Anamika Gupta - Academia.edu (original) (raw)

Papers by Anamika Gupta

BMC Infectious Diseases, 2020

Background Molecular epidemiological studies of Mycobacterium tuberculosis (MTB) are the core of ... more Background Molecular epidemiological studies of Mycobacterium tuberculosis (MTB) are the core of current research to find out the association of the M. tuberculosis genotypes with its outbreak and transmission. The high prevalence of the Beijing genotype strain among multidrug resistance (MDR) TB has already been reported in various studies around India. The overall objective of this study was to detect the prevalence of Beijing genotype strains of MDR M. tuberculosis and their association with the clinical characteristics of TB patients. Methods In this study 381 M. tuberculosis clinical isolates were obtained from sputum samples from 2008 to 2014. The multiplex-PCR and Spoligotyping (n = 131) methods were used to investigate the prevalence of the Beijing genotype strain by targeting the Rv2820 gene and their association with drug resistance and clinical characteristics of TB patients. The drug susceptibility testing of first-line anti-TB drugs was performed by using the proportion...

Oncotarget, 2017

Pancreatic ductal adenocarcinomas (PDACs) are highly aggressive malignancies, associated with poo... more Pancreatic ductal adenocarcinomas (PDACs) are highly aggressive malignancies, associated with poor clinical prognosis and limited therapeutic options. Oncogenic KRAS mutations are found in over 90% of PDACs, playing a central role in tumor progression. Global gene expression profiling of PDAC reveals 3-4 major molecular subtypes with distinct phenotypic traits and pharmacological vulnerabilities, including variations in oncogenic KRAS pathway dependencies. PDAC cell lines of the aberrantly differentiated endocrine exocrine (ADEX) subtype are robustly KRAS-dependent for survival. The KRAS gene is located on chromosome 12p11-12p12, a region amplified in 5-10% of primary PDACs. Within this amplicon, we identified co-amplification of KRAS with the STK38L gene in a subset of primary human PDACs and PDAC cell lines. Therefore, we determined whether PDAC cell lines are dependent on STK38L expression for proliferation and viability. STK38L encodes a serine/threonine kinase, which shares homology with Hippo pathway kinases LATS1/2. We show that STK38L expression is elevated in a subset of primary PDACs and PDAC cell lines displaying ADEX subtype characteristics, including overexpression of mutant KRAS. RNAimediated depletion of STK38L in a subset of ADEX subtype cell lines inhibits cellular proliferation and induces apoptosis. Concomitant with these effects, STK38L depletion causes increased expression of the LATS2 kinase and the cell cycle regulator p21. LATS2 depletion partially rescues the cytostatic and cytotoxic effects of STK38L depletion. Lastly, high STK38L mRNA expression is associated with decreased overall patient survival in PDACs. Collectively, our findings implicate STK38L as a candidate targetable vulnerability in a subset of molecularly-defined PDACs.

The Indian journal of tuberculosis, 2015

The growing emergence of multidrug resistant tuberculosis (MDR-TB) strains is obstructing efforts... more The growing emergence of multidrug resistant tuberculosis (MDR-TB) strains is obstructing efforts for the control and management of TB. Proper management of MDR-TB relies on early recognition of drug resistance followed by timely treatment initiation. Several diagnostic methods, both phenotypic and molecular, have been developed in last few years for rapid identification of drug resistant (DR)-TB. Revised national tuberculosis control programmes (RNTPs) may find it tough to choose from the puzzling variety of rapid tests. Here, we present an outline of the available methods, discussing their basis, advantages and deficiencies.

Indian journal of medical microbiology

We sought to determine the characteristics and relative frequency of transmission of MDR-TB in No... more We sought to determine the characteristics and relative frequency of transmission of MDR-TB in North India and their association with the clinical and epidemiological characteristics of TB-patients. To achieve the objectives PCR-SSCP, MAS-PCR and direct DNA sequencing were used against 101 Mycobacterium tuberculosis isolates. Multidrug-resistant-TB isolates were found to be significantly higher (P=0.000) in previously treated patients in comparison to newly diagnosed patients. Further, significant differences (P=0.003) were observed between different age groups (Mean±SD, 28.6±11.77) of the TB patients and multidrug resistance. Most frequent mutations were observed at codons 531 and 315 of rpoB and katG genes, respectively, in MDR-TB isolates. Routine surveillance of resistance to anti-TB drugs will improve timely recognition of MDR-TB cases and help prevent further transmission in Northern India.

