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Biomedical subjects

A A Mahdi

Publications and source records attributed to A A Mahdi.

At least 19 recordsLinked to original sources
PubMed2006

1H NMR spectroscopy in the diagnosis of Klebsiella pneumoniae-induced urinary tract infection.

The (1)H NMR spectroscopic method is suggested and its utility is demonstrated for the diagnosis of Klebsiella pneumoniae (K. pneumoniae) in urinary tract infection (UTI). K. pneumoniae have the specific property of metabolizing glycerol to 1,3-propanediol (1,3-PD), acetate, ethanol and succinate. The quantity of 1,3-PD produced correlates well with the viable bacterial count. Other common bacteria causing UTI (except for Citrobacter frundii), such as Escherichia coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa), Enterobacter aerogenes, Acinetobacter baumanii, Proteus mirabilis, Enterococcus faecalis, Streptococcus gp B and Staphylococcus aureus do not metabolize glycerol under similar conditions. Citrobacter frundii (C. frundii) also gives the same NMR results but is easily differentiated as being motile on direct microscopic examination of urine and it is not common nosocomial infectious agent in urinary tract infection. The method provides a single-step documentation of K. pneumoniae (and C. frundii) qualitatively as well as quantitatively. Out of the total 614 subjects considered, clinical diagnosis of UTI was obtained in 516 cases (84%). The NMR-based screening had a sensitivity of 90%, a specificity of 100% and a false negativity of 10% relative to the conventional quantitative culture method. In the present authors' experience, the results of NMR spectroscopy based screening show a very good correlation with the diagnosis of urinary tract infected patients.

Bacteria↗
PubMed2005

(1)H NMR spectroscopy in the diagnosis of Pseudomonas aeruginosa-induced urinary tract infection.

The utility of (1)H NMR spectroscopy is suggested and demonstrated for the diagnosis of Pseudomonas aeruginosa in urinary tract infection (UTI). The specific property of P. aeruginosa of metabolizing nicotinic acid to 6-hydroxynicotinic acid (6-OHNA) is exploited. The quantity of 6-OHNA produced correlates well with the viable bacterial count. Other common bacteria causing UTI such as Escherichia coli, Klebsiella pneumonia, Enterobacter aerogenes, Acinetobacter baumanii, Proteus mirabilis, Citrobacter frundii, Enterococcus faecalis, Streptococcus gp B and Staphylococcus aureus do not metabolize nicotinic acid under similar conditions. The method provides a single-step documentation of P. aeruginosa qualitatively as well as quantitatively. The NMR method is demonstrated on urine samples from 30 patients with UTI caused by P. aeruginosa.

Biomarkers↗
PubMed2000

Characterisation of the catalytically active form of RecG helicase.

Replication of DNA is fraught with difficulty and chromosomes contain many lesions which may block movement of the replicative machinery. However, several mechanisms to overcome such problems are beginning to emerge from studies with Escherichia coli. An important enzyme in one or more of these mechanisms is the RecG helicase, which may target stalled replication forks to generate a four-stranded (Holliday) junction, thus facilitating repair and/or bypass of the original lesion. To begin to understand how RecG might catalyse regression of fork structures, we have analysed what the catalytically active form of the enzyme may be. We have found that RecG exists as a monomer in solution as measured by gel filtration but when bound to junction DNA the enzyme forms two distinct protein-DNA complexes that contain one and two protein molecules. However, mutant inhibition studies failed to provide any evidence that RecG acts as a multimer in vitro. Additionally, there was no evidence for cooperativity in the junction DNA-stimulated hydrolysis of ATP. These data suggest that RecG functions as a monomer to unwind junction DNA, which supports an 'inchworm' rather than an 'active rolling' mechanism of DNA unwinding. The observed in vivo inhibition of wild-type RecG by mutant forms of the enzyme was attributed to occlusion of the DNA target and correlates with the very low abundance of replication forks within an E.COLI: cell, even during rapid growth.

Amino Acid Sequence↗
PubMed2000

Circadian periodicity of urinary volume, creatinine and 5-hydroxyindole acetic acid excretion in healthy Indians.

