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H N Shah

Publications and source records attributed to H N Shah.

At least 19 recordsLinked to original sources
PubMed2006

Long-term storage and safe retrieval of DNA from microorganisms for molecular analysis using FTA matrix cards.

We assessed the potential use of Whatman FTA paper as a device for archiving and long-term storage of bacterial cell suspensions of over 400 bacterial strains representing 61 genera, the molecular applications of immobilised DNA on FTA paper, and tested its microbial inactivation properties. The FTA paper extracted bacterial DNA is of sufficiently high quality to successfully carryout the molecular detection of several key genes including 16S rRNA, esp (Enterococcus surface protein), Bft (Bacteroides fragilis enterotoxin) and por (porin protein) by PCR and for DNA fingerprinting by random amplified polymorphic DNA-PCR (RAPD-PCR). To test the long-term stability of the FTA immobilised DNA, 100 of the 400 archived bacterial samples were randomly selected following 3 years of storage at ambient temperature and PCR amplification was used to monitor its success. All of the 100 samples were successfully amplified using the 16S rDNA gene as a target and confirmed by DNA sequencing. Furthermore, the DNA was eluted into solution from the FTA cards using a new alkaline elution procedure for evaluation by real-time PCR-based assays. The viability of cells retained on the FTA cards varied among broad groups of bacteria. For the more fragile gram-negative species, no viable cells were retained even at high cell densities of between 10(7) and 10(8) colony forming units (cfu) ml(-1), and for the most robust species such as spore-formers and acid-fast bacteria, complete inactivation was achieved at cell densities ranging between 10(1) and 10(4) cfu ml(-1). The inactivation of bacterial cells on FTA cards suggest that this is a safe medium for the storage and transport of bacterial nucleic acids.

Bacteria↗
PubMed2006

Incidence and antimicrobial susceptibility of Porphyromonas gingivalis isolated from mixed endodontic infections.

AIM: To investigate the prevalence of Porphyromonas gingivalis in root canals of infected teeth with periapical abscesses and to investigate the antimicrobial susceptibility of this species to some frequently prescribed antibiotics. METHODOLOGY: Samples were obtained from 70 root canals of abscessed teeth. Microbial sampling, isolation and bacterial identification were accomplished using appropriate culture methods for anaerobic species. The antimicrobial susceptibility of the 20 strains of P. gingivalis isolated was determined by using the E-test. The antimicrobial agents tested were amoxicillin, amoxicillin + clavulanate, azythromycin, benzylpenicillin, cephaclor, clindamycin, erythromycin, metronidazole and tetracycline. RESULTS: A total of 352 individual strains, belonging to 69 different species, were isolated. Eighty three percent of the strains were strict anaerobes and 47.5% of the isolated bacteria were Gram-negative. Porphyromonas gingivalis was found in 20 root canals and was most frequently found in symptomatic cases. Statistically, the presence of P. gingivalis was related to purulent exudates and pain on palpation (both P < 0.05). All P. gingivalis strains were sensitive to amoxicillin, amoxicillin + clavulanate, cephaclor, clindamycin, benzylpenicyllin, metronidazole and tetracycline. The lowest range of minimum inhibitory concentration (MIC) (0.026-0.125 microg mL(-1)) was observed against amoxicillin + clavulanate and clindamycin. The lowest MIC 90 was observed against clindamycin (0.064 microg mL(-1)). One strain was resistant to erythromycin and eight strains were resistant to azythromycin. CONCLUSION: Porphyromonas gingivalis pathogen is isolated with frequency from root canals of infected teeth with periapical abscesses. Amoxicillin, as well as amoxicillin-clavulanic acid and benzylpenicillin were effective against P. gingivalis.

Adolescent↗
PubMed2000

The enigma of cobalamin (Vitamin B12) biosynthesis in Porphyromonas gingivalis. Identification and characterization of a functional corrin pathway.