The Indian journal of medical research, 2014

One-fifth of the world's new tuberculosis (TB) cases and two-thirds of cases in the South Eas... more One-fifth of the world's new tuberculosis (TB) cases and two-thirds of cases in the South East Asian region occur in India. Molecular typing of Mycobacterium tuberculosis isolates has greatly facilitated to understand the transmission of TB. This study was aimed to investigate the molecular epidemiology of M. tuberculosis genotypes in Varanasi, north India, and their association with clinical presentation among patients with pulmonary TB. M. tuberculosis isolates from 104 TB patients attending a tertiary referral hospital of north India were screened for susceptibility to isoniazid (INH), rifampicin (RIF), ethambutol (EMB) and streptomycin (STR) by proportion method and multiplex-allele-specific-polymerase chain reaction (MAS-PCR). These were genotyped by spoligotyping. The spoligotype patterns were compared with those in the international SITVIT2 spoligotyping database. Eighty three of 104 isolates were distributed in 38 SITs, of which SIT3366 was newly created within the prese...

Asian Pacific Journal of Tropical Disease, 2012

ABSTRACT Objective: To evaluate the effect of extract of Murraya paniculata Linn. (Family - Rutac... more ABSTRACT Objective: To evaluate the effect of extract of Murraya paniculata Linn. (Family - Rutaceae) on bdlioaobde tigcl uacnods en, ocnh-odleiastbeertoilc, rtraitgsl.y Mceeritdheo dans:d hliypdirdo -leavleclo haonldic a enxtitoraxcidt aonf t Mst.a ptuasn iicnu alalltoax alena vineds u(1c0e0d, t2r0i0g layncde r4id00e sm agn/kdg l) iwpiads laedvmeli nwiestreer eedst iomraaltleyd f oirn 1s4e druamys. and its effect on blood glucose, cholesterol, and antioxidant Liver free radical (lipid peroxidation, LPO) (Super oxide dismutase, SOD; catalase, CAT; and reduced glutathione peroxidase, GwPasx ) ewsteirmea atelsdo amfteear sured after 14 days treatment with extract. Glucose level in non-diabetic rats of M. paniculata ext2r1a cdta ys treatment with M. paniculata extract. Results: Oral administrations blood glucose, cholestero(l1, 0a0n, d2 0t0r igalnydc e4r0i0d em agn/kdg l)i pfoidr 1l4e vdeal.y s significantly reduced the levels of reduced and antioxidants Liver free radical (LPO) significantly of extract in diabetic rats.( SMOD. p, aCnAiTcu alnadta G Px) status significantly increase after 14 days treatment in non-diabetic rats after 200 and 400 mg/kg significantly decrease glucose level 21 day and caused hypoglycemia in normal rats. Conclusions: M. paniculata leaves extract posses hypoglycemic effect in oxidative stress condition and also in ninocnr-eadsiianbge teiict hceorn tdhiet iopnan. cHryepatoigcl yseccermetiico na cotfi oinn smulainy fbreo mb yb eptoat ecnetlilas toinf gi solef tsth oef ilnasnugleirnh aenffse cotr bitys wreilteha asen tiforoxmid atnhte pbrooupnerdt ifeosr.m .

Journal of Pharmacy Research, 2013

Background/aims: Present study evaluates the potential of three different Indian plants against d... more Background/aims: Present study evaluates the potential of three different Indian plants against drug resistant clinical pathogens, which are already known to provide relief in microbial infections. Methods: A total of nine extracts from leaves of Arum maculatum, Tinospora cardifolia and Andrographis paniculata were investigated to evaluate their antibacterial activities against two reference strains of human pathogenic bacteria. The antibacterial activities of the extracts were assessed by agar well diffusion method and minimal inhibition concentration (MIC). The efficacy of the extracts was compared to commercially prepared antibiotic (Streptomycin) discs. The extract showing antibacterial activity was fractionated by TLC and the purified active fraction was chemically characterized by different phytochemical tests. Results: Methanol extract of A. paniculata leaves exhibited strong in vitro antibacterial activity against Gram positive bacteria including clinical isolates of Mycobacterium tuberculosis, Enterococcus faecalis and methicillin resistant Staphylococcus aureus. Phytochemical investigations of TLC purified active fraction from this extract showed the presence of terpenoids in it. Conclusion: The study concludes that the terpenoids present in methanol extract of A. paniculata leaves have enough potential to kill drug resistant Gram positive bacteria.

Journal of Health, Population and Nutrition, 2011

The objective of the study was to evaluate the performance of nitrate reductase assay (NRA) as a ... more The objective of the study was to evaluate the performance of nitrate reductase assay (NRA) as a rapid, reliable and inexpensive method for drug-susceptibility testing (DST) of Mycobacterium tuberculosis against firstline antitubercular drugs, such as rifampicin (RIF), isoniazid (INH), streptomycin (STR), and ethambutol (EMB). In total, 286 isolates were subjected to test by proportion method (PM) and NRA. By comparing the results of NRA with those of the gold standard PM, sensitivities and specificities were 98.4%, 97%, 88.5%, and 94.2% and 100%, 100%, 94%, and 99% for RIF, INH, STR, and EMB respectively. The positive predictive values were 100%, 100%, 95%, and 98% for RIF, INH, STR, and EMB respectively. The negative values were 99%, 98%, 87%, and 96% for RIF, INH, STR, and EMB respectively. The median time of obtaining results was shorter using NRA (10 days) compared to PM (28 days). An excellent agreement was observed between the two phenotypic tests with the κ values of 0.98, 0.97, 0.81, and 0.93 for RIF, INH, STR, and EMB respectively. The results demonstrated that NRA is suitable for the early determination of INH and RIF resistance and has the potential to be a useful tool for rapid drug-sensitivity test of M. tuberculosis in resource-constrained settings.

