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Chot E, Medicherla KM, Reddy MS. Comparative transcriptome analysis of ectomycorrhizal fungus Pisolithus albus in response to individual and combined stress of copper and cadmium. Environ Sci Pollut Res Int 2023; 30:118616-118633. [PMID: 37917254 DOI: 10.1007/s11356-023-30592-8] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
An ectomycorrhizal fungus Pisolithus albus establishes the natural symbiosis with plant roots on extreme heavy metal (HM)-rich soil and enables their survival in toxic metal concentrations. Understanding P. albus key genes and pathways behind strong metal tolerance is crucial for its successful application in the rehabilitation of metal-contaminated barren lands. Therefore, this study aimed to analyze the whole transcriptome profile of P. albus under individual and combined metal stress of copper (Cu) and cadmium (Cd). At 480 µM Cu and 16 µM Cd toxic concentrations, P. albus has shown growth and survival and accumulated high metal (1.46 µg Cu and 1.13 µg Cd per mg of dry mycelia). The study found a stronger response of P. albus to single-metal stress in high concentration as compared to multi-metal stress in relatively lower concentration. Hence, the intensity of fungal response to HM stress is mainly determined by the metal concentration involved in stress. We have found a total of 11 pathways significantly associated with HM stress, among which amino acid, lipid, and carbohydrate metabolisms were highly affected. The functional enrichment of differentially expressed genes has shown the induced biosynthesis of arginine, melanin, metal chelating agents, membrane phospholipids, fatty acids, folate, pantothenate, ergothioneine, and other antioxidant agents; upregulation of zinc ion uptake, potassium transporters, and lysine degradation; and reduction of phosphatidylcholine degradation, incorrect protein folding, iron uptake, and potassium efflux as the top efficient tolerance mechanisms of P. albus against HM stress. The current study would contribute to understanding fungal HM tolerance and its further utilization in the bioremediation of metal-contaminated abandoned lands. The validation of RNA-sequencing analysis with RT-qPCR of selected genes showed the high credibility of the presented data.
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Affiliation(s)
- Eetika Chot
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Bhadson Road, Patiala, Punjab, 147004, India
| | | | - Mondem Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Bhadson Road, Patiala, Punjab, 147004, India.
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Pritam M, Dutta S, Medicherla KM, Kumar R, Singh SP. Computational analysis of spike protein of SARS-CoV-2 (Omicron variant) for development of peptide-based therapeutics and diagnostics. J Biomol Struct Dyn 2023:1-19. [PMID: 37498146 DOI: 10.1080/07391102.2023.2239932] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
In the last few years, the worldwide population has suffered from the SARS-CoV-2 pandemic. The WHO dashboard indicated that around 504,079,039 people were infected and 6,204,155 died from COVID-19 caused by different variants of SARS-CoV-2. Recently, a new variant of SARS-CoV-2 (B.1.1.529) was reported by South Africa known as Omicron. The high transmissibility rate and resistance towards available anti-SARS-CoV-2 drugs/vaccines/monoclonal antibodies, make Omicron a variant of concern. Because of various mutations in spike protein, available diagnostic and therapeutic treatments are not reliable. Therefore, the present study explored the development of some therapeutic peptides that can inhibit the SARS-CoV-2 virus interaction with host ACE2 receptors and can also be used for diagnostic purposes. The screened linear B cell epitopes derived from receptor-binding domain of spike protein of Omicron variant were evaluated as peptide inhibitor/vaccine candidates through different bioinformatics tools including molecular docking and simulation to analyze the interaction between Omicron peptide and human ACE2 receptor. Overall, in-silico studies revealed that Omicron peptides OP1-P12, OP14, OP20, OP23, OP24, OP25, OP26, OP27, OP28, OP29, and OP30 have the potential to inhibit Omicron interaction with ACE2 receptor. Moreover, Omicron peptides OP20, OP22, OP23, OP24, OP25, OP26, OP27, and OP30 have shown potential antigenic and immunogenic properties that can be used in design and development vaccines against Omicron. Although the in-silico validation was performed by comparative analysis with the control peptide inhibitor, further validation through wet lab experimentation is required before its use as therapeutic peptides.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manisha Pritam
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Somenath Dutta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Department of Bioinformatics, Pondicherry Central University, Puducherry, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
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Gupta S, Mathur P, Mishra AK, Medicherla KM, Bandapalli OR, Suravajhala P. Whole Exome-Trio Analysis Reveals Rare Variants Associated with Congenital Pouch Colon. Children (Basel) 2023; 10:children10050902. [PMID: 37238450 DOI: 10.3390/children10050902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023]
Abstract
Anorectal malformations (ARM) are individually common, but Congenital Pouch Colon (CPC) is a rare anorectal anomaly that causes a dilated pouch and communication with the genitourinary tract. In this work, we attempted to identify de novo heterozygous missense variants, and further discovered variants of unknown significance (VUS) which could provide insights into CPC manifestation. From whole exome sequencing (WES) performed earlier, the trio exomes were analyzed from those who were admitted to J.K. Lon Hospital, SMS Medical College, Jaipur, India, between 2011 and 2017. The proband exomes were compared with the unaffected sibling/family members, and we sought to ask whether any variants of significant interest were associated with the CPC manifestation. The WES data from a total of 64 samples including 16 affected neonates (11 male and 5 female) with their parents and unaffected siblings were used for the study. We examined the role of rare allelic variation associated with CPC in a 16 proband/parent trio family, comparing the mutations to those of their unaffected parents/siblings. We also performed RNA-Seq as a pilot to find whether or not the genes harboring these mutations were differentially expressed. Our study revealed extremely rare variants, viz., TAF1B, MUC5B and FRG1, which were further validated for disease-causing mutations associated with CPC, further closing the gaps of surgery by bringing intervention in therapies.
