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Gewolb IH, Schwalbe RS, Taciak VL, Harrison TS, Panigrahi P. Stool microflora in extremely low birthweight infants. Arch Dis Child Fetal Neonatal Ed 1999; 80:F167-73. [PMID: 10212075 PMCID: PMC1720923 DOI: 10.1136/fn.80.3.f167] [Citation(s) in RCA: 247] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
AIM To serially characterise aerobic and anaerobic stool microflora in extremely low birthweight infants and to correlate colonisation patterns with clinical risk factors. METHODS Stool specimens from 29 infants of birthweight <1000 g were collected on days 10, 20, and 30 after birth. Quantitative aerobic and anaerobic cultures were performed. RESULTS By day 30, predominant species were Enterococcus faecalis, Escherichia coli, Staphylococcus epidermidis, Enterbacter cloacae, Klebsiella pneumoniae, and Staphylococcus haemolyticus. Lactobacillus and Bifidobacteria spp were identified in only one infant. In breast milk fed (but not in formula fed) infants, the total number of bacterial species/stool specimen increased significantly with time (2.50 (SE 0.34) on day 10; 3.13 (0.38) on day 20; 4.27 (0.45) on day 30) as did quantitative bacterial counts; Gram negative species accounted for most of the increase. On day 30, significant inverse correlations were found between days of previous antibiotic treatment and number of bacterial species (r=0.491) and total organisms/g of stool (r=0.482). Gestational age, birthweight, maternal antibiotic or steroid treatment, prolonged rupture of the membranes, and mode of delivery did not seem to affect colonisation patterns. CONCLUSIONS The gut of extremely low birthweight infants is colonised by a paucity of bacterial species. Breast milking and reduction of antibiotic exposure are critical to increasing fecal microbial diversity.
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Johnson JA, Salles CA, Panigrahi P, Albert MJ, Wright AC, Johnson RJ, Morris JG. Vibrio cholerae O139 synonym bengal is closely related to Vibrio cholerae El Tor but has important differences. Infect Immun 1994; 62:2108-10. [PMID: 8168977 PMCID: PMC186475 DOI: 10.1128/iai.62.5.2108-2110.1994] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Although Vibrio cholerae O139 synonym Bengal strains, from the current epidemics in India and Bangladesh, are closely related to seventh-pandemic strains, as shown by multilocus enzyme electrophoresis, Bengal strains are encapsulated and portions of the O1 antigen biosynthetic complex genes found in O1 strains are altered or lacking. Encapsulated Bengal strains showed resistance to killing by normal human serum. The presence of the capsule suggests the potential for bloodstream invasion in susceptible hosts and has profound implications for vaccine development.
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31 |
127 |
3
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Wassenaar TM, Panigrahi P. Is a foetus developing in a sterile environment? Lett Appl Microbiol 2014; 59:572-9. [PMID: 25273890 DOI: 10.1111/lam.12334] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/12/2014] [Accepted: 09/19/2014] [Indexed: 12/27/2022]
Abstract
Novel findings in microbiology question the long-standing paradigm that a healthy pregnancy implies a sterile uterus. It now seems that the placenta is frequently colonized with bacteria, and a placental microbiome has been identified. Recent literature findings are summarized here, and an attempt is made to separate pathological bacterial presence from a naturally occurring microbiome.
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Review |
11 |
94 |
4
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Morris JG, Sztein MB, Rice EW, Nataro JP, Losonsky GA, Panigrahi P, Tacket CO, Johnson JA. Vibrio cholerae O1 can assume a chlorine-resistant rugose survival form that is virulent for humans. J Infect Dis 1996; 174:1364-8. [PMID: 8940236 DOI: 10.1093/infdis/174.6.1364] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Vibrio cholerae can shift to a "rugose" colonial morphology associated with expression of an amorphous exopolysaccharide that promotes cell aggregation. Flow cytometric studies indicated that up to 3% of particles in rugose cultures represented aggregates of >5 bacterial cells. Rugose variants of our test strains displayed resistance to killing by chlorine, with viable cells persisting for >30 min in 2 mg/L free chlorine; strains also showed resistance to killing by complement-mediated serum bactericidal activity. Six volunteers fed 10(6) cfu of a rugose variant of V. cholerae O1 El Tor Inaba N16961 developed symptoms typical of cholera, with a mean diarrheal stool volume of 2.2 L (range, 1.4-4.3). Isolates recovered from the stool of infected volunteers retained the rugose phenotype. The data suggest that rugose strains cause human disease. The role of these strains in the epidemiology of cholera remains to be determined.
