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S Agrawal

Publications and source records attributed to S Agrawal.

At least 55 records · Page 3Linked to original sources
PubMed2001

NMR structure of a 2',5' RNA favors A type duplex with compact C2'endo nucleotide repeat.

In order to provide a structural basis for the unusual properties of 2',5' nucleic acids, especially their unsuitability as information molecules, we report here a high resolution NMR structure of a 2',5' RNA fragment r(GCCGCGGC). It forms an A type duplex with C2'endo compact nucleotide repeat, instead of the familiar C3'endo compact nucleotide (seen in RNA) supporting the deductions made earlier from stereochemical considerations. This data together with the observation that 2',5' nucleic acids require mandatory slide and displacement for duplex and triplex structure formation suggest their reluctance to form the biologically relevant B type duplex. It is argued that this lack of flexibility for helical polymorphism and other inadequacies as a consequence of this may be a contributing factor for the rejection of 2',5' links by nature. The structure exhibits interesting features such as the syn glycosyl conformation for the terminal guanine and a hydrogen bond between O3' hydroxyl and anionic oxygen of the phosphate.

Base Sequence↗
PubMed2001

The 3' end of hepatitis E virus (HEV) genome binds specifically to the viral RNA-dependent RNA polymerase (RdRp).

Hepatitis E virus (HEV) is the major cause of acute epidemic and sporadic hepatitis in the developing world. It is a positive-strand RNA virus with a genome length of about 7.2 kb. The replication mechanism of this virus is virtually unexplored. Identification of the regulatory elements involved in initiation of replication may help in designing specific inhibitors for therapy. In the positive-stranded RNA viruses the initiation of replication requires interaction of the 3' end of genome with its RNA-dependent RNA polymerase (RdRp) and possibly host-derived cofactors for synthesis of the minus-strand replicative intermediate. Secondary structure prediction of the conserved 3' end of the infectious HEV genome was carried out to identify possible stem-loop structures necessary for RNA-protein interaction and the model was confirmed by structure probing experiments. Electrophoretic mobility-shift assays showed specific binding of purified and refolded recombinant HEV RdRp protein to the 3' end of its RNA genome containing the poly(A) stretch. Mutations at the 3' end, in which the stem-loop structures were partially or completely destroyed or recreated revealed that the two stem-loop structures SL1 and SL2 at the 3' end and the poly(A) stretch are necessary for this binding. The interacting nucleotides in such an interaction were further identified by generating footprints of the complex by Pb(II)-induced hydrolysis. This specific binding of viral RdRp to the 3' end of HEV RNA directs the synthesis of complementary-strand RNA and thus such a binding domain might assume the role of a possible cis-acting element as a potential site for the initiation of replication.

3' Untranslated Regions↗
PubMed2001

Effect of 2'-O-methyl antisense ORNs on expression of thymidylate synthase in human colon cancer RKO cells.

Translation of thymidylate synthase (TS) mRNA is controlled by its own protein end-product TS in a negative autoregulatory manner. Disruption of this regulation results in increased synthesis of TS and may lead to the development of cellular drug resistance to TS-directed anticancer agents. As a strategy to inhibit TS expression, antisense 2'-O-methyl RNA oligoribonucleotides (ORNs) were designed to directly target the 5' upstream cis-acting regulatory element (nucleotides 80-109) of TS mRNA. A 30 nt ORN, HYB0432, inhibited TS expression in human colon cancer RKO cells in a dose-dependent manner but had no effect on the expression of beta-actin, alpha-tubulin or topoisomerase I. TS expression was unaffected by treatment with control sense or mismatched ORNs. HYB0504, an 18 nt ORN targeting the same core sequence, also repressed expression of TS protein. However, further reduction in oligo size resulted in loss of antisense activity. Following HYB0432 treatment, TS protein levels were reduced by 60% within 6 h and were maximally reduced by 24 h. Expression of p53 protein was inversely related to that of TS, suggesting that p53 expression may be directly linked to intracellular levels of TS. Northern blot analysis demonstrated that TS mRNA was unaffected by HYB0432 treatment. The half-life of TS protein was unchanged after antisense treatment suggesting that the mechanism of action of antisense ORNs is mediated through a process of translational arrest. These findings demonstrate that an antisense ORN targeted at a critical cis-acting element on TS mRNA can specifically inhibit expression of TS protein in RKO cells.

Colonic Neoplasms↗
PubMed2001

Stabilization of the MDM2 oncoprotein by mutant p53.

