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Anaplastic histology and distinct molecular features in a small series of spinal cord ependymomas. Acta Neuropathol 2024; 147:83. [PMID: 38735021 PMCID: PMC11089008 DOI: 10.1007/s00401-024-02740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
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Integrated proteomics spotlight the proteasome as a therapeutic vulnerability in embryonal tumors with multilayered rosettes. Neuro Oncol 2024; 26:935-949. [PMID: 38158710 PMCID: PMC11066909 DOI: 10.1093/neuonc/noad265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Embryonal tumors with multilayered rosettes (ETMR) are rare malignant embryonal brain tumors. The prognosis of ETMR is poor and novel therapeutic approaches are desperately needed. Comprehension of ETMR tumor biology is currently based on only few previous molecular studies, which mainly focused on the analyses of nucleic acids. In this study, we explored integrated ETMR proteomics. METHODS Using mass spectrometry, proteome data were acquired from 16 ETMR and the ETMR cell line BT183. Proteome data were integrated with case-matched global DNA methylation data, publicly available transcriptome data, and proteome data of further embryonal and pediatric brain tumors. RESULTS Proteome-based cluster analyses grouped ETMR samples according to histomorphology, separating neuropil-rich tumors with neuronal signatures from primitive tumors with signatures relating to stemness and chromosome organization. Integrated proteomics showcased that ETMR and BT183 cells harbor proteasome regulatory proteins in abundance, implicating their strong dependency on the proteasome machinery to safeguard proteostasis. Indeed, in vitro assays using BT183 highlighted that ETMR tumor cells are highly vulnerable toward treatment with the CNS penetrant proteasome inhibitor Marizomib. CONCLUSIONS In summary, histomorphology stipulates the proteome signatures of ETMR, and proteasome regulatory proteins are pervasively abundant in these tumors. As validated in vitro, proteasome inhibition poses a promising therapeutic option in ETMR.
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Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation. Acta Neuropathol 2024; 147:22. [PMID: 38265489 PMCID: PMC10808175 DOI: 10.1007/s00401-023-02668-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/28/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024]
Abstract
Ependymomas encompass multiple clinically relevant tumor types based on localization and molecular profiles. Tumors of the methylation class "spinal ependymoma" (SP-EPN) represent the most common intramedullary neoplasms in children and adults. However, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical relevance have been described in a large, epigenetically defined series. Transcriptomic (n = 72), epigenetic (n = 225), genetic (n = 134), and clinical data (n = 112) were integrated for a detailed molecular overview on SP-EPN. Additionally, we mapped SP-EPN transcriptomes to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. The integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord revealed that SP-EPN display the highest similarities to mature adult ependymal cells. Unsupervised hierarchical clustering of transcriptomic data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype A tumors primarily carried previously known germline or sporadic NF2 mutations together with 22q loss (bi-allelic NF2 loss), resulting in decreased NF2 expression. Furthermore, they more often presented as multilocular disease and demonstrated a significantly reduced progression-free survival as compared to SP-EP subtype B. In contrast, subtype B predominantly contained samples without NF2 mutation detected in sequencing together with 22q loss (monoallelic NF2 loss). These tumors showed regular NF2 expression but more extensive global copy number alterations. Based on integrated molecular profiling of a large multi-center cohort, we identified two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.
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Mouse models of pediatric high-grade gliomas with MYCN amplification reveal intratumoral heterogeneity and lineage signatures. Nat Commun 2023; 14:7717. [PMID: 38001143 PMCID: PMC10673884 DOI: 10.1038/s41467-023-43564-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Pediatric high-grade gliomas of the subclass MYCN (HGG-MYCN) are highly aggressive tumors frequently carrying MYCN amplifications, TP53 mutations, or both alterations. Due to their rarity, such tumors have only recently been identified as a distinct entity, and biological as well as clinical characteristics have not been addressed specifically. To gain insights into tumorigenesis and molecular profiles of these tumors, and to ultimately suggest alternative treatment options, we generated a genetically engineered mouse model by breeding hGFAP-cre::Trp53Fl/Fl::lsl-MYCN mice. All mice developed aggressive forebrain tumors early in their lifetime that mimic human HGG-MYCN regarding histology, DNA methylation, and gene expression. Single-cell RNA sequencing revealed a high intratumoral heterogeneity with neuronal and oligodendroglial lineage signatures. High-throughput drug screening using both mouse and human tumor cells finally indicated high efficacy of Doxorubicin, Irinotecan, and Etoposide as possible therapy options that children with HGG-MYCN might benefit from.
