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Radhakrishnan A, Gangopadhyay R, Sharma C, Kapardar RK, Sharma NK, Srivastav R. Unwinding Helicase MCM Functionality for Diagnosis and Therapeutics of Replication Abnormalities Associated with Cancer: A Review. Mol Diagn Ther 2024; 28:249-264. [PMID: 38530633 DOI: 10.1007/s40291-024-00701-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
The minichromosome maintenance (MCM) protein is a component of an active helicase that is essential for the initiation of DNA replication. Dysregulation of MCM functions contribute to abnormal cell proliferation and genomic instability. The interactions of MCM with cellular factors, including Cdc45 and GINS, determine the formation of active helicase and functioning of helicase. The functioning of MCM determines the fate of DNA replication and, thus, genomic integrity. This complex is upregulated in precancerous cells and can act as an important tool for diagnostic applications. The MCM protein complex can be an important broad-spectrum therapeutic target in various cancers. Investigations have supported the potential and applications of MCM in cancer diagnosis and its therapeutics. In this article, we discuss the physiological roles of MCM and its associated factors in DNA replication and cancer pathogenesis.
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Affiliation(s)
| | - Ritwik Gangopadhyay
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | | | | | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr. DY Patil Biotechnology and Bioinformatics Institute, Dr. DY Patil Vidyapeeth, Pune, Maharashtra, India
| | - Rajpal Srivastav
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India.
- Department of Science and Technology, Ministry of Science and Technology, New Delhi, India.
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Radhakrishnan A, Sharma C, Malviya VN, Srivastav R. Deciphering the molecular functionality of Cdc45 in replisomal complex. Biochem Biophys Rep 2024; 37:101643. [PMID: 38298211 PMCID: PMC10828582 DOI: 10.1016/j.bbrep.2024.101643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
The members of DHH superfamily have been reported with diverse substrate spectrum and play pivotal roles in replication, repair, and RNA metabolism. This family comprises phosphatases, phosphoesterase and bifunctional enzymes having nanoRNase and phosphatase activities. Cell cycle factor Cdc45, a member of this superfamily, is crucial for movement of the replication fork during DNA replication and an important component of the replisome. The specific protein-protein interactions of Cdc45 with other factors along with helicase moderate the faithful DNA replication process. However, the exact biochemical functions of this factor are still unknown and need further investigation. Here, we studied the biochemical roles of Cdc45 and its molecular interactions within the replisomal complex. The alteration in the level of protein, observed when DNA damage is induced in-vivo, suggests its association with DNA replication stress. We analyzed protein Cdc45, providing new insights about the molecular and biochemical functionality of this replisomal factor.
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Affiliation(s)
| | - Chandresh Sharma
- Translational Health Science and Technology Institute, Haryana, India
| | - Viveka Nand Malviya
- Department of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Gottingen, Germany
| | - Rajpal Srivastav
- Amity Institute of Biotechnology, Amity University Uttar Pardesh, Noida, India
- Department of Science & Technology, Ministry of Science & Technology, New Delhi, India
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Hayne D, Stockler M, Martin A, Mccombie S, Zebic D, Krieger L, Anderson P, Bastick P, Beardsley E, Blatt A, Frydenberg M, Green W, Grummet J, Hawks C, Ischia J, Mitterdorfer A, Patel M, Roberts M, Sengupta S, Srivastav R, Winter M, Redfern A, Davis I. Adding Mitomycin to BCG as adjuvant intravesical therapy for high-risk, non-muscle-invasive -bladder cancer: A randomised phase 3 trial: The BCG+MM Study (ANZUP1301). Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00567-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Kumar D, Baligar P, Srivastav R, Narad P, Raj S, Tandon C, Tandon S. Stem Cell Based Preclinical Drug Development and Toxicity Prediction. Curr Pharm Des 2021; 27:2237-2251. [PMID: 33076801 DOI: 10.2174/1381612826666201019104712] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/22/2020] [Indexed: 01/09/2023]
Abstract
Stem cell based toxicity prediction plays a very important role in the development of the drug. Unexpected adverse effects of the drugs during clinical trials are a major reason for the termination or withdrawal of drugs. Methods for predicting toxicity employ in vitro as well as in vivo models; however, the major drawback seen in the data derived from these animal models is the lack of extrapolation, owing to interspecies variations. Due to these limitations, researchers have been striving to develop more robust drug screening platforms based on stem cells. The application of stem cells based toxicity testing has opened up robust methods to study the impact of new chemical entities on not only specific cell types, but also organs. Pluripotent stem cells, as well as cells derived from them, can be evaluated for modulation of cell function in response to drugs. Moreover, the combination of state-of-the -art techniques such as tissue engineering and microfluidics to fabricate organ- on-a-chip, has led to assays which are amenable to high throughput screening to understand the adverse and toxic effects of chemicals and drugs. This review summarizes the important aspects of the establishment of the embryonic stem cell test (EST), use of stem cells, pluripotent, induced pluripotent stem cells and organoids for toxicity prediction and drug development.
