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Chang L, Wang D, Peng C, Wang Q, Xu B, Tong Z. A method for high-concentration agarose gel preparation and its application in high-resolution separation of low-molecular-weight nucleic acids and proteins. Int J Biol Macromol 2023; 231:123358. [PMID: 36693602 DOI: 10.1016/j.ijbiomac.2023.123358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
Separation of nucleic acids and proteins using gels has always been a crucial part of molecular biology research. For low-molecular-weight nucleic acids and proteins, low- and medium-concentration agarose gels cannot achieve the high resolution as polyacrylamide gels. We found that 6 %-14 % high-concentration agarose gels (HAGs) could be easily dissolved in an autoclave and the vertical gel cast can be effortlessly filled using an easy-made plastic box. Coupled with the improved buffer condition, HAG electrophoresis resulted in a good resolution of DNA and protein bands. With conventional TBE buffer plus 0.2 % NaCl, DNA fragments that differ by 2-5-bp within the 50-200-bp size range can be resolved on 6 %-8 % HAGs. By using TBE without NaCl, DNA fragments that differ by 2-bp or 2-nt within the 10-100-bp size range can be well resolved on >8 % HAGs. Using a buffer system comprising 1 M Tris-Cl for gel preparation, 0.2 M Tris-Cl/0.2 % SDS as upper tank buffer, and 0.2 M Tris-Cl as the lower tank buffer, HAGs achieved good molecular weight separation of total bacterial and plant proteins in the 10-200 kDa range. In conclusion, we developed a method for HAG preparation and electrophoresis of low-molecular-weight nucleic acids and proteins.
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Affiliation(s)
- Lili Chang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Dan Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Cunzhi Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Qi Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Bingqiang Xu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
| | - Zheng Tong
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China.
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Kanapeckaitė A, Burokienė N, Mažeikienė A, Cottrell GS, Widera D. Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies. BIOPHYSICAL REPORTS 2021; 1:100028. [PMID: 36425454 PMCID: PMC9680810 DOI: 10.1016/j.bpr.2021.100028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/24/2021] [Indexed: 06/16/2023]
Abstract
Epigenetic research holds great promise to advance our understanding of biomarkers and regulatory processes in health and disease. An increasing number of new approaches, ranging from molecular to biophysical analyses, enable identifying epigenetic changes on the level of a single gene or the whole epigenome. The aim of this review is to highlight how the field is shifting from completely molecular-biology-driven solutions to multidisciplinary strategies including more reliance on biophysical analysis tools. Biophysics not only offers technical advancements in imaging or structure analysis but also helps to explore regulatory interactions. New computational methods are also being developed to meet the demand of growing data volumes and their processing. Therefore, it is important to capture these new directions in epigenetics from a biophysical perspective and discuss current challenges as well as multiple applications of biophysical methods and tools. Specifically, we gradually introduce different biophysical research methods by first considering the DNA-level information and eventually higher-order chromatin structures. Moreover, we aim to highlight that the incorporation of bioinformatics, machine learning, and artificial intelligence into biophysical analysis allows gaining new insights into complex epigenetic processes. The gained understanding has already proven useful in translational and clinical research providing better patient stratification options or new therapeutic insights. Together, this offers a better readiness to transform bench-top experiments into industrial high-throughput applications with a possibility to employ developed methods in clinical practice and diagnostics.
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Affiliation(s)
- Austė Kanapeckaitė
- Algorithm379, Laisvės g. 7, LT 12007, Vilnius, Lithuania
- Reading School of Pharmacy, Whiteknights, Reading, UK, RG6 6UB
| | - Neringa Burokienė
- Clinics of Internal Diseases, Family Medicine and Oncology, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio str. 21/27, LT-03101 Vilnius, Lithuania
| | - Asta Mažeikienė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, M. K. Čiurlionio str. 21/27, LT-03101 Vilnius, Lithuania
| | | | - Darius Widera
- Reading School of Pharmacy, Whiteknights, Reading, UK, RG6 6UB
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Gurbanov R, Tunçer S, Mingu S, Severcan F, Gozen AG. Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 198:111580. [DOI: 10.1016/j.jphotobiol.2019.111580] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 07/07/2019] [Accepted: 07/29/2019] [Indexed: 01/27/2023]
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4
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Pan S, Bruford MW, Wang Y, Lin Z, Gu Z, Hou X, Deng X, Dixon A, Graves JAM, Zhan X. Transcription-Associated Mutation Promotes RNA Complexity in Highly Expressed Genes-A Major New Source of Selectable Variation. Mol Biol Evol 2018; 35:1104-1119. [PMID: 29420738 PMCID: PMC5913671 DOI: 10.1093/molbev/msy017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Alternatively spliced transcript isoforms are thought to play a critical role for functional diversity. However, the mechanism generating the enormous diversity of spliced transcript isoforms remains unknown, and its biological significance remains unclear. We analyzed transcriptomes in saker falcons, chickens, and mice to show that alternative splicing occurs more frequently, yielding more isoforms, in highly expressed genes. We focused on hemoglobin in the falcon, the most abundantly expressed genes in blood, finding that alternative splicing produces 10-fold more isoforms than expected from the number of splice junctions in the genome. These isoforms were produced mainly by alternative use of de novo splice sites generated by transcription-associated mutation (TAM), not by the RNA editing mechanism normally invoked. We found that high expression of globin genes increases mutation frequencies during transcription, especially on nontranscribed DNA strands. After DNA replication, transcribed strands inherit these somatic mutations, creating de novo splice sites, and generating multiple distinct isoforms in the cell clone. Bisulfate sequencing revealed that DNA methylation may counteract this process by suppressing TAM, suggesting DNA methylation can spatially regulate RNA complexity. RNA profiling showed that falcons living on the high Qinghai-Tibetan Plateau possess greater global gene expression levels and higher diversity of mean to high abundance isoforms (reads per kilobases per million mapped reads ≥18) than their low-altitude counterparts, and we speculate that this may enhance their oxygen transport capacity under low-oxygen environments. Thus, TAM-induced RNA diversity may be physiologically significant, providing an alternative strategy in lifestyle evolution.
