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Sharma MP, Shukla S, Misra G. Recent advances in breast cancer cell line research. Int J Cancer 2024; 154:1683-1693. [PMID: 38230499 DOI: 10.1002/ijc.34849] [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: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
Breast cancer, a formidable global health challenge, needs continuous translational research to understand the complexity of mechanisms and improve therapeutic and diagnostic strategies. Breast cancer cell lines are of paramount importance as they significantly contribute to the initial stage of research to understand cancer biology. This review provides insights into targeted therapies and immunotherapies that have emerged using in vitro models and microbiome analysis. It focuses on therapeutic development using cell lines and the limitations of tumor heterogeneity and microenvironment. We explore the evolving landscape of breast cancer cell lines from two-dimensional (2-D) cultures to patient-derived xenograft (PDX) models advancing both fundamental and translational research. Patient-derived xenografts, cell line-derived xenografts (CDX), three-dimensional (3-D) cultures, organoids, and circulating tumor cells (CTC) models provide promising alternatives that capture the intricacies of the tumor microenvironment. This review bridges the gap between traditional cell lines and newer developments exploring the therapeutic and diagnostic advancements and needs for cell lines to expedite the progress in breast cancer research and treatment.
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Affiliation(s)
- Manika P Sharma
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), Noida, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Supriya Shukla
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), Noida, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Gauri Misra
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), Noida, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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2
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Rymbai E, Sugumar D, Chakkittukandiyil A, Kothandan R, Selvaraj D. Molecular insights into the potential effects of selective estrogen receptor β agonists in Alzheimer's and Parkinson's diseases. Cell Biochem Funct 2024; 42:e4014. [PMID: 38616346 DOI: 10.1002/cbf.4014] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/19/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024]
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common neurodegenerative disorders. Pathologically, AD and PD are characterized by the accumulation of misfolded proteins. Hence, they are also called as proteinopathy diseases. Gender is considered as one of the risk factors in both diseases. Estrogens are widely accepted to be neuroprotective in several neurodegenerative disorders. Estrogens can be produced in the central nervous system, where they are called as neurosteroids. Estrogens mediate their neuroprotective action mainly through their actions on estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ). However, ERα is mainly involved in the growth and development of the primary and secondary sexual organs in females. Hence, the activation of ERα is associated with undesired side effects such as gynecomastia and increase in the risk of breast cancer, thromboembolism, and feminization. Therefore, selective activation of ERβ is often considered to be safer. In this review, we explore the role of ERβ in regulating the expression and functions of AD- and PD-associated genes. Additionally, we discuss the association of these genes with the amyloid-beta peptide (Aβ) and α-synuclein mediated toxicity. Ultimately, we established a correlation between the importance of ERβ activation and the process underlying ERβ's neuroprotective mechanisms in AD and PD.
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Affiliation(s)
- Emdormi Rymbai
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Tamil Nadu, India
| | - Deepa Sugumar
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Tamil Nadu, India
| | - Amritha Chakkittukandiyil
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Tamil Nadu, India
| | - Ram Kothandan
- Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, Tamil Nadu, India
| | - Divakar Selvaraj
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Tamil Nadu, India
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Saini P, Bandsode V, Singh A, Mendem SK, Semmler T, Alam M, Ahmed N. Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment. mBio 2024; 15:e0354523. [PMID: 38376265 PMCID: PMC10936179 DOI: 10.1128/mbio.03545-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations. IMPORTANCE Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.
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Affiliation(s)
- Poorvi Saini
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Viraj Bandsode
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Anuradha Singh
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | - Suresh Kumar Mendem
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
| | | | - Munirul Alam
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Niyaz Ahmed
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, University of Hyderabad, Hyderabad, Telangana State, India
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Sharma P, Chaturvedi S, Khan MA, Rai Y, Bhatt AN, Najmi AK, Akhtar M, Mishra AK. Nanoemulsion potentiates the anti-cancer activity of Myricetin by effective inhibition of PI3K/AKT/mTOR pathway in triple-negative breast cancer cells. Med Oncol 2024; 41:56. [PMID: 38218749 DOI: 10.1007/s12032-023-02274-5] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/28/2023] [Indexed: 01/15/2024]
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous tumor with a poor prognosis and high metastatic potential, resulting in poor clinical outcomes, necessitating investigation to devise effective therapeutic strategies. Multiple studies have substantiated the anti-cancer properties of the naturally occurring flavonoid "Myricetin" in various malignancies. However, the therapeutic application of Myricetin is impeded by its poor water solubility and low oral bioavailability. To overcome this limitation, we aimed to develop nanoemulsion of Myricetin (Myr-NE) and evaluate its advantage over Myricetin alone in TNBC cells. The nanoemulsion was formulated using Capryol 90 (oil), Tween 20 (surfactant), and Transcutol HP (co-surfactant). The optimized nano-formulation underwent an evaluation to determine its size, zeta potential, morphology, stability, drug encapsulation efficiency, and in vitro release properties. The anti-cancer activity of Myr-NE was further studied to examine its distinct impact on intracellular drug uptake, cell-viability, anti-tumor signaling, oxidative stress, clonogenicity, and cell death, compared with Myricetin alone in MDA-MB-231 (TNBC) cells. The in vitro drug release and intracellular drug uptake of Myricetin was significantly increased in Myr-NE formulation as compared to Myricetin alone. Moreover, Myr-NE exhibited significant inhibition of cell proliferation, clonogenicity, and increased apoptosis with ~ 2.5-fold lower IC50 as compared to Myricetin. Mechanistic investigation revealed that nanoemulsion augmented the anti-cancer efficacy of Myricetin, most likely by inhibiting the PI3K/AKT/mTOR pathway, eventually leading to enhanced cell death in TNBC cells. The study provides substantial experimental evidence to support the notion that the Myr-NE formulation has the potential to be an effective therapeutic drug for TNBC treatment.
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Affiliation(s)
- Preeti Sharma
- Department of Pharmacology, School of Pharmaceutical Education and Research (SPER), Jamia Hamdard (Hamdard University), New Delhi, 110062, India
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, Timarpur, Delhi, 110054, India
| | - Shubhra Chaturvedi
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, Timarpur, Delhi, 110054, India
| | - Mohammad Ahmed Khan
- Department of Pharmacology, School of Pharmaceutical Education and Research (SPER), Jamia Hamdard (Hamdard University), New Delhi, 110062, India
| | - Yogesh Rai
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, Timarpur, Delhi, 110054, India
| | - Anant Narayan Bhatt
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, Timarpur, Delhi, 110054, India
| | - Abul Kalam Najmi
- Department of Pharmacology, School of Pharmaceutical Education and Research (SPER), Jamia Hamdard (Hamdard University), New Delhi, 110062, India
| | - Mohd Akhtar
- Department of Pharmacology, School of Pharmaceutical Education and Research (SPER), Jamia Hamdard (Hamdard University), New Delhi, 110062, India.
| | - Anil Kumar Mishra
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, Timarpur, Delhi, 110054, India.
