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Bhandary S, Singh RK, Sinha AK, Badhu BP, Karki P. Sinonasal inverted papilloma in eastern part of Nepal. Kathmandu Univ Med J (KUMJ) 2006; 4:431-435. [PMID: 18603949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
OBJECTIVE To evaluate the clinicopathological profile of sinonasal inverted papilloma in a tertiary referral center in eastern part of Nepal. METHODS A prospective study consisting of total 28 histologically proven cases of sinonasal inverted papilloma was conducted in the ENT department of the center. The study period was from April 2002 to November 2005. RESULT Out of 28 cases studied, 21 were males and 7 were females with male to female ratio of 3:1. The highest incidence was seen in the 5th and 6th decades of life. The duration of symptoms varied from 5 months to 20 years with mean duration of 3.9 years. The lateral nasal wall and nasal cavity involvement was seen in all 28 cases. Maxillary sinus was involved in 27(96.4%) subjects followed by ethmoid (20), sphenoid (10) and the frontal sinus (7). The principle presenting symptom was nasal obstruction seen in 96.4% of the patients. Twenty two cases were treated by lateral rhinotomy with medial maxillectomy while, orbital exenteration was done in two cases. Associated carcinoma was noticed in 10.15% of all the subjects studied. CONCLUSION Sinonasal papilloma mostly presented in fifth to six decades of life mainly affecting the male patients. Majority of the patients were treated by lateral Rhinotomy with medial maxillectomy surgery. Early presentation would have given chances for endoscopic surgery.
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Dhar P, Muthuchelvan D, Sanyal A, Kaul R, Singh RP, Singh RK, Bandyopadhyay SK. Sequence analysis of the haemagglutinin and fusion protein genes of peste-des-petits ruminants vaccine virus of Indian origin. Virus Genes 2006; 32:71-8. [PMID: 16525737 DOI: 10.1007/s11262-005-5847-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2005] [Revised: 07/27/2005] [Accepted: 07/27/2005] [Indexed: 11/28/2022]
Abstract
The amino acid composition of the two surface proteins of peste-des-petits ruminants vaccine virus belonging to lineage four from India were deduced from the nucleotide sequence. The fusion (F) protein gene of PPRV Sungri/96 is 2405 nucleotides long and in relation to the length, it is 80 nucleotides longer than that of PPRV Nigeria/75/1 which are found to be present at the 5'UTR of this virus. The complete F gene alignment with other morbillivirus reveals a homology of 89% with PPRV/Nigeria/75/1 and 48-51% with other morbilliviruses. The F protein of PPRV Sungri/96 exhibited characteristics similarity to those of other morbillivirus F proteins. The overall amino acid similarity with its counterpart PPRV Nigeria/75/1 was 96%; with other morbilliviruses it is 65-74%. The PPRV Sungri/96 haemagglutinin (H) protein gene is 1954 nucleotides long and showed a sequence homology of 90.7% with PPRV/Nigeria/75/1 and with other morbilliviruses it ranged from 33% to 45%. At amino acids level, PPRV Sungri/96 showed a homology of 92.3% with PPRV/Nigeria/75/1 and 34-49% with other morbilliviruses. The phylogenetic tree constructed for F and H gene reveals four separate groups which is very similar to that found in other genes. To the best of our knowledge this is the first report describing the F and H genes of an Indian isolate.
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Singh RK, Mohta A, Kumar S. An unusual cause of abdominal mass in a child. Diagnosis: plasma cell type of Castleman's disease arising from transverse mesocolon. Gut 2006; 55:939, 999. [PMID: 16766751 PMCID: PMC1856357 DOI: 10.1136/gut.2005.083006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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Sundar S, Singh RK, Maurya R, Kumar B, Chhabra A, Singh V, Rai M. Serological diagnosis of Indian visceral leishmaniasis: direct agglutination test versus rK39 strip test. Trans R Soc Trop Med Hyg 2006; 100:533-7. [PMID: 16325874 DOI: 10.1016/j.trstmh.2005.08.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2005] [Revised: 08/24/2005] [Accepted: 08/24/2005] [Indexed: 11/23/2022] Open
Abstract
We evaluated the direct agglutination test (DAT), using freeze-dried (FD) and aqueous (AQ) antigen, and the rK39 immunochromatographic strip test in the diagnosis of Indian visceral leishmaniasis (VL). Sera from 508 subjects (150 parasitologically confirmed patients with VL, 100 and 153 healthy controls drawn from non-endemic and endemic regions, respectively, and 105 patients with other diseases presenting with fever and/or splenomegaly) were tested. The sensitivity of the tests were as follows: DAT (FD), 96% (95% CI 91-98); DAT (AQ), 97% (95% CI 93-99); rK39 strip test, 99% (95% CI 95-100). The specificity of DAT (FD), DAT (AQ) and rK39 strip tests were 85% (95% CI 81-88), 87% (95% CI 83-91) and 89% (95% CI 86-92), respectively. A significant correlation (high degree of agreement) was observed between all tests (kappa>0.80). We conclude that the sensitivity of FD antigen is comparable to that of AQ antigen. Similarly, the rK39 strip test is as sensitive as the DAT, but the strip test's greater convenience of use makes it a better tool for diagnosis of VL in peripheral areas of endemic regions.
