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D Ahmad

Publications and source records attributed to D Ahmad.

At least 19 recordsLinked to original sources
PubMed2006

A new rapid technique for screening the potential of implanted microorganisms to tolerate and grow on petroleum oily sludges.

Standard experimental protocols for biodegrading petroleum hydrocarbons employ microbiological and/or analytical analysis, and require advanced machines and specialized professionals to carry them out. Furthermore, the obtained results involve a high margin of error. In this paper, a new experimental technique was developed to facilitate the study of microbial capability to degrade petroleum oily sludges. The technique is based on growing microorganisms on 0.22 microm filter membranes laid over oily sludge placed in metallic cups. The microbial growth was assessed using the plate counts technique. Sludge degradation was assessed using Fourier Transform Infrared Spectrometry (FTIR), and compared to the decrease in total petroleum hydrocarbons (TPH) using solvent extraction. The protocol was tested using three types of inocula: fungal inoculum containing Paecilomyces variotii; bacterial inoculum containing Bacillus cereus; and fungal-bacterial inoculum containing both strains. Both, fungal and bacterial, strains were isolated from the oily sludge used in the present study, and were tentatively identified as oil degraders. The results of the newly developed technique helped to assess the potential of these cultures to tolerate and grow on the oily sludge.

Bacillus cereus↗
PubMed2002

Subsurface irrigation as a microbial delivery tool for bioaugmentation: transport, distribution and survival in large packed soil columns.

Traditionally, soil surface inoculation and surface irrigation are used for delivery, transport and distribution of bacteria for agricultural and in-situ environmental decontamination applications. The objective of this study was to test whether subsurface irrigation with a water table management (WTM) system, successfully used previously for nutrient delivery, could also be used to deliver bacteria to soil depths. Twelve stainless steel columns, 1000 mm in length and 200 mm in diameter, were packed with a sandy loam soil. Four experimental treatments, two subsurface irrigation and two surface irrigation, were randomly allocated, in triplicate, to the twelve columns. The transport, implantation and survival of Sinorhizobium (Rhizobium) meliloti, strain A-025, in these columns were monitored at different depths and times after surface and subsurface irrigation. Even though the transport of bacterial cells was slower with the subsurface irrigation regime than with surface irrigation, more bacteria were implanted at different depths with subsurface irrigation. The numbers of bacterial cells distributed with subsurface irrigation were 1.6x10(5), 1.3x10(5), 2.6x10(5) and 2.9x10(5) cfu (colony forming units) x g(-1) of soil at 60, 300, 500 and 700 mm depths, respectively, whereas with surface irrigation the numbers were 2.0x10(4), 3.0x10(4), 1.9x10(5), 9.0x10(2) cfu x g(-1) of soil. These results dearly indicate that subirrigation can be used effectively to bioaugment a sandy loam soil matrix.

Agriculture↗
PubMed2001

Biofiltration of residual fertilizer nitrate and atrazine by Rhizobium meliloti in saturated and unsaturated sterile soil columns.

This study was undertaken to investigate whether microbial bioaugmentation of subsurface soil with subsurface irrigation could be used as a biofiltration/biocontrol technology for agricultural pollutants. Nine Plexiglas columns, 458 mm long x 139 mm in diameter, were packed with a sterilized sandy loam soil. Subsurface irrigation, through a controlled water table management system, was used to deliver bacteria, Rhizobium meliloti A-025, to the soil and to maintain aerobic (unsaturated) or anaerobic (saturated) conditions in the columns. Nitrate and atrazine, a fertilizer and a corn herbicide, were applied to the soil surface, and leaching was affected by simulated rainfall events. The soil and drainage waters were analyzed for nitrate and atrazine residues after each rainfall simulation throughout the experimental period during which the soil was kept saturated for a total of 80 days and unsaturated for a total of 70 days. The monitoring of transport and survival of the implanted bacterial strain (A-025) showed that subsurface irrigation was successful in introducing and transporting the bacteria throughout the soil columns. During the saturated period, significantly more (95% probability) nitrate-N leached into the drainage waters from the control columns than from the bioaugmented columns; the increase being 450% or more for the abiotic control columns. The amount of atrazine that leached into the drainage waters during the unsaturated period was also significantly more from control columns as opposed to bioaugmented columns, with the increase being 262%.

Atrazine↗
PubMed2001

Effect of bioaugmentation on microbial transport, water infiltration, moisture loss, and surface hardness in pristine and contaminated soils.

Three different soils, a clay, a pristine sandy loam and a PCB-contaminated sandy loam, were bioaugmented to determine the influence of clay content and contaminants on the transport of bacteria in unsaturated soils, using surface irrigation water as a transport medium. The results indicate that the transport of the implanted bacteria was influenced negatively more by the presence of PCBs than by the clay content of the soil. Transport was directly related to the frequency of irrigation and length of the intervals between irrigation periods, making these variables important factors to consider when applying bioaugmentation via downward percolating water. Other parameters measured after bacterial bioaugmentation were water infiltration, moisture loss, and surface hardness of these soils. Surface water infiltration was affected more by the soil clay content than by the hydrophobic contaminant. Infiltration was significantly but differently influenced by bioaugmentation, positively in clay, negatively in sandy loam, and negatively (to a lesser extent) in the PCB-contaminated sandy loam soils. Moisture loss was slower in the bioaugmented soil than in the control soils, with this difference being most pronounced in the PCB soil. High moisture loss in the bioaugmented clay soil rendered it the hardest soil for surface penetration.