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5
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Comstock LE, Maneval D, Panigrahi P, Joseph A, Levine MM, Kaper JB, Morris JG, Johnson JA. The capsule and O antigen in Vibrio cholerae O139 Bengal are associated with a genetic region not present in Vibrio cholerae O1. Infect Immun 1995; 63:317-23. [PMID: 7528734 PMCID: PMC172994 DOI: 10.1128/iai.63.1.317-323.1995] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Vibrio cholerae O139 Bengal, although closely related to V. cholerae O1 El Tor, produces a polysaccharide capsule and has a distinct O antigen. We have identified a chromosomal region of at least 11 kb, as defined by three TnphoA mutations, that is required for the expression of both polysaccharides. Electron microscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis show that these TnphoA mutants have lost the abilities both to express capsule and to produce lipopolysaccharide beyond the core oligosaccharide. Reactivity with O139 typing serum and resistance to serum are also lost in the mutants. DNA probes for this region do not hybridize with O1 V. cholerae but do react with other vibrios, implying that the region was recently acquired.
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Panigrahi P, Gewolb IH, Bamford P, Horvath K. Role of glutamine in bacterial transcytosis and epithelial cell injury. JPEN J Parenter Enteral Nutr 1997; 21:75-80. [PMID: 9084009 DOI: 10.1177/014860719702100275] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND L-Glutamine is the principal energy source for small intestinal enterocytes. Diminution of intestinal function, mucosal atrophy, and increased bacterial translocation have been noted during total parenteral nutrition (TPN). In a rat model of glutamine starvation, we previously showed that luminal glutamine is essential for optimal intestinal function. In this study, we examined the effect of apical vs basolateral glutamine on bacterial translocation in a Caco-2 cell culture system and bacteria-induced tissue injury in a weanling rabbit ileal loop model. METHODS Caco-2 cells were grown in a transwell system. After confluence, apical and basolateral chambers received defined media, and glutamine deprivation was carried out over a 4- to 48-hour period. Escherichia coli transcytosis and structure/function studies were then performed. In a second series of experiments, the effect of intraluminal glutamine supplementation was evaluated in an E. coli-induced tissue injury model in weanling rabbit ileal loops. RESULTS Expression of disaccharidases, glucoamylase, and Na+/K(+)-adenosine 5'-triphosphatase (ATPase) were significantly reduced when cells were deprived of glutamine from the apical side, and there was increased bacterial translocation across the monolayer. Transepithelial epithelial resistance (TEER) across the monolayer was also reduced in the glutamine-free cultures. Glutamine replenishment over 24 to 48 hours restored the original functions. Basolateral deprivation had a smaller effect on the Caco-2 cells. Typical necrotic mucosal injury caused by E. coli in the ileal loops was blocked by co-infiltration of the loops with glutamine. CONCLUSIONS This study demonstrates for the first time that the supply of glutamine from the apical side is of critical importance for maintaining optimal structure and function of the enterocytes. The effects are not acute or energy related. These observations have important clinical implications in the management of patients under critical care, including premature infants and patients receiving TPN, for whom lack of glutamine from the luminal side could produce mucosal dysfunction, resulting ultimately in severe atrophic/necrotic complications.
