Utility of polymerase chain reaction using two probes for rapid diagnosis of tubercular pleuritis in comparison to conventional methods

We have used polymerase chain reaction (PCR) with IS6110 and a new set of primers from an insertion element like repetitive sequence, (TRC4) to detect Mycobacterium tuberculosis in pleural effusion samples from 50 patients having pleuritis. The results of PCR were compared with the results of conventional methods like smear, culture and adenosine deaminase activity. Thirty six specimens were positive and 14 were negative by PCR. Among the 36 samples, 33 were from patients with clinical evidence of tuberculosis including response to anti-tuberculosis therapy. Only six samples were positive by the gold standard which is culture, and three were positive by smear. The measurement of adenosine deaminase activity classified 19 samples as positives. The overall sensitivity and specificity of PCR was 100 and 85 per cent respectively. PCR using IS6110 and TRC4 primers is a sensitive test as compared to conventional tests for detection of M. tuberculosis from pleural fluid samples of patients with tubercular pleuritis

The fate of Mycobacterium tuberculosis in activated human macrophages

Human peripheral blood monocytes, that are unstimulated in vitro, permit free multiplication of intracellular Mycobacterium tuberculosis after 72 h in culture. There was no killing of bacilli in the intracellular environment even after in vitro activation of monocytes with a cocktail of lipopolysaccharide, phorbol myristate acetate, interferon gamma and tumour necrosis factor-alpha. We also tested the ability of adenosine triphosphate (ATP) in reducing the intracellular viability of mycobacteria. Infected monocytes upon ATP treatment underwent cell death, but no loss in the intracellular viability of M. tuberculosis or M. smegmatis could be observed

Isolation and characterization of an insertion element-like repetitive sequence specific for Mycobacterium tuberculosis complex

We report the characterization of an insertion-like repetitive sequence containing the clone of Mycobacterium tuberculosis. This repetitive sequence contains seven inverted repeats. Restriction fragment length polymorphism studies using this probe have shown that it is not a highly polymorphic probe but rather shows conservative fingerprint pattern. Out of the 150 strains tested, only three showed different fingerprint patterns. It has several direct and inverted repeats. Homology studies of the putative protein coding region show that this repeat element might code for a metalloproteinase of M. tuberculosis. Homology studies also implicate this repeat element to be from a very essential region of the M. tuberculosis genome participating in recombination. This repeat has been found to be an ideal target for polymerase chain reaction to detect M. tuberculosis

Ginsparg-Wilson Fermions: A study in the Schwinger Model

Qualitative features of Ginsparg-Wilson fermions, as formulated by Neuberger, coupled to two dimensional U(1) gauge theory are studied. The role of the Wilson mass parameter in changing the number of massless flavors in the theory and its connection with the index of the Dirac operator is studied. Although the index of the Dirac operator is not related to the geometric definition of the topological charge for strong couplings, the two start to agree as soon as one goes to moderately weak couplings. This produces the desired singularity in the quenched chiral condensate which appears to be very difficult to reproduce with staggered fermions. The fermion determinant removes the singularity and reproduces the known chiral condensate and the meson mass within understandable errors.Comment: Corrected a few typos and changed some references. Minor changes to the conten

Fermion-scalar interactions with domain wall fermions

Domain wall fermions are defined on a lattice with an extra direction the size of which controls the chiral properties of the theory. When gauge fields are coupled to domain wall fermions the extra direction is treated as an internal flavor space. Here it is found that this is not the case for scalar fields. Instead, the interaction takes place only along the link that connects the boundaries of the extra direction. This reveals a richness in the way different spin particles are coupled to domain wall fermions. As an application, 4-Fermi models are studied using large N techniques and the results are supported by numerical simulations with N=2. It is found that the chiral properties of domain wall fermions in these models are good across a large range of couplings and that a phase with parity-flavor broken symmetry can develop for negative bare masses if the number of sites along the extra direction is finite.Comment: LaTeX, 17 pages, 8 eps figures; comment regarding the width of Aoki phase added in sec. 3; references adde

