Douglas J. Cork

Microbial transformations of herbicides and pesticides

Publisher Summary This chapter discusses the microbial transformations of herbicides and pesticides. Herbicide and pesticide usage has benefited modern society by improving the quality and quantity of the worlds food supply while keeping the cost of that food supply reasonable. However, increased usage of chemicals has resulted in environmental concerns. The development and integration of microbes or their activities with the use of herbicides and pesticides can enhance the beneficial effects of chemical usage while eliminating some of the environmental concerns. Microbes can also provide a means to eliminate unwanted residues from the environment, protect previously susceptible crops from herbicide or pesticide damage, and provide a source of genetic material for the development of herbicide-resistant crops or pesticide-producing plants. A fundamental understanding of a microbes degradative kinetics under various conditions, its biochemical systems, and its molecular biology are vital in maximizing the potential benefits of its use. The chapter describes the widespread use of xenobiotics with emphasis on the usage and detoxication of haloaromatic herbicides and pesticides.

Computer visualization of long genomic sequences

Human beings find it difficult to analyze local and global oligonucleotide patterns in the linear primary sequences of a genome. In this paper, we present a family of iterated function systems (IFS) that can be used to generate a set of visual models of a DNA sequence. A new visualization function, the W-curve, that is derived from this IFS family is introduced. Using W-curves, a user can readily compare subsequences within a long genomic sequence - or between genomic sequences - and can visually evaluate the effect of local variations (mutations) upon the global genomic information content.<<ETX>>

Subsurface contaminant bioremediation engineering

Abstract The ability to predict the release and flow of contaminants from the waste source is a critical step in assessing the impact to the environment and designing bioremediation strategies. The contaminant mixtures in the subsurface are subject to simultaneous action of diverse chemical and microbiological processes. Many factors and variables are involved in the migration of contaminants in the subsurface. Some of these factors are the adsorptive capacity of the soil and adsorption of a particular contaminant or mixture of contaminants. The microbial transfer from sorption and adsorption of microorganisms can affect the migration of contaminants. The environmental conditions of the subsurface, such as the availability of oxygen, the pH, and the temperature also can affect migration rates. Predictions of solute transport, chemical identity, and form of constituents originating in the wastes must be made. This article reviews typical engineering considerations for in situ bioremediation focusing on con...

Detection, isolation, and stability of megaplasmid-encoded chloroaromatic herbicide-degrading genes within Pseudomonas species.

Dicamba is used as a model system for microbial degradation of chloroaromatic benzoic acids. The detection, isolation, and stability of a megaplasmid within a Pseudomonas sp. is described as the first step in optimizing the growth of this microorganism and other microorganisms similar to it. A large plasmid, pDK1, consisting of approximately 250 kb, was purified from dicamba-degrading Pseudomonas sp. PXM. This plasmid was purified by the method of Allen (personal communication, 1994), which is a modified version of several that have been attempted for the isolation of large plasmids (Lee and Rasheed, 1990). The restriction analysis of this plasmid (pDK1) from PXM. revealed many distinctive bands on agarose gel electrophoresis. Based on the preliminary restriction enzyme analysis, the estimated size of this plasmid is 250 kb, which could make it one of the largest procaryotic plasmids encoding for chloroaromatic degrading enzymes. Allens methodology results in very high purity and reproducibility compared to the other methods used in this study. As described in this work, the method of Kado and Liu (1981) is easier to perform and results in a more reproducible plasmid preparation than the method of Casse et al. (1979). Casses protocol requires the use of a highly alkaline SDS solution (pH 12.45) in order to eliminate the chromosomal DNA. However, only incomplete removal of the chromosomal DNA results. Compared to the Casse et al. protocol, the Kado and Liu protocol requires the use of a highly alkaline solution (pH 12.6) and a high temperature (55-65 degrees C) to eliminate the chromosomal DNA. This results in a nearly complete removal of the chromosomal DNA. The high temperature treatment also quickly eliminates the RNA. Another advantage of the protocol of Kado and Liu over the protocol of Casse et al. is that the former uses phenol-chloroform extraction while the latter uses only phenol extraction. The phenol-chloroform extraction step denatures the DNA along with the proteins. In addition to this, the phenol-chloroform mixture minimizes the formation of a brown oxidation pigment that usually occurs with phenol extraction alone. Finally, the time needed to complete the Kado and Liu protocol is much shorter (2 hr) than the time needed to complete the Casse protocol (8 hr). As described previously, a highly purified plasmid preparation with minimal chromosomal DNA was prepared by following the suggestions of L. Allen.(ABSTRACT TRUNCATED AT 400 WORDS)

Quantum efficiency requirements for an anaerobic photobioreactor

SummaryThe effect of light intensity, surface area of illuminated bioreactor, H2S flow rate and various wavelength regions of light on oxidative sulfur metabolism byChlorobium was examined. The regulation of oxidative sulfur metabolism by light intensity led to the determination of the photobioreaction quantum efficiency (PQE) for this system. This efficiency is defined as the molecules of sulfur (So) produced per photon utilized and can be used in designing a light efficient photobioreactor. Included in our analysis of requirements for a light efficient photobioreactor is a summary of some fed-batch equations which can be used to model a productive path for the formation of sulfur duringChlorobiums photosynthesis. It is suggested that the incorporation of PQE and fed-batch formulae into expressions for wavelength dependent rates of photosynthetic product formation will lead to a more accurate mathematical model for anoxygenic as well as oxygenic photosynthesis.

