Characterisation of the gene encoding type II DNA topoisomerase from Leishmania donovani: a key molecular target in antileishmanial therapy

The gene encoding type II DNA topoisomerase from the kinetoplastid hemoflagellated protozoan parasite Leishmania donovani (LdTOP2) was isolated from a genomic DNA library of this parasite. DNA sequence analysis revealed an ORF of 3711 bp encoding a putative protein of 1236 amino acids with no introns. The deduced amino acid sequence of LdTOP2 showed strong homologies to TOP2 sequences from other kinetoplastids, namely Crithidia and Trypanosoma spp. with estimated identities of 86 and 68%, respectively. LdTOP2 shares a much lower identity of 32% with its human homologue. LdTOP2 is located as a single copy on a chromosome in the 0.7 Mb region in the L.donovani genome and is expressed as a 5 kb transcript. 5'-Mapping studies indicate that the LdTOP2 gene transcript is matured post-transcriptionally with the trans-splicing of the mini-exon occurring at -639 from the predicted initiation site. Antiserum raised in rabbit against glutathione S-transferase fusion protein containing the major catalytic portion of the recombinant L.donovani topoisomerase II protein could detect a band on western blots at approximately 132 kDa, the expected size of the entire protein. Use of the same antiserum for immunolocalisation analysis led to the identification of nuclear, as well as kinetoplast, antigens for L.donovani topoisomerase II. The in vitro biochemical properties of the full-length recombinant LdTOP2 when overexpressed in E.coli were similar to the Mg(II) and ATP-dependent activity found in cell extracts of L.donovani.

Gene expression of the key enzymes of melatonin synthesis in extrapineal tissues of the rat

Besides the pineal gland, melatonin is reported to be produced in a number of extrapineal sites, where it could act as an intracellular mediator or paracrine signal in addition to its endocrine effects. In view of the suggested immunoregulatory role of melatonin, we compared lymphoid organs and several other tissues of the rat for their potential to synthesize melatonin. Using the reverse transcription-polymerase chain reaction (RT-PCR) method, we determined the tissue-specific expression of mRNAs encoding two key enzymes of the melatonin biosynthesis: serotonin-N-acetyltransferase (NAT) and hydroxyindole-O-methyltransferase (HIOMT). The minimal number of PCR cycles required to obtain a positive signal served as a measure for the abundance of a given mRNA. NAT and HIOMT mRNAs were detected in all tested tissues at high numbers of PCR cycles (40 and 45, respectively). At 35 cycles, only gut, testis, spinal cord, raphe nuclei, stomach fundus and striatum yielded positive signals for both enzymes. In conclusion, the presence of NAT and HIOMT mRNAs in a wide range of tissues corroborates and extends the notion of extrapineal melatonin synthesis. Comparatively low levels of the HIOMT messages in lymphoid organs, however, indicate a limited significance of melatonin synthesis within the immune system.

A 1.8 A resolution structure of pig muscle 3-phosphoglycerate kinase with bound MgADP and 3-phosphoglycerate in open conformation: new insight into the role of the nucleotide in domain closure

3-phosphoglycerate kinase (PGK) is a typical kinase with two structural domains. The domains each bind one of the two substrates, 3-phosphoglycerate (3-PG) and MgATP. For the phospho-transfer reaction to take place the substrates must be brought closer by a hinge-bending domain closure. Open and closed structures of the enzyme with different relative domain positions have been determined from different species, but a comprehensive description of this conformational transition is yet to be attained. Crystals of pig muscle PGK in complex with MgADP and 3-phosphoglycerate were grown under the conditions which have previously resulted in crystals of the closed, catalytically competent conformation of Trypanosoma brucei PGK. The X-ray structure of the pig muscle ternary complex was determined at 1.8 A and the model was refined to R=20.8% and Rfree=24.1%. Contrary to expectation, however, it represents an essentially open conformation compared to that of T. brucei PGK. In addition, the beta-phosphate group of ADP is mobile in the new structure, in contrast to its well-defined position in T. brucei PGK. An extensive comparison of the ternary complexes from these remote species has been carried out in order to establish general differences between the two conformations and is reported here. A second pair of the open and closed structures was also compared. These analyses have made it possible to define several characteristic changes which accompany the structural transition, in addition to those identified previously: (1) the operation of a hinge at beta-strand L in the inter-domain region which greatly affects the relative domain positions; (2) the rearrangement and movement of helix 8, regulated through the interactions with the nucleotide phosphate; and (3) the existence of another hinge between helix 14 and the rest of the C-terminal part of the chain, which allows fine adjustment of the N-domain position. The main hinge at beta-strand L acts in concert with the C-terminal hinge at helix 7 described previously. Simultaneous interactions of the nucleotide phosphate groups with the loop that precedes helix 8, beta-strand J and the N terminus of helix 13 are required for propagation of the nucleotide effect towards the beta-strand L molecular hinge. A detailed description of the role of nucleotide binding in the hinge operation is presented.