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Akhilesh, Uniyal A, Mehta A, Tiwari V. Combination chemotherapy in rodents: a model for chemotherapy-induced neuropathic pain and pharmacological screening. Metab Brain Dis 2024; 39:43-65. [PMID: 37991674 DOI: 10.1007/s11011-023-01315-2] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/09/2023] [Indexed: 11/23/2023]
Abstract
Chemotherapy-induced neuropathic pain (CINP) remains a therapeutic challenge, with no US-FDA approved drugs or effective treatments available. Despite significant progress in unravelling the pathophysiology of CINP, the clinical translation of this knowledge into tangible outcome remains elusive. Here, we employed behavioural and pharmacological approaches to establish and validate a novel combination-based chemotherapeutic model of peripheral neuropathy. Male Sprague Dawley rats were subjected to chemotherapy administration followed by assessment of pain behaviour at different time-points post-chemotherapy. Paclitaxel-treated animals displayed an enhanced thermal and mechanical hypersensitivity from day four onwards which continued till day thirty-five post last paclitaxel injection. Notably, rats subjected to combination chemotherapy, displayed prolonged hypersensitivity that emerged on day four and persisted until day fifty-six. RT-PCR analysis revealed significant upregulation in DRG and spinal mRNA expressions of TRP channels (TRPA1, TRPV1, & TRPM8), pro-inflammatory cytokines (TNF-α & IL-1β) and neuropeptides, Substance P and CGRP in both the pain models. Interestingly, the combination chemotherapy model demonstrated a significant increase in DRG and spinal NR2B expressions compared to rats solely treated with paclitaxel. Pharmacological investigations revealed that gabapentin treatment substantially mitigates pain hypersensitivity in both the combined chemotherapy and paclitaxel-administered groups, with the simultaneous reversal of cellular and molecular changes observed in the lumbar DRG and spinal cord of rats. The findings from this study suggests that combination chemotherapy model exhibits heightened and prolonged hypersensitivity in comparison to the conventional paclitaxel-induced neuropathic pain model. This model not only recapitulates clinical biomarkers of neuropathy but also presents a potential alternative platform for screening analgesic drugs targeted at CINP.
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Affiliation(s)
- Akhilesh
- Neuroscience and Pain Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - Ankit Uniyal
- Neuroscience and Pain Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - Anuj Mehta
- Neuroscience and Pain Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - Vinod Tiwari
- Neuroscience and Pain Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India.
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Vashisht A, Gahlay GK. Understanding seminal plasma in male infertility: emerging markers and their implications. Andrology 2023. [PMID: 38018348 DOI: 10.1111/andr.13563] [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: 09/01/2023] [Revised: 10/26/2023] [Accepted: 11/11/2023] [Indexed: 11/30/2023]
Abstract
Infertility affects a significant proportion of the reproductive-aged population, with male-associated factors contributing to over half of the cases. However, current diagnostic tools have limitations, leading to an underestimation of the true prevalence of male infertility. While traditional semen parameters provide some insights, they fail to determine the true fertility potential in a substantial number of instances. Therefore, it is crucial to investigate additional molecular targets responsible for male infertility to improve understanding and identification of such cases. Seminal plasma, the main carrier of molecules derived from male reproductive glands, plays a crucial role in reproduction. Amongst its multifarious functions, it regulates processes such as sperm capacitation, sperm protection and maturation, and even interaction with the egg's zona pellucida. Seminal plasma offers a non-invasive sample for urogenital diagnostics and has shown promise in identifying biomarkers associated with male reproductive disorders. This review aims to provide an updated and comprehensive overview of seminal plasma in the diagnosis of male infertility, exploring its composition, function, methods used for analysis, and the application of emerging markers. Apart from the application, the potential challenges of seminal plasma analysis such as standardisation, marker interpretation and confounding factors have also been addressed. Moreover, we have also explored future avenues for enhancing its utility and its role in improving diagnostic strategies. Through comprehensive exploration of seminal plasma's diagnostic potential, the present analysis seeks to advance the understanding of male infertility and its effective management.
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Affiliation(s)
- Ashutosh Vashisht
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Gagandeep Kaur Gahlay
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
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Agrawal A, Vindal V. Competing endogenous RNAs in head and neck squamous cell carcinoma: a review. Brief Funct Genomics 2023:elad049. [PMID: 37941447 DOI: 10.1093/bfgp/elad049] [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: 07/25/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023] Open
Abstract
Our understanding of RNA biology has evolved with recent advances in research from it being a non-functional product to molecules of the genome with specific regulatory functions. Competitive endogenous RNA (ceRNA), which has gained prominence over time as an essential part of post-transcriptional regulatory mechanism, is one such example. The ceRNA biology hypothesis states that coding RNA and non-coding RNA co-regulate each other using microRNA (miRNA) response elements. The ceRNA components include long non-coding RNAs, pseudogene and circular RNAs that exert their effect by interacting with miRNA and regulate the expression level of its target genes. Emerging evidence has revealed that the dysregulation of the ceRNA network is attributed to the pathogenesis of various cancers, including the head and neck squamous cell carcinoma (HNSCC). This is the most prevalent cancer developed from the mucosal epithelium in the lip, oral cavity, larynx and pharynx. Although many efforts have been made to comprehend the cause and subsequent treatment of HNSCC, the morbidity and mortality rate remains high. Hence, there is an urgent need to understand the holistic progression of HNSCC, mediated by ceRNA, that can have immense relevance in identifying novel biomarkers with a defined therapeutic intervention. In this review, we have made an effort to highlight the ceRNA biology hypothesis with a focus on its involvement in the progression of HNSCC. For the identification of such ceRNAs, we have additionally highlighted a number of databases and tools.