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MYC overexpression and SMARCA4 loss cooperate to drive medulloblastoma formation in mice. Acta Neuropathol Commun 2023; 11:174. [PMID: 37919824 PMCID: PMC10621315 DOI: 10.1186/s40478-023-01654-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/17/2023] [Indexed: 11/04/2023] Open
Abstract
Group 3 medulloblastoma is one of the most aggressive types of childhood brain tumors. Roughly 30% of cases carry genetic alterations in MYC, SMARCA4, or both genes combined. While overexpression of MYC has previously been shown to drive medulloblastoma formation in mice, the functional significance of SMARCA4 mutations and their suitability as a therapeutic target remain largely unclear. To address this issue, we combined overexpression of MYC with a loss of SMARCA4 in granule cell precursors. Both alterations did not increase proliferation of granule cell precursors in vitro. However, combined MYC overexpression and SMARCA4 loss successfully induced tumor formation in vivo after orthotopic transplantation in recipient mice. Resulting tumors displayed anaplastic histology and exclusively consisted of SMARCA4-negative cells although a mixture of recombined and non-recombined cells was injected. These observations provide first evidence for a tumor-promoting role of a SMARCA4 deficiency in the development of medulloblastoma. In comparing the transcriptome of tumors to the cells of origin and an established Sonic Hedgehog medulloblastoma model, we gathered first hints on deregulated gene expression that could be specifically involved in SMARCA4/MYC driven tumorigenesis. Finally, an integration of RNA sequencing and DNA methylation data of murine tumors with human samples revealed a high resemblance to human Group 3 medulloblastoma on the molecular level. Altogether, the development of SMARCA4-deficient medulloblastomas in mice paves the way to deciphering the role of frequently occurring SMARCA4 alterations in Group 3 medulloblastoma with the perspective to explore targeted therapeutic options.
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WCN23-0439 TRANSESOPHAGEAL ECHOCARDIOGRAPHY IN PATIENTS WITH CUFFED TUNNELLED HAEMODIALYSIS CATHETERS – A BRIDGE TO THE MISSED DIAGNOSIS? Kidney Int Rep 2023. [DOI: 10.1016/j.ekir.2023.02.711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023] Open
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OTHR-42. Missing data tolerant integration of proteomic datasets enables the identification and characterization of brain cancer subtypes. Neuro Oncol 2022. [PMCID: PMC9164826 DOI: 10.1093/neuonc/noac079.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Investigating the proteome can add a significant layer of information to manifold existing methylation, mutation, and transcriptome data on brain tumors as proteins represent the pharmacologically addressable phenotype of a disease. Small cohorts limit the usability and validity of statistical methods, and variable technical setups and high numbers of missing values make data integration from public sources challenging. Using a newly developed framework being able to reduce batch effects without the need for data reduction or missing value imputation, we show –based on in-house and publicly available datasets- successful integration of proteomic data across different tissue types, quantification platforms, and technical setups. Exemplarily, data of a Sonic hedgehog (Shh) medulloblastoma mouse model were analyzed, showing efficient data integration independent of tissue preservation strategy or batch. We further integrated batches of publicly available data of human brain tumors, confirming proposed proteomic cancer subtypes correlating with clinical features. We show that, missing value tolerant reduction of technical variances may be helpful to identify biomarkers, proteomic signatures, and altered pathways characteristic for molecular brain cancer subtypes.
