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Díez Pérez T, Tafoya AN, Peabody DS, Lakin MR, Hurwitz I, Carroll NJ, López GP. Isolation of nucleic acids using liquid-liquid phase separation of pH-sensitive elastin-like polypeptides. Sci Rep 2024; 14:10157. [PMID: 38698072 PMCID: PMC11065875 DOI: 10.1038/s41598-024-60648-9] [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: 07/25/2023] [Accepted: 04/25/2024] [Indexed: 05/05/2024] Open
Abstract
Extraction of nucleic acids (NAs) is critical for many methods in molecular biology and bioanalytical chemistry. NA extraction has been extensively studied and optimized for a wide range of applications and its importance to society has significantly increased. The COVID-19 pandemic highlighted the importance of early and efficient NA testing, for which NA extraction is a critical analytical step prior to the detection by methods like polymerase chain reaction. This study explores simple, new approaches to extraction using engineered smart nanomaterials, namely NA-binding, intrinsically disordered proteins (IDPs), that undergo triggered liquid-liquid phase separation (LLPS). Two types of NA-binding IDPs are studied, both based on genetically engineered elastin-like polypeptides (ELPs), model IDPs that exhibit a lower critical solution temperature in water and can be designed to exhibit LLPS at desired temperatures in a variety of biological solutions. We show that ELP fusion proteins with natural NA-binding domains can be used to extract DNA and RNA from physiologically relevant solutions. We further show that LLPS of pH responsive ELPs that incorporate histidine in their sequences can be used for both binding, extraction and release of NAs from biological solutions, and can be used to detect SARS-CoV-2 RNA in samples from COVID-positive patients.
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Affiliation(s)
- Telmo Díez Pérez
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ashley N Tafoya
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - David S Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Matthew R Lakin
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Computer Science, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ivy Hurwitz
- Department of Internal Medicine, Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Nick J Carroll
- Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Gabriel P López
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA.
- Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, NM, 87131, USA.
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA.
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2
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Wang Y, Xiong Y, Shi K, Effah CY, Song L, He L, Liu J. DNA nanostructures for exploring cell-cell communication. Chem Soc Rev 2024; 53:4020-4044. [PMID: 38444346 DOI: 10.1039/d3cs00944k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The process of coordinating between the same or multiple types of cells to jointly execute various instructions in a controlled and carefully regulated environment is a very appealing field. In order to provide clearer insight into the role of cell-cell interactions and the cellular communication of this process in their local communities, several interdisciplinary approaches have been employed to enhance the core understanding of this phenomenon. DNA nanostructures have emerged in recent years as one of the most promising tools in exploring cell-cell communication and interactions due to their programmability and addressability. Herein, this review is dedicated to offering a new perspective on using DNA nanostructures to explore the progress of cell-cell communication. After briefly outlining the anchoring strategy of DNA nanostructures on cell membranes and the subsequent dynamic regulation of DNA nanostructures, this paper highlights the significant contribution of DNA nanostructures in monitoring cell-cell communication and regulating its interactions. Finally, we provide a quick overview of the current challenges and potential directions for the application of DNA nanostructures in cellular communication and interactions.
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Affiliation(s)
- Ya Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Yamin Xiong
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kangqi Shi
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Clement Yaw Effah
- The First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou 450003, China
| | - Lulu Song
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Leiliang He
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China.
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3
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Nienaber-Rousseau C. Understanding and applying gene-environment interactions: a guide for nutrition professionals with an emphasis on integration in African research settings. Nutr Rev 2024:nuae015. [PMID: 38442341 DOI: 10.1093/nutrit/nuae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Noncommunicable diseases (NCDs) are influenced by the interplay between genetics and environmental exposures, particularly diet. However, many healthcare professionals, including nutritionists and dietitians, have limited genetic background and, therefore, they may lack understanding of gene-environment interactions (GxEs) studies. Even researchers deeply involved in nutrition studies, but with a focus elsewhere, can struggle to interpret, evaluate, and conduct GxE studies. There is an urgent need to study African populations that bear a heavy burden of NCDs, demonstrate unique genetic variability, and have cultural practices resulting in distinctive environmental exposures compared with Europeans or Americans, who are studied more. Although diverse and rapidly changing environments, as well as the high genetic variability of Africans and difference in linkage disequilibrium (ie, certain gene variants are inherited together more often than expected by chance), provide unparalleled potential to investigate the omics fields, only a small percentage of studies come from Africa. Furthermore, research evidence lags behind the practices of companies offering genetic testing for personalized medicine and nutrition. We need to generate more evidence on GxEs that also considers continental African populations to be able to prevent unethical practices and enable tailored treatments. This review aims to introduce nutrition professionals to genetics terms and valid methods to investigate GxEs and their challenges, and proposes ways to improve quality and reproducibility. The review also provides insight into the potential contributions of nutrigenetics and nutrigenomics to the healthcare sphere, addresses direct-to-consumer genetic testing, and concludes by offering insights into the field's future, including advanced technologies like artificial intelligence and machine learning.