Indian Journal of Pathology and Microbiology, 2009

Traditional drug susceptibility testing for Mycobacterium tuberculosis takes weeks and/or expensi... more Traditional drug susceptibility testing for Mycobacterium tuberculosis takes weeks and/or expensive. In this study, we evaluated nitrate reductase assay for drug susceptibility testing which is faster than the visual detection of colonies. 32 clinical specimens (direct microscopy positive for AFB with 1+, 2+ or 3+ grading) were decontaminated and the sediment was inoculated onto the L-J medium with INH or Rifampicin incorporated with Potassium nitrate and the same medium without antibiotics at 1;10 dilution as control. After 2 weeks, the control was first tested for color change with addition of nitrate reductase reagents. If found positive, the media with antibiotics were tested and compared. Futher incubation was done if the control was found to be negative. The results obtained was compared with standard direct proportion method for drug susceptibility testing. Resistance of isolates as shown by both methods for INH and Rifampicin was 37.5% and 31.3% respectively. The results showed that NRA and proportion method do not differ significantly ( P &amp;amp;amp;amp;amp;lt; 0.05 for both drugs). Thus an excellent agreement between the results of NRA and proportion method was found for two primary anti-tubercular drugs, 87.5% for INH and 97% for Rifampicin. Nitrate reductase assay is a rapid and inexpensive method for susceptibility testing of M. tuberculosis for primary anti-tubercular drugs and could be an alternative to existing methods, particularly in resource poor settings.

Annals of Clinical Microbiology and Antimicrobials, 2017

Background: The Mycobacterium tuberculosis (M.tb) protein kinase B (PknB) which is now proved to ... more Background: The Mycobacterium tuberculosis (M.tb) protein kinase B (PknB) which is now proved to be essential for the growth and survival of M.tb, is a transmembrane protein with a potential to be a good drug target. However it is not known if this target remains conserved in otherwise resistant isolates from clinical origin. The present study describes the conservation analysis of sequences covering the inhibitor binding domain of PknB to assess if it remains conserved in susceptible and resistant clinical strains of mycobacteria picked from three different geographical areas of India. Methods: A total of 116 isolates from North, South and West India were used in the study with a variable profile of their susceptibilities towards streptomycin, isoniazid, rifampicin, ethambutol and ofloxacin. Isolates were also spoligotyped in order to find if the conservation pattern of pknB gene remain consistent or differ with different spoligotypes. The impact of variation as found in the study was analyzed using Molecular dynamics simulations. Results: The sequencing results with 115/116 isolates revealed the conserved nature of pknB sequences irrespective of their susceptibility status and spoligotypes. The only variation found was in one strains wherein pnkB sequence had G to A mutation at 664 position translating into a change of amino acid, Valine to Isoleucine. After analyzing the impact of this sequence variation using Molecular dynamics simulations, it was observed that the variation is causing no significant change in protein structure or the inhibitor binding. Conclusions: Hence, the study endorses that PknB is an ideal target for drug development and there is no pre-existing or induced resistance with respect to the sequences involved in inhibitor binding. Also if the mutation that we are reporting for the first time is found again in subsequent work, it should be checked with phenotypic profile before drawing the conclusion that it would affect the activity in any way. Bioinformatics analysis in our study says that it has no significant effect on the binding and hence the activity of the protein.

There is a growing need to develop rapid laboratory research methods to counter the menace of dru... more There is a growing need to develop rapid laboratory research methods to counter the menace of drug resistant tuberculosis (MDR-TB) cases worldwide especially in developing countries. The present study was undertaken to investigate the type and frequency of rpoB and katG mutations in rifampicin (RIF) and isoniazid (INH) resistant strains respectively of Mycobacterium tuberculosis (MTB) circulating in Northern India and to explore the utility of multiplex-allele-specific (MAS)-PCR assay for detection of drug-resistant MTB isolates in low resource set up. Phenotypic and genotypic drug susceptibility testing (DST) was performed on 354 MTB isolates. Mutation in rpoB gene was found most frequently at codons 531, 526 and 516 (59.83%, 45.29% and 22.22%, respectively). Further, combinations of 2-3 point mutations were also observed in 19.66% of RIF-resistant MTB strains. The frequency of mutations in katG gene was found at codon 315 among 82.95% of the INH-resistant MTB isolates. MAS-PCR detected rpoB and katG mutations in phenotypically resistant isolates with sensitivities of 93% and 83% respectively. MAS-PCR assays can be used for rapid detection of drug-resistant TB strains in routine diagnostic practice, enabling early administration of appropriate treatment regimens to the affected patients.