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Affiliation(s)
- Avantika Agrawal
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - Vaibhav Vindal
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India
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Hussain Y, Singh J, Meena A, Sinha RA, Luqman S. Escin enhanced the efficacy of sorafenib by autophagy-mediated apoptosis in lung cancer cells. Phytother Res 2023; 37:4819-4837. [PMID: 37468281 DOI: 10.1002/ptr.7948] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/21/2023]
Abstract
Combining anti-cancer drugs has been exploited as promising treatment strategy to target lung cancer. Synergistic chemotherapies increase anti-cancer effect and reduce effective drug doses and side effects. In this study, therapeutic potential of escin in combination with sorafenib has been explored. 3-(4,5-Dimethylthiazol-2-yl)-2 5-diphenyltetrazolium bromide assay was used to calculate IC50 values. The synergy was evaluated using Chou-Talaly algorithm. Cellular reactive oxygen species, mitochondrial membrane potential, annexin V, and cell-cycle studies were done by flow-cytometer, and autophagy biomarkers expression were determined using western blotting. Moreover, autophagy was knocked down using ATG5 siRNA to confirm its role, diethylnitrosamine-induced lung cancer model was used to check the synergy of sorafenib/escin. Escin significantly reduced the IC50 of sorafenib in A549 and NCIH460 cells. The combination of sorafenib/escin produced a 2.95 and 5.45 dose reduction index for sorafenib in A549 and NCI-H460 cells. The combination of over-expressed p62 and LC3-II reflects autophagy block-mediated late apoptosis. This phenomenon was reconfirmed by ATG5 knockdown. This combination also selectively targeted G0/G1 phase of cancer cells. In in vivo study, the combination reduced tumour load and lower elevated serum biochemical parameters. The combination of sorafenib/escin synergistically inhibits autophagy to induce late apoptosis in lung cancer cells' G0/G1 phase.
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Affiliation(s)
- Yusuf Hussain
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Jyoti Singh
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Jawaharlal Nehru University, New Delhi, India
| | - Abha Meena
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Rohit Anthony Sinha
- Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Suaib Luqman
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
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Teli G, Pal R, Maji L, Sengupta S, Raghavendra NM, Matada GSP. Medicinal Chemistry Perspectives on Recent Advances in Src Kinase Inhibitors as a Potential Target for the Development of Anticancer Agents: Biological Profile, Selectivity, Structure-Activity Relationship. Chem Biodivers 2023; 20:e202300515. [PMID: 37563848 DOI: 10.1002/cbdv.202300515] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 08/05/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023]
Abstract
The physiological Src proto-oncogene is a protein tyrosine kinase receptor that served as the essential signaling pathway in different types of cancer. Src kinase receptor is divided into different domains: a unique domain, an SH3 domain, an SH2 domain, a protein tyrosine kinase domain, and a regulatory tail, which runs from the N-terminus to the C-terminus. Src kinase inhibitors bind in the kinase domain and are activated by phosphorylation. The etiology of cancer involved various signaling pathways and Src signaling pathways are also involved in those clusters. Although the dysregulation of Src kinase resulted in cancer being discovered in the late 19th century it is still considered a cult pathway because it is not much explored by different medicinal chemists and oncologists. The Src kinase regulated through different kinase pathways (MAPK, PI3K/Akt/mTOR, JAK/STAT3, Hippo kinase, PEAK1, and Rho/ROCK pathways) and proceeded downstream signaling to conduct cell proliferation, angiogenesis, migration, invasion, and metastasis of cancer cells. There are numerous FDA-approved drugs flooded the market but still, there is a huge demand for the creation of novel anticancer drugs. As the existing drugs are accompanied by several adverse effects and drug resistance due to rapid mutation in proteins. In this review, we have elaborated about the structure and activation of Src kinase, as well as the development of Src kinase inhibitors. Our group also provided a comprehensive overview of Src inhibitors throughout the last two decades, including their biological activity, structure-activity relationship, and Src kinase selectivity. The Src binding pocket has been investigated in detail to better comprehend the interaction of Src inhibitors with amino acid residues. We have strengthened the literature with our contribution in terms of molecular docking and ADMET studies of top compounds. We hope that the current analysis will be a useful resource for researchers and provide glimpse of direction toward the design and development of more specific, selective, and potent Src kinase inhibitors.
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Affiliation(s)
- Ghanshyam Teli
- Integrated Drug Discovery Center, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | - Rohit Pal
- Integrated Drug Discovery Center, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | - Lalmohan Maji
- Integrated Drug Discovery Center, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | - Sindhuja Sengupta
- Integrated Drug Discovery Center, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
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Kumar Pal S, Kumar S. Indole-based LpxC (UDP-3-O-(R-3-hydroxyacyl)-N-acetylglucosaminedeacetylase) inhibitors for Salmonella typhi: rational drug discovery through in silico screening. 3 Biotech 2023; 13:281. [PMID: 37496977 PMCID: PMC10366066 DOI: 10.1007/s13205-023-03699-5] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023] Open
Abstract
Salmonella typhi is an infectious bacteria that causes typhoid fever and poses a significant risk to human health. The emergence of antibiotic resistance has become a growing concern in the management of this disease. In this work, a structure-based drug design approach was used to identify inhibitors for zinc-dependent metalloamidase LpxC, the enzyme responsible for the biosynthesis of lipid A. Using an in silico approach (virtual screening, docking, and molecular dynamics (MD) simulations), from a library of 59,000 indole derivatives, we were able to identify promising lead molecules with high binding affinity to the LpxC. Of these, five molecules (compound 435 (CID: 12253558), compound 436 (CID: 122514279), compound 1812 (CID: 90797680), compound 2584 (CID: 57056726), and compound 2545 (CID: 59897361)) have passed all the filtering criteria. This finding was verified by molecular dynamics (MD) simulation as well as post-dynamics free energy calculations. The five compounds that have been identified have shown the most promise compared to other compounds that are already recognized. To further validate the positive outcome of this study, experimental validation and optimization are necessary. These lead compounds may help to develop new antibiotics for antibiotic-resistant Salmonella typhi and improve typhoid fever treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03699-5.