Stabilizing C-terminal tails on AraC

We examined the effects of the metabolic stability of random sequences appended to the C-terminus of the dimerization domain of the regulatory protein of the Escherichia coli arabinose operon, AraC. Genetic scoring utilized the trans dominant negative effect of the dimerization domain on the activity of intact AraC, and physical scoring used sodium dodecyl sulfate (SDS) gel electrophoresis. We confirmed previous results obtained with Arc and lambda repressors that C-terminal charged residues tend to be stabilizing and that hydrophobic residues are destabilizing. Additionally, we found that the provision of a single, charged C-terminal residue conferred significant stability that was independent of interior sequence. Hence, it appears that in the engineering of proteins, flexible tails may be freely added, with only the identity of the C-terminal amino acid being restricted. Proteins 2001;42:177-181.

Apoptosis in squamous cell carcinoma of the lung: correlation with survival and clinicopathological features

AIMS

Apoptosis is recognised as a physiological mechanism for controlling cell numbers and its subversion is thought to contribute to carcinogenesis. The aims of this study were to measure the apoptotic index (AI) in a series of squamous cell carcinomas (SCCs) of the lung using standard histological staining and confirm this by immunohistology using an antibody to an apoptosis specific protein (ASP), and to seek to correlate the AI with clinicopathological parameters.

METHODS

Sections of 134 SCCs were stained by haematoxylin and eosin (H&E) for counting apoptotic bodies of determine the AI (number of apoptotic bodies/10,000 tumour cells); 26 of these were also stained with anti-ASP antibody and the proportion of ASP positive cells counted. Clinical data were obtained from hospital notes.

RESULTS

The mean AI obtained by H&E staining of all 134 SCCs was 30.3 (SD, 24.75). Anti-ASP staining allowed easy identification of apoptotic bodies, and generated a somewhat higher index (mean, 51.4; SD 39); this was not a result of the selection of tumours because the AI by H&E in the subset stained with anti-ASP was 31.1. Regression analysis showed that the correlation between the two values of AI was highly significant (Rs = 0.9760; p < 0.001), indicating that the two methods were both reliable measures of apoptosis but that the anti-ASP staining is the more sensitive method. The tumours were grouped into high AI (> 50) and low AI (< 50) and survival analysis was carried out. The mean survival of the high AI group was 109 weeks and of the low AI group 72 weeks (p = 0.036).

CONCLUSIONS

Anti-ASP staining is a reliable, easy, and sensitive method for assessing apoptosis in tumour sections and confirms the validity of the AI obtained by H&E staining. AI is a guide to the behaviour of SCCs of the lung.