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Affiliation(s)
- Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Amity Institute of Biotechnology, Amity University Rajasthan, Kant Kalwar, Jaipur 303002, India
| | - Praveen Mathur
- Department of Pediatric Surgery, SMS Medical College and Hospital, JLN Marg, Jaipur 302004, India
| | | | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Department of Bioengineering, Birla Institute of Technology, Mesra, Jaipur Campus, 27-Malaviya Industrial, Area, Jaipur 302017, India
| | | | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita University, Vallikavu, Clappana P.O. Box 690525, Kerala, India
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Shukla N, Kour B, Sharma D, Vijayvargiya M, Sadasukhi TC, Medicherla KM, Malik B, Bissa B, Vuree S, Lohiya NK, Suravajhala P. Towards Understanding the Key Signature Pathways Associated from Differentially Expressed Gene Analysis in an Indian Prostate Cancer Cohort. Diseases 2023; 11:diseases11020072. [PMID: 37218885 DOI: 10.3390/diseases11020072] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent cancers among men in India. Although studies on PCa have dealt with genetics, genomics, and the environmental influence in the causality of PCa, not many studies employing the Next Generation Sequencing (NGS) approaches of PCa have been carried out. In our previous study, we identified some causal genes and mutations specific to Indian PCa using Whole Exome Sequencing (WES). In the recent past, with the help of different cancer consortiums such as The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC), along with differentially expressed genes (DEGs), many cancer-associated novel non-coding RNAs have been identified as biomarkers. In this work, we attempt to identify differentially expressed genes (DEGs) including long non-coding RNAs (lncRNAs) associated with signature pathways from an Indian PCa cohort using the RNA-sequencing (RNA-seq) approach. From a cohort of 60, we screened six patients who underwent prostatectomy; we performed whole transcriptome shotgun sequencing (WTSS)/RNA-sequencing to decipher the DEGs. We further normalized the read counts using fragments per kilobase of transcript per million mapped reads (FPKM) and analyzed the DEGs using a cohort of downstream regulatory tools, viz., GeneMANIA, Stringdb, Cytoscape-Cytohubba, and cbioportal, to map the inherent signatures associated with PCa. By comparing the RNA-seq data obtained from the pairs of normal and PCa tissue samples using our benchmarked in-house cuffdiff pipeline, we observed some important genes specific to PCa, such as STEAP2, APP, PMEPA1, PABPC1, NFE2L2, and HN1L, and some other important genes known to be involved in different cancer pathways, such as COL6A1, DOK5, STX6, BCAS1, BACE1, BACE2, LMOD1, SNX9, CTNND1, etc. We also identified a few novel lncRNAs such as LINC01440, SOX2OT, ENSG00000232855, ENSG00000287903, and ENST00000647843.1 that need to be characterized further. In comparison with publicly available datasets, we have identified characteristic DEGs and novel lncRNAs implicated in signature PCa pathways in an Indian PCa cohort which perhaps have not been reported. This has set a precedent for us to validate candidates further experimentally, and we firmly believe this will pave a way toward the discovery of biomarkers and the development of novel therapies.