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Affiliation(s)
- Sudhir Kumar Pal
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, 632014 Tamil Nadu India
| | - Sanjit Kumar
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, 632014 Tamil Nadu India
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Saptarshi AN, More TA, Dongerdiye R, Kedar P. Congenital Dyserythropoietic Anemia Type II: High Prevalence of c.1385A>G, (p.Tyr462Cys) Mutation in the Indian Population. Indian J Pediatr 2023; 90:840. [PMID: 37204595 DOI: 10.1007/s12098-023-04662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/03/2023] [Indexed: 05/20/2023]
Affiliation(s)
- Arati Nandan Saptarshi
- Department of Hematogenetics, ICMR-National Institute of Immunohematology, Indian Council of Medical Research, 13th Floor, New Multi-storeyed Building, King Edward Memorial (KEM.) Hospital Campus, Parel, Mumbai, 400012, India
| | - Tejashree A More
- Department of Hematogenetics, ICMR-National Institute of Immunohematology, Indian Council of Medical Research, 13th Floor, New Multi-storeyed Building, King Edward Memorial (KEM.) Hospital Campus, Parel, Mumbai, 400012, India
| | - Rashmi Dongerdiye
- Department of Hematogenetics, ICMR-National Institute of Immunohematology, Indian Council of Medical Research, 13th Floor, New Multi-storeyed Building, King Edward Memorial (KEM.) Hospital Campus, Parel, Mumbai, 400012, India
| | - Prabhakar Kedar
- Department of Hematogenetics, ICMR-National Institute of Immunohematology, Indian Council of Medical Research, 13th Floor, New Multi-storeyed Building, King Edward Memorial (KEM.) Hospital Campus, Parel, Mumbai, 400012, India.
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Saptarshi AN, Dongerdiye RK, More TA, Kedar PS. Development of High-Resolution Melting Curve Analysis for rapid detection of SEC23B gene mutation causing Congenital Dyserythropoietic Anemia type II in Indian population. Ital J Pediatr 2023; 49:84. [PMID: 37455305 DOI: 10.1186/s13052-023-01493-w] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/09/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Congenital dyserythropoietic anemias (CDAs) are a very rare and heterogeneous group of disorders characterized by ineffective erythropoiesis. CDA II is caused by mutations in the SEC23B gene. The most common mutation reported in India is c.1385 A > G, p.Y462C. There is no simple and cost-effective confirmatory diagnostic test available for CDA, and therefore, many patients remain undiagnosed. High-resolution melting curve (HRM) analysis is a polymerase chain reaction (PCR) based technique applied to identify genetic differences and scan nucleic acid sequences. HRM can be used to rapidly screen the common mutation causing CDA II in the Indian population. Thus, we studied the use of High-Resolution Melting Curve Analysis to detect common mutation causing CDA II in the Indian population. METHOD 11 patients having SEC23B (Y462C) mutation causing CDA II are considered for this study. HRM was used to check the presence of Y462C mutation. To verify the accuracy of the HRM analysis, we compared HRM results with the results of Sanger sequencing. This helped us to confirm the diagnosis. RESULTS We have described the clinical, hematological, and genetic data of eleven patients suffering from CDAII. According to HRM and Sanger sequencing, a homozygous SEC23B (Y462C) mutation was present in all patients, whereas a heterozygous Y462C mutation was present in their parents. CONCLUSION Our data showed that High-Resolution Melting (HRM) analysis could be used to rapidly screen common SEC23B mutation that causes CDA II in the Indian population.
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Affiliation(s)
- Arati Nandan Saptarshi
- Department of Haematogenetics, ICMR- National Institute of Immunohaematology, 13th Floor, New Multi Storeyed Building, KEM Hospital Campus, Parel, Mumbai, 400012, India
| | - Rashmi K Dongerdiye
- Department of Haematogenetics, ICMR- National Institute of Immunohaematology, 13th Floor, New Multi Storeyed Building, KEM Hospital Campus, Parel, Mumbai, 400012, India
| | - Tejashree Anil More
- Department of Haematogenetics, ICMR- National Institute of Immunohaematology, 13th Floor, New Multi Storeyed Building, KEM Hospital Campus, Parel, Mumbai, 400012, India
| | - Prabhakar S Kedar
- Department of Haematogenetics, ICMR- National Institute of Immunohaematology, 13th Floor, New Multi Storeyed Building, KEM Hospital Campus, Parel, Mumbai, 400012, India.
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Szal T, Chauhan SS, Lewe P, Rachad FZ, Madre M, Paunina L, Witt S, Parthasarathi R, Windshügel B. Efflux Pump-Binding 4(3-Aminocyclobutyl)Pyrimidin-2-Amines Are Colloidal Aggregators. Biomolecules 2023; 13:1000. [PMID: 37371580 DOI: 10.3390/biom13061000] [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: 02/14/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Efflux pumps are a relevant factor in antimicrobial resistance. In E. coli, the tripartite efflux pump AcrAB-TolC removes a chemically diverse set of antibiotics from the bacterium. Therefore, small molecules interfering with efflux pump function are considered adjuvants for improving antimicrobial therapies. Several compounds targeting the periplasmic adapter protein AcrA and the efflux pump AcrB have been identified to act synergistically with different antibiotics. Among those, several 4(3-aminocyclobutyl)pyrimidin-2-amines have been shown to bind to both proteins. In this study, we intended to identify analogs of these substances with improved binding affinity to AcrA using virtual screening followed by experimental validation. While we succeeded in identifying several compounds showing a synergistic effect with erythromycin on E. coli, biophysical studies suggested that 4(3-aminocyclobutyl)pyrimidin-2-amines form colloidal aggregates that do not bind specifically to AcrA. Therefore, these substances are not suited for further development. Our study emphasizes the importance of implementing additional control experiments to identify aggregators among bioactive compounds.