Using Fuzzy Logic to Confirm the Integrity of a Pattern Recognition Algorithm for Long Genomic Sequences

Abstract: The W‐curve is a numerical mapping algorithm that provides tertiary information content of long and short genomic sequences. The most popular genomic pattern recognition algorithms depend on string matching of the primary information content of short genomic sequences. Herein, we describe a way to define the fuzzy properties of the W‐curve. This approach improves a distance (dissimilarity) between two or more homologous long genomic sequences. Fourier analysis of W‐curves delivers a smoother function for gap‐stripped regions. Calculation of respective Fourier energies may improve the accuracy of the distance metric used to generate a phylogenetic tree of analyzed genomic sequences. This is especially the case for long genomic sequences that have been gap‐stripped and aligned with the aid of previously published heuristic methods. These previous methods involved W‐curve alignments used in concert with such programs as Clustal that use linear dynamic programming to align multiple gap‐stripped W‐curves.

Specificity of a Flavobacterium in the metabolism of substituted chlorobenzoates.

SummaryA strain ofFlavobacterium breve capable of utilizing 3,5-dichlorosalicylate as a sole source of carbon and energy was identified. Degradation of 3,5-dichlorosolicylate, was specific as this strain did not metabolize dicamba (3,6-dichloro-2-methoxybenzoic acid), 3,5-dicamba (3,5-dichloros2-methoxybenzoic acid), or 3,6-dichlorosalicylate. The organism was able to remove completely 3,5-dichlorosalicylate in the presence of three times as much 3,6-dichlorosalicylate being degraded. The organism was able to utilize 3,5-dichlorosalicylate at concentrations up to 1000μg/ml. A mixture of 3,5 and 3,6-dichlorosalicylate isomers purified by biological destruction of the unwanted isomer (3,5-dichlorosalicylate) would be useful for producing isomerically pure dicamba, an important herbicide.

Microcomputer interfacing to mass flow type gas controllers for biotechnology applications

SummaryAn Apple IIe microcomputer with an Isaac analog-digital package has been interfaced to Tylan proportionating mass flow gas controllers to regulate three substrate gases which are introduced into an anaerobic bioreactor. Advantages of the system include: straightforward interfacing and programming, accurate monitoring and controlling, and advanced real time control capabilities.

W-Curve Alignments for HIV-1 Genomic Comparisons

Background The W-curve was originally developed as a graphical visualization technique for viewing DNA and RNA sequences. Its ability to render features of DNA also makes it suitable for computational studies. Its main advantage in this area is utilizing a single-pass algorithm for comparing the sequences. Avoiding recursion during sequence alignments offers advantages for speed and in-process resources. The graphical technique also allows for multiple models of comparison to be used depending on the nucleotide patterns embedded in similar whole genomic sequences. The W-curve approach allows us to compare large numbers of samples quickly. Method We are currently tuning the algorithm to accommodate quirks specific to HIV-1 genomic sequences so that it can be used to aid in diagnostic and vaccine efforts. Tracking the molecular evolution of the virus has been greatly hampered by gap associated problems predominantly embedded within the envelope gene of the virus. Gaps and hypermutation of the virus slow conventional string based alignments of the whole genome. This paper describes the W-curve algorithm itself, and how we have adapted it for comparison of similar HIV-1 genomes. A treebuilding method is developed with the W-curve that utilizes a novel Cylindrical Coordinate distance method and gap analysis method. HIV-1 C2-V5 env sequence regions from a Mother/Infant cohort study are used in the comparison. Findings The output distance matrix and neighbor results produced by the W-curve are functionally equivalent to those from Clustal for C2-V5 sequences in the mother/infant pairs infected with CRF01_AE. Conclusions Significant potential exists for utilizing this method in place of conventional string based alignment of HIV-1 genomes, such as Clustal X. With W-curve heuristic alignment, it may be possible to obtain clinically useful results in a short time—short enough to affect clinical choices for acute treatment. A description of the W-curve generation process, including a comparison technique of aligning extremes of the curves to effectively phase-shift them past the HIV-1 gap problem, is presented. Besides yielding similar neighbor-joining phenogram topologies, most Mother and Infant C2-V5 sequences in the cohort pairs geometrically map closest to each other, indicating that W-curve heuristics overcame any gap problem.

Achieving Congruency of Phylogenetic Trees Generated by W-Curves of Genomic Sequences

Abstract: Comparative genomic analysis at its most fundamental level involves alignment and analysis of linear strings of DNA. Many useful and powerful tools, such as BlastN and ClustalW are able to respectively, search for, and align similar strings of DNA from a variety of species. However, interesting genomic patterns cannot be immediately visualized within the information contact embedded in long genomic strings without extensive a priori knowledge. More problematic is the question of whether we will be able to crystallize long genomic sequences and analyze their true secondary and tertiary structures. It is, of course, these putative motifs that are binding to the three‐dimensional structures of proteins and inducing replication and transcription events. The W‐curve is a numerical mapping algorithm that allows one to geometrically visualize the information content of genomic motifs. Patterns of ALU, LINES, SINEs, and duplication sequences may be easily visualized with the W‐curve. It is our hope that this pattern recognition algorithm will lead to visualization tools to track the evolutionary history of motif patterns. The combinatorics of DNA motif crossover‐recombination events will be more easily followed as we continue to sequence more and more genomes. In our laboratory we are currently collaborating with mathematicians and computer scientists to develop and test tools, such as the W‐curve, for analyzing patterns of long genomic sequences. In this paper, we examine the limitations of using the W‐curve to infer the phylogenetic history of species.