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Affiliation(s)
- Dhruv Kumar
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida, Uttar Pradesh 201313, India
| | - Prakash Baligar
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida, Uttar Pradesh 201313, India
| | - Rajpal Srivastav
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Priyanka Narad
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Sibi Raj
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida, Uttar Pradesh 201313, India
| | - Chanderdeep Tandon
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Simran Tandon
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida, Uttar Pradesh 201313, India
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Grover R, Burse SA, Shankrit S, Aggarwal A, Kirty K, Narta K, Srivastav R, Ray AK, Malik G, Vats A, Motiani RK, Thukral L, Roy SS, Bhattacharya S, Sharma R, Natarajan K, Mukerji M, Pandey R, Gokhale RS, Natarajan VT. Myg1 exonuclease couples the nuclear and mitochondrial translational programs through RNA processing. Nucleic Acids Res 2019; 47:5852-5866. [PMID: 31081026 PMCID: PMC6582341 DOI: 10.1093/nar/gkz371] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 04/12/2019] [Accepted: 04/30/2019] [Indexed: 01/25/2023] Open
Abstract
Semi-autonomous functioning of mitochondria in eukaryotic cell necessitates coordination with nucleus. Several RNA species fine-tune mitochondrial processes by synchronizing with the nuclear program, however the involved components remain enigmatic. In this study, we identify a widely conserved dually localized protein Myg1, and establish its role as a 3′-5′ RNA exonuclease. We employ mouse melanoma cells, and knockout of the Myg1 ortholog in Saccharomyces cerevisiae with complementation using human Myg1 to decipher the conserved role of Myg1 in selective RNA processing. Localization of Myg1 to nucleolus and mitochondrial matrix was studied through imaging and confirmed by sub-cellular fractionation studies. We developed Silexoseqencing, a methodology to map the RNAse trail at single-nucleotide resolution, and identified in situ cleavage by Myg1 on specific transcripts in the two organelles. In nucleolus, Myg1 processes pre-ribosomal RNA involved in ribosome assembly and alters cytoplasmic translation. In mitochondrial matrix, Myg1 processes 3′-termini of the mito-ribosomal and messenger RNAs and controls translation of mitochondrial proteins. We provide a molecular link to the possible involvement of Myg1 in chronic depigmenting disorder vitiligo. Our study identifies a key component involved in regulating spatially segregated organellar RNA processing and establishes the evolutionarily conserved ribonuclease as a coordinator of nucleo-mitochondrial crosstalk.
