Papers by Samanta S. Khora
Indian Journal of Microbiology, 2014
Coenzyme Q 10 (CoQ 10) is a blockbuster nutraceutical molecule which is often used as an oral sup... more Coenzyme Q 10 (CoQ 10) is a blockbuster nutraceutical molecule which is often used as an oral supplement in the supportive therapy for cardiovascular diseases, cancer and neurodegenerative diseases. It is commercially produced by fermentation process, hence constructing the high yielding CoQ 10 producing strains is a prerequisite for cost effective production. Paracoccus denitrificans ATCC 19367, a biochemically versatile organism was selected to carry out the studies on CoQ 10 yield improvement. The wild type strain was subjected to iterative rounds of mutagenesis using gamma rays and NTG, followed by selection on various inhibitors like CoQ 10 structural analogues and antibiotics. The screening of mutants were carried out using cane molasses based optimized medium with feeding strategies at shake flask level. In the course of study, the mutant P-87 having marked resistance to gentamicin showed 1.25-fold improvements in specific CoQ 10 content which was highest among all tested mutant strains. P-87 was phenotypically differentiated from the wild type strain on the basis of carbohydrate assimilation and FAME profile. Molecular differentiation technique based on AFLP profile showed intra specific polymorphism between wild type strain and P-87. This study demonstrated the beneficial outcome of induced mutations leading to gentamicin resistance for improvement of CoQ 10 production in P. denitrificans mutant strain P-87. To investigate the cause of gentamicin resistance, rpIF gene from P-87 and wild type was sequenced. No mutations were detected on the rpIF partial sequence of P-87; hence gentamicin resistance in P-87 could not be conferred with rpIF gene. However, detecting the mutations responsible for gentamicin resistance in P-87 and correlating its role in CoQ 10 overproduction is essential. Although only 1.25-fold improvement in specific CoQ 10 content was achieved through mutant P-87, this mutant showed very interesting characteristic, differentiating it from its wild type parent strain P. denitrificans ATCC 19367, which are presented in this paper. Keywords Coenzyme Q 10 Á Paracoccus denitrificans Á Gamma rays Á Gentamicin Á AFLP Á rpIF gene Á Strain improvement Electronic supplementary material The online version of this article (
Advances in Bioscience and Biotechnology, 2014
Coenzyme Q 10 (CoQ 10), an important antioxidant molecule playing a major role in electron transp... more Coenzyme Q 10 (CoQ 10), an important antioxidant molecule playing a major role in electron transport chain, has been commercially produced by fermentation process for the use in oral nutraceutical formulations. Constructing the high-yielding CoQ 10 producing strains is a prerequisite for cost-effective production. A superior mutant strain P-87 generated from Paracoccus denitrificans ATCC 19367, which showed 1.25-fold improvement in specific CoQ 10 content higher than the wild type strain at shake flask level, was selected to carry out the studies on CoQ 10 yield improvement through fermenter process optimization. In the course of study, initially the cane-molasses-based medium and fed-batch fermentation strategy using pHBA in combination with sucrose were standardized in shake flask using wild type strain. This strategy was subsequently translated at 2 L laboratory fermenter while optimizing the fermentation process parameters using improved mutant strain P-87. Under optimized fermentation condition, mutant strain P-87 produced 49.85 mg/L of CoQ10 having specific content of 1.63 mg/g of DCW, which was 1.36 folds higher than the specific CoQ 10 content of wild-type strain under similar optimized condition. The temperature and DO were found to be critical parameters for CoQ 10 production by mutant strain P-87. The optimum temperature was found to be 32˚C and the optimum DO concentration to be maintained throughout the fermentation cycle was found to be 30% of air saturation. Overall, a new cost-effective process has been established for the production of CoQ 10 using the cheaper substrate "cane molasses" and higher CoQ 10 producing mutant strain P-87.