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Singh RK, Dhiman RC, Mittal PK. Mosquito larvicidal properties of Momordica charantia Linn (family: Cucurbitaceae). J Vector Borne Dis 2006; 43:88-91. [PMID: 16967822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
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331
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Hosamani M, Bhanuprakash V, Scagliarini A, Singh RK. Comparative sequence analysis of major envelope protein gene (B2L) of Indian orf viruses isolated from sheep and goats. Vet Microbiol 2006; 116:317-24. [PMID: 16777357 DOI: 10.1016/j.vetmic.2006.04.028] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Revised: 04/20/2006] [Accepted: 04/28/2006] [Indexed: 11/25/2022]
Abstract
Orf virus (ORFV), the type species of Parapoxvirus, is responsible for contagious ecthyma in sheep and goats. In the present report, sequence analysis of major envelope gene (B2L) of four Indian orf virus isolates originating two each from sheep and goats was carried out. These recent isolates belonged to different outbreaks that occurred in Kumaon hills and adjoining plains during 2004-2005. Preliminary screening of the scab samples was carried out by diagnostic PCR. Full-length B2L gene encoding for immunogenic major envelope protein from all the four ORFV isolates was amplified by PCR and the amplicons (1206 bp) were cloned and sequenced. Comparative sequence analysis revealed an open reading frame of 1137 nucleotides (nt) encoding a polypeptide of 378 amino acids (aa). Indian isolates were highly related amongst themselves with sequence identity of over 97% at the nt and aa level. Further, they showed 97-98% sequence identity with sequences of other ORFV isolates from around the world; while 94-95 and 82.7-83.8% sequence identity was observed, respectively, with pseudocowpox and bovine papular stomatitis viruses--the other members of the genus. Phylogenetic analysis also showed that these Parapoxviruses from sheep and goats are closely related to other orf viruses reported worldwide.
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Singh RK, Maulik S, Mitra S, Mondal RK, Basu PS, Roychowdhury S, Panda CK. Human papillomavirus prevalence in postradiotherapy uterine cervical carcinoma patients: correlation with recurrence of the disease. Int J Gynecol Cancer 2006; 16:1048-54. [PMID: 16803484 DOI: 10.1111/j.1525-1438.2006.00550.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
To understand the role of human papillomavirus (HPV) in recurrence of uterine cervical cancer (CA-CX) after radiotherapy, we have analyzed the HPV prevalence in the exfoliated cells of 56 patients and their corresponding plasma. HPV DNA was detected in exfoliated cells of 78% (44/56) patients (HPV-16, 68%; HPV-18, 14%; HPV-X [other than 16, 18], 11%; and mixed infection of HPV-16 and HPV-18 in three cases). HPV DNA in plasma was present in only 25% (11/44) of the HPV-positive exfoliated cells (positive predictive value, 100%; negative predictive value, 27%) with concordance in HPV types. The recurrence of the disease was significantly associated with the presence of HPV in the exfoliated cell (P= 0.01) and plasma (P= 0.007) as well as high viral load in the exfoliated cell (P= 0.0002). Kaplan-Meier disease-free estimates have also shown the significant association between HPV prevalence in plasma and recurrence of the disease (P= 0.045). Thus, it indicates that in postradiotherapy CA-CX patients, the high viral load in the exfoliated cell as well as HPV presence in the plasma samples could be used in early detection of the patients at increased risk for disease recurrence and progression.