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Affiliation(s)
- Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhumandeep Kour
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144001, India
| | - Devendra Sharma
- Department of Urology, Rukmani Birla Hospital, Jaipur 302018, India
| | - Maneesh Vijayvargiya
- Department of Pathology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - T C Sadasukhi
- Department of Urology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Bioengineering, Birla Institute of Technology, Mesra Jaipur Campus, 27-Malaviya Industrial Area, Jaipur 302017, India
| | - Babita Malik
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhawana Bissa
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Sugunakar Vuree
- Bioclues.org, Hyderabad 500072, India
- MNR Foundation for Research & Innovation, MNR University, Sangareddy 502294, India
| | - Nirmal Kumar Lohiya
- Department of Zoology, Center for Advanced Studies, University of Rajasthan, Jaipur 302004, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
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5
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Chot E, Suravajhala P, Medicherla KM, Reddy MS. Characterization and genome-wide sequence analysis of an ectomycorrhizal fungus Pisolithus albus, a potential source for reclamation of degraded lands. 3 Biotech 2023; 13:58. [PMID: 36714549 PMCID: PMC9873894 DOI: 10.1007/s13205-023-03483-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023] Open
Abstract
Pisolithus albus is a ubiquitous ectomycorrhizal fungus that establishes symbiosis with a wide range of woody plants around the globe. The symbiotic association of this fungus plays a crucial role in the nutrient cycling of their host plants and enables them to thrive in adverse environmental conditions. Based on its ecological importance and lack of genomic studies, whole-genome sequencing was carried out to analyze P. albus sequences through an Illumina HiSeq X system. The functional annotations were performed against various databases to explore genomic patterns and traits possibly attributing to its specialization. Comparative genomics of P. albus with phylogenetically related Pisolithus microcarpus and Pisolithus tinctorius (only available genomes of Pisolithus at NCBI till now) led to the identification of their unique and shared basic functional and stress adaptation capabilities. The de novo assembled genome of 56.15 Mb with 91.8% BUSCO completeness is predicted to encode 23,035 genes. The study is aimed to generate solid genomic data resources for P. albus, forming the theoretical basis for future transcriptomic, proteomic and metabolomic studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03483-5.
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Affiliation(s)
- Eetika Chot
- Thapar Institute of Engineering and Technology, Bhadson Road, Patiala, Punjab 147004 India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O, Kollam, Kerala 690525 India
| | | | - Mondem Sudhakara Reddy
- Thapar Institute of Engineering and Technology, Bhadson Road, Patiala, Punjab 147004 India
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6
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Rout M, Kour B, Vuree S, Lulu SS, Medicherla KM, Suravajhala P. Diabetes mellitus susceptibility with varied diseased phenotypes and its comparison with phenome interactome networks. World J Clin Cases 2022; 10:5957-5964. [PMID: 35949812 PMCID: PMC9254192 DOI: 10.12998/wjcc.v10.i18.5957] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/02/2022] [Accepted: 04/22/2022] [Indexed: 02/06/2023] Open
Abstract
An emerging area of interest in understanding disease phenotypes is systems genomics. Complex diseases such as diabetes have played an important role towards understanding the susceptible genes and mutations. A wide number of methods have been employed and strategies such as polygenic risk score and allele frequencies have been useful, but understanding the candidate genes harboring those mutations is an unmet goal. In this perspective, using systems genomic approaches, we highlight the application of phenome-interactome networks in diabetes and provide deep insights. LINC01128, which we previously described as candidate for diabetes, is shown as an example to discuss the approach.
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Affiliation(s)
- Madhusmita Rout
- Department of Pediatrics, University of Oklahoma Health Sciences Centre, Oklahoma City, OK 73104, United States
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, Rajasthan, India
| | - Bhumandeep Kour
- Department of Biotechnology, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Sugunakar Vuree
- Department of Biotechnology, Lovely Professional University, Phagwara 144001, Punjab, India
| | - Sajitha S Lulu
- Department of Biotechnology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, Rajasthan, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Vallikavu PO, Amritapuri, Clappana, Kollam 690525, Kerala, India
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Rajagopal S, Gupta A, Parveen R, Shukla N, Bhattacharya S, Naravula J, Kumar S A, Mathur P, Simlot A, Mehta S, Bihari C, Mehta S, Mishra AK, Nair BG, Medicherla KM, Reddy GB, Sreenivasulu N, Kishor PK, Suravajhala P. Vitamin K in human health and metabolism: A nutri-genomics review. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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8
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Kaur A, Chopra M, Bhushan M, Gupta S, Kumari P H, Sivagurunathan N, Shukla N, Rajagopal S, Bhalothia P, Sharma P, Naravula J, Suravajhala R, Gupta A, Abbasi BA, Goswami P, Singh H, Narang R, Polavarapu R, Medicherla KM, Valadi J, Kumar S A, Chaubey G, Singh KK, Bandapalli OR, Kavi Kishor PB, Suravajhala P. The Omic Insights on Unfolding Saga of COVID-19. Front Immunol 2021; 12:724914. [PMID: 34745097 PMCID: PMC8564481 DOI: 10.3389/fimmu.2021.724914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
The year 2019 has seen an emergence of the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease of 2019 (COVID-19). Since the onset of the pandemic, biological and interdisciplinary research is being carried out across the world at a rapid pace to beat the pandemic. There is an increased need to comprehensively understand various aspects of the virus from detection to treatment options including drugs and vaccines for effective global management of the disease. In this review, we summarize the salient findings pertaining to SARS-CoV-2 biology, including symptoms, hosts, epidemiology, SARS-CoV-2 genome, and its emerging variants, viral diagnostics, host-pathogen interactions, alternative antiviral strategies and application of machine learning heuristics and artificial intelligence for effective management of COVID-19 and future pandemics.