Aluminum Silicates↗
PubMed2001

Biotransformation and partial mineralization of the explosive 2,4,6-trinitrotoluene (TNT) by rhizobia.

Three strains, T10, B5, and M8, each belonging to a different species of the family Rhizobiaceae and isolated from atrazine-contaminated soils, were tested for their ability to transform 2,4,6-trinitrotoluene (TNT) (50 microg x mL(-1)) in liquid cultures using glucose as the C-source. All three strains were able to transform TNT to hydroxylaminodinitrotoluenes (2-HADNT, 4-HADNT), aminodinitrotoluenes (2-ADNT, 4-ADNT), and diaminonitrotoluene (2,4-DANT). The transformation was significantly faster in the presence of glutamate. Furthermore, the major metabolites that accumulated in cultures were 2-ADNT with glucose, and 4-ADNT with glutamate plus glucose. Rhizobium trifolii T10 was also tested for its ability to transform high levels of TNT (approximately 350 microg x mL(-1)) in a soil slurry. Almost 60% of the TNT was transformed within 2 days in bioaugmented soil slurries, and up to 90% when cultures were supplemented with glucose and glutamate. However, mineralization was minimal in all cases, less than 2% in 78 days. This is the first report on the degradation of TNT by rhizobial strains, and our findings suggest that rhizobia have the potential to play an important role in the safe decontamination of soils and sites contaminated with TNT if bioaugmentation with rhizobia is shown to have no ecotoxicological consequence.

Biodegradation, Environmental↗
PubMed1998

Biphenyl-associated meta-cleavage dioxygenases from Comamonas testosteroni B-356.

In addition to 2,3-dihydroxybiphenyl 1,2-dioxygenase (B1,2O), biphenyl-grown cells of Comamonas testosteroni B-356 were shown to produce a catechol 2,3-dioxygenase (C2,3O). B1,2O showed strong sequence homology with B1,2Os found in other biphenyl catabolic pathways, while partial sequence analysis of the C2,3O of B-356 suggested a relationship with xylEII-encoded C2,3O. The coexistence of two meta-cleavage dioxygenases in this strain prompted a comparison between the catalytic properties of the two enzymes. C2,3O has a much broader substrate specificity than native or His-tagged B1,2O: both enzymes were inhibited by chlorocatechols, but B1,2O was more sensitive than C2,3O. The results are discussed in terms of the physiological implications of interaction between metabolites from the lower biphenyl-chlorobiphenyl pathway and enzymes of the upper pathway.

Amino Acid Sequence↗
PubMed1998

Desmoid tumour of the thoracic outlet: an unusual cause of thoracic outlet syndrome.

Desmoid tumour is an unusual and aggressive tumour associated with a high recurrence rate. A 35-year-old man presented with recurrent debilitating left arm pain 2 years after undergoing bilateral transaxillary first rib resection for thoracic outlet syndrome. Nerve conduction studies demonstrated impairment of nerve conduction in the left arm. Magnetic resonance imaging of the brachial plexus demonstrated a mass at the apex of the left hemithorax involving the lower cord of the brachial plexus. Subsequent percutaneous needle biopsies failed to provided a definitive diagnosis. A cervicothoracic approach as described by Dartevelle was used to resect the lesion. Histologic and ultrastructural studies confirmed the diagnosis of a desmoid tumour. This report describes the atypical presentation of this unusual tumour and the application of the novel Dartevelle approach to secure its complete excision.

Adult↗
PubMed1996

Sequencing of Comamonas testosteroni strain B-356-biphenyl/chlorobiphenyl dioxygenase genes: evolutionary relationships among Gram-negative bacterial biphenyl dioxygenases.

In a previous work, all three components of Comamonas testosteroni B-356 biphenyl (BPH)/chlorobiphenyls (PCBs) dioxygenase (dox) have been purified and characterized. They include an iron-sulphur protein (ISPBPH) which is the terminal oxygenase composed of two subunits (encoded by bphA and bphE), a ferredoxin (FERBPH) encoded by bphF and a reductase (REDBPH) encoded by bphG. bphG Is not located in the neighbourhood of bphAEF in B-356. We are reporting the cloning of B-356-bphG and the sequencing of B-356-BPH dox genes. Comparative analysis of the genes provided genetic evidence showing that two BPH dox lineages have emerged in Gram-negative bacteria. The main features of the lineage that includes B-356 are the location of bphG outside the bph gene cluster and the structure of REDBPH which is very distinct from all other aryl dioxygenase-reductases.

Amino Acid Sequence↗
PubMed1996

Biodegradation of polychlorinated biphenyls by rhizobia: a novel finding.