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Affiliation(s)
- Tania Szal
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany
- School of Science, Constructor University, 28759 Bremen, Germany
| | - Shweta Singh Chauhan
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Philipp Lewe
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), 22607 Hamburg, Germany
| | - Fatima-Zahra Rachad
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany
| | - Marina Madre
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Laura Paunina
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Susanne Witt
- Centre for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), 22607 Hamburg, Germany
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, 22525 Hamburg, Germany
- School of Science, Constructor University, 28759 Bremen, Germany
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Basu S, Debroy R, Kumar H, Singh H, Ramaiah S, Anbarasu A. Bioactive phytocompounds against specific target proteins of Borrelia recurrentis responsible for louse-borne relapsing fever: Genomics and structural bioinformatics evidence. Med Vet Entomol 2023; 37:213-218. [PMID: 36377635 DOI: 10.1111/mve.12623] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/20/2022] [Indexed: 05/18/2023]
Abstract
Louse-borne relapsing fever (LBRF) with high untreated mortality caused by spirochete Borrelia recurrentis is predominantly endemic to Sub-Saharan Africa and has re-emerged in parts of Eastern Europe, Asia and Latin America due to population migrations. Despite subtractive evolution of lice-borne pathogenic Borrelia spp. from tick-borne species, there has been no comprehensive report on conservation of protein targets across tick and lice-borne pathogenic Borrelia nor exploration of phytocompounds that are toxic to tick against lice. From the 19 available whole genomes including B. recurrentis, B. burgdorferi, B. hermsii, B. parkeri and B. miyamotoi, conservation of seven drug targets (>80% domain identity) viz. 30 S ribosomal subunit proteins (RSP) S3, S7, S8, S14, S19, penicillin-binding protein-2 and 50 S RSP L16 were deciphered through multiple sequence alignments. Twelve phytocompounds (hydroxy-tyrosol, baicalein, cis-2-decanoic acid, morin, oenin, rosemarinic acid, kaempferol, piceatannol, rottlerin, luteolin, fisetin and monolaurin) previously explored against Lyme disease spirochete B. burgdorferi when targeted against LBRF-causing B. recurrentis protein targets revealed high multi-target affinity (2%-20% higher than conventional antibiotics) through molecular docking. However, based on high binding affinity against all target proteins, stable coarse-grained dynamics (fluctuations <1 Å) and safe pharmacological profile, luteolin was prioritized. The study encourages experimental evaluation of the potent phytocompounds and similar protocols for investigating other emerging vector-borne diseases.
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Affiliation(s)
- Soumya Basu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
- Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
| | - Reetika Debroy
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
- Department of Bio Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
| | - Hithesh Kumar
- Department of Bio Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
| | - Harpreet Singh
- Division of Biomedical Informatics, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
- Department of Bio Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
- Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, India
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Sinha P, Ponnuraja C, Gupte N, Prakash Babu S, Cox SR, Sarkar S, Mave V, Paradkar M, Cintron C, Govindarajan S, Kinikar A, Priya N, Gaikwad S, Thangakunam B, Devarajan A, Dhanasekaran M, Tornheim JA, Gupta A, Salgame P, Christopher DJ, Kornfeld H, Viswanathan V, Ellner JJ, Horsburgh CR, Gupte AN, Padmapriyadarsini C, Hochberg NS. Impact of Undernutrition on Tuberculosis Treatment Outcomes in India: A Multicenter, Prospective, Cohort Analysis. Clin Infect Dis 2023; 76:1483-1491. [PMID: 36424864 PMCID: PMC10319769 DOI: 10.1093/cid/ciac915] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/10/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Undernutrition is the leading risk factor for tuberculosis (TB) globally. Its impact on treatment outcomes is poorly defined. METHODS We conducted a prospective cohort analysis of adults with drug-sensitive pulmonary TB at 5 sites from 2015-2019. Using multivariable Poisson regression, we assessed associations between unfavorable outcomes and nutritional status based on body mass index (BMI) nutritional status at treatment initiation, BMI prior to TB disease, stunting, and stagnant or declining BMI after 2 months of TB treatment. Unfavorable outcome was defined as a composite of treatment failure, death, or relapse within 6 months of treatment completion. RESULTS Severe undernutrition (BMI <16 kg/m2) at treatment initiation and severe undernutrition before the onset of TB disease were both associated with unfavorable outcomes (adjusted incidence rate ratio [aIRR], 2.05; 95% confidence interval [CI], 1.42-2.91 and aIRR, 2.20; 95% CI, 1.16-3.94, respectively). Additionally, lack of BMI increase after treatment initiation was associated with increased unfavorable outcomes (aIRR, 1.81; 95% CI, 1.27-2.61). Severe stunting (height-for-age z score <-3) was associated with unfavorable outcomes (aIRR, 1.52; 95% CI, 1.00-2.24). Severe undernutrition at treatment initiation and lack of BMI increase during treatment were associated with a 4- and 5-fold higher rate of death, respectively. CONCLUSIONS Premorbid undernutrition, undernutrition at treatment initiation, lack of BMI increase after intensive therapy, and severe stunting are associated with unfavorable TB treatment outcomes. These data highlight the need to address this widely prevalent TB comorbidity. Nutritional assessment should be integrated into standard TB care.
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Affiliation(s)
- Pranay Sinha
- Section of Infectious Diseases, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Chinnaiyan Ponnuraja
- Indian Council of Medical Research, National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Nikhil Gupte
- Byramjee Jeejeebhoy Government Medical College, Sassoon General Hospitals–Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
- Center for Infectious Diseases in India, Johns Hopkins India, Pune, Maharashtra, India
- Division of Infectious Diseases, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | | | - Samyra R Cox
- Division of Infectious Diseases, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Sonali Sarkar
- Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Vidya Mave
- Byramjee Jeejeebhoy Government Medical College, Sassoon General Hospitals–Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
- Center for Infectious Diseases in India, Johns Hopkins India, Pune, Maharashtra, India
- Division of Infectious Diseases, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Mandar Paradkar
- Byramjee Jeejeebhoy Government Medical College, Sassoon General Hospitals–Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
- Center for Infectious Diseases in India, Johns Hopkins India, Pune, Maharashtra, India
| | - Chelsie Cintron
- Section of Infectious Diseases, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - S Govindarajan
- Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
- National Tuberculosis Elimination Program, Puducherry, India
| | - Aarti Kinikar
- Byramjee Jeejeebhoy Government Medical College and Sassoon General Hospitals, Pune, Maharashtra, India
| | - Nadesan Priya
- Christian Medical College, Vellore, Tamil Nadu, India
| | - Sanjay Gaikwad
- Byramjee Jeejeebhoy Government Medical College and Sassoon General Hospitals, Pune, Maharashtra, India
| | | | | | | | - Jeffrey A Tornheim
- Division of Infectious Diseases, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Amita Gupta
- Division of Infectious Diseases, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Padmini Salgame
- Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA
| | | | - Hardy Kornfeld
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Vijay Viswanathan