Substituting leucine for alanine-86 in the tether region of the iron-sulfur protein of the cytochrome bc1 complex affects the mobility of the [2Fe2S] domain

Mutating three conserved alanine residues in the tether region of the iron-sulfur protein of the yeast cytochrome bc(1) complex resulted in 22-56% decreases in enzymatic activity [Obungu et al. (2000) Biochim. Biophys. Acta 1457, 36-44]. The activity of the cytochrome bc(1) complex isolated from A86L was decreased 60% compared to the wild-type without loss of heme or protein and without changes in the 2Fe2S cluster or proton-pumping ability. The activity of the bc(1) complex from mutant A92R was identical to the wild-type, while loss of both heme and activity was observed in the bc(1) complex isolated from mutant A90I. Computer simulations indicated that neither mutation A86L nor mutation A92R affects the alpha-helical backbone in the tether region; however, the side chain of the leucine substituted for Ala-86 interacts with the side chain of Leu-89. The Arrhenius plot for mutant A86L was apparently biphasic with a transition observed at 17-19 degrees C and an activation energy of 279.9 kJ/mol below 17 degrees C and 125.1 kJ/mol above 17 degrees C. The initial rate of cytochrome c(1) reduction was lowered 33% in mutant A86L; however, the initial rate of cytochrome b reduction was unaffected, suggesting that movement of the tether region of the iron-sulfur protein is necessary for maximum rates of enzymatic activity. Substituting a leucine for Ala-86 impedes the unwinding of the alpha-helix and hence movement of the tether.

Cyclooxygenase expression in the gallbladder

The COX expressions were evaluated separately in the epithelium and in the stroma of gallbladder cancer, chronic cholecystitis, xanthogranulomatous cholecystitis (XGC) and the normal gallbladder. In normal gallbladder COX-2 expression rate was significantly higher in the epithelium than in the stroma. The COX-2 expression rate in the epithelium of non-cancerous adjacent epithelium to cancerous lesion was significantly lower than those not only of cancer, but also chronic cholecystitis, XGC and normal gallbladder. In stroma, the COX-2 expression rate in cancer, chronic cholecystitis and XGC were significantly higher than that of the normal gallbladder. The rate in non-cancerous adjacent stroma to cancer is significantly lower than that of cancer and XGC. However, the difference of rate between of normal and of chronic cholecystitis was not significant. The COX-2 expression rates were significantly higher in both the epithelium and the stroma in the well and moderately differentiated cancer group than in the poorly and undifferentiated cancer group. Our results suggest that COX-2 expression in the gallbladder may be regulated by various factors and not directly related to carcinogenesis. The significance of its repression in the non-cancerous adjacent tissue to cancer lesion should be re-evaluated.

Infantile-onset leukoencephalopathy with discrepant mild clinical course

Four children characterised by megalencephaly and cerebral leukoencephalopathy with infantile onset, defined on the basis of clinical and neuroimaging findings are reported. The course of the disease is characterised by stabilization of the macrocephaly and slow clinical deterioration. The CT scan findings include supratentorial diffuse hypodensities in the white matter and swelling. The characteristic MRI findings include the discrepant severity in comparison with the clinical picture, diffuse supratentorial white matter abnormalities with subcortical cysts. The basic defect of the disease is unknown. Considering the high rate of consanguinity among the parents and the presence of two affected sibs in one family, an autosomal recessive inheritance is assumed. We report four unrelated cases of this entity.

Fraser-cryptophthalmos syndrome

Fraser or Cryptophthalmos syndrome is a variable syndrome to the extent that cryptophthalmos might not be present in all cases. However, the main features are a "hidden eye", other craniofacial abnormalities, renal abnormalities, syndactyly and abnormal genitalia. It may be classified as isolated cryptophthalmos or cryptophthalmos sequence and cryptophthalmos syndrome. The cryptophthalmos syndrome has an autosomal recessive mode of inheritance. Isolated cryptophthalmos has been reported as an autosomal dominant trait. Prenatal diagnosis is possible using ultrasonography and fetoscopy. We report three cases of cryptophthalmos. One with renal agenesis had cryptophthalmos syndrome and the other two had isolated cryptophthalmos or cryptophthalmos sequence.