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Morris JG, Losonsky GE, Johnson JA, Tacket CO, Nataro JP, Panigrahi P, Levin MM. Clinical and immunologic characteristics of Vibrio cholerae O139 Bengal infection in North American volunteers. J Infect Dis 1995; 171:903-8. [PMID: 7706818 DOI: 10.1093/infdis/171.4.903] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Vibrio cholerae O139 Bengal has recently emerged as a cause of epidemic cholera in Asia. To evaluate clinical and immunologic responses to infection, V. cholerae O139 Bengal AI1837 was administered to healthy adult North American volunteers. Two of 4 persons ingesting 10(4) cfu became ill (incubation period, 48 h; mean diarrheal stool, 1873 g), as did 7 of 9 persons receiving 10(6) cfu (incubation period, 28 h; mean diarrheal stool, 4548 g). Ill volunteers did not demonstrate a vibriocidal antibody response to the challenge strain or other V. cholerae. Three months later, volunteers were rechallenged with the homologous O139 Bengal strain. Only 1 of 6 persons who had been ill on initial challenge had diarrhea, compared with 11 of 13 controls (P = .01; protective efficacy = 80%). V. cholerae O139 Bengal can cause severe diarrhea typical of cholera, with clinical characteristics and a dose-response similar to those seen with V. cholerae O1 El Tor. A moderately high level of protection against subsequent disease is provided by initial clinical infection.
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Panigrahi P, Gupta S, Gewolb IH, Morris JG. Occurrence of necrotizing enterocolitis may be dependent on patterns of bacterial adherence and intestinal colonization: studies in Caco-2 tissue culture and weanling rabbit models. Pediatr Res 1994; 36:115-21. [PMID: 7936830 PMCID: PMC7086551 DOI: 10.1203/00006450-199407001-00021] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Necrotizing enterocolitis (NEC) is one of the leading causes of death in neonatal intensive care units. The underlying pathophysiology of NEC is poorly defined, although there is a suggestion that bacterial agents play an important role in the process. In this study, we evaluated bacterial isolates from 17 NEC cases and matched asymptomatic control infants. Isolates from NEC patients were no more likely than control isolates to be adherent to enterocytes, as assessed by a Caco-2 cell tissue culture model. Adherent Escherichia coli isolates, from both NEC cases and controls, were able to cause pathologic changes typical of NEC in a weanling rabbit ileal loop model. Adherence of E. coli strains to Caco-2 cells, and subsequent production of disease in weanling rabbits, could be blocked by coinfection with Gram-positive isolates from control children. In contrast, in three of four instances, adherent E. coli from NEC cases retained their adherence and caused illness in rabbits when coinfected with Gram-positive isolates from the homologous child. Our data suggest that patterns of intestinal adherence, as influenced by the underlying intestinal microbial ecology, play a role in the pathophysiology of NEC.
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Johnson JA, Panigrahi P, Morris JG. Non-O1 Vibrio cholerae NRT36S produces a polysaccharide capsule that determines colony morphology, serum resistance, and virulence in mice. Infect Immun 1992; 60:864-9. [PMID: 1311706 PMCID: PMC257566 DOI: 10.1128/iai.60.3.864-869.1992] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Non-O1 Vibrio cholerae produced two distinct colony types, designated as opaque and translucent. NRT36S, a clinical isolate shown to be virulent in volunteers, produced predominantly opaque colonies, but translucent colonies appeared on subculture. Opaque variants were recovered exclusively following exposure to normal human serum or animal passage. A nonreverting translucent mutant of NRT36S, JVB52, was isolated following mutagenesis with the transposon Tn5 IS50L::phoA (TnphoA). Only translucent colonies were produced by a nonpathogenic environmental isolate, A5. Electron microscopic examination of the opaque form of NRT36S revealed thick, electron-dense, fibrous capsules surrounding polycationic ferritin-stained cells. The ferritin-stained material around translucent NRT36S or A5 was patchy or absent. JVB52 had a thin but contiguous capsular layer. The amount of ferritin-stained capsular material correlated with the amount of surface polysaccharide determined by phenol-sulfuric acid assay: opaque NRT36S had approximately three times as much polysaccharide as translucent NRT36S or A5 and four times as much as JVB52. The encapsulated, opaque variant of NRT36S was protected from serum bactericidal activity, while translucent non-O1 V. cholerae was readily killed. The encapsulated form also had increased virulence in mice. Our data provide the first indication that non-O1 V. cholerae strains can have a polysaccharide capsule. This capsule may be important in protecting the organism from host defenses and may contribute to the ability of some non-O1 V. cholerae strains to cause septicemia in susceptible hosts.
