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Ani V, Sreevidya KV, Unnikrishnan K, Sindhu Mol A, Chacko PM, Shafeeca A. Technical Note: A simple FTA® based method for the direct STR amplification of human foetal tissues. Forensic Sci Int 2024; 357:111971. [PMID: 38447344 DOI: 10.1016/j.forsciint.2024.111971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/05/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024]
Abstract
Short tandem repeats (STRs) or microsatellites are short, tandemly repeated DNA sequences that involve a repetitive unit of 1-6 bp. DNA isolation and purification from a large number and often compromised samples gives problems to forensic labs for STR typing. Many of the conventional methods used in the isolation and purification of DNA from forensic samples are time consuming, expensive, hazardous for health and are often associated with greater risks of cross contamination. FTA® technology is a method designed to simplify the collection, shipment, archiving and purification of nucleic acid from a wide variety of biological samples. We report a new method for the direct STR amplification which can amplify STR loci from human foetal tissues spotted on FTA cards, bye-passing the need of DNA purification. The STR loci amplified by this method was compared with conventional method of STR profiling and was found absolutely matching. Therefore, this new method is demonstrated to be very useful for fast, less expensive and non- hazardous forensic DNA analysis.
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Affiliation(s)
- V Ani
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India.
| | - K V Sreevidya
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India
| | - K Unnikrishnan
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India
| | - A Sindhu Mol
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India
| | - Priya Mary Chacko
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India
| | - A Shafeeca
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India
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Luo J, Jin G, Cui S, Wang H, Liu Q. Regulatory mechanism of FCGR2A in macrophage polarization and its effects on intervertebral disc degeneration. J Physiol 2024; 602:1341-1369. [PMID: 38544414 DOI: 10.1113/jp285871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Intervertebral disc degeneration (IDD) poses a significant health burden, necessitating a deeper understanding of its molecular underpinnings. Transcriptomic analysis reveals 485 differentially expressed genes (DEGs) associated with IDD, underscoring the importance of immune regulation. Weighted gene co-expression network analysis (WGCNA) identifies a yellow module strongly correlated with IDD, intersecting with 197 DEGs. Protein-protein interaction (PPI) analysis identifies ITGAX, MMP9 and FCGR2A as hub genes, predominantly expressed in macrophages. Functional validation through in vitro and in vivo experiments demonstrates the pivotal role of FCGR2A in macrophage polarization and IDD progression. Mechanistically, FCGR2A knockdown suppresses M1 macrophage polarization and NF-κB phosphorylation while enhancing M2 polarization and STAT3 activation, leading to ameliorated IDD in animal models. This study sheds light on the regulatory function of FCGR2A in macrophage polarization, offering novel insights for IDD intervention strategies. KEY POINTS: This study unveils the role of FCGR2A in intervertebral disc (IVD) degeneration (IDD). FCGR2A knockdown mitigates IDD in cellular and animal models. Single-cell RNA-sequencing uncovers diverse macrophage subpopulations in degenerated IVDs. This study reveals the molecular mechanism of FCGR2A in regulating macrophage polarization. This study confirms the role of the NF-κB/STAT3 pathway in regulating macrophage polarization in IDD.
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Affiliation(s)
- Jiaying Luo
- School of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Guoxin Jin
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, P. R. China
| | - Shaoqian Cui
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, P. R. China
| | - Huan Wang
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, P. R. China
| | - Qi Liu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, P. R. China
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Jordan D, Mills D. Resolving human DNA mixtures with F-108 polymer and capillary electrophoresis single-strand conformational polymorphism analysis. J Sep Sci 2020; 43:3327-3332. [PMID: 32506742 DOI: 10.1002/jssc.202000194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/17/2020] [Accepted: 06/03/2020] [Indexed: 11/10/2022]
Abstract
Current technologies have increased the sensitivity for analyzing forensic DNA samples, especially those considered "touch samples." Because of this, there has been an increase in the number of forensic mixtures-two or more contributors within a single sample-submitted to the crime laboratories. Therefore, the need to resolve these mixtures has increased as well. Several technologies are currently utilized, but many of them are time consuming and do not resolve the entire profile. Therefore, CE-Single-Strand Conformational Polymorphisms coupled with the Pluronic F-108 polymer was assessed for its ability to resolve human forensic mixtures. This technique has been able to detect sequence variation, such as single nucleotide polymorphism in short tandem repeat loci, such as D7S820 and vWA. Samples were first analyzed with the Performance Optimized Polymer-7, and mixtures created from samples that shared alleles. These samples were sequenced to detect single base-pair mutations and evaluated with the F-108 and CE-Single Strand Conformational Polymorphism analysis. Results from this study indicated the method would serve as a valuable screening tool to detect base sequence variation between individuals when they share alleles in a mixture and before using Massive Parallel Sequencing technology to distinguish which bases differ.
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Affiliation(s)
- Deidra Jordan
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,International Forensic Research Institute, Florida International University, Miami, FL, USA
| | - DeEtta Mills
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,International Forensic Research Institute, Florida International University, Miami, FL, USA
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You HS, Lee SH, Ok YJ, Kang HG, Sung HJ, Lee JY, Kang SS, Hyun SH. Influence of swabbing solution and swab type on DNA recovery from rigid environmental surfaces. J Microbiol Methods 2019; 161:12-17. [PMID: 31004622 DOI: 10.1016/j.mimet.2019.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023]
Abstract
Determination of the metagenome has become an important component of forensic identification, which requires efficient environmental sampling techniques. Therefore, in this study, we compared the efficiency of sample collection using swabbing with cotton swabs and three types of medical swabs (S7, S22, S24) along with three different solutions: phosphate-buffered saline (PBS), 1% Tween 20 + 1% glycerol in PBS (TG), and GS commercial solution (Noble Bio, Hwaseong, Republic of Korea). Combinations of the three solutions with the three types of swabs were tested at different volumes (cotton swab, S7: 0, 30, 50, 70 μL; S22, S24: 0, 70, 100, 130 μL). Escherichia coli and Staphylococcus aureus were selected as representative environmental microbial samples, and the number of colony-forming units (CFUs), DNA concentration, and DNA copy numbers were compared across groups. The sampling process had a clear effect on the efficiency of extraction, which allowed for determination of a more efficient sample sampling method. In particular, cotton swabs showed 2-10-fold greater CFUs of both species than the medical swabs, and resulted in significantly greater amounts of extracted DNA. TG was found to be the most efficient solution for bacterial DNA extraction, with higher CFUs and DNA obtained than with the other three solutions at all volumes tested. This study highlights the need for a standardized sampling method that can be applied to all environmental samples, especially for microbial quantification, and provides valuable reference data for the efficient collection of environmental samples for metagenomic analyses in microbial-based forensic assessments.
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Affiliation(s)
- Hee Sang You
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea; Department of Biomedical Laboratory Science, Eulji University, School of Medicine, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea
| | - Song Hee Lee
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea; Department of Biomedical Laboratory Science, Eulji University, School of Medicine, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea
| | - Yeon Jeong Ok
- Department of Biomedical Laboratory Science, Eulji University, School of Medicine, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea
| | - Hee-Gyu Kang
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea; Department of Biomedical Laboratory Science, Eulji University, School of Medicine, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea
| | - Ho Jung Sung
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea; Department of Biomedical Laboratory Science, Eulji University, School of Medicine, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea
| | - Ji Yeong Lee
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea
| | - Sang Sun Kang
- Department of Biology Education, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk 28644, Republic of Korea
| | - Sung Hee Hyun
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea; Department of Biomedical Laboratory Science, Eulji University, School of Medicine, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea.
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