The ability of Porphyromonas gingivalis to biosynthesize tetrapyrroles de novo has been investigated. Extracts of the bacterium do not possess activity for 5- aminolevulinic-acid dehydratase or porphobilinogen deaminase, two key enzymes involved in the synthesis of uroporphyrinogen III. Similarly, it was not possible to detect any genetic evidence for these early enzymes with the use of degenerate polymerase chain reaction. However, the bacterium does appear to harbor some of the enzymes for cobalamin biosynthesis since cobyric acid, a pathway intermediate, was converted into cobinamide. Furthermore, degenerate polymerase chain reaction with primers to cbiP, which encodes cobyric-acid synthase, produced a fragment with a high degree of identity to Salmonella typhimurium cbiP. Indeed, the recently released genome sequence data confirmed the presence of cbiP together with 14 other genes of the cobalamin pathway. A number of these genes were cloned and functionally characterized. Although P. gingivalis harbors all the genes necessary to convert precorrin-2 into cobalamin, it is missing the genes for the synthesis of precorrin-2. Either the organism has a novel pathway for the synthesis of precorrin-2, or more likely, it has lost this early part of the pathway. The remainder of the pathway may be being maintained to act as a salvage route for corrin synthesis.

Base Sequence↗
PubMed1997

The use of a 16s rDNA directed PCR for the detection of endodontopathogenic bacteria.

The study evaluates a 16S rDNA directed polymerase chain reaction (PCR) to detect and differentiate bacteria in necrotic root canal samples. The examination focused on species that are fastidious concerning culture or are difficult to differentiate after culturing by biochemical methods. In the described PCR assay, a universal 16S rDNA directed forward primer in combination with a highly specific reversed one was used to amplify taxon specific gene fragments of 230 to 950 bp length. A similar PCR reaction using a universal 16S rDNA reversed primer was also established to demonstrate bacteria in root canal specimens in general. A first application of this method revealed the presence of Actinomycetales-species, Fusobacterium nucleatum, "Streptococcus milleri," and, presumably for the first time described in infected root canals, Bacteroides forsythus. The identity of amplificons was confirmed by generating sequence information and comparison to gene databanks.

Adult↗
PubMed1996

Demonstration that 1-trans-epoxysuccinyl-L-leucylamido-(4-guanidino) butane (E-64) is one of the most effective low Mr inhibitors of trypsin-catalysed hydrolysis. Characterization by kinetic analysis and by energy minimization and molecular dynamics simulation of the E-64-beta-trypsin complex.

1-trans-Epoxysuccinyl-L-leucylamido(4-guanidino)butane (E-64) was shown to inhibit beta-trypsin by a reversible competitive mechanism; this contrasts with the widely held view that E-64 is a class-specific inhibitor of the cysteine proteinases and reports in the literature that it does not inhibit a number of other enzymes including, notably, trypsin. The K1, value (3 x 10(-5) M) determined by kinetic analysis of the hydrolysis of N alpha-benzoyl-L-arginine 4-nitroanilide in Tris/HCl buffer, pH 7.4, at 25 degrees C, I = 0.1, catalysed by beta-trypsin is comparable with those for the inhibition of trypsin by benzamidine and 4-aminobenzamidine, which are widely regarded as the most effective low Mr inhibitors of this enzyme. Computer modelling of the beta-trypsin-E64 adsorptive complex, by energy minimization, molecular dynamics simulation and Poisson-Boltzmann electrostatic-potential calculations, was used to define the probable binding mode of E-64; the ligand lies parallel to the active-centre cleft, anchored principally by the dominant electrostatic interaction of the guanidinium cation at one end of the E-64 molecule with the carboxylate anion of Asp-171 (beta-trypsin numbering from Ile-1) in the S1-subsite, and by the interaction of the carboxylate substituent on C-2 of the epoxide ring at the other end of the molecule with Lys-43; the epoxide ring of E-64 is remote from the catalytic site serine hydroxy group. The possibility that E-64 might bind to the cysteine proteinases clostripain (from Clostridium histolyticum) and alpha-gingivain (one of the extracellular enzymes from phyromonas gingivalis) in a manner analogous to that deduced for the beta-trypsin-E-64 complex is discussed.

Amino Acid Sequence↗
PubMed1996

Characterization of Prevotella intermedia and Prevotella nigrescens by enzyme production, restriction endonuclease and ribosomal RNA gene restriction analyses.