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10
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Kumar Y, Zhang L, Panigrahi P, Dholakia BB, Dewangan V, Chavan SG, Kunjir SM, Wu X, Li N, Rajmohanan PR, Kadoo NY, Giri AP, Tang H, Gupta VS. Fusarium oxysporum mediates systems metabolic reprogramming of chickpea roots as revealed by a combination of proteomics and metabolomics. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1589-603. [PMID: 26801007 PMCID: PMC5066658 DOI: 10.1111/pbi.12522] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 05/05/2023]
Abstract
Molecular changes elicited by plants in response to fungal attack and how this affects plant-pathogen interaction, including susceptibility or resistance, remain elusive. We studied the dynamics in root metabolism during compatible and incompatible interactions between chickpea and Fusarium oxysporum f. sp. ciceri (Foc), using quantitative label-free proteomics and NMR-based metabolomics. Results demonstrated differential expression of proteins and metabolites upon Foc inoculations in the resistant plants compared with the susceptible ones. Additionally, expression analysis of candidate genes supported the proteomic and metabolic variations in the chickpea roots upon Foc inoculation. In particular, we found that the resistant plants revealed significant increase in the carbon and nitrogen metabolism; generation of reactive oxygen species (ROS), lignification and phytoalexins. The levels of some of the pathogenesis-related proteins were significantly higher upon Foc inoculation in the resistant plant. Interestingly, results also exhibited the crucial role of altered Yang cycle, which contributed in different methylation reactions and unfolded protein response in the chickpea roots against Foc. Overall, the observed modulations in the metabolic flux as outcome of several orchestrated molecular events are determinant of plant's role in chickpea-Foc interactions.
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9 |
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11
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Rice EW, Johnson CJ, Clark RM, Fox KR, Reasoner DJ, Dunnigan ME, Panigrahi P, Johnson JA, Morris JG. Chlorine and survival of "rugose" Vibrio cholerae. Lancet 1992; 340:740. [PMID: 1355849 DOI: 10.1016/0140-6736(92)92289-r] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Letter |
33 |
43 |
12
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Panigrahi P, Jere A, Anamika K. FusionHub: A unified web platform for annotation and visualization of gene fusion events in human cancer. PLoS One 2018; 13:e0196588. [PMID: 29715310 PMCID: PMC5929557 DOI: 10.1371/journal.pone.0196588] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 04/16/2018] [Indexed: 12/15/2022] Open
Abstract
Gene fusion is a chromosomal rearrangement event which plays a significant role in cancer due to the oncogenic potential of the chimeric protein generated through fusions. At present many databases are available in public domain which provides detailed information about known gene fusion events and their functional role. Existing gene fusion detection tools, based on analysis of transcriptomics data usually report a large number of fusion genes as potential candidates, which could be either known or novel or false positives. Manual annotation of these putative genes is indeed time-consuming. We have developed a web platform FusionHub, which acts as integrated search engine interfacing various fusion gene databases and simplifies large scale annotation of fusion genes in a seamless way. In addition, FusionHub provides three ways of visualizing fusion events: circular view, domain architecture view and network view. Design of potential siRNA molecules through ensemble method is another utility integrated in FusionHub that could aid in siRNA-based targeted therapy. FusionHub is freely available at https://fusionhub.persistent.co.in.
