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Siuta J, Dobosz A, Kawecki J, Dobosz T. DNA Content of Various Fluids and Tissues of the Human Body. Genes (Basel) 2023; 15:17. [PMID: 38275599 PMCID: PMC10815331 DOI: 10.3390/genes15010017] [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: 11/03/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Due to the scarcity of literature data on the DNA content of different human tissues, this study aimed to isolate DNA from different tissues and fluids of the human body together with the determination of its content in the samples studied. Material was collected and tests were performed between 1990 and 2010, during autopsies performed for prosecutor's offices in the Department of Forensic Medicine. Goiter and thyroid cancer tissues were obtained from the Department of General Surgery, Gastroenterology and Endocrinology of Wroclaw Medical University. Isolated samples were measured spectrophotometrically, yielding an R 260/280 nm between 1.5 and 1.6. In some cases (when a sufficiently pure preparation could not be obtained), isolation was continued using the silica-based commercial QIAquick PCR Purification Kit (Qiagen). If the sampling tissues showed signs of decomposition such as bad odour or colour, the results were calibrated by Real-Time PCR, using the Quantifiler DNA assay (Thermo Fisher Scientific, Applied Biosystems). The results have shown that the maximum amount of genetic material was obtained from hair roots, adrenal glands, gonads and lymph nodes. The lowest DNA content per gram or milliliter of tissue or body fluid was found in adipose tissue, blood, saliva, bile, sweat, tears and the vitreous body of the eye. The presented findings indicate the best sources of high-quality DNA from the human body: gonads, kidneys, muscle (including heart), blood and bones (after decalcification).
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Affiliation(s)
- Jędrzej Siuta
- Department of Forensic Medicine, Wroclaw Medical University, Mikulicza-Redeckiego 4, 50-345 Wroclaw, Poland (T.D.)
| | - Agnieszka Dobosz
- Division of Basic Medical Science, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
| | - Jerzy Kawecki
- Department of Forensic Medicine, Wroclaw Medical University, Mikulicza-Redeckiego 4, 50-345 Wroclaw, Poland (T.D.)
| | - Tadeusz Dobosz
- Department of Forensic Medicine, Wroclaw Medical University, Mikulicza-Redeckiego 4, 50-345 Wroclaw, Poland (T.D.)
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Butto T, Mungikar K, Baumann P, Winter J, Lutz B, Gerber S. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing. Cells 2023; 12:cells12071051. [PMID: 37048124 PMCID: PMC10093037 DOI: 10.3390/cells12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.
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Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Peter Baumann
- Faculty of Biology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center Mainz, 55128 Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
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Asamba MN, Mugendi EN, Oshule PS, Essuman S, Chimbevo LM, Atego NA. Molecular characterization of chlorpyrifos degrading bacteria isolated from contaminated dairy farm soils in Nakuru County, Kenya. Heliyon 2022; 8:e09176. [PMID: 35846483 PMCID: PMC9280583 DOI: 10.1016/j.heliyon.2022.e09176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Chlorpyrifos (CP) is an organophosphate widely used as an insecticide and acaricide. Extensive application of CP contaminates ecosystems, polluting the environment and food products, creating health complications to humans due to its neurotoxicity. The study evaluated CP bioremediation by bacteria isolated from dairy farm soils in Nakuru County, Kenya, through enrichment culture technique. The growth response of the bacteria and degradation of chlorpyrifos was monitored every five days using UV-VIS Spectrophotometer (600nm). Enrichment culture technique led to the isolation of eighteen (MA1-MA18) potential CP degraders belonging to the genera Pseudomonas, Stenotrophomonas, Bacillus, Alicaligenes, and Achromobacter. The efficacy of four (4) strains was further investigated using Gas Chromatography-Mass Spectrometry (GC-MS) analysis. The results showed that all four strains significantly degraded chlorpyrifos in Minimum Salt Medium (MSM): Lysinibacillus sp.HBUM206408 (87.16 %), Stenotrophomonas maltophilia (82.04 %), Pseudomonas putida (89.52 %), and Achromobacter insuavis (91.08 %) within 16 days, producing 2-Hydroxy-3, 5, 6-trichloropyridine (TCP) as the main metabolite. Therefore, these strains can be used to degrade chlorpyrifos in contaminated soil. There is a need for further studies to determine the possible mechanisms and other metabolites of chlorpyrifos degradation by the isolates obtained in the study. Besides, future studies should explore the efficacy and survival of the organisms in the contaminated environment.