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HGG-15. Generation of a novel mouse model for brain tumors of the DNA methylation class “GBM MYCN”. Neuro Oncol 2022. [PMCID: PMC9164702 DOI: 10.1093/neuonc/noac079.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Multiple recent publications have described a highly aggressive subgroup of pediatric glioblastoma, which is clearly separable from other pediatric and adult glioblastoma based on its DNA methylation profile (GBM MYCN). These tumors almost exclusively occur in children and have a median overall survival of only 14 months. Many tumors in this group are driven by MYCN amplifications and harbor TP53 mutations. Otherwise, information about these tumors are still sparse and treatment is ineffective and causes severe side effects in many cases. In order to further investigate the biology and treatment options of these tumors, preclinical models are urgently needed. Here, we describe the generation of hGFAP-cre::TP53Fl/Fl::lsl-MYCN mice, which carry a loss of TP53 and show aberrant MYCN expression in neural precursors of the central nervous system. These animals develop large forebrain tumors within the first 80 days of life with 100 % penetrance. These tumors resemble human GBM MYCN tumors by histology, global gene expression, and DNA methylation. In order to understand the developmental biology and intratumoral heterogeneity, we employed single cell RNA sequencing (scRNAseq) to the murine tumors with first results indicating a resemblance of tumor cells to committed oligodendrocyte precursors. We further show that both murine and human tumor cells are sensitive to AURKA inhibition in vitro, suggesting a potential new therapeutic option for improved patient care. We believe that further characterization and utilization of the model will pave the way to improved treatment strategies for patients with these highly aggressive tumors.
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First impression of teeth design on others: A facial and personality analysis in the Central Indian population. Niger J Clin Pract 2019; 22:1503-1508. [PMID: 31719271 DOI: 10.4103/njcp.njcp_135_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Facial features and personality types vary with different geographical boundaries, culture, and ethnicity. The impression created by teeth design differs with the face and personality of males and females. Aims This study evaluated the dominant facial and personality types and their correlation among males and females in Central Indian population. Subjects and Methods The full-face photographs of 120 people, with a broad smile and visible dentition, were calibrated to generate a facial map with digital software. The participants filled a personality questionnaire. Facial form and personality type were classified as a combination of strong, dynamic, delicate, and calm. Descriptive and inferential statistics using Chi-square and Kappa tests. Results The dominant facial form was calm (66.67%, 71.67%) with the second dominant facial form being dynamic (50%, 51.67%) both for males and females respectively. While the dominant personality type was dynamic (50%), the second dominant personality type was calm (35%, 30%) for both males and females. Kappa analysis showed moderate agreement between the dominant facial and personality types (P = 0.41 in males, P = 0.10 in females). The software used was SPSS 22.0 version and P < 0.05 is considered as the level of significance. Conclusions A varying number of combinations are essential in characterizing the face. The personality type has a predominance of one type over other. The interpretation of these combinations in dentistry can help to select appropriate tooth forms and design a harmonious smile.