Development of DNA probes for M. tuberculosis

Attempts were made to develop DNA probes for M. tuberculosis. Random library of M. tuberculosis was constructed in plasmid pGEM -4. Selection of recombinant clones was made by hybridisation with 32P labelled M. tuberculosis probe. Ten recombinant clones were selected on the basis of strong signals from the random library. These 10 clones named pTRC1-10 were subjected to tests for specificity and sensitivity. On this basis, pTRC4 was chosen and this is also, useful in restriction fragment length polymorphism (RFLP) studies

Domain Wall Fermions in Quenched Lattice QCD

We study the chiral properties and the validity of perturbation theory for domain wall fermions in quenched lattice QCD at beta=6.0. The explicit chiral symmetry breaking term in the axial Ward-Takahashi identity is found to be very small already at Ns=10, where Ns is the size of the fifth dimension, and its behavior seems consistent with an exponential decay in Ns within the limited range of Ns we explore. From the fact that the critical quark mass, at which the pion mass vanishes as in the case of the ordinary Wilson-type fermion, exists at finite Ns, we point out that this may be a signal of the parity broken phase and investigate the possible existence of such a phase in this model at finite Ns. The rho and pi meson decay constants obtained from the four-dimensional local currents with the one-loop renormalization factor show a good agreement with those obtained from the conserved currents

On the continuum limit of fermionic topological charge in lattice gauge theory

It is proved that the fermionic topological charge of SU(N) lattice gauge fields on the 4-torus, given in terms of a spectral flow of the Hermitian Wilson--Dirac operator, or equivalently, as the index of the Overlap Dirac operator, reduces to the continuum topological charge in the classical continuum limit when the parameter $m_0$ is in the physical region $0<m_0<2$.Comment: latex, 18 pages. v2: Several comments added. To appear in J.Math.Phy

Domain-wall fermions with U(1)U(1) dynamical gauge fields

We have carried out a numerical simulation of a domain-wall model in $(2+1)$-dimensions, in the presence of a dynamical gauge field only in an extra dimension, corresponding to the weak coupling limit of a ( 2-dimensional ) physical gauge coupling. Using a quenched approximation we have investigated this model at $\beta_{s} ( = 1 / g^{2}_{s} ) =$ 0.5 ( ``symmetric'' phase), 1.0, and 5.0 (``broken'' phase), where $g_s$ is the gauge coupling constant of the extra dimension. We have found that there exists a critical value of a domain-wall mass $m_{0}^{c}$ which separates a region with a fermionic zero mode on the domain-wall from the one without it, in both symmetric and broken phases. This result suggests that the domain-wall method may work for the construction of lattice chiral gauge theories.Comment: 27 pages (11 figures), latex (epsf style-file needed

Identification of the promoter of amidase gene for expression of useful mycobacterial genes

The genetics of mycobacteria has lagged behind because of several reasons. Mycobacteria grow very slowly. their generation time ranging anywhere between 12-24 hrs. Mycobacteria are rather hydrophobic and tend to grow in clusters and there is difficulty in purifying individual cells for genetic analysis. Very few genetic markers have been found in mycobacteria because there is no known naturally occurring genetic exchange in mycobacteria. With the creation of genomic libraries of M. tuberculosis more than 50 genes have been characterised. Many of them are not expressed efficiently in Escherichia coli (E.coli) under the control of their own promoters, since very few mycobacterial promoters are recognised by the E. coli transcription machinery. This clearly shows that mycobacteria use a different system of gene regulation. Understanding the gene regulation of mycobacteria might throw light on the slow growth rate, about their persistence in a resting phase and also about their intracellular survival. Besides this if inducible or strong promoters are identified they can be used in over expression of genes coding for proteins useful in diagnosis and protection