Biomedical subjects

Kerry A Kinney

Publications and source records attributed to Kerry A Kinney.

6 recordsLinked to original sources

PubMed2006

Quantification of homogentisate-1,2-dioxygenase expression in a fungus degrading ethylbenzene.

A quantitative real time reverse transcription polymerase chain reaction (qRT-PCR) assay was utilized to quantify the expression of ElHDO in the fungus Exophiala lecanii-corni during the biodegradation of ethylbenzene and other volatile organic pollutants. The assay was applied to measure the impact of pollutant mixtures on ElHDO expression relative to that of a housekeeping gene (18S rRNA). Three compounds were tested in mixtures with ethylbenzene: methyl propyl ketone, phenylacetate and o-xylene. These chemicals repressed, induced, or had no effect on ethylbenzene degradation, respectively. The results demonstrate that the gene target expression value (T(N)) is a useful parameter for evaluating the effect of pollutant mixtures on gene expression. T(N) was found to reflect macroscopic changes in ethylbenzene utilization rates although these two parameters were not related in a linear fashion for all compounds. The assay was log-linear over 5 orders of magnitude of RNA concentration and reproducible between samples (the largest T(N) standard deviation was 20%). The comparative qRT-PCR assay used in this research represents a viable alternative to absolute quantification methods to monitor in situ fungal gene expression in natural and engineered environmental systems.

Benzene Derivatives↗

PubMed2005

Microbial response and elimination capacity in biofilters subjected to high toluene loadings.

Elimination capacity (EC) is frequently used as a performance and design criterion for vapor-phase biofilters without further verification of the microbial quantity and activity. This study was conducted to investigate how biofilters respond to high pollutant loadings and ultimately how this affects the EC of the biofilter. Two identical laboratory-scale biofilters were maintained at an initial toluene loading rate of 46 g m-3 h-1 for a period of 24 days. After the initial biofilm development stage, the loading rates were increased to 91 g m-3 h-1 and 137 g m-3 h-1, respectively. Following a short period of pseudo-steady state, toluene removal efficiencies rapidly declined in both biofilters, with a concurrent decline in both critical and maximum ECs. The decline was mainly due to deterioration in the biodegradation activity of the biofilm and a decline in the toluene-degrading bacterial population within the biofilm phase. The findings imply that high toluene loadings accelerated the deterioration in overall performance due to a rapid accumulation of inactive biomass. As a result, care must be used when relying on EC values for biofilter design and operational purposes, since the values do not appropriately reflect the temporal changes in biodegradation activity and active biomass quantities that can occur in biofilters subjected to high inlet loadings.

Air Pollutants↗

PubMed2005

Identification of a homogentisate-1,2-dioxygenase gene in the fungus Exophiala lecanii-corni: analysis and implications.

Exophiala lecanii-corni is a dimorphic fungus capable of degrading several volatile organic compounds (VOCs) including ethylbenzene, which has been classified as a hazardous air pollutant by the Environmental Protection Agency. In contrast to bacterial species, little is known about the mechanisms of fungal degradation of VOCs. The results described herein suggest a potential pathway for ethylbenzene degradation in E. lecanii-corni via styrene, phenylacetate and homogentisate. Consistent with this proposed pathway, a full-length homogentisate-1,2-dioxygenase gene (ElHDO) has been identified, cloned and sequenced. The nucleotide sequence of ElHDO consists of a 1,452-bp open reading frame encoding a protein with 484 amino acids. The expression of the gene product increases when grown on ethylbenzene, further suggesting that it could be involved in ethylbenzene degradation and may be responsible for the aromatic ring cleavage reaction. In addition, a 907-bp fragment isolated upstream from this gene shares 78% sequence identity at the amino acid level with the amino acid sequences of two fungal phenylacetate hydroxylase genes. This observation suggests that the genes responsible for ethylbenzene degradation may be clustered. This research constitutes the first step towards a better understanding of ethylbenzene degradation in E. lecanii-corni.

Amino Acid Sequence↗

PubMed2004

Characterization of two polyketide synthase genes in Exophiala lecanii-corni, a melanized fungus with bioremediation potential.

Exophiala lecanii-corni has significant bioremediation potential because it can degrade a wide range of volatile organic compounds. In order to identify sites for the insertion of genes that might enhance this potential, a genetic analysis of E. lecanii-corni was undertaken. Two polyketide synthase genes, ElPKS1 and ElPKS2, have now been discovered by a PCR-based strategy. ElPKS1 was isolated by a marker rescue technique. The nucleotide sequence of ElPKS1 consists of a 6576-bp open reading frame encoding a protein with 2192 amino acids, which was interrupted by a 60-bp intron near the 5' end and a 54-bp intron near the 3' end. Sequence analysis, results from disruption experiments, and physiological tests showed that ElPKS1 encoded a polyketide synthase required for melanin biosynthesis. Since ElPKS1 is non-essential, it is a desirable bioengineering target site for the insertion of native and foreign genes. The successful expression of these genes could enhance the bioremediation capability of the organism. ElPKS2 was cloned by colony hybridization screening of a partial genomic library with an ElPKS2 PCR product. ElPKS2 had a 6465-bp open reading frame that encoded 2155 amino acids and had introns of 56, 67, 54, and 71 bp. Although sequence analysis of the derived protein of ElPKS2 confirmed the polyketide synthase nature of its protein product, the function of that product remains unclear.

Amino Acid Sequence↗

PubMed2003

Nitrogen utilization in a vapor-phase biofilter.

The effect of media nitrogen levels on biofilter performance was investigated in a lab-scale biofilter treating toluene and p-xylene. Nitrogen utilization rates and the quantity of nitrogen recycled to meet microbial demand in the biofilm were estimated using a nitrogen balance approach. Experimental data imply that overall biofilter performance was a strong function of normalized nitrogen levels in the synthetic media. The biodegradation of p-xylene was found to be more sensitive to media nitrogen levels than was the degradation of toluene. However, increasing the nitrogen supply improved both toluene (>99%) and p-xylene removal efficiencies (>90%). Nitrogen balance calculations indicate that substantial recycling of nitrogen occurred in the biofilm even under nitrogen-rich conditions. The fraction of nitrogen demand met by recycling nitrogen increased when the external supply of nitrogen was terminated, and the biofilm became nitrogen limited. However, to avoid severe nitrogen limitation conditions, an external nitrogen source must be provided to sustain high pollutant removals in the biofilter.

Air Pollution↗

PubMed2002

A model to predict long-term performance of vapor-phase bioreactors: a cellular automaton approach.

A novel numerical model was constructed to predict performance of vapor-phase bioreactors (VPBs) operated over extended periods. This model incorporates two unique features to simulate changes in pollutant removal efficiency and biomass accumulation: (1) total biomass is divided into two microbial components, active and inactive biomass, and (2) biomass growth and biofilm thickness changes are simulated by means of a cellular automaton (CA) approach. The CA approach, a differential-discrete algorithm, numerically allows the excess quantity of biomass in each numerical element to move toward the biofilm surface as biomass accumulates. One set of experimental bioreactor data was used to estimate unknown model parameters. A 90-day simulation using the estimated parameters agreed with pollutant removal and biomass accumulation profiles determined experimentally. Four additional model simulations using the same estimated model parameters were generally consistent with experimental data collected from a series of toluene-degrading VPBs operated over a range of conditions. Model predictions imply that the decline in bioreactor performance observed over extended operation was caused by a decline in the active biomass fraction and a decrease in the biofilm specific surface area. This CA model provides insight into biomass accumulation during complex bioreactor operation and improves our capability to predict long-term VPB performance.

Biofilms↗