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ETHNIC DIFFERENCES IN SEDENTARY BEHAVIOR AND CARDIOMETABOLIC RISK BIOMARKERS IN POSTMENOPAUSAL WOMEN. Innov Aging 2018. [DOI: 10.1093/geroni/igy031.3461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Neoadjuvant chemotherapy followed by surgery (NACT-surgery) versus concurrent cisplatin and radiation therapy (CTRT) in patients with stage IB2 to IIB squamous carcinoma of cervix: A randomized controlled trial (RCT). Ann Oncol 2017. [DOI: 10.1093/annonc/mdx663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Neoadjuvant chemotherapy followed by surgery (NACT-surgery) versus concurrent cisplatin and radiation therapy (CTRT) in patients with stage IB2 to IIB squamous carcinoma of cervix: A randomized controlled trial (RCT). Ann Oncol 2017. [DOI: 10.1093/annonc/mdx440.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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RELATIONSHIP BETWEEN OBJECTIVELY MEASURED TRANSPORTATION BEHAVIOR AND HEALTH VARIABLES IN OLDER ADULTS. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.4347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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0852 SLEEP DISTURBANCES AND FEAR OF FALLING IN OLDEST ADULTS LIVING IN RETIREMENT COMMUNITY CAMPUS SETTINGS. Sleep 2017. [DOI: 10.1093/sleepj/zsx050.851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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0693 VARIATION IN ACTIGRAPHY-ESTIMATED REST-ACTIVITY PATTERNS BY DEMOGRAPHIC FACTORS. Sleep 2017. [DOI: 10.1093/sleepj/zsx050.692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Does the social environment moderate associations of the built environment with Latinas' objectively-measured neighborhood outdoor physical activity? Prev Med Rep 2016; 4:551-557. [PMID: 27818913 PMCID: PMC5094267 DOI: 10.1016/j.pmedr.2016.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 02/07/2023] Open
Abstract
Favorable perceptions of the built and social neighborhood environment may promote outdoor physical activity (PA). However, little is known about their independent and interactive effects on neighborhood-specific outdoor PA. We examined associations of perceived built and social neighborhood environment factors, and their interactions, with objectively-measured neighborhood outdoor moderate-to-vigorous physical activity (MVPA) among a sample of Latina women in San Diego, CA. Analyses included baseline data collected in 2011-2013 from 86 Latinas with ≥ 2 days of combined accelerometer and global positioning system data and complete survey measures. We examined objective neighborhood outdoor MVPA within 500-meter home buffers. Generalized linear mixed models examined associations of 3 perceived built (e.g., sidewalk maintenance) and 3 social environmental (e.g., safety from crime) factors with engaging in any daily neighborhood outdoor MVPA. Models tested interactions between the built and social environmental factors. Although the perceived neighborhood environmental factors were not significantly related to daily neighborhood outdoor MVPA, we found 2 significant interactions: perceived sidewalk maintenance x safety from crime (p = 0.05) and neighborhood aesthetics x neighborhood social cohesion (p = 0.03). Sidewalk maintenance was positively related to daily neighborhood outdoor MVPA only among Latinas that reported low levels of safety from crime. Neighborhood aesthetics was positively related to daily neighborhood outdoor MVPA only among Latinas with high neighborhood social cohesion. Findings suggest several built and social environmental factors interact to influence Latinas' neighborhood outdoor MVPA. Interventions are needed targeting both built and social neighborhood environmental factors favorable to outdoor PA in the neighborhood.
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HIV-infected CD4+ T Cells Use T-bet-dependent Pathway for Production of IL-10 Upon Antigen Recognition. Scand J Immunol 2016; 83:288-96. [PMID: 27028319 DOI: 10.1111/sji.12422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/15/2016] [Indexed: 01/11/2023]
Abstract
Interleukin (IL)-10 has been implicated in persistence of pathogens in a number of chronic infections. Infected CD4+ cells upon reactivation with HIV antigens were also shown to produce IL-10, which might contribute to their persistence. Hence, it is crucial to determine mechanisms regulating IL-10 production after activation with HIV antigens for devising effective blocking strategies. In this study, ERK-, T-bet- and FoxP3-dependent pathways were evaluated for their possible roles in IL-10 production by infected CD4+ cells after reactivation with HIV Env. Intracellular and secreted IL-10 levels were determined by flow cytometry and Bioplex assay after treating PBMCs with PD98059, tipifarnib and cyclosporin A for blocking of ERK-, T-bet-and FoxP3-dependent pathways, respectively. Baseline levels of T-bet, pERK were higher in P24+ CD4+ cells as compared to uninfected CD4+ cells, which increased further after activation with Env. Inhibition of T-bet resulted in 2.3-fold reduction of IL-10 expression whereas ERK and FoxP3 inhibition failed to cause suppression of IL-10 expression. Conversely, IL-10 secreted by PBMCs was inhibited maximally after ERK inhibition suggesting its role in regulation of cytokine secretory pathway. IFN-γ was found to be suppressed after treatment with inhibitors of all these pathways. Thus, the study highlighted need for IL-10 blockade along with the use of antigens for therapeutic vaccinations or latency reversal and identified the T-bet-dependent pathway as an important pathway regulating IL-10 production by infected CD4+ cells. However, simultaneous blockade of IFN-γ precludes use of inhibitor of this pathway as an IL-10 blocking strategy.