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Singh RK, Hosamani M, Balamurugan V, Satheesh CC, Rasool TJ, Yadav MP. Comparative sequence analysis of envelope protein genes of Indian buffalopox virus isolates. Arch Virol 2006; 151:1995-2005. [PMID: 16625321 DOI: 10.1007/s00705-006-0761-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Accepted: 03/04/2006] [Indexed: 11/25/2022]
Abstract
Buffalopox virus (BPXV) is considered to be a close variant of vaccinia virus (VACV), the prototype member of the genus Orthopoxvirus. In the present study, we have analyzed the sequences of H3L, A27L, and D8L gene-homologues of VACV in BPXV to elucidate its genetic relationship to VACV and other orthopoxviruses (OPVs). Products of these genes have been shown to be important in attachment of VACV to host cell surface receptors during viral entry. Additionally, the A27L gene is also responsible for cell fusion during infection, while the H3L gene is required for synthesis of the highly immunogenic major envelope protein p35. Full-length nucleotide sequences of H3L, A27L, and D8L genes of three BPXV isolates were determined by PCR amplification, cloning, and sequencing. The nucleotide (nt) sequence and the deduced amino acid (aa) sequences were compared with published sequences from other members of the genus Orthopoxvirus. Comparative sequence analysis of all the three genes revealed high sequence identity of BPXV isolates with VACV (close to 99% sequence identity) at both the nt and aa level. Phylogenetic analysis based on the deduced aa sequences of the H3L, A27L, and D8L genes also showed that BPXVs are more closely related to VACV than to any of the other OPVs.
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Bhandary S, Singh RK, Shrestha S. Regarding "Tonsillar microbial flora: a comparison of infected and non-infected tonsils". Kathmandu Univ Med J (KUMJ) 2006; 4:265. [PMID: 18807279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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335
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Zhou XD, Sens DA, Sens MA, Namburi VBRK, Singh RK, Garrett SH, Somji S. Metallothionein-1 and -2 expression in cadmium- or arsenic-derived human malignant urothelial cells and tumor heterotransplants and as a prognostic indicator in human bladder cancer. Toxicol Sci 2006; 91:467-75. [PMID: 16565513 DOI: 10.1093/toxsci/kfj174] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The goal of this study was to determine if the expression of the metallothionein (MT)-1/2 proteins might serve as a biomarker for the development of bladder cancer. A retrospective analysis of MT-1/2 staining was performed on 343 tissue sections from patients referred for the diagnosis of bladder cancer. The specimens were subdivided into six categories: benign, dysplastic, low-grade cancer, high-grade cancer with no evidence of invasion, high-grade cancer with evidence of invasion, and carcinoma in situ. There was no expression of MT-1/2 in benign lesions and low-grade cancers, a low incidence of expression in dysplastic lesions and high-grade cancers with no evidence of muscle invasion, and a significantly increased incidence of MT-1/2 in high-grade cancers that had invaded the underlying matrix. The expression of MT-1/2 varied in intensity from sample to sample and was focal in its expression. It was concluded from these findings that MT-1/2 may be a prognostic marker for cancers that are progressing to invade the underlying stroma of the bladder wall. The expression of MT-1/2 was also determined in a cell culture model of human urothelium that had been malignantly transformed by Cd2+ and As3+ and shown to be capable of tumor formation in nude mice. It was demonstrated that the expression of MT-1/2 in the tumor heterotransplants was similar to the pattern found in archival specimens of high-grade bladder cancers. The MT-1/2 staining in the heterotransplants was focal in pattern, varied in intensity, and highest in the less differentiated cells of the tumor. These findings indicate that the cell culture model may serve to help define the role of MT-1/2 expression in bladder cancer invasion.