A Preliminary Account on the Fish Fauna of the Estuaries of Ganjam District, Orissa
Records of the Zoological Survey of India
Studies on the Carcinological Fauna of Gopalpur Coast, Bay of Bengal 1. Non-Brachyrhynchan (Decapoda : Brachyura) (1)
Records of the Zoological Survey of India
Alginate: A Promising Biopolymer in Drug Delivery System
Marine Biomaterials, 2022
RESEARCH ARTICLE Meta-Analyses of Microarray Datasets Identifies ANO1 and FADD as Prognostic Markers of Head and Neck Cancer
The head and neck squamous cell carcinoma (HNSCC) transcriptome has been profiled extensively, ne... more The head and neck squamous cell carcinoma (HNSCC) transcriptome has been profiled extensively, nevertheless, identifying biomarkers that are clinically relevant and thereby with translational benefit, has been a major challenge. The objective of this study was to use a meta-analysis based approach to catalog candidate biomarkers with high potential for clini-cal application in HNSCC. Data from publically available microarray series (N = 20) profiled using Agilent (4X44K G4112F) and Affymetrix (HGU133A, U133A_2, U133Plus 2) platforms was downloaded and analyzed in a platform/chip-specific manner (GeneSpring software v12.5, Agilent, USA). Principal Component Analysis (PCA) and clustering analysis was car-ried out iteratively for segregating outliers; 140 normal and 277 tumor samples from 15 series were included in the final analysis. The analyses identified 181 differentially expressed, con-cordant and statistically significant genes; STRING analysis revealed interactions between 122 ...
International Journal of Drug Development and Research, 2013
Acalypha indica has been used in poisoning cases and are known to possess significant antioxidant... more Acalypha indica has been used in poisoning cases and are known to possess significant antioxidant activities. The objective of this study is to evaluate the protective effects of an aqueous extract (5 g/l) of A. indica (leaves and stems), on biochemical disorder, oxidative stress and histopathological changes induced by muscle extract of puffer fish Lagocephalus lunaris in swiss albino mice. Mice injected with L. lunaris muscle extract (1 ml/100g body weight) for 10 days showed (1) a reduced appetite and diarrhea resulting in a lower growth rate than controls, (2) an increase in serum Alanine aminotransferase, Aspartate aminotransferase, Alkaline phosphatase and Total & Direct bilirubin levels suggesting liver functional disorders, (3) an increase of serum creatinine and uric acid concentrations highlighting renal insufficiency and (4) increase in the level of serum triglycerides, total cholesterol, glucose and low density lipoproteins indicate the interference in the metabolism or ...
Toxicity studies on puffers from tropical waters
PLOS ONE, 2019
Head and neck squamous cell carcinomas (HNSCC) includes multiple subsites that exhibit differenti... more Head and neck squamous cell carcinomas (HNSCC) includes multiple subsites that exhibit differential treatment outcome, which is in turn reflective of tumor stage/histopathology and molecular profile. This study hypothesized that the molecular profile is an accurate prognostic adjunct in patients triaged based on clinico-pathological characteristics. Towards this effect, publically available micro-array datasets (n = 8), were downloaded, classified based on HPV association (n = 83) and site (tongue n = 88; laryngopharynx n = 53; oropharynx n = 51) and re-analyzed (Genespring; v13.1). The significant genes were validated in respective cohorts in The Cancer Genome Atlas (TCGA) for correlation with clinico-pathological parameters/survival. The gene entities (n = 3258) identified from HPV based analysis, when validated in TCGA identified the subset specifically altered in HPV+ HNSCC (n = 63), with three genes showing survival impact (RPP25, NUDCD2, NOVA1). Site-specific meta-analysis identified respective differentials (tongue: 3508, laryngopharynx: 4893, oropharynx: 2386); validation in TCGA revealed markers with high incidence (altered in >10% of patients) in tongue (n = 331), laryngopharynx (n = 701) and oropharynx (n = 404). Assessment