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Sunitinib in patients with imatinib-resistant gastrointestinal stromal tumor: A single center experience study. Indian J Cancer 2016; 52:320-3. [PMID: 26905126 DOI: 10.4103/0019-509x.176747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AIM The outcome of patients with advanced gastrointestinal stromal tumor (GIST) has improved with the use of imatinib. Despite high response rates with this drug resistance eventually develops in nearly all patients. We present an analysis of prospectively collected data on sunitinib efficacy and safety in patients with imatinib-resistant GIST. SUBJECTS AND METHODS Between November 2006 and October 2007, patients with GIST were accrued in an approved sunitinib patient access protocol. Key eligibility criteria included tumor resistance to imatinib and/or patient intolerance to this drug. Patients received sunitinib at a starting dose of 50 mg once daily for 4 weeks in a 6 week cycle, with standardized dose modification titrated to toxicity. Patients were continued on sunitinib until disease progression or unacceptable toxicity. The endpoints were safety, overall survival (OS) and objective response rate (ORR). RESULTS Fifteen patients, all of whom had imatinib resistance and none intolerance, with median age of 48 (26-69) years, were treated on the protocol. The most common sites of primary disease were small intestine (40%), stomach (26.7%) and retroperitoneal (26.7%). A median of 10 (1-47) cycles of sunitinib were delivered, 9 (60%) patients required dose reductions due to toxicity whereas dose delay of > 2 weeks was required in only one (6.7%) patient. There were no toxicity-related drug discontinuations. Hypothyroidism (n = 4; 26.7%) and hand-foot syndrome (n = 3; 20%) were the most common toxicities. There were no complete and 4 (26.7%) partial responses while prolonged disease stability was seen in 8 (53.3%) patients. At a median follow-up of 81 months in surviving patients, the median progression-free and overall survivals were 15.5 and 18.7 months, respectively. CONCLUSIONS Sunitinib appears to be an effective and well-tolerated treatment for Indian patients with imatinib-resistant GIST with outcomes similar to that reported previously. Adverse effects can be reasonably well managed using a dose modification strategy.
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Detection of dengue virus 4 from central India. Indian J Med Res 2012; 136:491-4. [PMID: 23041745 PMCID: PMC3510898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Indexed: 10/25/2022] Open
Abstract
BACKGROUND & OBJECTIVES Dengue is an important arboviral disease. All four dengue virus serotypes are reported to be circulating in India. It is also known that different serotypes, genotypes and clades of genotype determine outbreak severity. Dengue affected children are known to have serious disease outcome. We carried out this study to give reliable diagnosis of dengue infection in children and to detect circulating serotype in central India. METHODS Samples collected from paediatric patients suspected to have dengue fever were subjected to IgM and IgG ELISA to determine dengue virus infection. Samples collected within 0-5 days of onset of illness and positive by IgM ELISA were tested by nested reverse transcription polymerase chain reaction (nRT-PCR). The PCR products were sequenced and analyzed. RESULTS Of the 89 samples tested, 18 and 7 were positive for dengue IgM and IgG, respectively. Dengue activity was observed in both Jabalpur city and adjoining rural settings. One sample found positive by nRT-PCR was further sequenced to confirm dengue virus 4 as aetiological agent. INTERPRETATION & CONCLUSIONS Our findings demonstrated dengue virus infection in children and adolescent in central India. Because of continuous changing epidemiology, it is important to monitor dengue virus activity at both serological and molecular level in this part of the country for better patient care and management.