The circadian periodicity of urinary output, creatinine (Cr) and 5-hydroxyindole acetic acid (5-HIAA) excretion was studied under near-tropical conditions in 130 healthy volunteers (65 men and 65 women, 16-75 years of age) with a diurnal activity from about 06:30 to about 22:00 and nocturnal rest. These volunteers were divided into 4 groups, 16-30, 31-45, 46-60 and 61-75 years of age, comprising 20, 20, 15 and 10 participants of each gender, respectively. A marked circadian rhythm was recorded for urine volume, Cr and 5-HIAA excretion in healthy Indians of different ages. The acrophase tended to be delayed in the older age group. The relative amplitude decreased with advancing age, notably in women. Overall, men produced a larger urine volume as compared to women. Excretions of Cr and 5-HIAA in healthy Indian volunteers of different ages may be influenced by diet, societal relations, climate and/or geographic location. The contribution of such factors in metabolism and degradation warrants further study.

Adolescent↗
PubMed1997

DNA binding and helicase domains of the Escherichia coli recombination protein RecG.

The Escherichia coli RecG protein is a unique junction-specific helicase involved in DNA repair and recombination. The C-terminus of RecG contains motifs conserved throughout a wide range of DNA and RNA helicases and it is thought that this C-terminal half of RecG contains the helicase active site. However, the regions of RecG which confer junction DNA specificity are unknown. To begin to assign structure-function relationships within RecG, a series of N- and C-terminal deletions have been engineered into the protein, together with an N-terminal histidine tag fusion peptide for purification purposes. Junction DNA binding, unwinding and ATP hydrolysis were disrupted by mutagenesis of the N-terminus. In contrast, C-terminal deletions moderately reduced junction DNA binding but almost abolished unwinding. These data suggest that the C-terminus does contain the helicase active site whereas the N-terminus confers junction DNA specificity.

Bacterial Proteins↗
PubMed1997

Crystallization of E. coli RuvA gives insights into the symmetry of a Holliday junction/protein complex.

The E. coli protein RuvA (resistance to ultraviolet light) has been overexpressed in E. coli, purified and crystallized using the hanging-drop vapour-diffusion method with sodium chloride as the precipitant. The crystals, which diffract to beyond 1.9 A, belong to the tetragonal system, space group P4 with unit-cell dimensions of a = 83.7, c = 33.1 A with a monomer in the asymmetric unit. RuvA is known to be a tetramer and thus the crystal symmetry implies that its quaternary structure will be based on fourfold rotation symmetry rather than 222 symmetry. This is consistent with electron microscopy data on Holliday junction DNA complexes and implies that the arms of the four DNA duplexes involved in recombination adopt fourfold rotation symmetry.

Journal Article↗
PubMed1996

The RecG branch migration protein of Escherichia coli dissociates R-loops.

The RuvAB and RecG proteins of Escherichia coli promote branch migration of Holliday junction intermediates in genetic recombination. Both are structure-specific helicases that unwind and rewind DNA at the junction point. The helicase activities of these proteins were investigated using RNA:DNA hybrid molecules. RuvAB catalyses the unwinding of RNA:DNA partial duplexes of at least 218 bp in a reaction that requires both RuvA and RuvB, ATP and Mg2+. RecG failed to unwind these substrates even when the duplex region was reduced to 35 bp. In contrast, RecG rapidly removes a 218 nt RNA from an R-loop substrate, whereas RuvAB does not. RecG's ability to dissociate R-loops is correlated with an ability to reduce the copy number of pUC plasmids and other constructs based on the ColE1 replicon. Copy number is reduced severely when the plasmid carries recG+. RecG is assumed to reduce copy number by interfering with RNA II's ability to form an R-loop at the plasmid origin of replication and prime DNA synthesis. The dissociation of R-loops by RecG is discussed in terms of the functions needed to promote recombination and to prime DNA replication at D-loops formed during the early stages of RecA-mediated recombination.

Bacterial Proteins↗
PubMed1996

Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction.

The Escherichia coli DNA binding protein RuvA acts in concert with the helicase RuvB to drive branch migration of Holliday intermediates during recombination and DNA repair. The atomic structure of RuvA was determined at a resolution of 1.9 angstroms. Four monomers of RuvA are related by fourfold symmetry in a manner reminiscent of a four-petaled flower. The four DNA duplex arms of a Holliday junction can be modeled in a square planar configuration and docked into grooves on the concave surface of the protein around a central pin that may facilitate strand separation during the migration reaction. The model presented reveals how a RuvAB-junction complex may also accommodate the resolvase RuvC.

Bacterial Proteins↗
PubMed1996

Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82.