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Asamba MN, Mugendi EN, Oshule PS, Essuman S, Chimbevo LM, Atego NA. Molecular characterization of chlorpyrifos degrading bacteria isolated from contaminated dairy farm soils in Nakuru County, Kenya. Heliyon 2022; 8:e09176. [PMID: 35846483 DOI: 10.2139/ssrn.3940828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/18/2022] [Accepted: 03/17/2022] [Indexed: 05/28/2023] Open
Abstract
Chlorpyrifos (CP) is an organophosphate widely used as an insecticide and acaricide. Extensive application of CP contaminates ecosystems, polluting the environment and food products, creating health complications to humans due to its neurotoxicity. The study evaluated CP bioremediation by bacteria isolated from dairy farm soils in Nakuru County, Kenya, through enrichment culture technique. The growth response of the bacteria and degradation of chlorpyrifos was monitored every five days using UV-VIS Spectrophotometer (600nm). Enrichment culture technique led to the isolation of eighteen (MA1-MA18) potential CP degraders belonging to the genera Pseudomonas, Stenotrophomonas, Bacillus, Alicaligenes, and Achromobacter. The efficacy of four (4) strains was further investigated using Gas Chromatography-Mass Spectrometry (GC-MS) analysis. The results showed that all four strains significantly degraded chlorpyrifos in Minimum Salt Medium (MSM): Lysinibacillus sp.HBUM206408 (87.16 %), Stenotrophomonas maltophilia (82.04 %), Pseudomonas putida (89.52 %), and Achromobacter insuavis (91.08 %) within 16 days, producing 2-Hydroxy-3, 5, 6-trichloropyridine (TCP) as the main metabolite. Therefore, these strains can be used to degrade chlorpyrifos in contaminated soil. There is a need for further studies to determine the possible mechanisms and other metabolites of chlorpyrifos degradation by the isolates obtained in the study. Besides, future studies should explore the efficacy and survival of the organisms in the contaminated environment.
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Affiliation(s)
- Micah Nyabiba Asamba
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Ezekiel Njeru Mugendi
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Paul Sifuna Oshule
- Department of Medical Biochemistry, Mount Kenya University, Thika, Kenya
| | - Suliman Essuman
- Department of Medical Microbiology, Mount Kenya University, Thika, Kenya
| | - Lenny Mwagandi Chimbevo
- Department Pure and Applied Sciences, School of Applied and Health Sciences, Technical University of Mombasa, Mombasa, Kenya
| | - Norbert Adum Atego
- Department Pure and Applied Sciences, School of Applied and Health Sciences, Technical University of Mombasa, Mombasa, Kenya
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Chen XX, Chen W, Liu YL, Lin CX, Li M, Chen WJ, Xie SH, Lin DF, Cao SM. Development and validation of a flexible DNA extraction (PAN) method for liquid biopsy of multiple sample types. J Clin Lab Anal 2021; 35:e23962. [PMID: 34399000 PMCID: PMC8418477 DOI: 10.1002/jcla.23962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/07/2021] [Accepted: 08/03/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Liquid biopsy is gaining increasing popularity in cancer screening and diagnosis. However, there is no relatively mature DNA isolation method or commercial kit available that is compatible with different LB sample types. This study developed a PAN-sample DNA isolation method (PAN method) for liquid biopsy samples. METHODS The PAN method has two key steps, including biosample-specific pretreatments for various LB sample types and high concentration guanidine thiocyanate buffer for lysis and denaturation procedure. Subsequently, the performance of PAN method was validated by a series of molecular analyses. RESULTS The PAN method was used to isolate DNA from multiple sample types related to LB, including plasma, serum, saliva, nasopharyngeal swab, and stool. All purified DNA products showed good quality and high quantity. Comparison of KRAS mutation analysis using DNA purified using PAN method versus QIAamp methods showed similar efficiency. Epstein-Barr virus DNA was detected via Q-PCR using DNA purified from serum, plasma, nasopharyngeal swab, and saliva samples collected from nasopharyngeal carcinoma patients. Similarly, methylation sequencing of swab and saliva samples revealed good coverage of target region and high methylation of HLA-DPB1 gene. Finally, 16S rDNA gene sequencing of saliva, swab, and stool samples successfully defines the relative abundance of microbial communities. CONCLUSIONS This study developed and validated a PAN-sample DNA isolation method that can be used for different LB samples, which can be applied to molecular epidemiological research and other areas.
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Affiliation(s)
- Xiao-Xia Chen
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Chen
- Department of Pathology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yi-Long Liu
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Can-Xiang Lin
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Mengmeng Li
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen-Jie Chen
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shang-Hang Xie
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, and Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dong-Feng Lin
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Su-Mei Cao
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, and Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
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Real-time Assessment of the Development and Function of the Placenta Across Gestation to Support Therapeutics in Pregnancy. Clin Ther 2020; 43:279-286. [PMID: 33246660 DOI: 10.1016/j.clinthera.2020.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022]
Abstract
The placenta is vital to the health and development of the fetus, serving to deliver oxygen and nutrients, facilitate the removal of waste products, and provide a barrier to pathogens and other harmful substances present in the maternal circulation. When these processes fail to operate normally, they can lead to complications of pregnancy such as preeclampsia or fetal growth restriction. The development of novel therapeutics for the mother, fetus, or placenta requires a mechanistic understanding of the development and functions of the placenta. For the obstetric clinician, being able to monitor the placenta throughout the pregnancy and to measure the impact of any treatment modality on the mother and the developing fetus are essential for providing the best possible care. The Eunice Kennedy Shriver National Institute of Child Health and Human Development at the National Institutes of Health has been a longtime supporter of research on the placenta. In 2014, the Human Placenta Project was initiated to help to drive an understanding of the biology of the human placenta and to facilitate the development of novel tools and approaches to allow for safe, noninvasive, real-time assessment of the placenta across pregnancy. Those efforts, along with others from around the globe, are showing promise. Although not yet ready for clinical application, these advances are moving the field forward and are certain to have a tremendous impact on the development and assessment of therapeutics designed for treating conditions of pregnancy.
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