Biomedical subjects

Syed A Hashsham

Publications and source records attributed to Syed A Hashsham.

9 recordsLinked to original sources

PubMed2024

Transfer of antibiotic resistance genes from soil to rice in paddy field.

The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.

Oryza↗

PubMed2006

Stable colloidal dispersions of C60 fullerenes in water: evidence for genotoxicity.

Stable aqueous suspensions of colloidal C60 fullerenes free of toxic organic solvents were prepared by two methods: ethanol to water solvent exchange (EthOH/nC60 suspensions) and extended mixing in water (aqu/nC60 suspensions). The extended mixing method resulted in the formation of larger (dp approximately 178 nm) and less negatively charged (zeta approximately -13.5 mV) nC60 colloids than nC60 prepared by ethanol to water solvent exchange (dp approximately 122 nm, zeta approximately -31.6 mV). Genotoxicity of these suspensions was evaluated with respect to human lymphocytes using single-cell gel electrophoresis assay (Comet assay). The assay demonstrated genotoxicity for both types of suspensions with a strong correlation between the genotoxic response and nC60 concentration, and with genotoxicity observed at concentrations as low as 2.2 microg/L for aqu/nC60 and 4.2 microg/L for EtOH/nC60. The Olive tail moments (OTM) for these two concentrations were 1.54 +/- 0.24 and 1.34 +/- 0.07, respectively, which in comparison to the negative control OTM of 0.98 +/- 0.17 is statistically different with a p value of at least 0.05. Aqu/nC60 suspensions elicited higher genotoxic response than EthOH/nC60 for the same nC60 concentration. The results represent the first genotoxicity data for colloidal fullerenes produced by simple mixing in water.

Colloids↗

PubMed2006

Influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16S rRNA gene-based diagnostic arrays.

Dangling ends and surface-proximal tails of gene targets influence probe-target duplex formation and affect the signal intensity of probes on diagnostic microarrays. This phenomenon was evaluated using an oligonucleotide microarray containing 18-mer probes corresponding to the 16S rRNA genes of 10 waterborne pathogens and a number of synthetic and PCR-amplified gene targets. Signal intensities for Klenow/random primer-labeled 16S rRNA gene targets were dissimilar from those for 45-mer synthetic targets for nearly 73% of the probes tested. Klenow/random primer-labeled targets resulted in an interaction with a complex mixture of 16S rRNA genes (used as the background) 3.7 times higher than the interaction of 45-mer targets with the same mixture. A 7-base-long dangling end sequence with perfect homology to another single-stranded background DNA sequence was sufficient to produce a cross-hybridization signal that was as strong as the signal obtained by the probe-target duplex itself. Gibbs free energy between the target and a well-defined background was found to be a better indicator of hybridization signal intensity than the sequence or length of the dangling end alone. The dangling end (Gibbs free energy of -7.6 kcal/mol) was found to be significantly more prone to target-background interaction than the surface-proximal tail (Gibbs free energy of -64.5 kcal/mol). This study underlines the need for careful target preparation and evaluation of signal intensities for diagnostic arrays using 16S rRNA and other gene targets due to the potential for target interaction with a complex background.

Bacteria↗

PubMed2006

On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes.

Nucleic acid hybridization serves as backbone for many high-throughput systems for detection, expression analysis, comparative genomics and re-sequencing. Specificity of hybridization between probes and intended targets is always critical. Approaches to ensure and evaluate specificity include use of mismatch probes, obtaining dissociation curves rather than single temperature hybridizations, and comparative hybridizations. In this study, we quantify effects of mismatch type and position on intensity of hybridization signals and provide a new approach based on dissociation rate constants to evaluate specificity of hybridized signals in complex target mixtures. Using an extensive set of 18mer oligonucleotide probes on an in situ synthesized biochip platform, we demonstrate that mismatches in the center of the probe are more discriminating than mismatches toward the extremities of the probe and mismatches toward the attached end are less discriminating than those toward the loose end. The observed destabilizing effect of a mismatch type agreed in general with predictions using the nearest neighbor model. Use of a new parameter, specific dissociation temperature (T(d-w), temperature of maximum specific dissociation rate constant), obtained from probe-target duplex dissociation profiles considerably improved the evaluation of specificity. These results have broad implications for hybridization data obtained from complex mixtures of nucleic acids.

Base Pair Mismatch↗

PubMed2004

Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs.

Development of parallel detection tools using microarrays is critically reviewed in view of the need for screening multiple microorganisms in a single test. Potential research needs with respect to probe design and specificity, validation, sample concentration, selective target enrichment and amplification, and data analysis are discussed. Data illustrating selected probe design issues for detecting multiple targets in mixed microbial systems is presented. Challenges with respect to cost, time, and ease of use compared to other methods are also summarized.