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7 |
39 |
13
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Panigrahi P, Losonsky G, DeTolla LJ, Morris JG. Human immune response to Campylobacter jejuni proteins expressed in vivo. Infect Immun 1992; 60:4938-44. [PMID: 1399004 PMCID: PMC258251 DOI: 10.1128/iai.60.11.4938-4944.1992] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Campylobacter jejuni 81-176 grown in vivo in rabbit ileal loops expresses novel proteins that are not expressed under standard laboratory culture conditions. A new protein with a molecular mass of ca. 180 kDa is expressed at 14, 24, and 48 h of infection. Three other proteins, with molecular masses of ca. 66, 43, and 35 kDa, are overexpressed during different phases of infection. Expression of these proteins stops immediately during the first passage in laboratory media, and they do not elicit a human immune response. Two other proteins, with molecular masses of ca. 84 and 47 kDa, expressed 48 h after infection can be identified by using convalescent sera from human volunteers who were immune to C. jejuni infection upon rechallenge; these proteins were not visualized on sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels by Coomassie blue staining or silver staining. Antibodies to the 84- and 47-kDa proteins are of the immunoglobulin G class. Both preinfection and convalescent human sera react strongly to the C. jejuni flagellin (a 58-kDa protein), suggesting the presence of cross-reactive antibodies to this protein in healthy humans. Major outer membrane protein and flagella may play a role in providing protection against C. jejuni disease, but our data suggest that there are other proteins expressed only during in vivo growth of the organism that elicit a strong immune response in human C. jejuni infections.
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33 |
36 |
14
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Panigrahi P, Tall BD, Russell RG, Detolla LJ, Morris JG. Development of an in vitro model for study of non-O1 Vibrio cholerae virulence using Caco-2 cells. Infect Immun 1990; 58:3415-24. [PMID: 2205582 PMCID: PMC313669 DOI: 10.1128/iai.58.10.3415-3424.1990] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Non-O1 Vibrio cholerae strains have been reported as a causative agent of diarrhea throughout the world. We recently reported that non-O1 V. cholerae strains cause diarrhea in human volunteers. In this study we evaluated the virulence of three strains of non-O1 V. cholerae in a Caco-2 cell adherence assay by light and electron microscopy. A-5 is an environmental isolate which failed to colonized volunteers and did not cause diarrhea. It exhibited low numbers of organisms adherent to Caco-2 cells, leaving the microvilli intact. Strain 2076-79, isolated from a patient with diarrhea, colonized human volunteers without producing disease. It adhered to Caco-2 cells in moderate numbers without producing any damage to the microvilli. Strain NRT36S, a clinical isolate, colonized human volunteers and produced significant diarrhea disease. This strain adhered in very large numbers to Caco-2 cells and caused damage to the brush borders. Membrane-bound bacteria were also seen within the cytoplasm of these cells. Scanning electron microscopy confirmed the generalized adherence of NRT36S to the microvilli of Caco-2 cells. The three strains did not appear to compete with each other for binding sites on Caco-2 cells and were not adherent when assays were conducted at 4 degrees C. Our results with strains A-5, 2076-79, and NRT36S correlate well with observations in human volunteer studies, suggesting that Caco-2 cells provide an appropriate in vitro system for further investigation of the pathogenesis of non-O1 V. cholerae gastroenteritis.
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research-article |
35 |
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15
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Panigrahi P, Bamford P, Horvath K, Morris JG, Gewolb IH. Escherichia coli transcytosis in a Caco-2 cell model: implications in neonatal necrotizing enterocolitis. Pediatr Res 1996; 40:415-21. [PMID: 8865278 DOI: 10.1203/00006450-199609000-00009] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Necrotizing enterocolitis (NEC) is a serious gastrointestinal disorder of preterm infants. Other than an association with prematurity and gastrointestinal feeding, no single factor or mechanism has been consistently linked to this disease. We have previously demonstrated that Escherichia coli isolates obtained from the stool of infants with NEC caused NEC-like injury in a weanling rabbit ileal loop model; this injury, in turn, could be blocked by coinfection with selected Gram(+) bacteria (Enterococcus faecium) isolated from asymptomatic controls. Using Caco-2 cells in a trans-well system, we now demonstrate that the same E. coli isolates can cross epithelial cell monolayers in the absence of ultrastructural change or damage. These results with E. coli contrast with those seen with Salmonella typhimurium, which passed through the monolayer at a higher rate and were associated with striking ultrastructural damage. Transcytosis of E. coli was reduced 3-5-fold in the presence of E. faecium previously shown to block NEC-like injury in the loop model. There was a mild increase in the rate of E. coli transcytosis when studies were conducted with younger, undifferentiated cells; these immature cells had no brush border, had decreased production of brush border-specific enzymes, but retained well defined tight junctions, as demonstrated by transepithelial electrical resistance and electron microscopy. A further reduction/ complete blockage of E. coli transcytosis was observed when E. faecium was used as the coinfectant in studies with these undifferentiated cells. We hypothesize that the ability of E. coli to cross epithelial cell layer is a critical initial step in the cascade of events which lead ultimately to NEC; blockage or reduction in E. coli transcytosis in the presence of certain Gram(+) organisms may play a significant role in prevention of NEC.
