Biomedical subjects

Andrew C Singer

Publications and source records attributed to Andrew C Singer.

13 recordsLinked to original sources

PubMed2006

Nutrient amendments in soil DNA stable isotope probing experiments reduce the observed methanotroph diversity.

Stable isotope probing (SIP) can be used to analyze the active bacterial populations involved in a process by incorporating 13C-labeled substrate into cellular components such as DNA. Relatively long incubation times are often used with laboratory microcosms in order to incorporate sufficient 13C into the DNA of the target organisms. Addition of nutrients can be used to accelerate the processes. However, unnatural concentrations of nutrients may artificially change bacterial diversity and activity. In this study, methanotroph activity and diversity in soil was examined during the consumption of 13CH4 with three DNA-SIP experiments, using microcosms with natural field soil water conditions, the addition of water, and the addition of mineral salts solution. Methanotroph population diversity was studied by targeting 16S rRNA and pmoA genes. Clone library analyses, denaturing gradient gel electrophoresis fingerprinting, and pmoA microarray hybridization analyses were carried out. Most methanotroph diversity (type I and type II methanotrophs) was observed in non-amended SIP microcosms. Although this treatment probably best reflected the in situ environmental conditions, one major disadvantage of this incubation was that the incorporation of 13CH4 was slow and some cross-feeding of 13C occurred, thereby leading to labeling of nonmethanotroph microorganisms. Conversely, microcosms supplemented with mineral salts medium exhibited rapid consumption of 13CH4, resulting in the labeling of a less diverse population of only type I methanotrophs. DNA-SIP incubations using water-amended microcosms yielded faster incorporation of 13C into active methanotrophs while avoiding the cross-feeding of 13C.

Carbon Isotopes↗

PubMed2006

Phytoremediation of mixed-contaminated soil using the hyperaccumulator plant Alyssum lesbiacum: evidence of histidine as a measure of phytoextractable nickel.

In this study we examine the effects of polycyclic aromatic hydrocarbons (PAHs) on the ability of the hyperaccumulator plant Alyssum lesbiacum to phytoextract nickel from co-contaminated soil. Planted and unplanted mesocosms containing the contaminated soils were repeatedly amended with sorbitan trioleate, salicylic acid and histidine in various combinations to enhance the degradation of two PAHs (phenanthrene and chrysene) and increase nickel phytoextraction. Plant growth was negatively affected by PAHs; however, there was no significant effect on the phytoextraction of Ni per unit biomass of shoot. Exogenous histidine did not increase nickel phytoextraction, but the histidine-extractable fraction of soil nickel showed a high correlation with phytoextractable nickel. These results indicate that Alyssum lesbiacum might be effective in phytoextracting nickel from marginally PAH-contaminated soils. In addition, we provide evidence for the broader applicability of histidine for quantifying and predicting Ni phytoavailability in soils.

Biodegradation, Environmental↗

PubMed2006

Quantitative in situ assay of salicylic acid in tobacco leaves using a genetically modified biosensor strain of Acinetobacter sp. ADP1.

Salicylic acid (SA) plays important roles in plants, most notably in the induction of systemic acquired resistance (SAR) against pathogens. A non-destructive in situ assay for SA would provide new insights into the functions of SA in SAR and other SA-regulated phenomena. We assessed a genetically engineered strain of Acinetobacter sp. ADP1, which proportionally produces bioluminescence in response to salicylates including SA and methylsalicylate, as a reporter for salicylate accumulation in the apoplast of plant leaves. SA was measured quantitatively in situ in NN genotype tobacco (Nicotiana tabacum L. cv Xanthi-nc) leaves inoculated with tobacco mosaic virus (TMV). The biosensor revealed accumulation of apoplastic SA before the visible appearance of hypersensitive response (HR) lesions. When the biosensor was infiltrated into TMV-inoculated leaves displaying HR lesions at 90 and 168 h post-inoculation, salicylate accumulation was detected predominantly in tissues surrounding the lesions and in veins adjacent to HR lesions. These images are consistent with previous data demonstrating that SA accumulation occurs prior to and following the onset of visible HR lesions. We also used the biosensor to observe apoplastic SA accumulation in tobacco leaves inoculated with virulent and HR-eliciting strains of the bacterial plant pathogen Pseudomonas syringae. The work demonstrates that the Acinetobacter sp. ADP1 biosensor is a useful new tool to non-destructively assay salicylates in situ and to map their spatial distribution in plant tissues.

Acinetobacter↗

PubMed2005

Insight into pollutant bioavailability and toxicity using Raman confocal microscopy.