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Fluconazole resistant non-albicans vaginal yeast in HIV seronegative women with vaginal discharge in Pune, India. Int J Infect Dis 2004; 8:251-2. [PMID: 15234330 DOI: 10.1016/j.ijid.2003.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2003] [Revised: 10/19/2003] [Accepted: 11/20/2003] [Indexed: 11/17/2022] Open
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Preparation and characterization of biodegradable poly-3-hydroxybutyrate-starch blend films. BIORESOURCE TECHNOLOGY 2003; 86:33-37. [PMID: 12421006 DOI: 10.1016/s0960-8524(02)00110-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacterial polyesters have attracted much attention as biodegradable biocompatible polymers. Poly-3-hydroxybutyrate, a microbially produced thermoplastic, has similar material properties to polypropylene. Its potential application as biodegradable and biocompatible plastics is well documented. However, due to high cost it is used mainly in biomaterials for medical applications. Materials with useful properties may result from blending bacterial polyhydroxybutyrate (PHB) with other polymers. In this paper, the compatibility of PHB with starch for improved properties and cost reduction is discussed. The thermal and mechanical properties of the blended films were studied by means of thermogravimetry, differential scanning calorimetry and an automated material testing system. The results revealed that blend films had a single glass transition temperature for all the proportions of PHB:starch tested. The nature of all combinations was found to be crystalline. The tensile strength was optimum for the PHB:starch ratio of 0.7:0.3 (wt/wt). The variation in tensile strength, Young's modulus, extension needed to break, thermal stability, glass transition temperature, melting temperature, for the different proportions of PHB:starch are discussed.
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Measuring denatured state energetics: deviations from random coil behavior and implications for the folding of iso-1-cytochrome c. J Mol Biol 2000; 296:217-28. [PMID: 10656828 DOI: 10.1006/jmbi.1999.3454] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The changes in the free energy of the denatured state of a set of yeast iso-1-cytochrome c variants with single surface histidine residues have been measured in 3 M guanidine hydrochloride. The thermodynamics of unfolding by guanidine hydrochloride is also reported. All variants have decreased stability relative to the wild-type protein. The free energy of the denatured state was determined in 3 M guanidine hydrochloride by evaluating the strength of heme-histidine ligation through determination of the pK(a) for loss of histidine binding to the heme. The data are corrected for the presence of the N-terminal amino group which also ligates to the heme under similar solution conditions. Significant deviations from random coil behavior are observed. Relative to a variant with a single histidine at position 26, residual structure of the order of -1.0 to -2.5 kcal/mol is seen for the other variants studied. The data explain the slower folding of yeast iso-1-cytochrome c relative to the horse protein. The greater number of histidines and the greater strength of ligation are expected to slow conversion of the histidine-misligated forms to the obligatory aquo-heme intermediate during the ligand exchange phase of folding. The particularly strong association of histidine residues at positions 54 and 89 may indicate regions of the protein with strong energetic propensities to collapse against the heme during early folding events, consistent with available data in the literature on early folding events for cytochrome c.
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Abstract
Pichia pastoris was transformed with the Trichoderma reesei cbh1 gene, and the recombinant enzyme was purified and analyzed kinetically and by circular dichroism. The P. pastoris rCBH I was recognized by MoAb raised to T. reesei CBH I but was found in multiple molecular weight species on SDS-PAGE gels. Carbohydrate content determination and SDS-PAGE western analysis indicated that the recombinant protein was hyperglycosylated, although a species very similar in molecular weight to the T. reesei enzyme could be isolated chromatographically. The P. pastoris rCBH I also demonstrated activity toward soluble and insoluble substrates (i.e., pNPL and Sigmacell), although at a level significantly lower than the wild-type enzyme. More seriously, the yeast-expressed enzyme showed non-wild-type secondary structure by circular dichroism. We conclude that P. pastoris may not serve as an adequate host for the site-directed mutagenesis of T. reesei CBH I.