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Affiliation(s)
- Arvinpreet Kaur
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
- Bioclues.org, Hyderabad, India
| | - Mehak Chopra
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mahak Bhushan
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Sonal Gupta
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | | | - Narmadhaa Sivagurunathan
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Nidhi Shukla
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Shalini Rajagopal
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Purva Bhalothia
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Purnima Sharma
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
| | - Jalaja Naravula
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Renuka Suravajhala
- Bioclues.org, Hyderabad, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Ayam Gupta
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Bilal Ahmed Abbasi
- Functional Genomics Unit, Council of Scientific and Industrial Research- Institute of Genomics & Integrative Biology (CSIR-IGIB), Delhi, India
| | - Prittam Goswami
- Department of Biotechnology, Haldia Institute of Technology, West Bengal, India
| | - Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Punjab, India
- Bioclues.org, Hyderabad, India
| | - Rahul Narang
- Department of Microbiology, All India Institute of Medical Sciences, Bibinagar, Hyderabad, India
| | | | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Jayaraman Valadi
- Bioclues.org, Hyderabad, India
- Department of Computer Science, Flame University, Pune, India
| | - Anil Kumar S
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Benaras Hindu University, Varanasi, India
| | - Keshav K. Singh
- Department of Genetics, University of Alabama, Birmingham, AL, United States
| | - Obul Reddy Bandapalli
- Bioclues.org, Hyderabad, India
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Department of Applied Biology, Council of Scientific and Industrial Research-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, India
| | - Polavarapu Bilhan Kavi Kishor
- Bioclues.org, Hyderabad, India
- Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Guntur, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kerala, India
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Zhang D, Peng Y, Chan CL, On H, Wai HKF, Shekhawat SS, Gupta AB, Varshney AK, Chuanchuen R, Zhou X, Xia Y, Liang S, Fukuda K, Medicherla KM, Tun HM. Metagenomic Survey Reveals More Diverse and Abundant Antibiotic Resistance Genes in Municipal Wastewater Than Hospital Wastewater. Front Microbiol 2021; 12:712843. [PMID: 34526976 PMCID: PMC8435860 DOI: 10.3389/fmicb.2021.712843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/21/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Alongside antibiotic resistance, co-selection of antibiotics, biocides, and metal resistance is a growing concern. While hospital wastewater is considered a hotspot for antibiotic-resistant bacteria (ARB) and genes (ARGs), the scenario in India, one of the biggest consumers of antibiotics, remains poorly described. In this study, we used metagenomic sequencing to characterize ARGs and biocide/metal resistance genes (BMRGs) in four wastewater treatment plants (WWTPs) in Jaipur City of India. We observed a significantly lower richness and abundance of ARGs in the influent of a WWTP exclusively receiving hospital wastewater when compared to other three WWTPs involving municipal wastewater treatment. Several tetracycline and macrolide-lincosamide-streptogramin resistance genes were enriched in influents of these three municipal wastewater-related treatment plants, whereas hospital wastewater had a higher abundance of genes conferring resistance to disinfectant-related compounds such as synergize and wex-cide-128, reflecting the patterns of antibiotic/disinfectant use. Of note, in the wastewater system with more chemicals, there was a strong correlation between the numbers of ARGs and BMRGs potentially harbored by common hosts. Our study highlights significant influxes of ARGs from non-hospital sources in Jaipur City, and thus more attention should be paid on the emergence of ARGs in general communities.