Raman confocal microscopy was used to discriminate between cultures of Burkholderia xenovorans LB400 exposed to four different common environmental pollutants: phenanthrene, dodecane, 3-chlorobiphenyl and pentachlorophenol. Evidence is presented for the application of Raman spectroscopy as a bioassay for pollutant bioavailability and toxicity.

Alkanes↗

PubMed2005

Perspectives and vision for strain selection in bioaugmentation.

Notwithstanding the phenomenally large and ever-increasing resource of pollutant-degrading microbial isolates in laboratories around the globe, inoculum survival remains the 'Achilles' heel' for bioaugmentation of contaminated land. Considerable effort has been invested into inoculum strain selection to facilitate pollutant biodegradation, ranging from the isolation of 'superbugs,' which are microorganisms highly resilient to environmental stresses, harboring catabolically superior pollutant-degrading enzymes, to the other extreme in 'priming', where pollutant degradation is carried out through the addition of soil enriched with an undefined consortium of pollutant-degrading microorganisms.

Bacteria, Aerobic↗

PubMed2005

Bioaugmentation for bioremediation: the challenge of strain selection.

Despite its long-term use in bioremediation, bioaugmentation of contaminated sites with microbial cells continues to be a source of controversy within environmental microbiology. This largely results from its notoriously unreliable performance record. In this article, we argue that the unpredictable nature of the approach comes from the initial strain selection step. Up until now, this has been dictated by the search for catabolically competent microorganisms, with little or no consideration given to other essential features that are required to be functionally active and persistent in target habitats. We describe how technical advances in molecular biology and analytical chemistry, now enable assessments of the functional diversity and spatial distribution of microbial communities to be made in situ. These advances now enable microbial populations, targeted for exploitation, to be differentiated to the cell level, an advance that is bound to improve microbial selection and exploitation. We argue that this information-based approach is already proving to be more effective than the traditional 'black-box' approach of strain selection. The future perspectives and opportunities for improving selection of effective microbial strains for bioaugmentation are also discussed.

Bacteria↗

PubMed2005

Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate.

Acinetobacter sp. ADP1 is a common soil-associated bacterium with high natural competency, allowing it to efficiently integrate foreign DNA fragments into its chromosome. This property was exploited to engineer salicylate-inducible luxCDABE and green fluorescent protein (GFP) variants of Acinetobacter sp. ADP1. Specifically, Acinetobacter sp. ADPWH_lux displayed the higher sensitivity when comparing the two variants (minimum detection c. 0.5-1 microM salicylate) and a faster turnover of the lux marker gene, making it suitable for whole-cell luminescence assays of salicylate concentration. In contrast, the longer maturation and turnover times of the GFP protein make the Acinetobacter sp. ADPWH_gfp variant more suited to applications involving whole-cell imaging of the presence of salicylate. The sensitivity of the luxCDABE variant was demonstrated by assaying salicylate production in naphthalene-degrading cultures. Assays using ADPWH_lux specifically mapped the kinetics of salicylate production from naphthalene and were similar to that observed by high-performance liquid chromatography (HPLC) data. However, ADPWH_lux exhibited the higher sensitivity, when compared with HPLC, for detecting salicylate production during the first 24 h of naphthalene metabolism. These data demonstrate that the engineered Acinetobacter variants have significant potential for salicylate detection strategies in laboratory and field studies, especially in scenarios where genetic stability of the construct is required for in situ monitoring.

Acinetobacter↗

PubMed2004

The tritrophic trinity: a source of pollutant-degrading enzymes and its implications for phytoremediation.

Barring bioavailability and nutritional limitations, virtually all organic anthropogenic chemicals can be naturally biodegraded. It is to this phenomenon we owe thanks to the long established 'tritrophic trinity' of microbe-plant-insect interactions. Over hundreds of millennia these organisms have coevolved, producing hundreds of thousands of different chemicals that are used to attract, defend, antagonize, monitor and misdirect one another. In comparison, the numbers of truly novel chemicals of anthropogenic origin are negligible. It is only now that we are beginning to appreciate the fortuitous evolution of xenobiotic-degrading enzymes from these interactions. We argue that success in phytoremediation can be hastened through understanding the structure, sources, uses and targets of these secondary metabolites. Owing to recent developments in molecular biology, particularly stable isotope probing, we eagerly anticipate highly significant insights into trophic interactions, particularly in the rhizosphere, providing phytoremediation with a solid mechanistic understanding.