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Affiliation(s)
- Ritika Grover
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Shaunak A Burse
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Shambhavi Shankrit
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ayush Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Kritika Kirty
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kiran Narta
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajpal Srivastav
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ashwini Kumar Ray
- School of environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Garima Malik
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Archana Vats
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajender K Motiani
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Soumya Sinha Roy
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Sudha Bhattacharya
- School of environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | | | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
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Madhvi A, Hingane S, Srivastav R, Joshi N, Subramani C, Muthumohan R, Khasa R, Varshney S, Kalia M, Vrati S, Surjit M, Ranjith-Kumar CT. A screen for novel hepatitis C virus RdRp inhibitor identifies a broad-spectrum antiviral compound. Sci Rep 2017; 7:5816. [PMID: 28725041 PMCID: PMC5517564 DOI: 10.1038/s41598-017-04449-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/16/2017] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) is a global pathogen and infects more than 185 million individuals worldwide. Although recent development of direct acting antivirals (DAA) has shown promise in HCV therapy, there is an urgent need for the development of more affordable treatment options. We initiated this study to identify novel inhibitors of HCV through screening of compounds from the National Cancer Institute (NCI) diversity dataset. Using cell-based assays, we identified NSC-320218 as a potent inhibitor against HCV with an EC50 of 2.5 μM and CC50 of 75 μM. The compound inhibited RNA dependent RNA polymerase (RdRp) activity of all six major HCV genotypes indicating a pan-genotypic effect. Limited structure-function analysis suggested that the entire molecule is necessary for the observed antiviral activity. However, the compound failed to inhibit HCV NS5B activity in vitro, suggesting that it may not be directly acting on the NS5B protein but could be interacting with a host protein. Importantly, the antiviral compound also inhibited dengue virus and hepatitis E virus replication in hepatocytes. Thus, our study has identified a broad-spectrum antiviral therapeutic agent against multiple viral infections.
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Affiliation(s)
- Abhilasha Madhvi
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Smita Hingane
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Rajpal Srivastav
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Nishant Joshi
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
- Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Chandru Subramani
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Rajagopalan Muthumohan
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Renu Khasa
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Shweta Varshney
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Manjula Kalia
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - Sudhanshu Vrati
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Milan Surjit
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India
| | - C T Ranjith-Kumar
- Vaccine and Infectious Disease Research Center, Translational Health Science and Technology Institute, Faridabad, India.
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Srivastav R, Kumar D, Grover A, Singh A, Manjasetty BA, Sharma R, Taneja B. Unique subunit packing in mycobacterial nanoRNase leads to alternate substrate recognitions in DHH phosphodiesterases. Nucleic Acids Res 2014; 42:7894-910. [PMID: 24878921 PMCID: PMC4081065 DOI: 10.1093/nar/gku425] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
DHH superfamily includes RecJ, nanoRNases (NrnA), cyclic nucleotide phosphodiesterases and pyrophosphatases. In this study, we have carried out in vitro and in vivo investigations on the bifunctional NrnA-homolog from Mycobacterium smegmatis, MSMEG_2630. The crystal structure of MSMEG_2630 was determined to 2.2-Å resolution and reveals a dimer consisting of two identical subunits with each subunit folding into an N-terminal DHH domain and a C-terminal DHHA1 domain. The overall structure and fold of the individual domains is similar to other members of DHH superfamily. However, MSMEG_2630 exhibits a distinct quaternary structure in contrast to other DHH phosphodiesterases. This novel mode of subunit packing and variations in the linker region that enlarge the domain interface are responsible for alternate recognitions of substrates in the bifunctional nanoRNases. MSMEG_2630 exhibits bifunctional 3′-5′ exonuclease [on both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) substrates] as well as CysQ-like phosphatase activity (on pAp) in vitro with a preference for nanoRNA substrates over single-stranded DNA of equivalent lengths. A transposon disruption of MSMEG_2630 in M. smegmatis causes growth impairment in the presence of various DNA-damaging agents. Further phylogenetic analysis and genome organization reveals clustering of bacterial nanoRNases into two distinct subfamilies with possible role in transcriptional and translational events during stress.