- Prof. M. Viswanathan Diabetes Research Centre, Chennai, Tamil Nadu, India
| | - Jerrold J Ellner
- Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, New Jersey, USA
| | - C Robert Horsburgh
- Section of Infectious Diseases, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Akshay N Gupte
- Division of Infectious Diseases, Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | | | - Natasha S Hochberg
- Section of Infectious Diseases, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
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B.R. R, Shah N, Joshi P, Madhusudan MS, Balasubramanian N. Kinetics of Arf1 inactivation regulates Golgi organisation and function in non-adherent fibroblasts. Biol Open 2023; 12:bio059669. [PMID: 36946871 PMCID: PMC10187640 DOI: 10.1242/bio.059669] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/13/2023] [Indexed: 03/23/2023] Open
Abstract
Arf1 belongs to the Arf family of small GTPases that localise at the Golgi and plasma membrane. Active Arf1 plays a crucial role in regulating Golgi organisation and function. In mouse fibroblasts, loss of adhesion triggers a consistent drop (∼50%) in Arf1 activation that causes the Golgi to disorganise but not fragment. In suspended cells, the trans-Golgi (GalTase) disperses more prominently than cis-Golgi (Man II), accompanied by increased active Arf1 (detected using GFP-ABD: ARHGAP10 Arf1 binding domain) associated with the cis-Golgi compartment. Re-adhesion restores Arf1 activation at the trans-Golgi as it reorganises. Arf1 activation at the Golgi is regulated by Arf1 Guanine nucleotide exchange factors (GEFs), GBF1, and BIG1/2. In non-adherent fibroblasts, the cis-medial Golgi provides a unique setting to test and understand the role GEF-mediated Arf1 activation has in regulating Golgi organisation. Labelled with Man II-GFP, non-adherent fibroblasts treated with increasing concentrations of Brefeldin-A (BFA) (which inhibits BIG1/2 and GBF1) or Golgicide A (GCA) (which inhibits GBF1 only) comparably decrease active Arf1 levels. They, however, cause a concentration-dependent increase in cis-medial Golgi fragmentation and fusion with the endoplasmic reticulum (ER). Using selected BFA and GCA concentrations, we find a change in the kinetics of Arf1 inactivation could mediate this by regulating cis-medial Golgi localisation of GBF1. On loss of adhesion, a ∼50% drop in Arf1 activation over 120 min causes the Golgi to disorganise. The kinetics of this drop, when altered by BFA or GCA treatment causes a similar decline in Arf1 activation but over 10 min. This causes the Golgi to now fragment which affects cell surface glycosylation and re-adherent cell spreading. Using non-adherent fibroblasts this study reveals the kinetics of Arf1 inactivation, with active Arf1 levels, to be vital for Golgi organisation and function.
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Affiliation(s)
- Rajeshwari B.R.
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - Nikita Shah
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - Prachi Joshi
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - M. S. Madhusudan
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - Nagaraj Balasubramanian
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
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Aravindakshan MR, Maity SK, Paul A, Chakrabarti P, Mandal C, Sarkar J. Distinct pathoclinical clusters among patients with uncontrolled type 2 diabetes: results from a prospective study in rural India. BMJ Open Diabetes Res Care 2022; 10:10/1/e002654. [PMID: 35144941 PMCID: PMC8845217 DOI: 10.1136/bmjdrc-2021-002654] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/15/2022] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Inadequate glycemic control among patients with type 2 diabetes mellitus (T2DM) poses an enormous challenge. Whether this uncontrolled T2DM population is a heterogenous mix of disease subtypes remains unknown. Identification of these subtypes would result in a customized T2DM management protocol thereby paving the way toward personalized therapy. RESEARCH DESIGN AND METHODS Electronic health records of 339 patients with uncontrolled T2DM patients followed up for a median period of 14 months were analyzed using Uniform Manifold Approximation and Projection followed by density-based spatial clustering of applications with noise. Baseline clinical features and final diagnoses with drug combinations were selected in the analysis. A 30 min oral glucose tolerance test was next performed for assessing the underlying insulin resistance and β cell dysfunction. RESULTS Three major clusters were identified. The first cluster characterized by recent onset T2DM had moderately preserved β cell function. The second cluster with a longer duration of T2DM and associated hypertension showed the best glycemic control with dual antidiabetic therapy. The third cluster with the longest history of T2DM and no history of hypertension had the worst glycemic control in spite of the highest percentage of patients on triple therapy (34.58%) and quadruple therapy (8.41%). CONCLUSIONS Uncontrolled T2DM comprises a heterogeneous population with respect to disease duration, presence of co-morbidities and β cell function without significant difference in insulin resistance. Stratifying them on the basis of pathoclinical features is the first step toward a personalized management in T2DM.
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Affiliation(s)
| | - Sujay Krishna Maity
- Department of Cell Biology and Physiology, Indian Institute of Chemical Biology CSIR, Kolkata, West Bengal, India
| | - Avishek Paul
- Department of Cell Biology and Physiology, Indian Institute of Chemical Biology CSIR, Kolkata, West Bengal, India
| | - Partha Chakrabarti
- Department of Cell Biology and Physiology, Indian Institute of Chemical Biology CSIR, Kolkata, West Bengal, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Chittaranjan Mandal
- Department of Computer Science & Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Jit Sarkar
- Department of Cell Biology and Physiology, Indian Institute of Chemical Biology CSIR, Kolkata, West Bengal, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
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Krishnan R, Meera MS. Monitoring bioaccessibility of iron and zinc in pearl millet grain after sequential milling. J Food Sci Technol 2022; 59:784-795. [PMID: 35185191 PMCID: PMC8814269 DOI: 10.1007/s13197-021-05072-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/08/2021] [Accepted: 03/15/2021] [Indexed: 02/03/2023]
Abstract
The present study was to understand the effect of sequential milling on the distribution of inhibitory factors and their relation to iron-zinc bioaccessibility in the two pearl millet cultivars differing in grain shape and size. The studies revealed that the yield of decorticated grain and bran fractions differed between the cultivars. The initial bran fractions had lower iron content, which increased on increase of decortication duration (2.33-25.14 mg/100 g), while zinc did not follow this pattern. Among the inhibitory factors, polyphenols and phytic acid were low in the initial stages of milling and subsequently increased as the milling duration increased. Microscopic studies further confirmed that iron-zinc and inhibitory factors coexist in the same tissues of the grain. The β- carotene was more concentrated in the middle layers of the pericarp. It was observed that iron bioaccessibility was the highest in the 4 min milling bran (7.7%, 3.34%) and final decorticated grain fractions (13.79%, 18.45%) of both the cultivars. Iron bioaccessibility could not be related to any particular inhibitory factors, in bran insoluble fibre and phytic acid were prominent while in decorticated grain galloyls, catechols and phytic acid were the maxima. In both the cultivars, zinc bioaccessibility was high in fractions with low phytic acid and insoluble fibre. The data presented suggest that 6 min decortication that removed around 10-15% of the bran had the highest iron and zinc bioaccessibility. The iron-rich bran fraction after appropriate processing can also be used in speciality food and thereby addresses the problem of micronutrient deficiency. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13197-021-05072-x.