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Jabeen T, Sharma S, Singh N, Singh RK, Kaur P, Perbandt M, Betzel C, Srinivasan A, Singh TP. Crystal structure of a calcium-induced dimer of two isoforms of cobra phospholipase A2 at 1.6 A resolution. Proteins 2006; 59:856-63. [PMID: 15828003 DOI: 10.1002/prot.20464] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The calcium-induced formation of a complex between two isoforms of cobra venom phospholipase A2 reveals a novel interplay between the monomer-dimer and activity-inactivity transitions. The monodispersed isoforms lack activity in the absence of calcium ions while both molecules gain activity in the presence of calcium ions. At concentrations higher than 10 mg/ml, in the presence of calcium ions, they dimerize and lose activity again. The present study reports the crystal structure of a calcium-induced dimer between two isoforms of cobra phospholipase A2. In the complex, one molecule contains a calcium ion in the calcium binding loop while the second molecule does not possess an intramolecular calcium ion. However, there are two calcium ions per dimer in the structure. The second calcium ion is present at an intermolecular site and that is presumably responsible for the dimerization. The calcium binding loops of the two molecules adopt strikingly different conformations. The so-called calcium binding loop in the calcium-containing molecule adopts a normal conformation as generally observed in other calcium containing phospholipase A(2) enzymes while the conformation of the corresponding loop in the calcium free monomer deviates considerably with the formation of a unique intraloop Gly33 (N)-Cys27 (O) = 2.74 A backbone hydrogen bond. The interactions of Arg31 (B) with Asp49 (A) and absence of calcium ion are responsible for the loss of catalytic activity in molecule A while interactions of Arg2 (B) with Tyr52 (B) inactivate molecule B.
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337
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Singh RK, Pandey HP, Sundar S. Visceral leishmaniasis (kala-azar): challenges ahead. Indian J Med Res 2006; 123:331-44. [PMID: 16778314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Indian visceral leishmaniasis (VL) is a parasitic disease caused by a haemoflagellete Leishmania donovani and transmitted by the bite of sand fly Phlebotomus argentipes. It affects various age groups. In India about 1,00,000 cases of VL are estimated to occur annually; of these, the State of Bihar accounts for over than 90 per cent of the cases. Diagnosis of VL typically relies on microscopic examination of tissue smears but serology and molecular methods are better alternatives currently. Notwithstanding the growing incidence of resistance, pentavalent antimony complex has been the mainstay for the treatment of VL during the last several decades. The second line drugs such as amphotericin B, lipid formulations of amphotericin B, paromomycin and recently developed miltefosine are the other alternatives. In spite of significant development in various areas of Leishmania research, there is a pressing need for the technological advancement in the understanding of immune response, drug resistance and the pathogenesis of leishmaniasis that could be translated into field applicable and affordable methods for diagnosis, treatment, and control of the disease.
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338
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Mondal S, Singh RK, Shanker R. Doppler effect in fluorine K-Auger line produced in electron-induced core ionization of SF6. J Chem Phys 2006; 124:034301. [PMID: 16438577 DOI: 10.1063/1.2158995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
An experimental evidence is reported on the observation of the Doppler effect in fluorine K-Auger line emitted from a core-ionized SF6 molecule under an impact of 16 keV electrons. The emitting source of the Auger line is found to acquire a kinetic energy of 4.7+/-0.3 keV. We propose that such large energy is released from the Coulomb repulsion taking place between F+ and SF5+ fragment ions under influence of an intense focusing field of the incident electrons. In the presence of the Coulomb field of these ions, the Auger line obtains a polarization P = 76%+/-7%.
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Singh RK, Nayak P, Niyogi UK, Khandal RK, Singh G. Gamma radiation process for destruction of toxic polychlorinated biphenyls (Pcbs) in transformer oils. JOURNAL OF ENVIRONMENTAL SCIENCE & ENGINEERING 2006; 48:45-50. [PMID: 17913201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Polychlorinated biphenyls (PCBs) are synthetic organic chemicals commercially used worldwide in many applications. PCBs were used in oils because of their excellent properties such as good thermal stability, flame resistance, dielectric constant, high break down voltage, high boiling point and low volatility. However, because of their adverse affects on environment and human health, the use of PCBs has been banned now. PCBs are today considered among the widespread pollutants in the global system. PCBs sources still exist in various industrial products and in waste streams such as capacitor oils, lubricating oils, transformer oils, hydraulic oils, paints, rubbers, cables, etc. Several such materials containing PCBs emanating from various sources need to be detoxified before their reuse or before going to landfill for final disposal. Various remedial technologies have been developed in the world to destroy toxic PCBs. The radiolysis has been investigated as an environment-friendly process for waste oil treatment contaminated with PCBs, which may be a better alternative to the globally most widely accepted incineration method. A study was undertaken to detoxify PCBs in transformer oil by gamma radiation using Cobalt 60 source. Analysis of PCBs in transformer oils before and after radiation was carried out by GC-MS instrument. The effect of radiation dose and destruction of PCBs in transformer oils are discussed in details in the present paper. The method used was found to be highly effective and destruction was as high as 79 %. Further, the transformer oil samples were also evaluated before and after radiation to check their quality. The properties of oils were not significantly altered by gamma radiation treatment as evident from the results given in the paper.