of these genes in clinical sub-cohorts of TCGA indicated that early stage tongue (MTFR1, C8ORF33, OTUD6B) and laryngeal cancers (TWISTNB, KLHL13 and UBE2Q1) were defined by distinct prognosticators. Similarly, correlation with perineural/angiolymophatic invasion, identified discrete marker panels with survival impact (tongue: NUDCD1, PRKC1; laryngopharynx: SLC4A1AP, PIK3CA, AP2M1). Alterations in ANO1, NUDCD1, PIK3CA defined survival in tongue cancer patients with nodal metastasis (node+ECS-), while EPS8 is a significant differential in node+ECS-laryngopharyngeal cancers. In oropharynx, wherein HPV is a major etiological factor, distinct prognosticators were identified in HPV+ (ECHDC2, HERC5, GGT6) and HPV-(GRB10, EMILIN1, FNDC1). Meta-analysis in combination with TCGA validation carried out in this study emphasized on the molecular heterogeneity inherent within HNSCC; the feasibility of leveraging this information for
Archives of Oral Biology, 2019
This study aimed to identify the cancer stem cell specific biomarkers that can be effective candi... more This study aimed to identify the cancer stem cell specific biomarkers that can be effective candidate prognosticators of oral squamous cell carcinoma. Design: Microarray-based meta-analysis derived transcriptional profile of head and neck cancers was compared with the Cancer Stem Cell database to arrive at a subset of markers. This subset was further co-related with clinico-pathological parameters, recurrence and survival of oral cancer patients (n = 313) in The Cancer Genome Atlas database and in oral cancer (n = 28) patients. Results: Meta-analysis in combination with database comparison identified a panel of 221 genes specific to head and neck cancers. Correlation of expression levels of these markers in the oral cancer cohort of The Cancer Genome Atlas (n = 313) with treatment outcome identified 54 genes (p < 0.05 or fold change > 2) associated with disease recurrence, 8 genes (NQO1, UBE2C, EDNRB, FKBP4, STAT3, HOXA1, RIT1, AURKA) being significant with high fold change. Assessment of the efficacy of the subset (n = 54) as survival predictors identified an additional 4 genes (CDK1, GINS2, PHF5 A, ERBB2) that co-related with poor disease-free survival (p < 0.05). CDK1 showed a significant association with the clinical stage, margin status and with advanced pathological parameters. Initial patient validation indicated that CDK1 and NQO1 significantly co-related with the poor disease-free and overall survival (p < 0.05). Conclusion: This panel of oral cancer specific, cancer stem cell associated markers identified in this study, a subset of which was validated, will be of clinical benefit subject to large scale validation studies.
ACS Biomaterials Science & Engineering, 2018
Oxidative stress is an important cause for several retinal aging diseases. Cell therapy using a d... more Oxidative stress is an important cause for several retinal aging diseases. Cell therapy using a decellularized human amniotic membrane (dHAM) as a tissue scaffold for retinal pigment epithelial cells has a potential therapeutic role in such pathological conditions. This is attributed by dHAM's anti-inflammatory, anti-microbial, low immunogenicity aspects apart from harboring a drug reservoir potential. The underlying mechanisms for maintaining the physiological properties of transplanted cells and their survival in a diseased milieu using dHAM has remained unexplored/unanswered. Hence, we investigated the potential role of dHAM in preserving the cellular functions of retinal pigment epithelium in an oxidative stress environment. Adult human retinal pigment epithelial (ARPE-19) cells were cultured on dHAM or tissue culture dishes under hyperoxia. Gene expression, immunofluorescence staining, enzyme-linked immunosorbent assay (ELISA) and scanning electron microscopy (SEM) were performed to assess the levels of reactive oxygen species, proliferation, apoptosis, epithelial-mesenchymal transition, phagocytosis and secretion of vascular endothelial factors. These results indicate that reduced epithelial-mesenchymal transition, generation of reactive oxygen species (p≤0.0001), and apoptosis (p≤0.