The RusA protein of Escherichia coli is an endonuclease that can resolve Holliday intermediates and correct the defects in genetic recombination and DNA repair associated with inactivation of RuvAB or RuvC. The structure of the rusA gene, its organisation in the genome, and its interaction with the Ruv and RecG proteins have been investigated. Recombinant plasmids carrying rusA were identified by their ability to make ruv mutants resistant to UV light. The gene was located to an open reading frame encoding a polypeptide of 120 amino acids. It forms the fifth gene in an operon containing a chain of short, interlinked open reading frames. A similar arrangement was found in the genome of the lambdoid bacteriophage, 82. The two rusA genes show 95% sequence identity. The E. coli operon forms part of the defective lambdoid prophage, DLP12, and is probably derived from a phage related to 82 and PA-2. rusA appears to be very poorly expressed in E. coli, but can be activated by insertion of IS2 or IS10 upstream of the coding sequence to promote transcription. These insertions arise spontaneously in ruv strains as suppressors of the mutant phenotype. Deletion of rusA from the chromosome of either wild-type or ruv mutant strains has no obvious effect on recombination or sensitivity to UV light. Multicopy plasmids expressing RusA alone make ruvA, ruvB, and ruvC mutants resistant to UV light. Suppression depends critically on RecG.

Amino Acid Sequence↗
PubMed1996

Modulation of recombination and DNA repair by the RecG and PriA helicases of Escherichia coli K-12.

The RecG protein of Escherichia coli is a structure-specific DNA helicase that targets strand exchange intermediates in genetic recombination and drives their branch migration along the DNA. Strains carrying null mutations in recG show reduced recombination and DNA repair. Suppressors of this phenotype, called srgA, were located close to metB and shown to be alleles of priA. Suppression depends on the RecA, RecBCD, RecF, RuvAB, and RuvC recombination proteins. Nine srgA mutations were sequenced and shown to specify mutant PriA proteins with single amino acid substitutions located in or close to one of the conserved helicase motifs. The mutant proteins retain the ability to catalyze primosome assembly, as judged by the viability of recG srgA and srgA strains and their ability to support replication of plasmids based on the ColE1 replicon. Multicopy priA+ plasmids increase substantially the recombination- and repair-deficient phenotype of recG strains and confer similar phenotypes on recG srgA double mutants but not on ruvAB or wild-type strains. The multicopy effect is eliminated by K230R, C446G, and C477G substitutions in PriA. It is concluded that the 3'-5' DNA helicase/translocase activity of PriA inhibits recombination and that this effect is normally countered by RecG.

Adenosine Triphosphatases↗
PubMed1994

Processing of intermediates in recombination and DNA repair: identification of a new endonuclease that specifically cleaves Holliday junctions.

The formation and subsequent resolution of Holliday junctions are critical stages in recombination. We describe a new Escherichia coli endonuclease that resolves Holliday intermediates by junction cleavage. The 14 kDa Rus protein binds DNA containing a synthetic four-way junction (X-DNA) and introduces symmetrical cuts in two strands to give nicked duplex products. Rus also processes Holliday intermediates made by RecA into products that are characteristic of junction resolution. The cleavage activity on X-DNA is remarkably similar to that of RuvC. Both proteins preferentially cut the same two strands at the same location. Increased expression of Rus suppresses the DNA repair and recombination defects of ruvA, ruvB and ruvC mutants. We conclude that all ruv strains are defective in junction cleavage, and discuss pathways for Holliday junction resolution by RuvAB, RuvC, RecG and Rus.

Bacterial Proteins↗
PubMed1993

Resolution of Holliday intermediates in recombination and DNA repair: indirect suppression of ruvA, ruvB, and ruvC mutations.

The ruvA, ruvB, and ruvC genes of Escherichia coli provide activities that catalyze branch migration and resolution of Holliday junction intermediates in recombination. Mutation of any one of these genes interferes with recombination and reduces the ability of the cell to repair damage to DNA. A suppressor of ruv mutations was identified on the basis of its ability to restore resistance to mitomycin and UV light and to allow normal levels of recombination in a recBC sbcBC strain carrying a Tn10 insertion in ruvA. The mutation responsible was located at 12.5 min on the genetic map and defines a new locus which has been designated rus. The rus suppressor works just as well in recBC sbcA and rec+ sbc+ backgrounds and is not allele specific. Mutations in ruvB and ruvC are suppressed to an intermediate level, except when ruvA is also inactive, in which case suppression is complete. In all cases, suppression depends on RecG protein, a DNA-dependent ATPase that catalyzes branch migration of Holliday junctions. The rus mutation activates an additional factor that probably works with RecG to process Holliday junction intermediates independently of the RuvAB and RuvC proteins. The possibility that this additional factor is a junction-specific resolvase is discussed.