Surface enhanced Raman scattering of 2,2' biquinoline adsorbed on colloidal silver particles

Surface enhanced Raman scattering (SERS) in silver sol and normal Raman spectra in the bulk and in solution of 2,2' biquinoline (BQ) molecule have been investigated. The observed Raman bands along with their corresponding FTIR bands have been assigned based on the established assignments of the vibrational bands of the parent napthalene and quinoline molecules. Existence of both the cis and trans form of the BQ molecule in solution and in the bulk are inferred from the normal Raman and FTIR spectra, whereas SERS study reveal that in the surface adsorbed state the molecule exists in the cis form. Definite evidence of the charge transfer interaction to the overall contribution in the SER enhancement have been reported. The excitation profile also supports the CT interaction. Estimated enhancement factor of the principal SERS bands indicate that the molecule is adsorbed on the silver surface through both the nitrogen atoms with the molecular plane almost perpendicular to the surface. This preferred orientation of the molecule is in conformity with its existence in the cis form in the surface adsorbed state.

Evaluation of a PCR primer based on the isocitrate dehydrogenase gene for detection of Helicobacter pylori in feces

In order to improve detection and identification of Helicobacter pylori in highly contaminated samples, we evaluated new specific primers based on the DNA base sequence within the isocitrate dehydrogenase (icd) gene to amplify a 1,200-bp DNA segment. The specificity of the icd primer was tested against DNA derived from various bacteria, including 7 Helicobacter species and a panel of 1 gram-variable, 2 gram-positive, and 16 gram-negative bacteria, as well as DNA from houseflies and feces from H. pylori-negative patients. The primers permitted the detection of all clinical H. pylori isolates tested, but no reactions were observed with negative controls. Several procedures for DNA extraction from feces were evaluated using PCR with icd primers. The lower limits of detection of H. pylori DNA from two different sources containing the same number of H. pylori organisms, a pure culture and feces spiked with H. pylori, were established for each extraction method tested. The results were 8.0 x 10(3) CFU/ml for cultures of pure H. pylori, and 8.0 x 10(6) CFU/ml for H. pylori from feces, using the phenol-chloroform method; 8.0 x 10(2) and 7.0 x 10(3) CFU/ml, respectively, for a glass matrix and chaotropic solution protocol; 8.0 x 10(2) and 7.0 x 10(3) CFU/ml, respectively, for the QIAamp tissue kit; and 5.0 x 10(2) and 5.0 x 10(3) CFU/ml, respectively, for the XTRAX DNA extraction kit. We conclude that the use of the icd gene as a primer for PCR represents a specific and sensitive assay for detection of H. pylori in highly contaminated samples.

Structure of human transthyretin complexed with bromophenols: a new mode of binding

The binding of two organohalogen substances, pentabromophenol (PBP) and 2,4,6-tribromophenol (TBP), to human transthyretin (TTR), a thyroid hormone transport protein, has been studied by in vitro competitive binding assays and by X-ray crystallography. Both compounds bind to TTR with high affinity, in competition with the natural ligand thyroxine (T(4)). The crystal structures of the TTR-PBP and TTR-TBP complexes show some unusual binding patterns for the ligands. They bind exclusively in the 'reversed' mode, with their hydroxyl group pointing towards the mouth of the binding channel and in planes approximately perpendicular to that adopted by the T(4) phenolic ring in a TTR-T(4) complex, a feature not observed before. The hydroxyl group in the ligands, which was previously thought to be a key ingredient for a strong binding to TTR, does not seem to play an important role in the binding of these compounds to TTR. In the TTR-PBP complex, it is primarily the halogens which interact with the TTR molecule and therefore must account for the strong affinity of binding. The interactions with the halogens are smaller in number in TTR-TBP and there is a decrease in affinity, even though the interaction with the hydroxyl group is stronger than that in the TTR-PBP complex.

pH-Dependent Surface-Enhanced Raman Scattering of 8-Hydroxy Quinoline Adsorbed on Silver Hydrosol

Surface-enhanced Raman scattering (SERS) of 8-hydroxy quinoline (HQ) adsorbed on silver hydrosols are compared with the FTIR and normal Raman spectrum in the bulk and in solution. Definite evidence of the charge transfer interaction to the overall contribution in the SER enhancement has been reported. The excitation profile study also supports the evidence of a charge transfer interaction. The effect of pH variation on the SER band intensity is explained in terms of chemisorption of the molecule on bare and chlorinated silver surfaces. The apparent enhancement factor calculations of the principal Raman bands indicate that in the surface-adsorbed state, an HQ molecule is oriented neither flat nor vertical to the silver surface but is tilted. Copyright 2000 Academic Press.