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Affiliation(s)
- Shengkai Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Michael W Bruford
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,Organisms and Environment Division, School of Biosciences and Sustainable Place Institute, Cardiff University, Cardiff, United Kingdom
| | - Yusong Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhenzhen Lin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China
| | - Zhongru Gu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xian Hou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xuemei Deng
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding, and Reproduction of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Andrew Dixon
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,Emirates Falconers' Club, Abu Dhabi, UAE
| | | | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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5
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Dahlhaus R. Of Men and Mice: Modeling the Fragile X Syndrome. Front Mol Neurosci 2018; 11:41. [PMID: 29599705 PMCID: PMC5862809 DOI: 10.3389/fnmol.2018.00041] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/31/2018] [Indexed: 12/26/2022] Open
Abstract
The Fragile X Syndrome (FXS) is one of the most common forms of inherited intellectual disability in all human societies. Caused by the transcriptional silencing of a single gene, the fragile x mental retardation gene FMR1, FXS is characterized by a variety of symptoms, which range from mental disabilities to autism and epilepsy. More than 20 years ago, a first animal model was described, the Fmr1 knock-out mouse. Several other models have been developed since then, including conditional knock-out mice, knock-out rats, a zebrafish and a drosophila model. Using these model systems, various targets for potential pharmaceutical treatments have been identified and many treatments have been shown to be efficient in preclinical studies. However, all attempts to turn these findings into a therapy for patients have failed thus far. In this review, I will discuss underlying difficulties and address potential alternatives for our future research.
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Affiliation(s)
- Regina Dahlhaus
- Institute for Biochemistry, Emil-Fischer Centre, University of Erlangen-Nürnberg, Erlangen, Germany
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6
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Jacobi CLJ, Stein C. Inflammatory-linked changes in CpG island methylation of three opioid peptide genes in a rat model for pain. PLoS One 2018; 13:e0191698. [PMID: 29352321 PMCID: PMC5774833 DOI: 10.1371/journal.pone.0191698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/09/2018] [Indexed: 11/19/2022] Open
Abstract
Expression of the opioid peptide genes proopiomelanocortin (Pomc), proenkephalin (Penk), and prodynorphin (Pdyn), in immune cells plays a key role in endogenous pain control. In a rat model of painful unilateral paw inflammation, we isolated cells from popliteal lymph nodes and evaluated the role of CpG island C5-methylation on the transcriptional activation of those genes. Using methylated DNA immunoprecipitation, we sorted gDNA into methylated (me) and non-me fractions and then determined the CpG island methylation status of each fraction via quantitative Real Time-PCR (qRT-PCR). In silico analysis by MethPrimer software identified one CpG island in Pdyn and three each in Pomc and Penk. No substantial changes in C5-methylation of any gene were observed. In conclusion, the CpG island methylation status does not seem to be a key regulator of opioid gene activation in immune cells during peripheral tissue inflammation.
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Affiliation(s)
- Charlotte Louise Justine Jacobi
- Klinik für Anästhesiologie und operative Intensivmedizin, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- * E-mail:
| | - Christoph Stein
- Klinik für Anästhesiologie und operative Intensivmedizin, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Chalmers G, Glushka JN, Foley BL, Woods RJ, Prestegard JH. Direct NOE simulation from long MD trajectories. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 265:1-9. [PMID: 26826977 PMCID: PMC4818662 DOI: 10.1016/j.jmr.2016.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/10/2016] [Accepted: 01/12/2016] [Indexed: 05/08/2023]
Abstract
A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected.
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Affiliation(s)
- G Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - J N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - B L Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - R J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - J H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States.
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