Down-regulated notch signaling in arpe-19 cells Cultured on denuded human Amniotic membrane
International Journal of pharma and Bio Science, 2017
Tumor Biology, 2017
Differentiation is a major histological parameter determining tumor aggressiveness and prognosis ... more Differentiation is a major histological parameter determining tumor aggressiveness and prognosis of the patient; cancer stem cells with their slow dividing and undifferentiated nature might be one of the factors determining the same. This study aims to correlate cancer stem cell markers (CD44 and CD147) with tumor differentiation and evaluate their subsequent effect on prognosis. Immunohistochemical analysis in treatment naïve oral cancer patients (n = 53) indicated that the expression of CD147 was associated with poorly differentiated squamous cell carcinoma and moderately differentiated squamous cell carcinoma (p < 0.01). Furthermore, co-expression analysis showed that 45% each of moderately differentiated squamous cell carcinoma and poorly differentiated squamous cell carcinoma patients were CD44 high /CD147 high as compared to only 10% of patients with well-differentiated squamous cell carcinoma. A threeway analysis indicated that differentiation correlated with recurrence and survival (p < 0.05) in only the patients with CD44 high /CD147 high cohort. Subsequently, relevance of these cancer stem cell markers in patterning the differentiation characteristics was evaluated in oral squamous cell carcinoma cell lines originating from different grades of oral cancer. Flowcytometry-based analysis indicated an increase in CD44 + /CD147 + cells in cell lines of poorly differentiated squamous cell carcinoma (94.35 ± 1.14%, p < 0.001) and moderately differentiated squamous cell carcinoma origin (93.49 ± 0.47%, p < 0.001) as compared to cell line of well-differentiated squamous cell carcinoma origin (23.12% ± 0.49%). Expression profiling indicated higher expression of cancer stem cell and epithelial-mesenchymal transition markers in SCC029B (poorly differentiated squamous cell carcinoma originated; p ≤ 0.001), which was further translated into increased spheroid formation, migration, and invasion (p < 0.001) as compared to cell line of well-differentiated squamous cell carcinoma origin. This study suggests that CD44 and CD147 together improve the prognostic efficacy of tumor differentiation; in vitro results further point out that these markers might be determinant of differentiation characteristics, imparting properties of increased self-renewal, migration, and invasion.
Indian Journal of Pharmaceutical Education and Research, 2017
Objective: The prime objective of this study is to determine the origin of Tetrodotoxin in the pu... more Objective: The prime objective of this study is to determine the origin of Tetrodotoxin in the pufferfish Takifugu oblongus. Methods: Ultracentrifugation was performed to separate the tissues into various cellular fractions. Mouse bioassay was done to analyse the toxicity of different fractions from skin, liver and ovary of T. oblongus. The toxic fractions were subjected to HPLC-UV detection, to detect the presence of tetrodotoxin and quantify it. Results: Cytosolic fractions of skin, liver and ovary were extremely toxic and the presence of tetrodotoxin was proved on comparison with the retention time of standard toxin. Conclusions: These results suggest that the origin of tetrodotoxin could be endogenous or biosynthesized by the pufferfishes themselves. Clarifying the contradictions about the origins of TTX in puffers would allow researchers to accurately identify its role and toxicogenesis of the organisms which possess tetrodotoxin.
PLOS ONE, 2016
The head and neck squamous cell carcinoma (HNSCC) transcriptome has been profiled extensively, ne... more The head and neck squamous cell carcinoma (HNSCC) transcriptome has been profiled extensively, nevertheless, identifying biomarkers that are clinically relevant and thereby with translational benefit, has been a major challenge. The objective of this study was to use a meta-analysis based approach to catalog candidate biomarkers with high potential for clinical application in HNSCC. Data from publically available microarray series (N = 20) profiled using Agilent (4X44K G4112F) and Affymetrix (HGU133A, U133A_2, U133Plus 2) platforms was downloaded and analyzed in a platform/chip-specific manner (GeneSpring software v12.5, Agilent, USA). Principal Component Analysis (PCA) and clustering analysis was carried out iteratively for segregating outliers; 140 normal and 277 tumor samples from 15 series were included in the final analysis. The analyses identified 181 differentially expressed, concordant and statistically significant genes; STRING analysis revealed interactions between 122 of them, with two major gene