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Affiliation(s)
- Rateesh Krishnan
- Department of Grain Science and Technology, CSIR-Central Food Technological Research Institute, Mysore, 570 020 India
| | - M. S. Meera
- Department of Grain Science and Technology, CSIR-Central Food Technological Research Institute, Mysore, 570 020 India
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Aftab M, Poojary SS, Seshan V, Kumar S, Agarwal P, Tandon S, Zutshi V, Das BC. Urine miRNA signature as a potential non-invasive diagnostic and prognostic biomarker in cervical cancer. Sci Rep 2021; 11:10323. [PMID: 33990639 PMCID: PMC8121812 DOI: 10.1038/s41598-021-89388-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/23/2021] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs as cancer biomarkers in serum, plasma, and other body fluids are often used but analysis of miRNA in urine is limited. We investigated the expression of selected miRNAs in the paired urine, serum, cervical scrape, and tumor tissue specimens from the women with cervical precancer and cancer with a view to identify if urine miRNAs could be used as reliable non-invasive biomarkers for an early diagnosis and prognosis of cervical cancer. Expression of three oncomiRs (miR-21, miR-199a, and miR-155-5p) and three tumor suppressors (miR-34a, miR-145, and miR-218) as selected by database search in cervical pre-cancer, cancer, and normal controls including cervical cancer cell lines were analyzed using qRT-PCR. The expression of miRNAs was correlated with various clinicopathological parameters, including HPV infection and survival outcome. We observed a significant overexpression of the oncomiRs and the downregulation of tumor suppressor miRNAs. A combination of miR-145-5p, miR-218-5p, and miR-34a-5p in urine yielded 100% sensitivity and 92.8% specificity in distinguishing precancer and cancer patients from healthy controls and it well correlates with those of serum and tumor tissues. The expression of miR-34a-5p and miR-218-5p were found to be independent prognostic factors for the overall survival of cervical cancer patients. We conclude that the evaluation of the above specific miRNA expression in non-invasive urine samples may serve as a reliable biomarker for early detection and prognosis of cervical cancer.
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Affiliation(s)
- Mehreen Aftab
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Campus, Sector-125, Noida, Uttar Pradesh, 201313, India
| | - Satish S Poojary
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Campus, Sector-125, Noida, Uttar Pradesh, 201313, India
| | - Vaishnavi Seshan
- Department of Gynecology and Obstetrics, Safdarjung Hospital, New Delhi, 110029, India
| | - Sachin Kumar
- Depatment of Medical Oncology, Dr. B R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Pallavi Agarwal
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Campus, Sector-125, Noida, Uttar Pradesh, 201313, India
| | - Simran Tandon
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Campus, Sector-125, Noida, Uttar Pradesh, 201313, India
| | - Vijay Zutshi
- Department of Gynecology and Obstetrics, Safdarjung Hospital, New Delhi, 110029, India
| | - Bhudev C Das
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Amity University Campus, Sector-125, Noida, Uttar Pradesh, 201313, India.
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Chakraborty S, Bhatia T, Sharma V, Antony N, Das D, Sahu S, Sharma S, Shriharsh V, Brar JS, Iyengar S, Singh R, Nimgaonkar VL, Deshpande SN. Psychometric properties of a screening tool for autism in the community-The Indian Autism Screening Questionnaire (IASQ). PLoS One 2021; 16:e0249970. [PMID: 33886585 PMCID: PMC8062015 DOI: 10.1371/journal.pone.0249970] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/29/2021] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Currently available screening questionnaires for Autism spectrum disorders were tested in developed countries, but many require additional training and many are unsuitable for older individuals, thus reducing their utility in lower/ middle- income countries. We aimed to derive a simplified questionnaire that could be used to screen persons in India. METHODS We have previously validated Indian Scale for Assessment of Autism (ISAA), that is now mandated for disability assessment by the Government of India. This detailed tool requires intensive training and it is time consuming. It was used to derive a new screening questionnaire: 1) items most frequently scored as positive by participants with autism in original ISAA validation study were modified for binary scoring following expert review. 2) In a new sample, clinically diagnosed individuals with/without autism were administered the screening tool and ISAA following written informed consent. Its psychometric properties were determined. RESULTS A 10-item scale named Indian Autism Screening Questionnaire (IASQ) was prepared in Hindi and English. Thereafter 145 parents/caregivers of participants (autism, n = 90, other psychiatric disorders, n = 55) (ages 3-18), were administered IASQ and ISAA (parents/caregivers plus observation) by separate interviewers, blind to each other and to diagnosis. At a cutoff of 1, sensitivity was 99%, specificity 62%, Positive Predictive Value 81%, and Negative Predictive Value 95%. Test-retest reliability was r = 0.767 (CI = 0.62-0.86) and interrater reliability- Krippendorff"s-alpha was 0.872. The area under Receiver Operating Characteristic Curve (ROC) was 95%. There was a significant difference on IASQ-scores between participants with and without a clinical diagnosis of Autism (t = 14.57, p<0.0001). DISCUSSION The IASQ is a simple, easy to use screening tool with satisfactory reliability and validity, that can be administered to caregivers in 15 minutes and provides information about DSM 5 criteria for autism. It may be applicable outside India, following additional adaptation, for community-based studies.