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Affiliation(s)
- Dengwei Zhang
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.,HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong SAR, China
| | - Ye Peng
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.,HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong SAR, China
| | - Chak-Lun Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.,HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong SAR, China
| | - Hilda On
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong SAR, China
| | - Hogan Kok-Fung Wai
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.,HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong SAR, China
| | | | | | - Alok Kumar Varshney
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Jaipur, India.,Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Mesra, Ranchi, India
| | - Rungtip Chuanchuen
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Xudong Zhou
- Institute of Social and Family Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yankai Xia
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Suisha Liang
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.,HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong SAR, China
| | - Keiji Fukuda
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Krishna Mohan Medicherla
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Jaipur, India.,Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Mesra, Ranchi, India
| | - Hein M Tun
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.,HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong SAR, China.,School of Public Health, Nanjing Medical University, Nanjing, China
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10
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Saxena A, Tiwari P, Wahi N, Soni A, Bansiwal RC, Kumar A, Sharma B, Punjabi P, Gupta N, Malik B, Medicherla KM, Suravajhala P, Mathur SK. Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian Indians. Adipocyte 2019; 8:125-136. [PMID: 30894049 PMCID: PMC6768216 DOI: 10.1080/21623945.2019.1595269] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Type 2 diabetes (T2D) is a complex disease with an elusive link between its molecular aetiology and clinical presentation. Although, the role of visceral adipose tissue in insulin-resistance and T2D is known, limited information is available on the role of peripheral-subcutaneous adipose tissue especially in Asian Indians. In this microarray-based study of diabetic and normal glucose tolerant Asian Indians, we generated the transcriptome of their thigh adipose tissue and analyzed differentially expressed genes (DEGs) using weighted gene co-expression network analysis; further we identified perturbed pathways implicated by these DEGs in relevant co-expression modules. We also attempted to link these pathways with known aspects of T2D pathophysiology in terms of their association with some of their intermediate traits, namely; adipocyte size, HOMA-B, HOMA-R, Hb1Ac, insulin, glucose-level, TNF-α, IL-6, VLDLs, LDLs, HDLs, and NEFAs. It was observed that several modules of co-expressed genes show an association with diabetes and some of its intermediate phenotypic traits mentioned above. Therefore, these findings suggest a role of peripheral subcutaneous adipose tissue in the pathophsiology of T2D in Asian Indians. Additionally, our study indicated that the peripheral subcutaneous adipose tissue in diabetics shows pathologic changes characterized by adipocyte hypertrophy and up-regulation of inflammation-related pathways.
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Affiliation(s)
- Aditya Saxena
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura, India
| | - Pradeep Tiwari
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur, India
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India
- Department of Chemistry, School of Basic Sciences, Manipal University, Jaipur, India
| | - Nitin Wahi
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura, India
| | - Arpana Soni
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur, India
| | - Ram Chandra Bansiwal
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur, India
| | - Anshul Kumar
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur, India
| | - Balram Sharma
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur, India
| | - Poonam Punjabi
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur, India
| | - Nidhi Gupta
- Department of Biotechnology, The IIS University, Jaipur, India
| | - Babita Malik
- Department of Chemistry, School of Basic Sciences, Manipal University, Jaipur, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India
| | - Sandeep Kumar Mathur
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur, India
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Pasam B, Medicherla KM, Rathore RS, Upadhyayula RS. Molecular dynamics insights on the role β-augmentation of the peptide N-terminus with binding site β-hairpin of proprotein convertase subtilisin/kexin 9. Chem Biol Drug Des 2019; 94:2073-2083. [PMID: 31452340 DOI: 10.1111/cbdd.13612] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/11/2019] [Accepted: 08/15/2019] [Indexed: 11/27/2022]
Abstract
PCSK9, a member of the proprotein convertase family, is a key negative regulator of hepatic low-density lipoprotein receptor (LDLR) concentrations in the blood plasma and is associated with the risk of coronary artery disease (CAD). Peptide inhibitors designed to block PCSK9-LDLR interactions could reduce the risk of CAD. We present a study of the interaction of a PCSK9 bound peptide and its design through modification by phosphorylation using molecular dynamics simulations. Extensive explicit solvent simulations of PCSK9 and its mutant (Asp374 → Tyr374) with designed peptides provide insights into the mechanism of peptide binding at the protein interface. We establish that β-augmentation is the key mechanism of peptide association with PCSK9. Position-specific phosphorylation of threonine residues is observed to have noticeable effect in modulating protein-peptide association. This study provides a handle to explore and improve the design of peptides bound to PCSK9 by incorporating knowledge-derived functional motifs into designing potent binders.