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Rao GS, Hussain T, Islam MS, Sagynbaeva M, Gupta D, Panigrahi P, Ahuja R. Adsorption mechanism of graphene-like ZnO monolayer towards CO₂ molecules: enhanced CO₂ capture. NANOTECHNOLOGY 2016; 27:015502. [PMID: 26599020 DOI: 10.1088/0957-4484/27/1/015502] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
This work aims to efficiently capture CO2 on two-dimensional (2D) nanostructures for effective cleaning of our atmosphere and purification of exhausts coming from fuel engines. Here, we have performed extensive first principles calculations based on density functional theory (DFT) to investigate the interaction of CO2 on a recently synthesized ZnO monolayer (ZnO-ML) in its pure, defected and functionalized form. A series of rigorous calculations yielded the most preferential binding configurations of the CO2 gas molecule on a ZnO-ML. It is observed that the substitution of one oxygen atom with boron, carbon and nitrogen on the ZnO monolayer resulted into enhanced CO2 adsorption. Our calculations show an enriched adsorption of CO2 on the ZnO-ML when substituting with foreign atoms like B, C and N. The improved adsorption energy of CO2 on ZnO suggests the ZnO-ML could be a promising candidate for future CO2 capture.
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Naqvi SR, Hussain T, Panigrahi P, Luo W, Ahuja R. Manipulating energy storage characteristics of ultrathin boron carbide monolayer under varied scandium doping. RSC Adv 2017. [DOI: 10.1039/c6ra24890j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report, for the first time we believe, a detailed investigation on hydrogen storage efficiency of scandium (Sc) decorated boron carbide (BC3) sheets using spin-polarized density functional theory (DFT).
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Russell RG, Sarmiento JI, Fox J, Panigrahi P. Evidence of reinfection with multiple strains of Campylobacter jejuni and Campylobacter coli in Macaca nemestrina housed under hyperendemic conditions. Infect Immun 1990; 58:2149-55. [PMID: 2365455 PMCID: PMC258790 DOI: 10.1128/iai.58.7.2149-2155.1990] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A prospective bacteriologic study of 18 infant pig-tailed macaques (Macaca nemestrina) housed in a nursery facility in which Campylobacter spp. are endemic was undertaken to determine the epidemiology of infection and reinfection. The isolates of Campylobacter jejuni and C. coli cultured from 8 of the 18 infants were characterized by serotyping, DNA hybridization, and polyacrylamide gel electrophoresis protein profiles. The chronology of infection was indicative of multiple reinfections with different strains of C. jejuni and C. coli during the 12-month study of each infant. The duration of infection with a particular strain was 3 to 4 weeks. Infants were also infected with nalidixic acid-resistant campylobacters. These observations indicated that long-term infections under endemic conditions are caused by continual reinfection. C. jejuni or C. coli infection correlated with diarrhea in 5 of the 18 infants at 1 to 4 months of age.
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Panigrahi P, Sule M, Ghanate A, Ramasamy S, Suresh CG. Engineering Proteins for Thermostability with iRDP Web Server. PLoS One 2015; 10:e0139486. [PMID: 26436543 PMCID: PMC4593602 DOI: 10.1371/journal.pone.0139486] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 09/13/2015] [Indexed: 11/18/2022] Open
Abstract
Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements.