Metabolism of simple aromatic compounds in rhizobial strains has been a subject of study for a few decades, due either to the significance of nutritional diversity in the inoculum survival during agricultural applications or to the importance of plant phenolics in the microbe-plant cross-talk and signal-transduction. Here, we report the capability of rhizobial strains to catabolize polychlorinated biphenyls (PCBs). In order to identify the genes in these strains that mediate the catabolism of PCBs we used the bphABC genes from Comamonas testosteroni strain B-356. Our results showed that genomic DNAs from all four rhizobial strains studied hybridized strongly with the Comamonas-derived probe, indicating the presence of a similar genetic system. This is a novel and interesting finding indicating for the first time, perhaps, of a role of rhizobia in recycling of aromatic compounds in nature and, certainly, opening a new avenue to be explored in the field of bioremediation.

Aroclors↗
PubMed1996

Characterization of active recombinant 2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase from Comamonas testosteroni B-356 and sequence of the encoding gene (bphB).

2,3-Dihydro-2,3-dihydroxybiphenyl-2,3-dehydrogenase (B2,3D) catalyzes the second step in the biphenyl degradation pathway. The nucleotide sequence of Comamonas testosteroni B-356 bphB, which encodes B2,3D, was determined. Structural analysis showed that the dehydrogenases involved in the bacterial degradation of aromatic compounds are related to each other and that their phylogenetic relationships are very similar to the relationships observed for dioxygenases that catalyze the initial reaction in the degradation pathway. The bphB sequence was used to produce recombinant active His-tagged B2,3D, which allowed us to describe for the first time some of the main features of a B2,3D. This enzyme requires NAD+, its optimal pH is 9.5, and its native M(r) was found to be 123,000, which makes it a tetramer. These characteristics are very similar to those reported for the related enzyme cis-toluene dihydrodiol dehydrogenase. The Km value and maximum rate of metabolism for 2,3-dihydro-2,3-dihydroxybiphenyl were 73 +/- 16 microM and 46 +/- 4 nmol min-1 microgram-1, respectively. Compared with the cis-toluene dihydrodiol dehydrogenase, B2,3D appeared to be more substrate specific since it was unable to attack cis-1,2-dihydroxy-cyclohexa-3,5-diene.

Amino Acid Sequence↗
PubMed1996

Sleep-disordered breathing in amyotrophic lateral sclerosis.

OBJECTIVE: The purpose of this study was to assess sleep and breathing in patients with amyotrophic lateral sclerosis (ALS) with bulbar muscle involvement. DESIGN: Prospective, controlled study of sleep and breathing measured during polysomnography. SETTING: University teaching hospital and referral center. PATIENTS: Patients with definite ALS and healthy age-matched control subjects. INTERVENTIONS: Eighteen ALS patients and 10 age-matched control subjects underwent one night of polysomnography. Thirteen patients with ALS were studied for a second night. RESULTS: The ALS patients had more arousals per hour (p = 0.008), more stage 1 sleep (p = 0.01), and a shorter total sleep time (TST) (279 +/- 69 vs 331.4 +/- 55.9 min, mean +/- SD, p = 0.04) than the control subjects. The ALS patients had mild sleep-disordered breathing with a greater apnea/hypopnea index (AHI) than the control subjects (p = 0.005). On the second night of polysomnography, there was an increase in TST (p = 0.003) and rapid eye movement (REM) sleep (p = 0.009), an improvement in sleep efficiency (p = 0.02), and less stage 1 sleep (p = 0.04). Eight ALS patients had sleep-disordered breathing consisting of periods of hypoventilation, predominantly during REM sleep. CONCLUSIONS: Sleep-disordered breathing occurs in patients with ALS and is similar to patients without ALS with respiratory muscle weakness. No obstructive sleep apnea was observed. One potential reason for its absence might be the inability of patients with respiratory muscle weakness to generate an inspiratory pressure greater than the upper airway closing pressure. This hypothesis should be addressed in future studies.

Aged↗
PubMed1995

Sequence of the bphD gene encoding 2-hydroxy-6-oxo-(phenyl/chlorophenyl)hexa-2,4-dienoic acid (HOP/cPDA) hydrolase involved in the biphenyl/polychlorinated biphenyl degradation pathway in Comamonas testosteroni: evidence suggesting involvement of Ser112 in catalytic activity.

The nucleotide sequence of bphD, encoding 2-hydroxy-6-oxo-(phenyl/chlorophenyl)hexa-2,4-dienoic acid hydrolase involved in the biphenyl/polychlorinated biphenyl degradation pathway of Comamonas testosteroni strain B-356, was determined. Comparison of the deduced amino-acid sequence with published sequences led to the identification of a 'lipase box', containing a consensus pentapeptide sequence GlyXaaSerXaaGly. This suggested that the mechanism of action of this enzyme may involve an Asp-Ser-His catalytic triad similar to that of classical lipases and serine hydrolases. Further biochemical and genetic evidence for the active-site involvement of Ser112 was obtained by showing that a semipurified enzyme was inhibited by PMSF, a classic inhibitor of serine hydrolases, and by site-directed Ser112-->Ala mutagenesis.

Amino Acid Sequence↗