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Affiliation(s)
- Bhargavi Pasam
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India.,Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Jaipur, India
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12
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Tiwari P, Saxena A, Gupta N, Medicherla KM, Suravajhala P, Mathur SK. Systems Genomics of Thigh Adipose Tissue From Asian Indian Type-2 Diabetics Revealed Distinct Protein Interaction Hubs. Front Genet 2019; 9:679. [PMID: 30671081 PMCID: PMC6331691 DOI: 10.3389/fgene.2018.00679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 07/03/2018] [Accepted: 12/07/2018] [Indexed: 12/13/2022] Open
Abstract
We performed a systematic analysis of genes implicated in thigh subcutaneous adipose tissue of Asian Indian Type 2 Diabetes Mellitus (AIT2DM) and created a phenome-interactome network. This analysis was performed on 60 subjects specific to limb thigh fat by integrating phenotypic traits and similarity scores associated with AIT2DM. Using a phenotypic attribute, a contextual neighbor was identified across all the traits, viz. body mass index (BMI) statistics, adipocyte size, lipid parameters, homeostatic model assessment- insulin resistance (HOMA-IR), HOMA-ß. In this work, we have attempted to characterize transcription signatures using the phenome-interactome maps where each of the traits under study including the intermediary phenotypes has a distinct set of genes forming the hubs. Furthermore, we have identified various clinical, biochemical, and radiological parameters which show significant correlation with distinct hubs. We observed a number of novel pathways and genes including those that are non-coding RNAs implicated in AIT2DM.We showed that they appear to be associated with pathways, viz. tyrosine kinase JAK2, NOTCH thereby recruiting signaling molecules such as STAT5 and Src family kinases on the cell surface regulated them and our analyses comprising significant hubs suggest that thigh subcutaneous adipose tissue plays a role in pathophysiology of AIT2DM.
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Affiliation(s)
- Pradeep Tiwari
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India.,Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur, India.,Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Aditya Saxena
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura, India
| | - Nidhi Gupta
- Department of Biotechnology, The IIS University, Jaipur, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Sandeep Kumar Mathur
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
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13
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Gupta S, Tiwari P, Gupta N, Nunia V, Saxena AK, Simlot A, Kothari SL, Suravajhala P, Medicherla KM, Mathur P. Is Pouch Specific to Colon and Not Ileum? Curr Pediatr Rev 2019; 15:259-264. [PMID: 31465285 PMCID: PMC7040526 DOI: 10.2174/1573396315666190829155930] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/01/2019] [Accepted: 08/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Congenital Pouch Colon (CPC) is an anorectal anomaly with an incidence of 3.5:1 in males and females, respectively. We have earlier reported CPC to be quite prevalent in north Indian tertiary care centers. OBJECTIVE In this article, we deliberate on the possible causes associated with CPC bringing the manifestation of the disease. In addition, we throw insights on the effective role of this congenital anomaly in Colon and provide systems genomic evaluation by comparing our recent analysis to that of Colon and Ileum based on Next-Generation Sequencing (NGS) studies. CONCLUSION In this commentary article, we argue that a host of epigenetic factors could be the reason why the disease is manifested in colon alone. We further hypothesize on the few unmet challenges linking epigenetics to understand the genetic variants.
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Affiliation(s)
- Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, RJ, India.,Department of Biotechnology, Amity University Rajasthan, Jaipur 303002 RJ, India
| | - Pradeep Tiwari
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, RJ, India
| | - Nidhi Gupta
- Department of Biotechnology, IIS (Deemed to be University), Mansarovar, Jaipur 302020, India
| | - Vandana Nunia
- Department of Zoology, University of Rajasthan, Jaipur 302004, RJ, India
| | - Amulya K Saxena
- Department of Pediatric Surgery, Imperial College London, United Kingdom
| | - Anita Simlot
- Department of Obstretrics and Gynaecology, SMS Medical College, JLN Marg, Jaipur 302004 RJ, India
| | - Shanker Lal Kothari
- Department of Biotechnology, Amity University Rajasthan, Jaipur 303002 RJ, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, RJ, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur 302001, RJ, India
| | - Praveen Mathur
- Department of Pediatric Surgery, SMS Medical College, JLN Marg, Jaipur 302004 RJ, India
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14
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Gupta S, Gupta N, Tiwari P, Menon S, Mathur P, Kothari SL, Nallapeta S, Medicherla KM, Suravajhala P. Lnc-EPB41-Protein Interactions Associated with Congenital Pouch Colon. Biomolecules 2018; 8:biom8030095. [PMID: 30227690 PMCID: PMC6163732 DOI: 10.3390/biom8030095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/12/2022] Open
Abstract
Congenital Pouch Colon (CPC) is a rare anorectal anomaly common to northwestern India, specifically Rajasthan. Despite efforts to understand the clinical genetic makeup of CPC, no attempt on identifying non-coding RNAs was done. We have earlier reported CPC’s rare variants from whole exome sequencing (WES) across 18 affected samples in a total of 64 subjects. A Smith–Waterman algorithm was used to infer a couple of lncRNAs from WES samples of CPC with predictions from the Noncode database. Further screening and quantification using polymerase chain reaction (PCR), we ascertained interactions using Micro Scale Thermophoresis (MST). We report the role of lnc-EPB41-1-1 shown to be promiscuously interacting with KIF13A substantiating their role in regulation.