Restriction endonuclease analysis, rRNA gene restriction analysis (ribotyping), multilocus enzyme electrophoresis and lipase production were investigated for their potential to differentiate isolates belonging to the closely-related species Prevotella intermedia and Prevotella nigrescens. Of 122 strains identified originally as P. intermedia, 52 were assigned to P. intermedia and 68 to P. nigrescens using multilocus enzyme electrophoresis. All 39 P. intermedia and 52 out of 53 P. nigrescens tested produced lipase. Restriction endonuclease analysis identified clonal variants, but did not facilitate the differentiation of strains into species. Taq I ribotyping of 99 strains revealed that all P. intermedia demonstrated a species-specific fragment of 0.40 kbp, which was always associated with a second fragment of 0.57 kbp, and all P. nigrescens tested shared a species-specific fragment of 2.21 kbp. Two strains atypical by multilocus enzyme electrophoresis had none of the above species-specific fragments. Thus, lipase production and restriction endonuclease analysis did not distinguish between P. intermedia and P. nigrescens, but Taq I ribotyping did and also allowed the characterization of individual strains.

Bacterial Typing Techniques↗
PubMed1995

Catalytic site targeted mutagenesis of the alpha-gingivain gene of Porphyromonas gingivalis using Tn-4351 to generate isogenic mutants.

The extracellular proteinases of the anaerobe Porphyromonas gingivalis, are implicated in the destruction of host defence mechanisms in periodontitis. We have previously purified one of these enzymes, alpha-gingivain, and established that it belongs to the cysteine proteinase family of enzymes. In the present study, transposon Tn4351 was used to alter the open reading frame encoding a region that includes the catalytic site of alpha-gingivain by targeted mutagenesis. Escherichia coli HB101 which harbours R751 was used to introduce the transposon into P. gingivalis ATCC 33277 by conjugal transfer. E. coli was transformed using the altered plasmid with a Cla I site insertion of a sequence common to the catalytic site histidine or cysteine of many cysteine proteinases. The frequency of the transconjugation was 4.5 x 10(5) while the recipient viable counts comprised 60% of the original P. gingivalis. The result of this targeted mutagenesis was inactivation of gingivains such that some colonies on skimmed-milk agar plates showed no clear surrounding zones of hydrolysis and their normal catalytic activity towards L-BAPNA was destroyed.

Journal Article↗
PubMed1995

Molecular analysis of surface-associated enzymes of Porphyromonas gingivalis.

There is now increasing evidence that surface-associated enzymes, previously considered to be involved in intermediary metabolism or virulence, play a role in physiological reactions such as signal transduction, transport systems, and metabolic processes. Herein we report the molecular aspects of two such enzymes, the cysteine proteinase gingivain and NAD-dependent glutamate dehydrogenase of Porphyromonas gingivalis. The gdh gene comprises an open reading frame of 1,335 base pairs that encodes a 49,000-M(r) protein of 445 amino acids. The gdh gene showed high homology (78.3%) with that of Clostridium symbiosum. Optimal codons accounted for 35.9% of the total codon usage, indicating high expression of this enzyme. These data are currently being used to carry out targeted mutagenesis, which was established here for gingivain. Conditions for targeted mutagenesis within the histidine domain of the catalytic site of gingivain using Tn 4351 was successfully achieved. Consequently, the catalytic functions, such as gingivain's capacity to hydrolyze the synthetic substrate alpha-benzoyl-arginine-4-nitroanilide, were disrupted.

Amino Acid Sequence↗
PubMed1995

The biochemical milieu of the host in the selection of anaerobic species in the oral cavity.

The periodontal pocket provides a unique structural site for studies on host/bacterial interactions. The pocket is colonized by a complex but characteristic anaerobic bacterial flora. Many new taxa have been described that have now been supported by comparative rRNA sequence analysis. Within recent years, several molecular approaches have been used to describe both cultivable and noncultivable species, and new genotypes have been reported. Microbial activity rather than the mere presence of a microorganism at a site must be a major factor in the process of disease development. Information on metabolic activities of species and identification of substrates are therefore essential to elucidate the complex interactions that are likely to occur in vivo. We have been using a variety of analytical procedures such as 13C substrate-enrichment nuclear magnetic resonance, 14C isotopic labeling experiments, enzyme assays, impedance measurements, and various chromatographic and electrophoretic procedures to study key species of this predominantly asaccharolytic flora. Results have so far indicated a major role for cationic and anionic acids as sources of energy, but the mechanisms of substrate processing may differ significantly between species. In this ecosystem, crevicular fluid is the likely source of nutrients for species. Components of this fluid appear to have a role in the selection of species in subgingival sites.