Structural basis for uracil DNA glycosylase interaction with uracil: NMR study

Two dimensional (2D) NMR and molecular dynamics simulations have been used to determine the three dimensional (3D) structure of a hairpin DNA, d-CTA-GAGGATCC-TUTT-GGATCCT (22mer; abbreviated as U2-hairpin), which has uracil at the second position from the 5' end of the tetraloop. The(1)H resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimization procedures have been used to describe the 3D structure of U2-hairpin. This study establishes that the stem of the hairpin adopts a right-handed B-DNA conformation, while the T(12)and T(15)nucleotides stack upon 3' and 5' ends of the stem, respectively. Further, T(14)stacks upon both T(12)and T(15). Though U(13)partially stacks upon T(14), no stacking interaction is observed between U(13)and T(12). All the individual nucleotide bases belonging to the stem and T(12)and T(15)of the loop adopt ' anti ' conformation with respect to their sugar moiety, while the U(13)and T(14)of the loop are in ' syn ' conformation. The turning phosphate in the loop is located between T(13)and T(14). This study and a concurrent NMR structural study on yet another hairpin DNA d-CTAGAGGAATAA-TTTU-GGATCCT (22mer; abbreviated as U4-hairpin), with uracil at the fourth position from the 5' end of the tetraloop throw light upon various interactions which have been reported between Escherichia coli uracil DNA glycosylase (UDG) and uracil containing DNA. The epsilon of T(12)and alpha, beta, gamma, epsilon and zeta of U(13)and gamma of T(14), which partially influence the local conformation of U(13)in U2-hairpin are all locked in ' trans ' conformation. Such stretched out backbone conformation in the vicinity of U(13)could be the reason as to why the U2-hairpin is found to be the poor substrate for its interaction with UDG compared to the other substrates in which the uracil is at first, third and fourth positions of the tetraloop from its 5' end, as reported earlier by Vinay and Varshney. This study shows that UDG actively promotes the flipping of uracil from a stacked conformation and rules out the possibility of UDG recognizing the flipped out uracil bases.

Stage-specific development of a novel adenosine transporter in Leishmania donovani amastigotes

Leishmania donovani, like all other kinetoplastida, is a purine auxotroph. Comparative studies of adenosine transport in L. donovani amastigotes and promastigotes revealed that, unlike the promastigote stage, the amastigote possesses two distinct adenosine transporters (T(1) and T(2)) both with high affinities (K(m), 1.14+/-0.05 and 2. 09+/-0.13 microM, respectively). One of these transporters (T(1)) appears to be identical with the adenosine/pyrimidine nucleoside transporter of the promastigote reported earlier. The other transporter (T(2)) is specific for the amastigote stage and transports only purine nucleosides. The biological significance of this stage-specific development of the second adenosine transporter has been briefly discussed.

Rapid detection of respiratory viruses by centrifugation enhanced cultures from children with acute lower respiratory tract infections

BACKGROUND

Acute respiratory tract infection (ARI) is the major cause of morbidity and mortality in young children in developing countries. Information on viral aetiology in ARI in India is very limited.

OBJECTIVE

The aim of the study was to define the role of viruses in acute lower respiratory tract infections (ALRTI) in children in India using centrifugation enhanced cultures followed by indirect immunofluorescence (IIF).

STUDY DESIGN

Nasopharyngeal aspirates (NPAs) were collected from children from September 1995 to April 1997, attending paediatric clinic of All India Institute of Medical Sciences (AIIMS) with symptoms of ALRTI. Virus isolation was done by centrifugation enhanced cultures using HEp-2, LLC-MK2 and MDCK cells. The viruses were identified at 24-48 h post inoculation by IIF staining using monoclonal antibodies to respiratory syncytial virus (RSV), parainfluenza virus (PIV), influenza virus and adenovirus.