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Bhanuprakash V, Indrani BK, Hosamani M, Singh RK. The current status of sheep pox disease. Comp Immunol Microbiol Infect Dis 2006; 29:27-60. [PMID: 16458357 DOI: 10.1016/j.cimid.2005.12.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2005] [Indexed: 11/19/2022]
Abstract
Sheep are the moving banks of shepherds and their economic contribution in terms of meat, wool and skin/hide is immense. Various infectious diseases jeopardize the optimum productivity; among which sheep pox is more important as the disease restricts the export of sheep and their products besides other economic losses. Although, clinical signs are indicative of the disease but a laboratory confirmation is necessary for unequivocal diagnosis and studying epidemiology. The causative agent, sheep pox virus (SPV), is antigenically and genetically closely related to goat pox virus (GPV) and lumpy skin disease virus (LSDV), the other members of the genus capripox virus. In some countries, SPV and GPV are cross infective to small ruminants posing problem in diagnosis and epidemiology. However, recent studies have showed that the viruses are phylogenetically distinct and can be differentiated by molecular tools. Prophylaxis using attenuated vaccines is the choice of control measure as the immunity is long lasting. Detailed information on isolation, identification, pathology, epidemiology, diagnosis and prophylaxis would not only help in updating the knowledge of scientific fraternity but will be useful to the policy makers in order to formulate appropriate measures for control and eradication of the disease. This synthesis is to present an up-to-date review of the disease and its control to provide the reader with an overview of the problem.
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Mathews L, Cherian S, Singh RK. Intraoperative Cardiac Arrest - Successful Resuscitation with Open Chest Cardiac Compression. Ann Card Anaesth 2006. [DOI: 10.4103/0971-9784.37915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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342
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Singh RK, Bhandary S, Wakode PT, Karki P. Cervical necrotizing fasciitis in an uncontrolled type II diabetic patient. Kathmandu Univ Med J (KUMJ) 2006; 4:105-108. [PMID: 18603881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We report a case of cervical necrotizing fasciitis (CNF) in a female having uncontrolled type II diabetes mellitus. The patient was presented to us after 20 days of preliminary symptoms. The aetiology of microbial inoculation in subdermal tissue was not known. The isolate was Staphylococcus aureus. In spite of the delay in presentation, the patient was successfully treated with combined antimicrobial and surgical intervention.
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Jabeen T, Singh N, Singh RK, Sharma S, Somvanshi RK, Dey S, Singh TP. Non-steroidal anti-inflammatory drugs as potent inhibitors of phospholipase A2: structure of the complex of phospholipase A2with niflumic acid at 2.5 Å resolution. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2005; 61:1579-86. [PMID: 16301791 DOI: 10.1107/s0907444905029604] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2005] [Accepted: 09/18/2005] [Indexed: 11/10/2022]
Abstract
Phospholipase A(2) (PLA(2); EC 3.1.3.4) catalyzes the first step of the production of proinflammatory compounds collectively known as eicosanoids. The binding of phospholipid substrates to PLA(2) occurs through a well formed hydrophobic channel. Surface plasmon resonance studies have shown that niflumic acid binds to Naja naja sagittifera PLA(2) with an affinity that corresponds to a dissociation constant (K(d)) of 4.3 x 10(-5) M. Binding studies of PLA(2) with niflumic acid were also carried out using a standard PLA(2) kit that gave an approximate binding constant, K(i), of 1.26 +/- 0.05 x 10(-6) M. Therefore, in order to establish the viability of PLA(2) as a potential target molecule for drug design against inflammation, arthritis and rheumatism, the three-dimensional structure of the complex of PLA(2) with the known anti-inflammatory agent niflumic acid [2-[3-(trifluoromethyl)anilino]nicotinic acid] has been determined at 2.5 Angstroms resolution. The structure of the complex has been refined to an R factor of 0.187. The structure determination reveals the presence of one niflumic acid molecule at the substrate-binding site of PLA(2). It shows that niflumic acid interacts with the important active-site residues His48 and Asp49 through two water molecules. It is observed that the niflumic acid molecule is completely buried in the substrate-binding hydrophobic channel. The conformations of the binding site in PLA(2) as well as that of niflumic acid are not altered upon binding. However, the orientation of the side chain of Trp19, which is located at the entry of the substrate-binding site, has changed from that found in the native PLA(2), indicating its familiar role.
