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Nandy K, Babu D, Rani S, Joshi G, Ijee S, George A, Palani D, Premkumar C, Rajesh P, Vijayanand S, David E, Murugesan M, Velayudhan SR. Efficient gene editing in induced pluripotent stem cells enabled by an inducible adenine base editor with tunable expression. Sci Rep 2023; 13:21953. [PMID: 38081875 PMCID: PMC10713686 DOI: 10.1038/s41598-023-42174-2] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/06/2023] [Indexed: 12/18/2023] Open
Abstract
The preferred method for disease modeling using induced pluripotent stem cells (iPSCs) is to generate isogenic cell lines by correcting or introducing pathogenic mutations. Base editing enables the precise installation of point mutations at specific genomic locations without the need for deleterious double-strand breaks used in the CRISPR-Cas9 gene editing methods. We created a bulk population of iPSCs that homogeneously express ABE8e adenine base editor enzyme under a doxycycline-inducible expression system at the AAVS1 safe harbor locus. These cells enabled fast, efficient and inducible gene editing at targeted genomic regions, eliminating the need for single-cell cloning and screening to identify those with homozygous mutations. We could achieve multiplex genomic editing by creating homozygous mutations in very high efficiencies at four independent genomic loci simultaneously in AAVS1-iABE8e iPSCs, which is highly challenging with previously described methods. The inducible ABE8e expression system allows editing of the genes of interest within a specific time window, enabling temporal control of gene editing to study the cell or lineage-specific functions of genes and their molecular pathways. In summary, the inducible ABE8e system provides a fast, efficient and versatile gene-editing tool for disease modeling and functional genomic studies.
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Affiliation(s)
- Krittika Nandy
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Dinesh Babu
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Sonam Rani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Gaurav Joshi
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Anila George
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, 695011, India
| | - Dhavapriya Palani
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Chitra Premkumar
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Praveena Rajesh
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - S Vijayanand
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Ernest David
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, 632115, India
| | - Mohankumar Murugesan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India
| | - Shaji R Velayudhan
- Center for Stem Cell Research (A Unit of inStem, Bengaluru, India), Christian Medical College, Tamil Nadu, Vellore, 632002, India.
- Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, 632004, India.
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Rani S, Thamodaran V, Nandy K, Fouzia NA, Maddali M, Rajesh P, Vijayanand S, David E, Velayudhan SR. Establishment and characterization of CSCRi006-A: an induced pluripotent stem cell line generated from a patient with Diamond-Blackfan Anemia (DBA) carrying ribosomal protein S19 (RPS19) mutation. Hum Cell 2023; 36:2204-2213. [PMID: 37603219 DOI: 10.1007/s13577-023-00946-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/21/2023] [Indexed: 08/22/2023]
Abstract
Diamond-Blackfan anemia (DBA) is a congenital hypoplastic anemia characterized by ineffective erythropoiesis. DBA is majorly caused by mutations in the ribosomal protein (RP) genes (Gadhiya and Wills in Diamond-Blackfan Anemia, https://www.statpearls.com/ ; 2023). A suitable disease model that yields a continuous supply of erythroid cells is required to study disease pathogenesis and drug discovery. Toward this, we reprogrammed dermal fibroblasts from a DBA patient with a heterozygous mutation c.22-23delAG in the RPS19 gene identified through exome sequencing. To generate induced pluripotent stem cells (iPSCs), we induced episomal expression of the reprogramming factors OTC3/4, L-MYC, LIN28, SOX2, and KLF4, and a p53 shRNA2. The DBA-iPSC line CSCRi006-A generated during this study was extensively characterized for its pluripotency and genome stability. The clone retained normal karyotype and showed high expression levels of pluripotency markers, OCT4, NANOG, SOX2, TRA-I-60, TRA-I-81, and SSEA4. It could differentiate into cells originating from all three germ cell layers, as identified by immunostaining for SOX17 (endoderm), Brachyury (mesoderm), and PAX6 (ectoderm). IPSCs provide a renewable source of cells for in vitro disease modeling. CSCRi006-A, a thoroughly characterized iPSC line carrying heterozygous RPS19 c.22-23delAG mutation, is a valuable cell line for the disease modeling of DBA. This iPSC line can be differentiated into different blood cell types to study the mechanisms of disease development and identify potential treatments.
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Affiliation(s)
- Sonam Rani
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Vasanth Thamodaran
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
- Tata Institute for Genetics and Society, Bangalore, India
| | - Krittika Nandy
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - N A Fouzia
- Department of Hematology, Christian Medical College, Vellore, India
| | - Madhavi Maddali
- Department of Hematology, Christian Medical College, Vellore, India
| | - Praveena Rajesh
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - S Vijayanand
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Ernest David
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Shaji R Velayudhan
- Centre for Stem Cell Research, Christian Medical College, Vellore, India.
