent endoscopy, gastric antral biopsy was performed for the rapid urease test (RUT), microbiological culture, and, in some patients, histology. Gastric juice samples were aspirated, and in 50 patients duodenal aspirate was collected. Polymerase chain reaction (PCR) with primers targeted to the 16S rRNA sequence of H. pylori was also employed for each of the specimens. In those patients where H. pylori was detected from multiple sites (dental plaque, gastric juice, gastric biopsy, and duodenal aspirate), restriction endonuclease digestion with Hae III was performed to determine if they were epidemiologically linked. The results indicated that 15/208 patients (7%) tested positively for H. pylori by PCR in dental plaque; only 2 samples were positive by culture. In none of the other oral sites sampled was H. pylori detected by any test used in the study. Gastric juice and gastric biopsy specimens from 36/ 208 patients (17%) and 114/208 patients (55%), respectively, were positive by PCR. Duodenal aspirate from 6/50 patients (12%) also tested positively by PCR. All specimens tested by restriction endonuclease digestion with Hae III (15/15 patients) were positive in both antral biopsy and gastric juice specimens, as well as 5 specimens from the duodenal aspirate. Four of the dental plaque strains had restriction patterns similar to those of the stomach and duodenal sites, providing evidence that these sites were infected with the same strain of H. pylori. In conclusion, the results suggest that H. pylori selects the gastric mucosa as its preferred site. The detection in dental plaque could indicate that the oral cavity may act as a reservoir or sanctuary for the organism. Whether H. pylori is a resident or transient oral microorganism is still unclear, although it is more likely to be transient in nature.

Bacterial Typing Techniques↗
PubMed1997

Production of 3R-hydroxy-polyenoic fatty acids by the yeast Dipodascopsis uninucleata.

Various fatty acids were fed to the yeast Dipodascopsis uninucleata UOFS Y 128, and the extracted samples were analyzed for the accumulation of 3-hydroxy metabolites with the help of electron impact gas chromatography-mass spectrometry. Fatty acids containing of 5Z,8Z-diene system (5Z,8Z,11Z-eicosatrienoic, 5Z,8Z,11Z,14Z-eicosatetraenoic, and 5Z,8Z,11Z,14Z,17Z-eicosapentaenoic acids) yielded the corresponding 3-hydroxy-all-Z-eicosapolyenoic acids. Moreover, linoleic acid (9Z,12Z-octadecadienoic acid) and 11Z,14Z,17Z-eicosatrienoic acid were converted to the 3-hydorxylated metabolites of shorter chain length, e,g., 3-hydroxy-5Z,8Z-tetradecadienoic acid and 3-hydroxy-5Z,8Z,11Z-tetradecatrienoic acid, respectively. In contrast, no accumulation of a 3-hydroxy metabolite was observed with oleic acid (9Z-octadecenoic acid), linolelaidic acid (9E,12E-octadecadienoic acid), gamma-linolenic acid (6Z,9Z,12Z-octadecatrienoic acid), and eicosanoic acid as substrate. These findings pinpoint that the 3-hydroxylation of a fatty acid in Dipodascopsis uninucleata requires a 5Z,8Z-diene system either directly or following initial incomplete beta-oxidation. Following analysis of the enantiomer composition, the arachidonic acid metabolite was identified as 3R-hydroxy-5Z,8Z,11Z,14Z-eicosatetraenoic acid, which rules out a normal beta-oxidation as biosynthetic route to this new class of oxylipins.

Arachidonic Acids↗