MDM2 is a short-lived protein that regulates p53 degradation. We report here that transient coexpression of MDM2 and several p53 hotspot mutants resulted in stabilization and increased expression of MDM2. Ectopic expression of the mutant p53(175H) allele by recombinant adenovirus infection or stable transfection also stabilized endogenous MDM2 in p53-null cells. A panel of human tumor cell lines expressing different endogenous mutant p53 alleles also contained stabilized nuclear MDM2 at elevated levels when compared with p53-null cells. MDM2 was present in complexes with mutant p53 in tumor cells, and stabilization of MDM2 required direct binding to mutant p53. These results reveal a novel property of mutant p53 and a unique feature of tumors with p53 missense mutations. Accumulation of stable MDM2 may contribute to tumorigenesis through its p53-independent transforming functions.

Humans↗
PubMed2001

Iridoschisis associated with lens subluxation.

The etiopathogenesis of iridoschisis is unclear, although age-related degeneration and angle-closure glaucoma are its most common associations. We report the case of a 50-year-old man with lens subluxation (familial) in 1 eye and ipsilateral iridoschisis. The inferotemporal edge of the lens was directed anteriorly, pushing the iris forward; this led to iridoschisis and shallowing of the anterior chamber. The patient had bilateral angle-closure glaucoma. A subluxated lens rubbing against the iris may be a mechanical precipitating factor in the development of iridoschisis.

Glaucoma, Angle-Closure↗
PubMed2001

Effect of chemical modifications of cytosine and guanine in a CpG-motif of oligonucleotides: structure-immunostimulatory activity relationships.

Oligodeoxynucleotides containing unmethylated CpG-motifs stimulate the innate immune system, including inducing B-cell proliferation and cytokine production. However, the mechanism of immunostimulation by CpG-oligonucleotides and the precise structural requirements and specific functional groups of cytosine and guanine necessary for recognition of and interaction with protein/receptor factors that are responsible for immune stimulation have not been elucidated. We sought to understand the critical role of each functional group of the cytosine and guanine moieties in a CpG-motif in inducing immunostimulatory activity. To this end, we examined structure-immunostimulatory activity relationships of phosphorothioate oligodeoxynucleotides (PS-oligos) containing YpG- and CpR-motifs (Y and R stand for pyrimidine and purine analogues, respectively). The PS-oligos containing a YpG-motif in which the natural deoxycytidine was replaced with deoxy-5-hydroxycytidine or deoxy-N4-ethylcytidine showed immunostimulatory activity. Substitution of deoxycytidine with a deoxy-5-methylisocytidine, deoxyuridine, or deoxy-P-base-nucleoside in the YpG-motif completely abolished the immunostimulatory activity, similar to the results observed with deoxy-5-methylcytidine. In the case of PS-oligos containing a CpR-motif, 7-deazaguanine substitution for natural guanine showed immunostimulatory activity similar to that of a parent PS-oligo. These studies suggest that the 2-keto, 3-imino and 4-amino groups of cytosine, and the 1-imino, 2-amino and 6-keto groups of guanine in a CpG-motif are important for the immunostimulatory activity of CpG-PS-oligos. The absence of N7 on guanine of the CpG-motif does not affect immunostimulatory activity significantly. These studies suggest that it is possible to develop YpG- and CpR-motifs as an alternative to CpG-motifs in PS-oligos for immunostimulatory studies.

Animals↗
PubMed2001

Immunostimulatory activity of CpG oligonucleotides containing non-ionic methylphosphonate linkages.

Bacterial DNA and synthetic oligodeoxynucleotides containing unmethylated CpG-motifs in a particular sequence context activate vertebrate immune cells. We examined the significance of negatively charged internucleoside linkages in the flanking sequences 5' and 3' to the CpG-motif on immunostimulatory activity. Cell proliferation and secretion of IL-12 and IL-6 in mouse spleen cell cultures, and spleen weights of mice increased significantly when a non-ionic linkage was placed at least four or more internucleoside linkages away from the CpG-motif in the 5'-flanking sequence. When the non-ionic linkage was placed closer than three internucleoside linkages in the 5'-flanking sequence to the CpG-motif, immunostimulatory activity was suppressed compared with that observed with the unmodified parent oligo. In general, the placement of non-ionic linkage in the 3'-flanking sequence to the CpG-motif either did not affect or slightly increased immunostimulatory activity compared with the parent oligo. These results have significance in understanding CpG oligonucleotide-receptor interactions and the development of potent immunomodulatory agents.

Adjuvants, Immunologic↗
PubMed2001

Gastric phytobezoar: treatment using meat tenderizer.

In summary bezoars are rarely symptomatic. CT scan of the abdomen is rapidly becoming the first tool of diagnosis, while endoscopy still remains the best diagnostic test. Medical treatment is usually successful, as in this case and rarely do patients require surgery.

Bezoars↗
PubMed2001

Post-kala-azar dermal leishmaniasis in Nepal.