Animals↗

PubMed2004

Factor graph methods for three-dimensional shape reconstruction as applied to LIDAR imaging.

Two methods based on factor graphs for reconstructing the three-dimensional (3D) shape of an object from a series of two-dimensional images are presented. First, a factor graph model is developed for image segmentation to obtain silhouettes from raw images; the shape-from-silhouette technique is then applied to yield the 3D reconstruction of the object. The second method presented is a direct 3D reconstruction of the object using a factor graph model for the voxels of the reconstruction. While both methods should be applicable to a variety of input data types, they will be developed and demonstrated for a particular application involving the LIDAR imaging of a submerged target. Results from simulations and from real LIDAR data are shown that detail the performance of the methods.

Journal Article↗

PubMed2003

Secondary plant metabolites in phytoremediation and biotransformation.

For millennia, secondary plant metabolites have antagonized microorganisms, insects and humans alike, ultimately generating a complex and dynamic mixture of facultative and obligate interactions from symbioses to pathogenicity. Secondary plant metabolites have an important role in developing the myriad of organic pollutant-degrading enzymes found in nature. The link between secondary plant metabolites and enzymatic diversity has yet to be exploited, with potential applications in fields as varied as pest management, bioremediation and fine chemical production.

Biodegradation, Environmental↗

PubMed2003

Impact of the plant rhizosphere and augmentation on remediation of polychlorinated biphenyl contaminated soil.

This study investigated the interactive effects of bioaugmentation, biostimulation, and the rhizosphere during remediation of Aroclor 1242-contaminated soil. Treatments were repeatedly augmented with polychlorinated bipheny (PCB)-degrading bacteria, inducers (carvone and salicylic acid), surfactant (sorbitan trioleate), minimal salts medium in a 20-cm high soil column, or a combination of these elements. Soils containing a single Brassica nigra plant achieved 61% PCB removal in the 0 to 2 and 2 to 6 cm depths after 9 weeks of bioaugmentation, whereas only 43 and 14% PCB removal, respectively, was achieved in unplanted controls. Gas diffusion coefficients of 13.0 and 5.0 x 10(-7) m2 s(-1) were calculated from a methane diffusion assay for planted and unplanted soils respectively, indicating the positive effect of plant roots on gas diffusion into the soil. A second, modified column study removed 87, 73, 63, and 45% of PCB after 12 weeks in the 0 to 5, 5 to 11, 11 to 26, and 26 to 35 cm depths, respectively, in planted-bioaugmented soils, whereas 65, 54, 53, and 47% of PCB was removed from the planted-minimal salts treatment, respectively. Shifts in the soil microbial community structure were demonstrated by denaturing gradient gel electrophoresis of bacterial 16S ribosomal DNA. Results support that Brassica nigra directly contributed to accelerated PCB removal by increased oxygen diffusion, amendment infiltration, and microbial enrichment.

Biodegradation, Environmental↗

PubMed2002

Bistatic receiver model for airborne lidar returns incident on an imaging array from underwater objects.

We develop a bistatic model for airborne lidar returns collected by an imaging array from underwater objects, incorporating additional returns from the surrounding water medium and ocean bottom. Our results provide a generalization of the monostatic model by Walker and McLean. In the bistatic scheme the transmitter and receiver are spatially separated or are not coaligned. This generality is necessary for a precise description of an imaging array such as a CCD, which may be viewed as a collection of receiver elements, with each transmitter-element pair forming a bistatic configuration. More generally, the receiver may consist of photomultiplier tubes, photodiodes, or any of a variety of optical receivers, and the imaging array can range in size from a CCD array to a multiple-platform airborne lidar system involving multiple aircraft. The majority of this research is devoted to a derivation of the bistatic lidar equations, which account for multiple scattering and absorption in the water column. We then describe the application of these equations to the modeling and simulation of an imaging array. We show an example of a simulated lidar return and compare it with a real ocean lidar return, obtained by a CCD array.

Journal Article↗

PubMed2002

Differential enantioselective transformation of atropisomeric polychlorinated biphenyls by multiple bacterial strains with different inducing compounds.

Five polychlorinated biphenyl (PCB)-degrading bacteria were tested for the ability to differentiate between the enantiomers of four atropisomeric PCB congeners (2,2',3,6-tetra-CB; 2,2',3,3',6-penta-CB; 2,2',3,4',6-penta-CB; and 2,2',3,5',6-penta-CB) after growth in the presence of tryptone-soytone, biphenyl, carvone, or cymene. Enantioselectivity was shown to vary with respect to strain, congener, and cosubstrate.

Bacteria↗