RESULTS

Of 200 NPA samples, 89 (44.5%) were positive for one or more viral pathogens. RSV was detected in 34 (17%) of all ALRTI cases followed by influenza viruses in 29 (14.5%), PIVs in 23 (11.5%) and adenoviruses in three (1.5%). In 79 children with bronchiolitis, RSV was most frequently isolated (25%) pathogen, while in bronchopneumonia cases (101) the most common viral pathogen was influenza virus (17%). In eight cases (4%) of ALRTI dual infections were detected. In 100 NPA specimens IIF staining on direct cell smears was carried out and viruses were detected in only 17%. RSV and influenza virus infection peaked from September to December, where as PIV infections were more frequent from January to April.

CONCLUSION

Respiratory viruses accounted for 44.5% of cases of ALRTI in India and the results of viral aetiology could be given in 24-48 h using centrifugation enhanced cultures. RSV was the most common viral agent associated with ALRTI in children under 5 years of age with greater association with bronchiolitis.

Evaluation of 2-(methylaminosulfonyl)-1-(arylsulfonyl)hydrazines as anticancer agents

Seven new 2-(methylaminosulfonyl)- 1-(arylsulfonyl)hydrazines were prepared and evaluated as potential antitumor agents in vivo against murine Ehrlich ascites carcinoma (EAC). Borderline in vivo activity in EAC was exhibited by two compounds. All of them were screened in vitro against a battery of human tumor cell lines at the National Cancer Institute (NCI), USA. One of them, namely compound 2f(NSC No. 649 752) displayed highly significant specificity in two different cell lines as non-small cell lung cancer line HOP-18 and in CNS cancer line SNB-19. The compounds assessed in vitro for anti-HIV activity also at the NCI, however, have not reached the criteria of significant activity. The alkylating activity of the compounds was determined by measuring the absorbance of the alkylated product of 4-(4-nitrobenzyl)pyridine. It was found that they are capable of acting as chemical alkylating agents.

Inhibition of phosphatase activity by positively-charged cyclodextrins

[formula: see text] Aminocyclodextrins are known to bind phosphate esters such as phosphotyrosine and p-nitrophenyl phosphate. This paper describes the inhibition of phosphate ester hydrolysis, as catalyzed by lambda-protein phosphatase and acid phosphatase, that is caused by such binding interactions. ROESY studies provide structural information about the cyclodextrin-aryl phosphate complexes. In addition, these experiments are used to generate approximations of the rates of dissociation of the noncovalent complexes.

CD40 and Bcl2 expression in squamous cell carcinoma of the lung: correlation with apoptosis, survival, and other clinicopathological factors

CD40 is a cell surface receptor which, when ligated, modulates apoptosis in some cell types, perhaps via activation of the expression of members of the Bcl2 gene family. This study sought to determine whether expression of CD40 in a series of 134 squamous cell carcinomas (SCCs) of the lung was related to apoptosis or clinical parameters, either alone or in connection with Bcl2 expression. Sections of SCCs were stained for CD40 and Bcl2 by immunohistochemical techniques. An index was determined for these two markers by counting stained and unstained malignant cells under high power. Sections were also stained by haematoxylin and eosin for determination of the apoptotic index by counting apoptotic bodies. About 40 per cent of SCCs expressed CD40 in at least some of the malignant cells, with about 10 per cent essentially uniformly stained. Similar proportions expressed Bcl2, with a tendency for expression to be mutually excluisve. Apoptosis did not correlate with CD40 expression, nor was there evidence of a co-operative or an antagonistic effect with Bcl2. Bcl2 expression, on the other hand, correlated significantly with the apoptosis score. CD40 expression showed no significant relationship with survival or any other clinicopathological parameter except ploidy. Bcl2 expression, however, correlated with longer survival. It is concluded that CD40 expression in SCC of the lung does not by itself relate to apoptosis, nor is it a useful indicator of prognosis.