Bacterial Proteins↗
PubMed1993

Circadian periodicity of urinary inhibitor of calcium oxalate crystallization in healthy Indians and renal stone formers.

The inhibitory activity (IA) of calcium oxalate crystallization was investigated in healthy Indians and renal stone formers. A marked circadian rhythm was observed in men and women of both groups. The rhythm pattern was similar on the basis of sex; however, it was different in stone formers as compared to normals. The acrophase for crystallization of calcium oxalate was observed, respectively, at 05.43 and 05.52 h in healthy men and women, and at 09.52 and 09.23 h in male and female renal stone formers. Moreover, the acrophase of percent inhibition by IA was observed at 17.44 and 17.52 h in healthy participants and at 21.52 and 21.27 h in male and female stone formers, respectively. Therefore, the acrophase suggests a highest risk of crystallization during the morning hours and a minimum one during the evening hours. The day-night rhythmic pattern of urinary calcium, magnesium and phosphorus is discussed in relation to the rhythm of IA.

Adolescent↗
PubMed1992

Role of free radicals in Plasmodium berghei infected Mastomys natalensis brain.

Lipid peroxide, lipid hydroperoxide, reduced glutathione, oxidised glutathione, lipofuscin contents and the activity of the enzyme superoxide dismutase were assessed in P. berghei infected M. natalensis brain. The results showed significant increase in the levels of lipid peroxides, lipid hydroperoxides and lipofuscin in brain subcellular fractions of P. berghei infected M. natalensis. Furthermore, a depressed superoxide dismutase activity was observed along with regulation in glutathione content. An elevated level of lipid peroxidation products along with depressed activity of scavengers in brain during malaria highlights the role of free radicals in malarial pathology.

Animals↗
PubMed1992

Biochemical studies on mouse liver following Plasmodium berghei infection.

The lipid composition of mouse liver following infection with P. berghei was investigated. The liver lipid contents of infected animals were greatly increased mainly due to the accumulation of triacylglycerides. There was enhanced lipid concentration (85.29%). Significantly (23.7%) depleted liver cholesterol was also found in the mice. Similarly, phospholipid contents of liver were also decreased by 19.90 per cent. The liver from P. berghei infected mouse produced more lipid peroxide, as compared to control animals (314%). Significant depletion was also observed in carbohydrate, glycogen and glucose (79.1, 86.26 and 78.6% respectively) contents of liver at high parasitaemia. The lower contents of nucleic acid in the infected hosts observed in the study may be partly due to the absorption of nucleic acids by the parasites from the host cells.

Animals↗
PubMed1991

Vaccination of rhesus monkeys against Plasmodium knowlesi with aqueous suspension of MDP as an adjuvant.

In these investigations two types of antigen preparations were used: (i) Whole Antigen (WAg), and (ii) Soluble Antigen (SAg). For immunization, Muramyl Dipeptide (MDP) was employed as an adjuvant. Highest reciprocal antibody titre values were recorded in ELISA and IHA tests from animals immunized by WAg-MDP. Skin reactions in animals sensitized with WAg-MDP combination showed a well developed zone of erythema with induration after 24 hours of intradermal injection. Animals immunized with WAg-MDP showed a maximum leukocyte migration inhibition. All the animals in experimental and control groups showed patent infection following challenge with live parasites. Animals belonging to the control groups showed 100% mortality. On the basis of these experiments it could be concluded that MDP preparation afforded some protection to the test animals.

Acetylmuramyl-Alanyl-Isoglutamine↗
PubMed1991

Pathogenesis of cerebral malaria.

Plasmodium knowlesi infected rhesus monkeys were employed for investigating brain tissue damage in experimentally induced cerebral malaria. Light microscopic studies revealed parasitic infiltration of virtually all the regions of CNS. Electron microscopic observations confirmed the light microscopic findings. These studies further revealed the presence of macrophages in the blood vessels of infected monkeys. In conclusion, the pathogenesis of cerebral malaria seems to be an outcome of a typical triad consisting of: (1) mechanical obstruction of the blood capillaries by parasitized RBCs; (2) biochemical events, involving free radicals, and (3) immunological dysfunction.

Animals↗