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Affiliation(s)
- Satabdi Chakraborty
- Department of Psychiatric Social Work, Centre of Excellence in Mental Health, Atal Bihari Vajpayee Institute of Medical Sciences-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Triptish Bhatia
- Indo-US Projects and NCU-ICMR, Department of Psychiatry and De-addiction, Centre of Excellence in Mental Health, Atal Bihari Vajpayee Institute of Medical Sciences-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Vikas Sharma
- NCU-ICMR, Department of Psychiatry and De-addiction, Centre of Excellence in Mental Health Atal Bihari Vajpayee Institute of Medical Sciences-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Nitin Antony
- Development and Validation of the Screening Version of ISAA, ICMR Project’, Dept. of Psychiatric Social Work, Centre of Excellence in Mental Health, Atal Bihari Vajpayee Institute of Medical Sciences-Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Dhritishree Das
- Development and Validation of the Screening Version of ISAA, ICMR Project’, Dept. of Psychiatric Social Work, Centre of Excellence in Mental Health, Atal Bihari Vajpayee Institute of Medical Sciences-Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Sushree Sahu
- Dyslexia Assessment for Languages of India, MoST Project, Department of Psychiatry and De-addiction, Centre of Excellence in Mental Health, Atal Bihari Vajpayee Institute of Medical Sciences-Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Satyam Sharma
- Department of Clinical Psychology, Centre of Excellence in Mental Health, Atal Bihari Vajpayee Institute of Medical Sciences-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Vandana Shriharsh
- Department of Clinical Psychology, Centre of Excellence in Mental Health, Atal Bihari Vajpayee Institute of Medical Sciences-Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Jaspreet S. Brar
- Department of Psychiatry and Consultant, Community Care Behavioral Health Organization, Western Psychiatric Hospital of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Satish Iyengar
- Department of Statistics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ravinder Singh
- Non Communicable Diseases, Indian Council for Medical Research, New Delhi, India
| | - Vishwajit L. Nimgaonkar
- Department of Psychiatry and Department of Human Genetics, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Smita Neelkanth Deshpande
- Department of Psychiatry, Centre of Excellence in Mental Health, Atal Bihari Vajpayee Institute of Medical Sciences-Dr. Ram Manohar Lohia Hospital, New Delhi, India
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Ali A, Gupta D, Khan AU. Role of non-active site residues in maintaining New Delhi metallo-β-lactamase-1(NDM-1) function: an approach of site-directed mutagenesis and docking. FEMS Microbiol Lett 2021; 368:fnz003. [PMID: 30624634 DOI: 10.1093/femsle/fnz003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/05/2019] [Indexed: 12/17/2023] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) has been known to hydrolyze nearly all β-lactam antibiotics, leading to a multidrug-resistant state. Hence, it is important to study its structure and function in relation to controlling infections caused by such resistant bacterial strains. Mutagenesis is one of the approaches used to explore it. No study has been performed to explore the role of non-active site residues in the enzyme activity. This study includes mutations of three non-active site residues to comprehend its structure and function simultaneously. Three non-active site laboratory mutants of NDM-1 were generated by site-directed mutagenesis. The minimum inhibitory concentrations of cefotaxime, cefoxitin, imipenem and meropenem were reduced by up to 4-fold for these mutants compared with wild-type. The hydrolytic activity of mutants was also found to be reduced. Mutants showed a significant change in secondary structure compared with wild-type, as determined by CD spectrophotometry. The catalytic properties and stability of these mutants were found to be reduced. Hence, it revealed an imperative role of non-active site residues in the enzymatic activity of NDM-1.
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Maan HS, Dhole TN, Chowdhary R. Identification and characterization of nonpolio enterovirus associated with nonpolio-acute flaccid paralysis in polio endemic state of Uttar Pradesh, Northern India. PLoS One 2019; 14:e0208902. [PMID: 30699113 PMCID: PMC6353074 DOI: 10.1371/journal.pone.0208902] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/27/2018] [Indexed: 11/18/2022] Open
Abstract
Despite polio eradication, nonpolio enterovirus (NPEV) detection amid polio surveillance, which is considered to have implications in paralysis, requires attention. The attributes of NPEV infections in nonpolio-AFP (NPAFP) cases from Uttar Pradesh (UP), India, remain undetermined and are thus investigated. A total of 1839 stool samples collected from patients with acute flaccid paralysis (AFP) from UP, India, between January 2010 and October 2011 were analyzed as per the WHO algorithm. A total of 359 NPAFP cases yielded NPEVs, which were subjected to microneutralization assay, partial VP1 gene-based molecular serotyping and phylogenetic analysis. Demographic and clinical-epidemiological features were also ascertained. Echoviruses (29%) and Coxsackievirus (CV)-B (17%) were the most common viruses identified by the microneutralization assay. The molecular genotyping characterized the NPEVs into 34 different serotypes, corresponding to Enterovirus (EV)-A (1.6%), EV-B (94%) and EV-C (5.3%) species. The rarely described EV serotypes, such as EV-C95, CV-A20, EV-C105, EV-B75, EV-B101, and EV-B107, were also identified. NPEV-associated AFP was more prevalent in younger male children, peaked in the monsoon months and was predominantly found in the central part of the state. The NPEV strains isolated in the study exhibited genetic diversity from those isolated in other countries. These form part of a different cluster or subcluster existing in cocirculation, limited to India only. This study augments the understanding of epidemiological features and demonstrates the extensive diversity exhibited by the NPEV strains in NPAFP cases from the polio-endemic region. It also underscores the need or effective long-term strategies to monitor NPEV circulation and its associated health risks in the post-polio eradication era.
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Affiliation(s)
- Harjeet Singh Maan
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Tapan N. Dhole
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
- * E-mail:
| | - Rashmi Chowdhary
- Department of Biochemistry, All Indian Institute of Medical Sciences, Bhopal, India
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Gangan MS, Athale CA. Threshold effect of growth rate on population variability of Escherichia coli cell lengths. R Soc Open Sci 2017; 4:160417. [PMID: 28386413 PMCID: PMC5367290 DOI: 10.1098/rsos.160417] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 01/23/2017] [Indexed: 05/24/2023]
Abstract
A long-standing question in biology is the effect of growth on cell size. Here, we estimate the effect of Escherichia coli growth rate (r) on population cell size distributions by estimating the coefficient of variation of cell lengths (CVL) from image analysis of fixed cells in DIC microscopy. We find that the CVL is constant at growth rates less than one division per hour, whereas above this threshold, CVL increases with an increase in the growth rate. We hypothesize that stochastic inhibition of cell division owing to replication stalling by a RecA-dependent mechanism, combined with the growth rate threshold of multi-fork replication (according to Cooper and Helmstetter), could form the basis of such a threshold effect. We proceed to test our hypothesis by increasing the frequency of stochastic stalling of replication forks with hydroxyurea (HU) treatment and find that cell length variability increases only when the growth rate exceeds this threshold. The population effect is also reproduced in single-cell studies using agar-pad cultures and 'mother machine'-based experiments to achieve synchrony. To test the role of RecA, critical for the repair of stalled replication forks, we examine the CVL of E. coli ΔrecA cells. We find cell length variability in the mutant to be greater than wild-type, a phenotype that is rescued by plasmid-based RecA expression. Additionally, we find that RecA-GFP protein recruitment to nucleoids is more frequent at growth rates exceeding the growth rate threshold and is further enhanced on HU treatment. Thus, we find growth rates greater than a threshold result in increased E. coli cell lengths in the population, and this effect is, at least in part, mediated by RecA recruitment to the nucleoid and stochastic inhibition of division.
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