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Comparative Study |
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Panigrahi P, Sule M, Sharma R, Ramasamy S, Suresh CG. An improved method for specificity annotation shows a distinct evolutionary divergence among the microbial enzymes of the cholylglycine hydrolase family. Microbiology (Reading) 2014; 160:1162-1174. [DOI: 10.1099/mic.0.077586-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bile salt hydrolases (BSHs) are gut microbial enzymes that play a significant role in the bile acid modification pathway. Penicillin V acylases (PVAs) are enzymes produced by environmental microbes, having a possible role in pathogenesis or scavenging of phenolic compounds in their microbial habitats. The correct annotation of such physiologically and industrially important enzymes is thus vital. The current methods relying solely on sequence homology do not always provide accurate annotations for these two members of the cholylglycine hydrolase (CGH) family as BSH/PVA enzymes. Here, we present an improved method [binding site similarity (BSS)-based scoring system] for the correct annotation of the CGH family members as BSH/PVA enzymes, which along with the phylogenetic information incorporates the substrate specificity as well as the binding site information. The BSS scoring system was developed through the analysis of the binding sites and binding modes of the available BSH/PVA structures with substrates glycocholic acid and penicillin V. The 198 sequences in the dataset were then annotated accurately using BSS scores as BSH/PVA enzymes. The dataset presented contained sequences from Gram-positive bacteria, Gram-negative bacteria and archaea. The clustering obtained for the dataset using the method described above showed a clear distinction in annotation of Gram-positive bacteria and Gram-negative bacteria. Based on this clustering and a detailed analysis of the sequences of the CGH family in the dataset, we could infer that the CGH genes might have evolved in accordance with the hypothesis stating the evolution of diderms and archaea from the monoderms.
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Kumar Y, Dholakia BB, Panigrahi P, Kadoo NY, Giri AP, Gupta VS. Metabolic profiling of chickpea-Fusarium interaction identifies differential modulation of disease resistance pathways. PHYTOCHEMISTRY 2015; 116:120-129. [PMID: 25935544 DOI: 10.1016/j.phytochem.2015.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 03/27/2015] [Accepted: 04/03/2015] [Indexed: 06/04/2023]
Abstract
Chickpea is the third most widely grown legume in the world and mainly used as a vegetarian source of human dietary protein. Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceri (Foc), is one of the major threats to global chickpea production. Host resistance is the best way to protect crops from diseases; however, in spite of using various approaches, the mechanism of Foc resistance in chickpea remains largely obscure. In the present study, non-targeted metabolic profiling at several time points of resistant and susceptible chickpea cultivars using high-resolution liquid chromatography-mass spectrometry was applied to better understand the mechanistic basis of wilt resistance or susceptibility. Multivariate analysis of the data (OPLS-DA) revealed discriminating metabolites in chickpea root tissue after Foc inoculation such as flavonoids, isoflavonoids, alkaloids, amino acids and sugars. Foc inoculated resistant plants had more flavonoids and isoflavonoids along with their malonyl conjugates. Many antifungal metabolites that were induced after Foc infection viz., aurantion-obstine β-glucosides and querecitin were elevated in resistant cultivar. Overall, diverse genetic and biochemical mechanisms were operational in the resistant cultivar for Foc defense as compared to the susceptible plant. The resistant chickpea plants employed the above-mentioned metabolic pathways as potential defense strategy against Foc.