- Department of Hematology, Christian Medical College, Vellore, India.
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Ashwini Ravi, Vijayanand S, Hemapriya J. Compilation of Analytical Techniques for Discrimination of Halophilic Archaea and Bacteria. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022130167] [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: 11/06/2022]
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Jagannathan K, Vijayanand S, Manoharan D, Indiran V. Perioral Rash in a Young Boy Due to Lip-Licking Dermatitis. Indian J Pediatr 2022; 89:513-514. [PMID: 34757572 DOI: 10.1007/s12098-021-04002-1] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]
Affiliation(s)
- Kokilavani Jagannathan
- VK General Health and Diabetic Care Clinic, 27A Nemilichery High Road, Bharathipuram, Chromepet, Chennai, Tamil Nadu, India
| | - S Vijayanand
- Department of Pediatrics, SRM Medical College Hospital and Research Center, Mahatma Gandhi Road, Potheri, SRM Nagar, Kattankulathur, Tamil Nadu, India
| | - D Manoharan
- Department of Dermatology, Sree Balaji Medical College and Hospital, Chennai, Tamil Nadu, India
| | - Venkatraman Indiran
- Department of Radiodiagnosis, Sree Balaji Medical College and Hospital, Chromepet, Chennai, Tamil Nadu, 600044, India. .,IVR Scans, Chromepet, Tamil Nadu, Chennai, India.
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Vijayanand S, Saravanan S. A deep learning model based anomalous behavior detection for supporting verifiable access control scheme in cloud servers. IFS 2022. [DOI: 10.3233/jifs-212572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Due to the growth of Big Data (BD) storage and access in cloud computing infrastructure, the detection of anomalies for Cloud Servers (CSs) is essential to ensure data confidentiality. Over the past decades, different security systems have been designed based on various methods like encryption, Access Policy (AP) control schemes, signcryption and so on. Among many security systems, a new Improved NTRU (INTRU) decryption based on the AP strategy has been suggested to secure the BD processed by the CSs. Also, the shared secret data was authenticated to defend the clients from anomalies in the cloud. But, the AP upgrade must not degrade the confidentiality of storing information, reveal trust in the CS or cause any different security challenges. It is not considered that such security challenges occur when the data owner shares its data with many CSs. Hence in this article, an INTRU with Detecting Anomalous in CS (INTRU-DACS) system is proposed that employs a deep learning-based Anomaly Detection System (ADS) to handle and secure the BD stored in the CSs. The main goal of this method is to effectively identify the abnormalities in the real world by the conduct utilization, i.e., the System Call Identifier Sequences (SCISs) created from CSs in which these conducts are associated with BD. Initially, effective data summarization is constructed via different feature states to analyze the SCISs of specific durations. After that, an anomaly identification algorithm is proposed to train and test the streaming of raw SC sequences. This observable SCs execution task of CSs is gathered from log files. The variations of such SCISs having a specified duration are random for usual and unusual sequences. So, the fact of current normal and abnormal services is recognized regarding their SCISs. Such normal and abnormal behavioral states are learned from Convolutional Neural Network-Hidden Markov Model (CNNHMM) classifier to identify the anomalies in CSs. But, it is still a challenging process because of the patterns of usual and unusual events. The performance is not effective since it models only the conduct of a huge number of SCISs created from a single CS. As a result, a Secure Access Control Scheme with DACS (SACS-DACS) system is proposed in which a Multidimensional Feature Misbehavior Server Detection method (MFMSD) is introduced for detecting anomalies in multiple CSs. In this method, large-scale SCISs of multiple CSs are extracted, including different features such as network traffic sequence features, CPU energy usage and memory usage from host logs. These extracted multidimensional features are fed to the CNNHMM that identifies the anomalies and maximizes the detection accuracy. At last, the simulation results demonstrate the effectiveness of the SACS-DACS and INTRU-DACS as compared to the INTRU.