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Muthuchelvan D, Sanyal A, Sreenivasa BP, Saravanan P, Dhar P, Singh RP, Singh RK, Bandyopadhyay SK. Analysis of the matrix protein gene sequence of the Asian lineage of peste-des-petits ruminants vaccine virus. Vet Microbiol 2005; 113:83-7. [PMID: 16297575 DOI: 10.1016/j.vetmic.2005.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Revised: 10/01/2005] [Accepted: 10/05/2005] [Indexed: 11/27/2022]
Abstract
The M gene nucleotide sequence of an Indian peste-des-petits ruminants (PPRV) vaccine virus ("PPRV Sungri/96") belonging to Asian lineage was determined. The gene is 1476 nucleotides long with a single open reading frame (ORF). The nucleotide and predicted amino acid sequence was compared with the homologous region of the African Lineage Vaccine virus "PPRV/Nigeria/75/1". The nucleotide sequence of the "PPRV Sungri/96" was 86% identical to that of "PPRV/Nigeria/75/1", while a homology of 93% and 95% could be observed in the ORF and amino acids level, respectively. The M gene encodes a protein of 335 amino acids, with a predicted molecular weight (MW) of 37.8 kDa. The ORF is flanked by a 3' untranslated region of 436 nucleotides and a high level of sequence divergence (approximately 30%) could be observed in this region between the vaccine viruses of Asian and African lineages. A high degree of conservation of several amino acids of this protein observed previously was also confirmed in this study.
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Jabeen T, Singh N, Singh RK, Jasti J, Sharma S, Kaur P, Srinivasan A, Singh TP. Crystal structure of a heterodimer of phospholipase A2 from Naja naja sagittifera at 2.3 Å resolution reveals the presence of a new PLA2-like protein with a novel cys 32-Cys 49 disulphide bridge with a bound sugar at the substrate-binding site. Proteins 2005; 62:329-37. [PMID: 16287060 DOI: 10.1002/prot.20708] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The crystal structure of the phospholipase A2 (PLA2) heterodimer from Naja naja sagittifera reveals the presence of a new PLA2-like protein with eight disulphide bridges. The heterodimer is formed between a commonly observed group I PLA2 having seven characteristic disulfide bonds and a novel PLA2-like protein (Cys-PLA2) containing two extra cysteines at two highly conserved sites (positions 32 and 49) of structural and functional importance. The crystals of the heterodimer belong to tetragonal space group P41212 with cell dimensions, a = b = 77.7 A and c = 68.4 A corresponding to a solvent content of 33%, which is one of the lowest values observed so far in the PLA2 crystals. The structure has been solved with molecular replacement method and refined to a final R value of 21.6% [Rfree = 25.6%]. The electron density revealed the presence of cysteines 32 and 49 that are covalently linked to give rise to an eighth disulphide bridge in the PLA2-like monomer. A non-protein high-quality electron density was also observed at the substrate-binding site in the PLA2-like protein that has been interpreted as N-acetylglucosamine. The overall tertiary folds of the two monomers are similar having all features of PLA2-type folding. A zinc ion is detected at the interface of the heterodimer with fivefold coordination while another zinc ion was found on the surface of Cys-PLA2 with sixfold coordination. The conformations of the calcium-binding loops of both monomers are significantly different from each other as well as from those in other group I PLA2s. The N-acetylglucosamine molecule is favorably placed in the substrate-binding site of Cys-PLA2 and forms five hydrogen bonds and several van der Waals interactions with protein atoms, thus indicating a strong affinity. It also provides clue of the possible mechanism of sugar recognition by PLA2 and PLA2-like proteins. The formation of heterodimer seems to have been induced by zinc ion.
