Last data update: Apr 22, 2024. (Total: 46599 publications since 2009)
Records 1-7 (of 7 Records) |
Query Trace: Shantanu R [original query] |
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Draft Chromosome Sequences of a Clinical Isolate of the Free-Living Ameba Naegleria fowleri.
Ali IKM , Kelley A , Joseph SJ , Park S , Roy S , Jackson J , Cope JR , Rowe LA , Burroughs M , Sheth M , Batra D , Loparev V . Microbiol Resour Announc 2021 10 (15) We present the chromosome sequences of a Naegleria fowleri isolate from a human primary amebic meningoencephalitis (PAM) case. The genome sequences were assembled from Illumina HiSeq and PacBio sequencing data and verified with the optical mapping data. This led to the identification of 37 contigs representing 37 chromosomes in N. fowleri. |
Entamoeba sp. infection in a bearded dragon (Pogona vitticeps)
Diana S , Karim AMI , Shantanu R , Lisa PM , Brandy K , David E . Vet Glas 2019 74 (1) 77-84 A 3-year-old, male intact, pet inland bearded dragon (Pogona vitticeps) presented with a history of diarrhea, progressive inappetence and weight loss. A palpable cranial celomic mass was identified on physical examination and confirmed to be hepatic in origin by celomic ultrasonography. Hematologic and biochemical abnormalities were mild and consistent with inflammation, regenerative anemia, and hepatocellular injury. Fine needle aspiration of the liver masses was suggestive of amoebiasis and the patient was humanely euthanized. PCR and Sanger DNA sequencing of liver aspirates were supportive of Entamoeba infection, although definitive speciation was not possible. Pathogenic amoebiasis due to infection by E. invadens has been reported in a wide range of reptiles and is an important cause of morbidity and mortality in these species. |
A real-time PCR assay for simultaneous detection and differentiation of four common Entamoeba species that infect humans.
Ali IKM , Roy S . J Clin Microbiol 2020 59 (1) There are over forty species within the genus Entamoeba, eight of which infect humans. Of these, four species (Entamoeba histolytica, E. dispar, E. moshkovskii, and E. bangladeshi) are morphologically indistinguishable from each other, yet differentiation is important for appropriate treatment decisions. Here, we developed a hydrolysis probe-based tetraplex real-time PCR assay that can simultaneously detect and differentiate these four species in clinical samples. In this assay, multi-copy SSU rDNA sequences were used as targets. We determined that the tetraplex real-time PCR can detect amebic DNA corresponding to as few as 0.1 trophozoite-equivalent of any of these species. We also determined that this assay can detect E. histolytica DNA in the presence of 10-fold more DNA from another Entamoeba species in the mixed infection scenarios. With a panel of more than 100 well-characterized clinical samples diagnosed and confirmed using a previously published duplex real-time PCR (capable of detecting E. histolytica and E. dispar), our tetraplex real-time PCR assay demonstrated comparable sensitivity and specificity with that of the duplex real-time PCR assay. The advantage of our assay over the duplex assay is that it can specifically detect two additional Entamoeba species and can be used in conventional PCR format. This newly-developed assay will allow further characterization of the epidemiology and pathogenicity of the four morphologically-identical Entamoeba species especially in low resource settings. |
HMG-CoA Reductase Inhibitors as Drug Leads against Naegleria fowleri .
Hahn HJ , Abagyan R , Podust LM , Roy S , Ali IKM , Debnath A . ACS Chem Neurosci 2020 11 (19) 3089-3096 Primary amebic meningoencephalitis (PAM), caused by the free-living ameba Naegleria fowleri, has a fatality rate of over 97%. Treatment of PAM relies on amphotericin B in combination with other drugs, but few patients have survived with the existing drug treatment regimens. Therefore, development of effective drugs is a critical unmet need to avert deaths from PAM. Since ergosterol is one of the major sterols in the membrane of N. fowleri, disruption of isoprenoid and sterol biosynthesis by small-molecule inhibitors may be an effective intervention strategy against N. fowleri. The genome of N. fowleri contains a gene encoding HMG-CoA reductase (HMGR); the catalytic domains of human and N. fowleri HMGR share <60% sequence identity with only two amino acid substitutions in the active site of the enzyme. Considering the similarity of human and N. fowleri HMGR, we tested well-tolerated and widely used HMGR inhibitors, known as cholesterol-lowering statins, against N. fowleri. We identified blood-brain-barrier-permeable pitavastatin as a potent amebicidal agent against the U.S., Australian, and European strains of N. fowleri. Pitavastatin was equipotent to amphotericin B against the European strain of N. fowleri; it killed about 80% of trophozoites within 16 h of drug exposure. Pretreatment of trophozoites with mevalonate, the product of HMGR, rescued N. fowleri from inhibitory effects of statins, demonstrating that HMGR of N. fowleri is the target of statins. Because of the good safety profile and availability for both adult and pediatric uses, consideration should be given to repurposing the fast-acting pitavastatin for the treatment of PAM. |
Rapid, Noninvasive Diagnosis of Balamuthia mandrillaris Encephalitis by a Plasma-Based Next-Generation Sequencing Test.