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Effect of pH on formation of a nativelike intermediate on the unfolding pathway of a Lys 73 --> His variant of yeast iso-1-cytochrome c. Biochemistry 1999; 38:487-95. [PMID: 9890932 DOI: 10.1021/bi981698k] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous work on a Lys 73 --> His (H73) variant of iso-1-cytochrome c at pH 7.5 [Godbole et al. (1997) Biochemistry 36, 119-126] showed that this variant unfolds through a nativelike intermediate that has properties consistent with replacement of the Met 80 heme ligand by His 73. Here, the pH dependence of the equilibrium unfolding of the wild type (WT) and H73 proteins have been investigated, since a characteristic pH dependence is expected for the stability of an intermediate stabilized by histidine-heme ligation. Stability has been evaluated using guanidine hydrochloride and pH denaturation methods. Above pH 5, the m-values from guanidine hydrochloride denaturation of the WT and H73 variants remain significantly different, consistent with continued population of this intermediate. At pH 4.5 the m-values for the two proteins are within error the same. To assess stability at lower pH, acid denaturation was carried out. The midpoint is about 3.3 for both proteins but the transition is broader for the H73 protein, suggestive of intermediates again being populated during the unfolding of the H73 protein at this lower pH. Heme ligation by Met 80 was monitored (695 nm absorbance) during gdnHCl (pH 4.5 and 5.0) and acid denaturation, confirming, respectively, the absence and presence of intermediates. A thermodynamic analysis demonstrates that this complex pH dependence for the presence of histidine ligation induced intermediates is expected and implicates a titratable group with a pKa of approximately 6.6. The analysis also demonstrates when the pH dependences of global stability and stability of an intermediate differ significantly, population of folding intermediates as a function of pH will show novel behavior.
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Cytochrome c folding traps are not due solely to histidine-heme ligation: direct demonstration of a role for N-terminal amino group-heme ligation. J Mol Biol 1998; 275:719-24. [PMID: 9480763 DOI: 10.1006/jmbi.1997.1493] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In previous work, heme ligation effects on the folding of cytochrome c have been attributed to histidine side-chains. A variant of yeast iso-1-cytochrome c designated TM, which lacks all histidine residues except His18, still shows evidence of denatured state heme ligation in the pH range between 5 and 6 where normally only histidine ligation is expected. Conversion of the N-terminal amino group of TM to a carbonyl group through a transamination reaction with glyoxylate produced a protein (ModTM) with no terminal amino group. The midpoint pH (pH1/2) for loss of heme ligation in 3 M guanidine-HCl shifts from 5.9 to 7.4 as a result of this modification, providing direct evidence for N-terminal amino group-heme ligation under these conditions. The N-terminal amino group thus competes with histidine for misligation of iso-1-cytochrome c under denaturing conditions. To assess the effect of denatured state N-terminal amino group-heme ligation on the folding of iso-1-cytochrome c, stopped-flow kinetics experiments were conducted. At pH 6.2, the major refolding lifetimes (3 M-->0.27 M guanidine-HCl) for ModTM, TM and the wild-type protein are 11.6 ms, 30 ms and 1.3 seconds, respectively. Denatured state ligation of the N-terminal amino group thus slows folding 2.6-fold.
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A histidine variant of yeast iso-1-cytochrome c that strongly affects the energetics of the denatured state. J Mol Biol 1997; 268:816-21. [PMID: 9180374 DOI: 10.1006/jmbi.1997.0999] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Iso-1-cytochrome c has been engineered to remove all histidine residues not involved in heme ligation in the native state to produce a variant designated TM. Single histidine residues were then introduced at positions 26, TM + His26, and 54, TM + His54. Since histidine residues not involved in native state heme ligation are known to replace the methionine 80 heme ligand in denatured cytochrome c, these variants were expected to affect the structure of the denatured state. Guanidine hydrochloride denaturations were performed to assess the stability of these proteins relative to the wild-type protein. The free energy difference for heme ligation in the denatured state was assessed by pH titration. The experimentally observed mutation-induced change (delta deltaG(D-state)) in the free energy of heme ligation for unfolded TM + His54 versus TM + His26 is -0.4 kcal/mol. The expected mutation-induced change in delta deltaG(D-state) calculated for a random coil unfolded state is +2 kcal/mol. Thus, unfolded TM + His54 has residual structure stabilizing its denatured state by -2.4 kcal/mol relative to TM + His26. The results imply that the denatured state can contribute significantly to mutation-induced changes in the free energy of unfolding of a protein.