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Jabeen T, Singh N, Singh RK, Ethayathulla AS, Sharma S, Srinivasan A, Singh TP. Crystal structure of a novel phospholipase A2 from Naja naja sagittifera with a strong anticoagulant activity. Toxicon 2005; 46:865-75. [PMID: 16269164 DOI: 10.1016/j.toxicon.2005.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Revised: 08/10/2005] [Accepted: 08/10/2005] [Indexed: 11/19/2022]
Abstract
This is the first PLA(2) crystal structure from group I that shows a strong anticoagulant property. The monomeric PLA(2) was purified from the venom of Naja naja sagittifera (Indian cobra). Its amino acid sequence has been determined using cDNA technique. The amino acid sequence of sPLA(2) contains three positively charged and two negatively charged residues in the segment 54-71 (numbering scheme of sPLA(2)) thus giving this region an overall cationic amphiphilic surface. This suggested the presence of an anticoagulant activity in sPLA(2). The enzyme was crystallized using hanging drop vapour diffusion method in the presence of calcium chloride. The crystals belong to space group P4(1) with cell dimensions of a=b=42.0A, c=65.9A. The X-ray crystal structure was determined at 1.8A resolution using molecular replacement method and refined to an R value of 0.179 for 10,023 reflections. The overall scaffolding of sPLA(2) is essentially similar to those observed for other group I PLA(2)s. However, the conformations of various surface loops were found to be significantly different. The most significant observation pertains to the anticoagulant loop in which both the acidic residues are engaged in intramolecular interactions whereas all the three basic residues are free to interact with other molecules. This makes the sPLA(2) a potentially strong anticoagulating molecule.
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Bakshi CS, Shah DH, Verma R, Singh RK, Malik M. Rapid differentiation of Mycobacterium bovis and Mycobacterium tuberculosis based on a 12.7-kb fragment by a single tube multiplex-PCR. Vet Microbiol 2005; 109:211-6. [PMID: 16005166 DOI: 10.1016/j.vetmic.2005.05.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2004] [Revised: 01/25/2005] [Accepted: 05/20/2005] [Indexed: 11/21/2022]
Abstract
The aim of this work was the design and validation of a rapid and easy single tube multiplex-PCR (m-PCR) assay for the unequivocal differential detection of Mycobacterium bovis and Mycobacterium tuberculosis. Oligonucleotide primers were based on the uninterrupted 229-bp sequence in the M. bovis genome and a unique 12.7-kb insertion sequence from the M. tuberculosis genome, which is responsible for species-specific genomic polymorphism between these two closely related pathogens. The m-PCR assay was optimized and validated using 22 M. bovis and 36 M. tuberculosis clinical strains isolated from diverse host species and 9 other non-tuberculous mycobacterial (NTM) strains. The designed primers invariably amplified a unique 168-bp (M. bovis-specific) and 337-bp (M. tuberculosis-specific) amplicon from M. bovis and M. tuberculosis strains, respectively. The accuracy of the assay, in terms of specificity, was 100%, as none of the NTM strains tested revealed any amplification product. As little as 20 pg of genomic DNA could be detected, justifying the sensitivity of the method. The m-PCR assay is an extremely useful, simple, reliable and rapid method for routine differential identification of cultures of M. bovis and M. tuberculosis. This m-PCR may be a valuable diagnostic tool in areas of endemicity, where bovine and human tuberculosis coexist, and the distinction of M. bovis from M. tuberculosis is required for monitoring the spread of M. bovis to humans.
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Singh R, Singh RK, Tripathi AK, Cornélissen G, Schwartzkopff O, Otsuka K, Halberg F. Chronomics of circulating plasma lipid peroxides and anti-oxidant enzymes and other related molecules in cirrhosis of liver. Biomed Pharmacother 2005; 59 Suppl 1:S229-35. [PMID: 16275500 PMCID: PMC2662331 DOI: 10.1016/s0753-3322(05)80037-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
BACKGROUND The chronome (from chronos, time, and nomos, rule; time structure) of lipid peroxidation and anti-oxidant defense mechanisms may relate to the efficacy and management of preventive and curative chronotherapy. PATIENTS AND METHODS Thirty patients with liver cirrhosis, 25-45 years of age, and 60 age-matched clinically healthy volunteers were synchronized for 1 week with diurnal activity from about 06:00 to about 22:00 and nocturnal rest. Breakfast was around 08:30, lunch around 13:30 and dinner around 20:30. Drugs known to affect the free-radical system were not taken. Blood samples were collected at 6-h intervals for 24 h under standardized, presumably 24-h synchronized conditions. Determinations included plasma lipid peroxides, in the form of malondialdehyde (MDA), blood superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and glutathione reductase (GR) activities, and serum total protein, albumin, ascorbic acid, and uric acid concentrations. RESULTS A marked circadian variation was demonstrated for each variable in each group by population-mean cosinor (P < 0.01). In addition to anticipated differences in overall mean value (MESOR), patients differed from healthy volunteers also in terms of their circadian pattern. CONCLUSION Mapping the broader time structure (chronome) with age and multifrequency rhythm characteristics of antioxidants and pro-oxidants is needed for exploring their putative role as markers in the treatment and management of liver cirrhosis.