Amino Acids↗
PubMed1995

Oligonucleotide probes to the 16S ribosomal RNA: implications of sequence homology and secondary structure with particular reference to the oral species Prevotella intermedia and Prevotella nigrescens.

Eight oligonucleotides based upon regions of the small subunit 16S ribosomal RNA gene sequences were analysed against a background of their position within the molecule and their two-dimensional structure to rationalise their use in recognising Prevotella intermedia and Prevotella nigrescens. The 41 clinical isolates from both oral and respiratory sites and two reference strains were subjected to DNA-DNA hybridisation and multilocus enzyme electrophoresis to confirm their identity. Alignment of oligonucleotide probes designated I Bi-2 to I Bi-6 (for P. intermedia) and 2Bi-2 (for P. nigrescens) with the 16S rRNA suggested that these probes lacked specificity or were constructed from hypervariable regions. A 52-mer oligonucleotide (designated Bi) reliably detected both species. Because of the high degree of concordance between the 16S rRNAs of both species, it was necessary to vary the stringency of hybridisation conditions for detection of both species. Thus probe I Bi-I recognised P. intermedia while I Bi-I detected both P. intermedia and P. nigrescens at low stringency. However, under conditions of high stringency only P. nigrescens was recognised by probe 2Bi-I. These probes were highly specific and did not hybridise with DNA from the closely related P. corporis, nor other periodontal pathogens such as Fusobacterium nucleatum, Actinobacillus actinomycetemcomitans, Treponema denticola and several pigmented species such as Prevotella melaninogenica, P. denticola, P. loescheii, Porphyromonas asaccharolytica, Py. endodontalis, Py. gingivalis, Py. levii, and Py. macacae.

Bacterial Typing Techniques↗
PubMed1995

Stable-isotope studies of glutamate catabolism in Fusobacterium nucleatum.

Catabolism of glutamate was investigated in Fusobacterium nucleatum, an anaerobic micro-organism that is strongly implicated in periodontal disease. The distribution of labels in acetate and butyrate derived from [13C]glutamates was determined by NMR spectroscopy and MS. The label from L-[5-13C]glutamate was not incorporated, whereas C-1 of acetate and butyrate were efficiently labelled by L-[1-13C]glutamate; these results indicated that the hydroxyglutarate pathway predominated. In butyrate, enrichment at C-3 was smaller than C-1; that this was not due to participation of the methylaspartate pathway was demonstrated by the incorporation of label from L-[4-13C]glutamate into only C-2 of acetate and C-4 (major)/C-2 (minor) of butyrate. The presence of label at a second site in butyrate was attributed to the synthesis of butyrate from acetate and verified by the incorporation of label from [1,2-13C2]- and [2H3]-acetate.

Acetates↗
PubMed1994

Malate dehydrogenase and glucose-6-phosphate dehydrogenase, key markers for studying the genetic diversity of Actinobacillus actinomycetemcomitans.

Cell-free extracts of strains belonging to the 5 serotypes of A. actinomycetemcomitans were screened for several enzymes. Enzymes representative of the pentose phosphate pathway/hexose monophosphate shunt and the TCA cycle were present. Of these glucose-6-phosphate dehydrogenase (G6PDH) and malate dehydrogenase (MDH) were the most readily detected and stable. MDH and G6PDH retained more than 50% of their activities at alkaline pHs (10-11) for up to 6 h and 3 h at 25 degrees C, respectively, while at pH 6.5, 50% of their activities were lost within 2-3 h. The Km for malate oxidation catalysed by MDH was 5.8 x 10(-4) M while that for glucose-6-phosphate oxidation was 2.0 x 10(-4) M. The pH optima for MDH and G6PDH oxidation activities were 10 and 9.5, respectively. Among the 5 designated serotypes of A. actinomycetemcomitans three groups were delineated by multilocus enzyme electrophoresis using MDH and G6PDH.

Aggregatibacter actinomycetemcomitans↗