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Endemic fluorosis with genu valgum syndrome in a village of district Mandla, Madhya Pradesh. Indian Pediatr 1997; 34:232-6. [PMID: 9282491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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A lysine 73-->histidine variant of yeast iso-1-cytochrome c: evidence for a native-like intermediate in the unfolding pathway and implications for m value effects. Biochemistry 1997; 36:119-26. [PMID: 8993325 DOI: 10.1021/bi961915m] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In this paper we report thermodynamic studies on a variant of yeast iso-1-cytochrome c in which a surface lysine residue at position 73 has been replaced with a histidine (H73). Guanidine hydrochloride denaturation studies monitored by circular dichroism spectroscopy indicated decreased thermodynamic stability (a lower delta G(o)(u)H20) and a smaller m value for the H73 protein as compared to the wild type (WT) protein. Further investigations to probe the causes for the thermodynamic stability differences between the two proteins involved guanidine hydrochloride and urea denaturations monitored by tryptophan fluorescence. The stability of heme ligation in the denatured state in the presence of either guanidine hydrochloride or urea was monitored by the spin-state transition of the heme iron induced by pH. None of these studies supported the hypothesis that the decreased m value was due to heme-His73 ligation in the denatured state. Guanidine hydrochloride denaturations monitored by the change in the extinction coefficient at 695 nm, which is sensitive to the presence of heme-Met80 ligation, revealed a native-like intermediate for the H73 protein, probably caused by displacement of the Met80 heme ligand by histidine 73 at guanidine hydrochloride concentrations much lower than required for full cooperative unfolding. Presence of the native-like intermediate is most likely the cause of the smaller m value and decreased thermodynamic stability for the CD-monitored H73 protein unfolding as compared to the unfolding of the WT protein. Guanidine hydrochloride denaturations in the presence of 200 mM imidazole provide further evidence in support of the proposed mechanism.
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Biodegradation of phenol: a comparative study with and without applying magnetic fields. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 1993; 56:73-76. [PMID: 7763365 DOI: 10.1002/jctb.280560113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The objective of this work was to study the effect of magnetic fields on the rate of phenol biodegradation using immobilized activated sludge. A recirculation flow bioreactor employing immobilized bacterial beads was used with phenol as the substrate to study the biodegradation process. This study was conducted by applying separately the north pole and the south pole magnetic fields to the bioreactor. Rate of dissolved oxygen consumption, phenol concentration and extracellular protein concentration were the parameters monitored during the process. It was observed that by applying a magnetic south pole to the process, biodegradation in the form of biological oxidation was enhanced. A 30% increase in biodegradation rate was obtained by applying a magnetic south pole of strength of 0.45 Tesla to the bioreactor with immobilized microbial beads as compared to the control. Magnetic north pole irradiation inhibited this type of biooxidation. This process has potential for biological treatment of organic wastes.
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Abstract
An epidemic of acute hemorrhagic conjunctivitis in 416 (10.8%) of 3,830 staff and students of the Christian Medical College and Hospital in Vellore, India, during September-December 1979 was studied. Virus was isolated in cultures of HeLa cells from 171 of the 249 persons cultured. Most of the viral isolates were identified as an antigenic variant of coxsackievirus A24. Success in isolating the virus from conjunctival swabs was inversely proportional to the time elapsed between the onset of illness and the time the specimens were collected. In general, titers of antibody to coxsackievirus A24 were low or undetectable. Three persons had subconjunctival hemorrhage with no other symptoms, and virologic evidence of infection with coxsackievirus A24 was obtained in two of them.
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