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Babu KS, Das A, Panigrahi P. Derivative expansion and the induced Chern-Simons term at finite temperature in 2+1 dimensions. PHYSICAL REVIEW. D, PARTICLES AND FIELDS 1987; 36:3725-3730. [PMID: 9958159 DOI: 10.1103/physrevd.36.3725] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Panigrahi P, Dhinakaran AK, Naqvi SR, Gollu SR, Ahuja R, Hussain T. Light metal decorated graphdiyne nanosheets for reversible hydrogen storage. NANOTECHNOLOGY 2018; 29:355401. [PMID: 29808826 DOI: 10.1088/1361-6528/aac84c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The sensitive nature of molecular hydrogen (H2) interaction with the surfaces of pristine and functionalized nanostructures, especially two-dimensional materials, has been a subject of debate for a while now. An accurate approximation of the H2 adsorption mechanism has vital significance for fields such as H2 storage applications. Owing to the importance of this issue, we have performed a comprehensive density functional theory (DFT) study by means of several different approximations to investigate the structural, electronic, charge transfer and energy storage properties of pristine and functionalized graphdiyne (GDY) nanosheets. The dopants considered here include the light metals Li, Na, K, Ca, Sc and Ti, which have a uniform distribution over GDY even at high doping concentration due to their strong binding and charge transfer mechanism. Upon 11% of metal functionalization, GDY changes into a metallic state from being a small band-gap semiconductor. Such situations turn the dopants to a partial positive state, which is favorable for adsorption of H2 molecules. The adsorption mechanism of H2 on GDY has been studied and compared by different methods like generalized gradient approximation, van der Waals density functional and DFT-D3 functionals. It has been established that each functionalized system anchors multiple H2 molecules with adsorption energies that fall into a suitable range regardless of the functional used for approximations. A significantly high H2 storage capacity would guarantee that light metal-doped GDY nanosheets could serve as efficient and reversible H2 storage materials.
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Avinash V, Panigrahi P, Suresh C, Pundle AV, Ramasamy S. Structural modelling of substrate binding and inhibition in penicillin V acylase from Pectobacterium atrosepticum. Biochem Biophys Res Commun 2013; 437:538-43. [DOI: 10.1016/j.bbrc.2013.06.109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 06/28/2013] [Indexed: 01/18/2023]
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Mehta DI, Horváth K, Chanasongcram S, Hill ID, Panigrahi P. Epidermal growth factor up-regulates sodium-glucose cotransport in enterocyte models in the presence of cholera toxin. JPEN J Parenter Enteral Nutr 1997; 21:185-91. [PMID: 9252942 DOI: 10.1177/0148607197021004185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Sodium-glucose cotransport by enterocytes is key to the successful implementation of oral rehydration in diarrhea. Confluent, differentiated Caco-2 cells have enterocyte-like characteristics. We have previously shown that short-term incubation of isolated rat jejunal enterocytes with epidermal growth factor (EGF) results in the up-regulation of sodium-glucose cotransport. The aim of this study was to examine the effect of EGF on Caco-2 cells in the presence of cholera toxin. METHODS Caco-2 cells grown on tissue culture dishes were used for glucose and sodium uptake studies and cells were grown on polycarbonate membranes for transport examinations. Effects of EGF on the kinetic parameters of sodium-glucose contransporter, thymidine transport, and on the activity of Na+/K(+)-ATPase were examined. The efficacy of basolateral vs apical EGF on sodium and glucose transport was compared after incubation of the monolayers with 10 nmol/L of cholera toxin. RESULTS EGF increased both glucose and sodium uptake and transport, and we observed a simultaneous increase in the activity of Na+/K(+)-adenosine triphosphatase (ATPase). Kinetic studies performed on brush-border membrane vesicles prepared from EGF-incubated confluent monolayers and on intact cells showed an increase in the maximum velocity but not the Michaelis constant, suggesting increased availability of transporters rather than conformational change. This effect was seen within minutes in both of the two putative transporters, high-affinity, low-capacity and low-affinity, high-capacity. There was no acute effect on thymidine uptake. Studies in the presence of cholera toxin demonstrated a significant up-regulation in sodium-glucose cotransport when EGF was applied from the basolateral side; the increase was smaller but significant with apical application. CONCLUSIONS Differentiated Caco-2 cells have two kinetically distinct sodium-glucose cotransporters. Short-term incubation of Caco-2 cells with EGF resulted in an up-regulation of sodium-glucose cotransport and subsequent increase in Na+/K(+)-ATPase activity. The effect of basolaterally applied EGF was more significant with or without incubation with cholera toxin. The early effect of EGF on glucose and sodium cotransport may have important therapeutic implications in diarrhea and dehydration states. The in vitro model described here uses a homogeneous cell population and provides a versatile system for uptake and transport studies.
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