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Affiliation(s)
- Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India.
- Department of Biotechnology, Amity University Rajasthan, Kant Kalwar, Jaipur 303002, India.
| | - Nidhi Gupta
- Department of Biotechnology, IIS University, Mansarovar, Jaipur 302020, India.
| | - Pradeep Tiwari
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India.
- Department of Chemistry, School of Basic Science, Manipal University, Jaipur 303007, India.
| | - Saji Menon
- NanoTemper Technologies, World Trade Centre, Bengaluru 302017, India.
| | - Praveen Mathur
- Department of Paediatric Surgery, SMS Medical College, JLN Marg, Jaipur 302004, India.
| | - Shanker Lal Kothari
- Department of Biotechnology, Amity University Rajasthan, Kant Kalwar, Jaipur 303002, India.
| | | | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India.
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302021, India.
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15
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Mathur P, Nunia V, Sharma R, Simlot A, Medicherla KM. Congenital Pouch Colon: Role of Genetics or Environmental Influence? Pathobiology 2018; 85:332-341. [PMID: 30223255 DOI: 10.1159/000492432] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 02/26/2018] [Accepted: 07/25/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Congenital pouch colon (CPC), a high type of anorectal malformation, is a sporadic disease and several environmental factors are known to be involved in its pathology. To the best of our knowledge, no familial incidence of CPC has been reported anywhere in the literature so far. AIM In the present study, which is first of its kind, we have reported the familial incidences of CPC and also tried to elucidate the role of genetics in this pathology. METHODS We have reported 1 familial pedigree of CPC and 2 incidences of dizygotic twins (DZ), out of them one is affected and another one is normal. Highly comprehensive microarray CytoScan HD from Affymetrix was employed to understand the defects underlying submicroscopic genomic imbalance like segment duplication and deletion of the twin patients vis-à-vis their parents and unaffected siblings in these DZ twins. RESULTS A total of 21 copy number variations (CNVs) were reported in the patient samples that did not overlap with the CNVs in normal parents and healthy sibling, including 5 loss, 3 LOH and 13 gain with size varied from 95 bp to 77 kbp. Genetic analysis revealed involvement of 12 potential genetic loci on Chr 1, 2, 3, 4, 6, 11, and 16. CONCLUSION Genetic study found that CPC could be a developmental disorder. These findings are important for further elucidating genetic causes of CPC pathogenesis.
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Affiliation(s)
- Praveen Mathur
- Department of Pediatric Surgery, SMS Medical College, Jaipur,
| | - Vandana Nunia
- Department of Zoology, University of Rajasthan, Jaipur, India
| | - Rakesh Sharma
- Bioinformatics Infrastructure Facility, University of Rajasthan, Jaipur, India
| | - Anita Simlot
- Department of Gynaecology and Obstetrics, SMS Medical College, Jaipur, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
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16
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Mathur P, Medicherla KM, Chaudhary S, Patel M, Bagali P, Suravajhala P. Author Correction: Whole exome sequencing reveals rare variants linked to congenital pouch colon. Sci Rep 2018; 8:13867. [PMID: 30206290 PMCID: PMC6131556 DOI: 10.1038/s41598-018-32119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Praveen Mathur
- Department of Pediatric Surgery, SMS Medical College and Hospital, JLN Marg, Jaipur, 302004 RJ, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, 302001 RJ, India
| | - Spandan Chaudhary
- Division of Genomics, Bioinformatics and Diagnostics, Xcelris Labs Limited, Ahmedabad, India
| | - Mruduka Patel
- Division of Genomics, Bioinformatics and Diagnostics, Xcelris Labs Limited, Ahmedabad, India
| | - Prashanth Bagali
- Division of Genomics, Bioinformatics and Diagnostics, Xcelris Labs Limited, Ahmedabad, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, 302001 RJ, India.