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Singh RK, Jabeen T, Sharma S, Kaur P, Srinivasan A, Singh TP. Crystal structure of a novel phospholipase A2 from crude venom of Indian cobra sub-species Naja naja sagittifera at 1.48 angstoms resolution. INDIAN JOURNAL OF BIOCHEMISTRY & BIOPHYSICS 2005; 42:279-286. [PMID: 23923535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Secretory phospholipase A2s (PLA2s), the structurally-homologous enzymes share a common qualitative catalytic site, but differ greatly in their pharmacological properties and toxicities. There has been a recognizable pattern of mutations in the primary sequence of PLA2s that alter their catalytic properties significantly. In the present study, the amino acid sequence and the three-dimensional structure of a new isoform of PLA2 from crude venom of Indian cobra sub-species Naja naja sagittifera (N.n.s.) has been determined by X-ray crystallography. The crystal structure has revealed several novel features of PLA2 folding and function. It contains 913 protein atoms and one each of Ca2+, phosphate and acetate ions with 142 solvent water molecules. A Ca2+ ion is present in the calcium-binding loop and forms a seven-fold coordination with a distorted pentagonal bipyramidal geometry. One of the coordination linkages is with the acetate ion, instead of the conserved water molecule. The presence of Lys at position 31 has a stabilizing effect on the loop Tyr 25-Cys 29 by interacting with carbonyl oxygen atoms of Tyr 25, Gly 26 and Cys 29. In turn, it lends stability to the Ca(2+)-binding loop as well. Another unique feature of the PLA2 structure is the formation of an intrastrand hydrogen bond, involving Ogamma of Thr 73 and Oepsilon2 of Glu 71, thus helping the beta-wing to act as a sharp arrow for insertion into other molecules. Yet another important feature of this PLA2 pertains to the conformation of its C-terminal segment, which is stabilized by a unique hydrogen bond through carbonyl oxygen of Lys 116 and Ndelta2 of Asn 120. This structural feature may be useful in the molecular recognition of the PLA2 through C-terminal segment.
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Cornélissen G, Delcourt A, Toussaint G, Otsuka K, Watanabe Y, Siegelova J, Fiser B, Dusek J, Homolka P, Singh RB, Kumar A, Singh RK, Sanchez S, Gonzalez C, Holley D, Sundaram B, Zhao Z, Tomlinson B, Fok B, Zeman M, Dulkova K, Halberg F. Opportunity of detecting pre-hypertension: worldwide data on blood pressure overswinging. Biomed Pharmacother 2005; 59 Suppl 1:S152-7. [PMID: 16275485 PMCID: PMC2581881 DOI: 10.1016/s0753-3322(05)80023-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Overswinging or CHAT (brief for Circadian Hyper-Amplitude-Tension), that is an excessive circadian variation in blood pressure (BP), has been associated with a large increase in cardiovascular disease risk, present even in the absence of an elevated BP itself. This usually asymptomatic condition is usually overlooked by current practice based on spot-checks, because to be diagnosed, measurements need to be taken around-the-clock, preferably for 7 days at the outset. Once diagnosed, however, a usual circadian BP pattern can be restored by means of certain non-pharmacologic or pharmacologic interventions timed appropriately. Thereby, it is possible to reduce the risk of cardiovascular morbidity and mortality, cerebral ischemic events and nephropathy in particular. For the preparation of guidelines regarding the diagnosis of BP disorders and for the institution of primary as well as secondary preventive measures, it is important to know what the incidence of CHAT is on a global basis. We found 191 cases of CHAT among 1602 mostly 7-day/24-h BP profiles, obtained from several centers in different countries participating in an ongoing project on the BIOsphere and the COSmos (BIOCOS). CHAT incidence is about the same between men and women, but it is diagnosed more often among patients with borderline hypertension or with glucose intolerance. It is also more common among MESOR-hypertensive than among MESOR-normotensive individuals. Priority should be given to the development of an unobtrusive and affordable device to automatically monitor BP and to analyze the data as-one-goes, so that cardiovascular disease risk can be prevented.
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