BACKGROUND: Post-kala-azar dermal leishmaniasis (PKDL) manifests as a skin eruption after healing of visceral leishmaniasis (VL), either spontaneously or as a result of treatment. This study was undertaken to describe the demographic, clinical, and histopathologic features of PKDL in Nepal. METHODS: Demographic, clinical, microbiologic, and histopathologic features and response to treatment were studied in 22 patients with PKDL from April 1998 to March 2000. RESULTS: PKDL accounted for 0.13% of all new dermatologic cases. There were 13 (59.1%) males and nine (40.9%) females. A past history of kala-azar was present in all but one patient. A family history of kala-azar was noted in eight (36.4%) patients. All patients presented with multiple types of lesion, except for two in whom only macular lesions were seen. Oral lesions in the form of nodules and plaques were seen in four patients. Generalized lymphadenopathy was present in five patients. Slit skin smears revealed Leishman-Donovan bodies (LDBs) in nine (40.9%) patients. In macular lesions, there was a sparse infiltrate of plasma cells, lymphocytes, or histiocytes in the upper dermis. There was a dense chronic inflammatory infiltrate comprising plasma cells, lymphocytes, histiocytes, and epithelioid cells in the entire dermis from papules, plaques, or nodules. Giemsa staining of biopsy specimens revealed LDBs in seven (38.9%) patients only. Fine needle aspiration from epitrochlear lymph nodes in two patients demonstrated LDBs. All patients responded well to treatment with minimal side-effects. CONCLUSIONS: This study emphasizes the need to be aware of the possibility of cases of PKDL in endemic regions of leprosy, as the conditions may be difficult to distinguish clinically and histopathologically.

Adolescent↗
PubMed2001

Survivin inhibition induces human neural tumor cell death through caspase-independent and -dependent pathways.

Survivin inhibits apoptosis during development and carcinogenesis and is absent in differentiated cells. To determine whether survivin inhibition induces cell death in neural tumor cells, survivin antisense oligonucleotides (SAO) were administered to a human neuroblastoma (MSN) and an oligodendroglioma (TC620) resulting in a dose-dependent reduction in survivin protein. Although 74% of the SAO-treated MSN cells were trypan blue(+), PARP cleavage or activated caspase-3 was not observed. However nuclear translocation of AIF occurred and XIAP increased dramatically. Co-administration of z-Val-Ala-Asp(OMe)-fluoromethyl ketone (zVAD-fmk) with SAO did not inhibit cell death suggesting a caspase-independent mechanism of cell death. Propidium iodide (PI) staining revealed multiple large macronuclei with no apoptotic bodies supporting a role for survivin in cell division. By contrast, while 70% of the SAO-treated TC620 cells were trypan blue(+), PARP was cleaved, cells were TUNEL(+) and PI-staining revealed macronuclei and numerous apoptotic bodies. Co-treatment of the TC620 cells with SAO and zVAD-fmk blocked cell death. While no macronuclei or apoptotic bodies were observed there was a two-fold increase in metaphase cells. Our results suggest that survivin inhibition decreases the viability of human neural tumor cells and as a result of mitotic catastrophe, cell death can be initiated by either a classic apoptotic mechanism or a caspase-independent mechanism.

Apoptosis↗
PubMed2001

Cross-cultural evaluation of two drinking assessment instruments: alcohol timeline followback and inventory of drinking situations.

This article describes the psychometric characteristics of two major assessment instruments used in a World Health Organization (WHO) clinical trial: (a) Alcohol Timeline Followback (TLFB, which assesses daily drinking patterns), and (b) Inventory of Drinking Situations (IDS, which assesses antecedents to "heavy" drinking). Clients (N = 308) were outpatient alcohol abusers from four countries (Australia, Canada, Mexico, and Sweden). Generally, the Alcohol TLFB and IDS were shown to be reliable and valid with outpatient alcohol abusers in four countries, and in three languages. These results suggest that the Alcohol TLFB and the IDS can be used in clinical and research settings with Swedish-, Spanish-, and English-speaking alcohol abusers.

Adult↗
PubMed2001

Alcohol and drug abusers' perceived reasons for self-change in Canada and Switzerland: computer-assisted content analysis.

Although many people recover from substance-use associated problems on their own, little is known about this phenomenon. The paper had two objectives: to use a new research method, computer-assisted content analysis, to understand alcohol and drug abusers' perceived reasons for self-change and to undertake a comparative evaluation across substances and cultures to validate previous findings about subjective appraisal processes. Three studies of natural recoveries of alcohol and drug abusers in two countries conducted tape-recorded interviews with 216 respondents. The taped responses were coded based on a content analytic dictionary approach using a computerized content analysis program. All three studies found several processes mediating the decision to change substance use. The computer content analysis confirmed a cognitive appraisal process regardless of the cultural setting or substance. The findings suggest that several procedures might have benefit in clinical interventions.