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Bajpai A, Shende KK, Meena N, Suravajhala P, Medicherla KM, Johri BN. Draft Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas protegens Strain BNJ-SS-45, Isolated from Rhizosphere Soil of Wheat (Triticum aestivum). Microbiol Resour Announc 2018; 7:e00926-18. [PMID: 30533914 PMCID: PMC6256506 DOI: 10.1128/mra.00926-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/01/2018] [Indexed: 11/20/2022] Open
Abstract
Here, we present the draft genome sequence of Pseudomonas protegens strain BNJ-SS-45, which was isolated from wheat rhizosphere. The genome is assembled with 7,116,445 bp with a GC content of 63.34% consisting of 32 scaffolds. The genome is useful in prediction of secondary metabolites, particularly rhizoxin, pyoverdine, and bacteriocin.
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Affiliation(s)
- Apekcha Bajpai
- Department of Biotechnology, Barkatullah University, Bhopal, MP, India
| | - Kishor K. Shende
- Department of Biotechnology, Barkatullah University, Bhopal, MP, India
| | - Narendra Meena
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, RJ, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, RJ, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, RJ, India
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18
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Mathur SK, Tiwari P, Gupta S, Gupta N, Nimesh S, Medicherla KM, Suravajhala P. Genetics of Lipodystrophy: Can It Help in Understanding the Pathophysiology of Metabolic Syndrome? Biomolecules 2018; 8:E47. [PMID: 29986445 PMCID: PMC6163883 DOI: 10.3390/biom8030047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 12/18/2022] Open
Abstract
Understanding phenotypes and their genetic determinants for metabolic syndrome (MetS) has been quite challenging. With the advent of systems genomic approaches, there is a need to decipher methods for identification and evaluating the functional role of phenotypic traits associated with complex diseases, such as MetS. The monogenic syndromes of lipodystrophy are well understood, but the molecular pathophysiology of insulin resistance (IR) underpinning the obesity, diabetes mellitus, and dyslipidemia is not well deciphered. In this commentary, we argue the role of pathophysiology of MetS, and its effects into possible understanding of genetic determinants associated with lipodystrophy-mediated diabetes mellitus.
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Affiliation(s)
| | - Pradeep Tiwari
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur 302001, India.
| | - Sonal Gupta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur 302001, India.
| | - Nidhi Gupta
- Department of Biotechnology, IIS University, Mansarovar, Jaipur 302020, India.
| | - Surendra Nimesh
- Department of Biotechnology, Central University of Rajasthan, Bandarsindri, N.H. 8, Kishangarh 305801, India.
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur 302001, India.
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Statue Circle, Jaipur 302001, India.
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Mathur P, Medicherla KM, Chaudhary S, Patel M, Bagali P, Suravajhala P. Whole exome sequencing reveals rare variants linked to congenital pouch colon. Sci Rep 2018; 8:6646. [PMID: 29703930 PMCID: PMC5923232 DOI: 10.1038/s41598-018-24967-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 11/06/2017] [Accepted: 04/05/2018] [Indexed: 01/07/2023] Open
Abstract
We demonstrate the application of whole exome sequencing to discover the rare variants for congenital pouch colon, acronymed CPC. For 18 affected individuals in a total of 64 samples, we sequenced coding regions to a mean coverage of 100×. A sufficient depth of ca. 94% of targeted exomes was achieved. Filtering against the public SNP/variant repositories, we identified a host of candidate genes, EPB41L4A and CTC1 associated with colon, neural/brain muscles and Dyskeratosis Congenita maladies. Furthermore, the stop gain mutations in the form of JAG1,OR5AR1,SLC22A24,PEX16,TSPAN32,TAF1B,MAP2K3 and SLC25A19 appears to be localized to Chromosomes 2, 11, 17 and 20 in addition to the three stop lost mutants across three genes, viz. OAS2, GBA3 and PKD1L2 affecting the colon tissue. While our results have paved way for transcendence of monogenic traits in identifying the genes underlying rare genetic disorders, it will provide helpful clues for further investigating genetic factors associated with anorectal anomalies, particularly CPC.
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Affiliation(s)
- Praveen Mathur
- Department of Pediatric Surgery, SMS Medical College and Hospital, JLN Marg, Jaipur, 302004 RJ, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, 302001 RJ, India
| | - Spandan Chaudhary
- Division of Genomics, Bioinformatics and Diagnostics, Xcelris Labs Limited, Ahmedabad, India
| | - Mruduka Patel
- Division of Genomics, Bioinformatics and Diagnostics, Xcelris Labs Limited, Ahmedabad, India
| | - Prashanth Bagali
- Division of Genomics, Bioinformatics and Diagnostics, Xcelris Labs Limited, Ahmedabad, India
| | - Prashanth Suravajhala
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, 302001 RJ, India.
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