clusters connected by multiple nodes (MYC, FOS and HSPA4). Validation in the HNSCC-specific database (N = 528) in The Cancer Genome Atlas (TCGA) identified a panel (ECT2, ANO1, TP63, FADD, EXT1, NCBP2) that was altered in 30% of the samples. Validation in treatment naïve (Group I; N = 12) and post treatment (Group II; N = 12) patients identified 8 genes significantly associated with the disease (Area under curve>0.6). Correlation with recurrence/re-recurrence showed ANO1 had highest efficacy (sensitivity: 0.8, specificity: 0.6) to predict failure in Group I. UBE2V2, PLAC8, FADD and TTK showed high sensitivity (1.00) in Group I while UBE2V2 and CRYM were highly sensitive (>0.8) in predicting re-recurrence in Group II. Further, TCGA analysis showed that ANO1 and FADD, located at 11q13, were co-expressed at transcript level and significantly
Cytotoxic Property of Cocos nucifera shell Extracts on HeLa Cells
ABSTRACT The main objective was to investigate the cytotoxic properties of Cocos nucifera shell c... more ABSTRACT The main objective was to investigate the cytotoxic properties of Cocos nucifera shell crude extract. The invitro antiproliferative activity against HeLa cells was measured by MTT assay which significantly decreased the number of HeLa cells by dose dependent manner with IC 50 of 1.77mg/ml. However, the cytotoxic activity was found due to the apoptosis induced in HeLa cells, which was demonstrated by DNA fragmentation analysis. The expression of apoptosis related genes, p53 and Bcl2 were analyzed by RT PCR. The apoptosis triggered by Cocos nucifera shell extract in HeLa cells was associated with the downregulation of Bcl-2 gene expression. These findings demonstrate that the shell extracts of Cocos nucifera presents excellent cytotoxic properties with beneficial virtues.
Marine Dinoflagellates-Associated Human Poisoning
Hb25_Springer Handbook of Marine Biotechnology, 2015
Seafood poisoning in humans is caused by consumption of toxin-containing seafood that is contamin... more Seafood poisoning in humans is caused by consumption of toxin-containing seafood that is contaminated with marine dinoflagellates. This has been a concern for many years. There are a number of dinoflagellate species that produce strong neurotoxins, which are often associated with the phenomenon called red tide. Outbreaks of red tide are caused by harmful algal blooms (HAB s). HABs are not a new phenomenon, with written references dating back to biblical times. The most common type of HAB is referred to as a red tide because the bloom discolors the water, making it appear red. Humans eating seafood from infested areas during dinoflagellate bloom can become poisoned. With respect to the contaminants of toxic dinoflagellates in seafood, there are two main types of poisoning in humans. The terms fish and shellfish are associated with these illnesses because the toxins are concentrated in fish and shellfish that ingest the harmful dinoflagellates. According to the species of toxigenic dinoflagellates the poisoning syndromes have been given the names paralytic (PSP ), diarrhetic (DSP ), neurotoxic (NSP ), and azaspiracid shellfish poisoning (AZP ). Another human illness, ciguatera fish poisoning (CFP ) is caused by the ciguatoxins produced by dinoflagellates that attach to surfaces in many coral reef communities [1]. Besides these well-known poisoning types, several new poisoning syndromes resulting from newly appearing dinoflagellate toxins, such as yessotoxin (YTX ) and palytoxin (PTX ), have been reported and characterized recently, and this has increased global public concerns regarding dinoflagellates associated with humans poisoning.
International Journal of Engineering Research and, 2017
The process for the production of Coenzyme Q10 (CoQ10) from a novel fusant strain PF-P1 has been ... more The process for the production of Coenzyme Q10 (CoQ10) from a novel fusant strain PF-P1 has been scaled up to 2 L laboratory fermenter level. At laboratory fermenter level, the strain PF-P1 produced 113.68 mg/L of CoQ10 at 96 h using fed batch [intermittent dosing of para Hydroxy Benzoic Acid (pHBA) at a concentration of 25 mg/L (final concentration) at 24 h followed by 30% of sucrose solution at 48 h and 72 h respectively] fermentation with optimized production medium containing carbon source as cane molasses and showed specific CoQ10 content of 2.4448 mg/g of dry cell weight (DCW). Optimized process resulted in significant improvement in biomass, CoQ10 titer and specific CoQ10 content than shake flask fermentation with PF-P1 strain.
Allergic Risks Associated with Seafood
Encyclopedia of Marine Biotechnology, 2020
Marine Collagen as a Source of Biomaterial
Encyclopedia of Marine Biotechnology, 2020
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Papers by Samanta S. Khora