Animals↗

PubMed2003

Customized cDNA microarray for expression profiling of environmentally important genes of Pseudomonas stutzeri strain KC.

DNA microarray is a powerful tool for parallel detection of multiple target genes in biological systems. In this study, a low-density DNA microarray has been custom designed by using Pseudomonas stutzeri strain KC ORFs that are implicated in carbon tetrachloride degradation. PCR amplified strain KC probes of varying lengths were obtained using ORF-specific primers. Purified short probes (80-120 bp) and full-length amplicons were directly immobilized on gamma-aminosilane coated and superaldehyde trade mark glass substrates without any chemical modification. The full-length amplicons exhibited a much higher signal compared to the shorter probes upon hybridization with the Cy5/Cy3-labeled unfragmented cDNA targets. The meager signal with the shorter probes limits the advantage of using the multiple probes of the same genes for enhancing the specificity of hybridization with environmental samples. Nevertheless, expression analysis of strain KC genome, under controlled laboratory conditions, revealed the constitutive expression of at least 11 putative ORFs of the pdt operon. Comparatively weaker hybridization signals with the cDNA from mutant cells suggested a low abundance of mRNA transcripts in the KC 1896 mutant. Similar expression levels of the pdt ORFs I, J, K, M, N, O, P, and fur gene both under iron-limiting conditions and in presence of iron (20 micro M Fe(3+)) suggested metal ion-independent regulation of the pdt operon. The tailor-made array with strain KC gene-specific probes served as a model for demonstrating the utility of cDNA microarray technology in monitoring the expression of environmentally important genes in bacteria.

Carbon Tetrachloride↗

PubMed2003

Adsorption of vitamin B12 to alumina, kaolinite, sand and sandy soil.

Vitamin B12 is an important component of media used to stimulate the growth of many anaerobic microbes that dechlorinate aliphatic compounds. Its delivery to the subsurface is therefore a concern for enhanced in situ bioremediation and bioaugmentation. In situ circulation of vitamin B12 and a chemical reductant has also been field tested for treatment of chlorinated methanes, ethanes, and ethenes. The objective of this study was to determine the extent of B12 (added as cyanocobalamin) adsorption to aquifer solids. Batch studies indicated a minor amount of adsorption to kaolinite clay (Freundlich Kf = 1.5 (microgram/g) (mL/microgram)1/n and 1/n = 0.39) and sand (Kf = 0.70 (microgram/g) (mL/microgram)1/n and 1/n = 0.84), and no detectable adsorption to alumina. Column studies using a 3H2O tracer and vitamin B12 in distilled water (10 microM) resulted in a B12 retardation factor (R) of approximately 2 for both sand (0.14% organic carbon) and a sandy soil (2.5% organic carbon). Using groundwater containing organic carbon (2.8 mg/L) in place of distilled water did not significantly change R. The relatively low value for R indicates vitamin B12 can be distributed throughout a contaminated aquifer without experiencing significant losses to adsorption.

Adsorption↗

PubMed2003

Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities.

Spotted oligonucleotide microarrays potentially offer a wide scope of applications for microbial ecology, especially as they improve the flexibility of design and the specificity of detection compared to PCR product based microarrays. Sensitivity, however, was expected to be problematic, as studies with the more sensitive PCR-based cDNA microarrays indicate that only genes from populations contributing to more than 5% of the community DNA can be detected. We evaluated several parameters to increase sensitivity and then tested applicability for bacterial functional genomics. The optimal parameters were the use of 5'-C6-amino-modified 70-mers printed on CMT-GAPS II substrates at a 40 micro M concentration combined with the use of Tyramide Signal Amplification labelling. This protocol allowed detection of single copy genes belonging to an organism contributing to 1% or more of the total community. To demonstrate its application, we detected the specific aromatic oxygenase genes in a soil community degrading polychlorinated biphenyls (PCBs). This increase in sensitivity is important if oligonucleotide microarrays are to be used for simultaneous monitoring of a range of functions performed by different microorganisms in the environment.

Bacteria↗

PubMed2002

Microbial dehalorespiration with 1,1,1-trichloroethane.

1,1,1-Trichloroethane (TCA) is a ubiquitous environmental pollutant because of its widespread use as an industrial solvent, its improper disposal, and its substantial emission to the atmosphere. We report the isolation of an anaerobic bacterium, strain TCA1, that reductively dechlorinates TCA to 1,1-dichloroethane and chloroethane. Strain TCA1 required H2 as an electron donor and TCA as an electron acceptor for growth, indicating that dechlorination is a respiratory process. Phylogenetic analysis indicated that strain TCA1 is related to gram-positive bacteria with low DNA G+C content and that its closest relative is Dehalobacter restrictus, an obligate H2-oxidizing, chloroethene-respiring bacterium.

Anaerobiosis↗