Kalyatanda G , Rand K , Lindner MS , Hong DK , Sait Albayram M , Gregory J , Kresak J , Ibne KMA , Cope JR , Roy S , Gary JM , Reddy V , Ahmed AA . Open Forum Infect Dis 2020 7 (7) ofaa189 Granulomatous amoebic encephalitis (GAE) caused by Balamuthia mandrillaris is a rare subacute infection with exceptionally high mortality. Diagnosis is typically made by brain biopsy or at autopsy. Detection of Balamuthia mandrillaris cell-free DNA by next-generation sequencing of plasma enabled rapid, noninvasive diagnosis in a case of amoebic encephalitis. |
The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans.
Delgado DA , Zhang C , Gleason K , Demanelis K , Chen LS , Gao J , Roy S , Shinkle J , Sabarinathan M , Argos M , Tong L , Ahmed A , Islam T , Rakibuz-Zaman M , Sarwar G , Shahriar H , Rahman M , Yunus M , Doherty JA , Jasmine F , Kibriya MG , Ahsan H , Pierce BL . Hum Genet 2018 138 (1) 49-60 Leukocyte telomere length (LTL) is a heritable trait with two potential sources of heritability (h(2)): inherited variation in non-telomeric regions (e.g., SNPs that influence telomere maintenance) and variability in the lengths of telomeres in gametes that produce offspring zygotes (i.e., "direct" inheritance). Prior studies of LTL h(2) have not attempted to disentangle these two sources. Here, we use a novel approach for detecting the direct inheritance of telomeres by studying the association between identity-by-descent (IBD) sharing at chromosome ends and phenotypic similarity in LTL. We measured genome-wide SNPs and LTL for a sample of 5069 Bangladeshi adults with substantial relatedness. For each of the 6318 relative pairs identified, we used SNPs near the telomeres to estimate the number of chromosome ends shared IBD, a proxy for the number of telomeres shared IBD (Tshared). We then estimated the association between Tshared and the squared pairwise difference in LTL ((DeltaLTL)(2)) within various classes of relatives (siblings, avuncular, cousins, and distant), adjusting for overall genetic relatedness (varphi). The association between Tshared and (DeltaLTL)(2) was inverse among all relative pair types. In a meta-analysis including all relative pairs (varphi > 0.05), the association between Tshared and (DeltaLTL)(2) (P = 0.01) was stronger than the association between varphi and (DeltaLTL)(2) (P = 0.43). Our results provide strong evidence that telomere length (TL) in parental germ cells impacts TL in offspring cells and contributes to LTL h(2) despite telomere "reprogramming" during embryonic development. Applying our method to larger studies will enable robust estimation of LTL h(2) attributable to direct transmission of telomeres. |
Genome-wide association study of telomere length among South Asians identifies a second RTEL1 association signal.
Delgado DA , Zhang C , Chen LS , Gao J , Roy S , Shinkle J , Sabarinathan M , Argos M , Tong L , Ahmed A , Islam T , Rakibuz-Zaman M , Sarwar G , Shahriar H , Rahman M , Yunus M , Jasmine F , Kibriya MG , Ahsan H , Pierce BL . J Med Genet 2018 55 (1) 64-71 BACKGROUND: Leucocyte telomere length (TL) is a potential biomarker of ageing and risk for age-related disease. Leucocyte TL is heritable and shows substantial differences by race/ethnicity. Recent genome-wide association studies (GWAS) report ~10 loci harbouring SNPs associated with leucocyte TL, but these studies focus primarily on populations of European ancestry. OBJECTIVE: This study aims to enhance our understanding of genetic determinants of TL across populations. METHODS: We performed a GWAS of TL using data on 5075 Bangladeshi adults. We measured TL using one of two technologies (qPCR or a Luminex-based method) and used standardised variables as TL phenotypes. RESULTS: Our results replicate previously reported associations in the TERC and TERT regions (P=2.2x10(-8) and P=6.4x10(-6), respectively). We observed a novel association signal in the RTEL1 gene (intronic SNP rs2297439; P=2.82x10(-7)) that is independent of previously reported TL-associated SNPs in this region. The minor allele for rs2297439 is common in South Asian populations (>/=0.25) but at lower frequencies in other populations (eg, 0.07 in Northern Europeans). Among the eight other previously reported association signals, all were directionally consistent with our study, but only rs8105767 (ZNF208) was nominally significant (P=0.003). SNP-based heritability estimates were as high as 44% when analysing close relatives but much lower when analysing distant relatives only. CONCLUSIONS: In this first GWAS of TL in a South Asian population, we replicate some, but not all, of the loci reported in prior GWAS of individuals of European ancestry, and we identify a novel second association signal at the RTEL1 locus. |
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