Behavior, Addictive↗
PubMed2001

Antituberculosis drugs and new drug development.

Tuberculosis affects more than 8 million people and has serious repercussions on economic, psychologic, and social status. Since its declaration as a global emergency in 1993 by the World Health Organization, significant development in the treatment and control of tuberculosis has been the implementation of the short-course directly observed treatment along with fixed dose combinations of existing drugs. However, the currently available therapeutic regimens have inherent disadvantages of long treatment duration, patient noncompliance, and risk of drug resistance. Hence, new antituberculosis drugs that are potent, are active against resistant strains and latent forms, and reduce the treatment period are needed to combat this disease. In this review, the authors discuss new chemical entities that in their opinion have a potential to become new antituberculosis drugs. This article emphasizes the role of biopharmaceutics and pharmacokinetics as an indispensable part in the development of new antituberculosis drugs to overcome the common hurdles such as exorbitant cost, time, and attrition rate involved in the process.

Animals↗
PubMed2001

TM Finder: a prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales.

Based on the principle of dual prediction by segment hydrophobicity and nonpolar phase helicity, in concert with imposed threshold values of these two parameters, we developed the automated prediction program TM Finder that can successfully locate most transmembrane (TM) segments in proteins. The program uses the results of experiments on a series of host-guest TM segment mimic peptides of prototypic sequence KK AAAXAAAAAXAAWAAXAAAKKKK-amide (where X = each of the 20 commonly occurring amino acids) through which an HPLC-derived hydropathy scale, a hydrophobicity threshold for spontaneous membrane insertion, and a nonpolar phase helical propensity scale were determined. Using these scales, the optimized prediction algorithm of TM Finder defines TM segments by first searching for competent core segments using the combination of hydrophobicity and helicity scales, and then performs a gap-joining operation, which minimizes prediction bias caused by local hydrophilic residues and/or the choice of window size. In addition, the hydrophobicity threshold requirement enables TM Finder to distinguish reliably between membrane proteins and globular proteins, thereby adding an important dimension to the program. A full web version of the TM Finder program can be accessed at http://www.bioinformatics-canada.org/TM/.

Animals↗
PubMed2001

Sexual habits and clinico-etiological profile of sexually transmitted diseases in Nepal.

A total of 100 patients giving histories suggestive of sexually transmitted disease (STDs) and attending the dermatology OPD at BPKIHS (B.P. Koirala Institute of Health Sciences) in Nepal over a period of one year from 1st July 1999 to 30th June 2000 were included in this study. Out of 10,400 new dermatology cases, a total of 100 cases (0.96%) of STDs were seen. Of these 73 were males, and the majority (53%) were in the age group of 21-30 years. Most of the patients were from Sunsari district (54%). The most common profession (21%) was businessman followed by housewife (19%). The most common age for first sexual contact was 16 to 19 years (45%). Eleven percent had their first sexual contact at the age of 15 or below 15 years. Premarital sexual exposure was recorded in 17% of the unmarried males. There were only 3 homosexuals and 1 bisexual patient. Multiple contacts were recorded in 55% of the patients. The most common source of contact was a commercial sex worker in 34.15%. Condoms were always used by only 7%. The various types of sexually trasmitted diseases (STDs) were syphilis (31%) followed by condylomata acuminata (16%), herpes genitalis (15%), gonorrhoea (9%), and mixed infections (12%). Despite their varied sexual behavior, none of the patients were HIV positive; however, it is always advisable to screen all STD patients for HIV antibody.

Adolescent↗
PubMed2001

A modified technique of devascularization for surgical management of portal hypertension in children.

In developing countries surgery is indicated in patients with portal hypertension for a variety of reasons. This study prospectively evaluates a modified technique of devascularization for secondary prophylaxis of variceal bleeding in patients with portal hypertension of different aetiologies. Transabdominal extensive oesophagogastric devascularization combined with transmural ligation of oesophageal and gastric varices was performed in 16 paediatric patients (nine with extrahepatic portal venous obstruction, and seven with non-cirrhotic portal fibrosis) in an elective setting. The Sugiura devascularization procedure was modified to minimize the operating time and to avoid the problems associated with oesophageal transection and anastomosis. The operative mortality rate as well as the oesophageal leak rate was zero. One patient developed an oesophageal stricture. During a 12-month follow-up, patients were seen with residual varices (2), recurrent varices (3) and rebleeding (1). Porto-systemic encephalopathy was seen in one patient only. This technique is a simple, straightforward, safe and effective modification of the Sugiura procedure in controlling bleeding, providing good quality of life with minimal porto-systemic encephalopathy.

Child↗