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Affiliation(s)
- Rajpal Srivastav
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
| | - Dilip Kumar
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
| | - Amit Grover
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
| | - Ajit Singh
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
| | - Babu A Manjasetty
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, Grenoble 38042, France Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, Grenoble 38042, France
| | - Rakesh Sharma
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
| | - Bhupesh Taneja
- CSIR-IGIB, Institute of Genomics and Integrative Biology, South Campus Mathura Road, New Delhi 110020, India
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Sumesh CK, Patel KD, Pathak VM, Srivastav R. Analysis of current - voltage - temperature characteristics of In and Cu contacts on n-type MoSe2 single crystals. Cryst Res Technol 2010. [DOI: 10.1002/crat.201000553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Sumesh CK, Patel KD, Pathak VM, Srivastav R. Investigation of carrier scattering mechanisms in molybdenum diselenide single crystals by hall effect measurements. Cryst Res Technol 2010. [DOI: 10.1002/crat.200900680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Goel D, Bansal KK, Singhal A, Srivastav R. Two-tier system of epilepsy evaluation: a useful method for developing countries. J Assoc Physicians India 2008; 56:937-941. [PMID: 19322971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
PURPOSE To test the usefulness of a simplified and clinically oriented, the Epidemiological Classification (EC), in determination of seizure types and appropriate drug selection in epileptic patients at the primary care level. METHODS The EC was applied to all epileptic patients over 5 years then compared with the currently recommended international classifications of seizures and epilepsy (ICES/ICEES). RESULTS A total of 1176 patients were enrolled with 2:1 male preponderance and 88% had onset of disease below 30 years of age. Based on EC, 682 (58%) had partial, 333 (28.3%) had generalized and 161 (13.7%) had undetermined seizures semiology. When ICES was applied, seizure typing was same in 86.2%, 68.5% and 26.7% patients of partial, generalized and unclassified seizures respectively. About 87% patients in generalized and partial seizure semiology had no change in selected antiepileptic drug even after the ICES, but 53.6% patients in undetermined group had change in selected AED. Only, 146 patients (12.5%) found to have symptomatic cause for seizure(s) on applying the EC system. After utilizing the ICEES on 1030 patients (87.5%) of "unknown etiology" cases after the EC system, almost 86.5% patients could be classified to a definite etiological class. CONCLUSION The EC was found useful for determination of seizure type and appropriate AEDs selection at the primary care level. The ICES/ICEES works better at the tertiary care level. This "two-tier" system can be more effective for overall epilepsy management in developing countries with limited facilities.
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Affiliation(s)
- D Goel
- Department of Neurology, Himalayan Institute of Medical Sciences, Dehradun, India
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Singh SK, Sarin D, Puliyel JM, Srivastav R, Gupta R, Kumar N, Mathews A. Melas syndrome. Indian J Pediatr 1999; 66:621-5. [PMID: 10798118 DOI: 10.1007/bf02727181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
An 11 year old male presented with headache, vomiting and weakness of right side of body. One day after admission he developed right focal seizures. He had 5 previous episodes of stroke, the first at 11 months age. His milestones were normal upto the first episode but subsequent mile stones were delayed. His serum and CSF lactic acids were raised. Muscle biopsy showed ragged red fibres on modified Gomori-trichrome staining. His EEG, CT scan and MRI were normal this time. The child improved spontaneously after 7 days. His recovery time progressively became shorter with each episode of stroke. Maximum time for recovery was noted during first episode and least in current episode. This is the first report of Melas syndrome in Indian literature.
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Affiliation(s)
- S K Singh
- Department of Pediatrics, St. Stephen's Hospital, Tis Hazari, Delhi
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Agarwal KS, Singh SK, Kumar N, Srivastav R, Rajkumar A. A study of current trends in enteric fever. J Commun Dis 1998; 30:171-4. [PMID: 10093424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The results of a study based on 68 cases of blood culture proven enteric fever are presented. Sensitivity to chloramphenicol, ampicillin and cotrimoxazole was found to be 55.88, 54.41, 38.23% respectively. Common clinical features were fever, vomiting, pain abdomen and cough in both the groups. There was no difference in complications in chloramphenicol sensitive against resistant cases. Of the chloramphenicol sensitive cases, 21.05% were resistant to cefotaxime. All cases were sensitive to ciprofloxacin. More than half the cases were sensitive to chloramphenicol and ampicillin.
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Affiliation(s)
- K S Agarwal
- Department of Paediatrics & Microbiology, St. Stephen's Hospital, Delhi
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