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Affiliation(s)
- S. Vijayanand
- Department of Computer Science & Engineering, The Kavery Engineering College, Salem, Tamilnadu, India
| | - S. Saravanan
- Department of Computer Science & Engineering, Narasus Sarathy Institute of Technology, Salem, Tamilnadu, India
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Thanuja B, Parimalavalli R, Vijayanand S, Alharbi RM, Abdel-Raouf N, Ibraheem IBM, Sholkamy EN, Durairaj K, Meansbo Hadish K. Anticancer and Cytotoxicity Activity of Native and Modified Black Rice Flour on Colon Cancer Cell Lines. Evid Based Complement Alternat Med 2022; 2022:8575026. [PMID: 35237334 PMCID: PMC8885193 DOI: 10.1155/2022/8575026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/06/2022] [Indexed: 12/16/2022]
Abstract
This study is intended to evaluate the cytotoxicity of native and dual-modified black rice flour against the colon cancer cell line (HCT116) and mouse embryo cell line (3T3-L1) by using the MTT assay. The modification techniques applied to prepare rice flour samples were enzymatic modification and heat moisture treatment. In this study, the IC50 of native black rice flour and modified black rice flour was 255.78 µg/mL and 340.85 µg/mL, respectively. The result confirms that the native black rice flour has significant cytotoxic and anticancer potential against human colon cancer cells. In addition, the IC50 of native black rice flour and modified black rice flour on the 3T3-L1 cell line was found to be 345.96 µg/mL and 1106.94 µg/mL, respectively. The results showed that the native black rice flour had weak cytotoxicity, and modified black rice flour was nontoxic in both the cell lines. The active component of phytochemicals present in black rice flour has a potential role in preventing colon cancer.
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Affiliation(s)
- B. Thanuja
- Department of Food Science and Nutrition, Periyar University, Salem 636 011, Tamil Nadu, India
| | - R. Parimalavalli
- Department of Food Science and Nutrition, Periyar University, Salem 636 011, Tamil Nadu, India
| | - S. Vijayanand
- Department of Biotechnology, Thiruvalluvar University, Serkadu, Vellore, India
| | - Reem Mohammed Alharbi
- Department of Biology, College of Science, University of Hafer Al-Baten, Hafer Al-Baten, Saudi Arabia
| | - Neveen Abdel-Raouf
- Department of Biology, College of Science and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef 65211, Egypt
| | | | - Essam Nageh Sholkamy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Kaliannan Durairaj
- Zoonosis Research Center, School of Medicine, Wonkwang University, Iksan, Republic of Korea
| | - Kibrom Meansbo Hadish
- Faculty of Mechanical Engineering, AMIT Campus, Arba Minch University, Arba Minch, Ethiopia
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Chhanwal H, Vijayanand S, Kheskani D, Natrajan P. A multicentric prospective study on clear plastic drape versus acrylic box during airway management of COVID-19 patients. Indian J Anaesth 2022; 66:602-606. [PMID: 36274802 PMCID: PMC9580595 DOI: 10.4103/ija.ija_57_22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 01/25/2023] Open
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Vijayanand S, Ranganatha N, Singh M, Babu R. Unusual Case of Acquired Capillary Hemangioma of the Eyelid in an Adult. Ann Maxillofac Surg 2017; 7:308-311. [PMID: 29264305 PMCID: PMC5717914 DOI: 10.4103/ams.ams_168_14] [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] [Indexed: 11/15/2022] Open
Abstract
Acquired capillary hemangioma of the eyelid is very uncommon in adults. To our knowledge, only eight such cases have been reported in the literature till date. We report the case of a 25-year-old female with acquired capillary hemangioma of the left lower eyelid treated by cutting diathermy followed by reconstruction of the cutaneous and cartilaginous defect. This patient had a history of a similar lesion in the left malar region treated 5 years back. This case is being presented to highlight the occurrence of such lesions in an adult and to discuss the dilemmas in the diagnosis and management.
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Affiliation(s)
- S. Vijayanand
- Department of Oral and Maxillofacial Surgery, Rajarajeswari Dental College and Hospital, Bengaluru, Karnataka, India
| | - Narahari Ranganatha
- Department of Oral and Maxillofacial Surgery, Rajarajeswari Dental College and Hospital, Bengaluru, Karnataka, India
| | - Madhumati Singh
- Department of Oral and Maxillofacial Surgery, Rajarajeswari Dental College and Hospital, Bengaluru, Karnataka, India
| | - Ramesh Babu
- Department of Plastic Surgery, Rajarajeswari Dental College and Hospital, Bengaluru, Karnataka, India
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V. Indra MD, J. Hemapriya NA, Vijayanand S. Antagonistic Activity of Biogenic TiO2 Nanoparticles against Staphylococcus aureus and Escherichia coli. ACTA ACUST UNITED AC 2017. [DOI: 10.20546/ijcmas.2017.603.281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gajendran P, Vijayanand S, Saraswathi R. Investigation of oxygen reduction at platinum loaded poly(o-phenylenediamine) electrode in acid medium. J Electroanal Chem (Lausanne) 2007. [DOI: 10.1016/j.jelechem.2006.10.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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