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Affiliation(s)
- Cornelie Nienaber-Rousseau
- Centre of Excellence for Nutrition, North-West University, Potchefstroom, South Africa
- SAMRC Extramural Unit for Hypertension and Cardiovascular Disease, Faculty of Health Sciences, North-West University, Potchefstroom, South Africa
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4
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Pietruszka M, Marzec M. Proton-polarized states in DNA. Biosystems 2024; 237:105125. [PMID: 38331379 DOI: 10.1016/j.biosystems.2024.105125] [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: 12/08/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
We observed signatures of a phase transition in the double-stranded DNA fragment of known length and sequences using a non-invasive semiconductor-electrolyte interface technique and statistical physics methods. Observations revealed a coherence peak in the electromotive force and a significant decline in calculated dynamic entropy at a critical temperature and pH. This behavior may arise from the dynamic interaction of proton (H+) pairs with opposite momentum and spin, carrying a charge q=2+ under critical conditions.
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Affiliation(s)
- Mariusz Pietruszka
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology, and Environmental Protection, 40-032 Katowice, Poland.
| | - Marek Marzec
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology, and Environmental Protection, 40-032 Katowice, Poland
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5
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Lynch A, Bradford S, Burkard ME. The reckoning of chromosomal instability: past, present, future. Chromosome Res 2024; 32:2. [PMID: 38367036 DOI: 10.1007/s10577-024-09746-y] [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: 01/11/2024] [Revised: 01/11/2024] [Accepted: 01/27/2024] [Indexed: 02/19/2024]
Abstract
Quantitative measures of CIN are crucial to our understanding of its role in cancer. Technological advances have changed the way CIN is quantified, offering increased accuracy and insight. Here, we review measures of CIN through its rise as a field, discuss considerations for its measurement, and look forward to future quantification of CIN.
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Affiliation(s)
- Andrew Lynch
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Shermineh Bradford
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Mark E Burkard
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA.
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA.
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA.
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6
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Xu Y, Liang X, Hyun CG. Isolation, Characterization, Genome Annotation, and Evaluation of Tyrosinase Inhibitory Activity in Secondary Metabolites of Paenibacillus sp. JNUCC32: A Comprehensive Analysis through Molecular Docking and Molecular Dynamics Simulation. Int J Mol Sci 2024; 25:2213. [PMID: 38396889 PMCID: PMC10889091 DOI: 10.3390/ijms25042213] [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: 01/12/2024] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
A potential strain, Paenibacillus sp. JNUCC32, was isolated and subjected to whole-genome sequencing. Genome functional annotation revealed its active metabolic capabilities. This study aimed to investigate the pivotal secondary metabolites in the biological system. Fermentation and extraction were performed, resulting in the isolation of seven known compounds: tryptophol (1), 3-(4-hydroxyphenyl)propionic acid (2), ferulic acid (3), maculosin (4), brevianamide F (5), indole-3-acetic acid (6), and butyric acid (7). Tryptophol exhibited favorable pharmacokinetic properties and demonstrated certain tyrosinase inhibitory activity (IC50 = 999 μM). For further analysis of its inhibition mechanism through molecular docking and molecular dynamics (MD) simulation, tryptophol formed three hydrogen bonds and a pro-Michaelis complex with tyrosinase (binding energy = -5.3 kcal/mol). The MD simulation indicated favorable stability for the tryptophol-mushroom tyrosinase complex, primarily governed by hydrogen bond interactions. The crucial residues VAL-283 and HIS-263 in the docking were also validated. This study suggests tryptophol as a potential candidate for antibrowning agents and dermatological research.
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Affiliation(s)
| | | | - Chang-Gu Hyun
- Department of Beauty and Cosmetology, Jeju Inside Agency and Cosmetic Science Center, Jeju National University, Jeju 63243, Republic of Korea; (Y.X.); (X.L.)
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7
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Arunkumar G. LncRNAs: the good, the bad, and the unknown. Biochem Cell Biol 2024; 102:9-27. [PMID: 37579511 DOI: 10.1139/bcb-2023-0155] [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] [Indexed: 08/16/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are significant contributors in maintaining genomic integrity through epigenetic regulation. LncRNAs can interact with chromatin-modifying complexes in both cis and trans pathways, drawing them to specific genomic loci and influencing gene expression via DNA methylation, histone modifications, and chromatin remodeling. They can also operate as building blocks to assemble different chromatin-modifying components, facilitating their interactions and gene regulatory functions. Deregulation of these molecules has been associated with various human diseases, including cancer, cardiovascular disease, and neurological disorders. Thus, lncRNAs are implicated as potential diagnostic indicators and therapeutic targets. This review discusses the current understanding of how lncRNAs mediate epigenetic control, genomic integrity, and their putative functions in disease pathogenesis.
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Affiliation(s)
- Ganesan Arunkumar
- The LncRNA, Epigenetics, and Genome Organization Laboratory, Department of Cell Biology and Physiology, School of Medicine, University of New Mexico, Albuquerque, NM, USA
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8
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Sial MU, Farooq T, Khalaf LK, Rahman S, Asad M, Ahamad Paray B. Two-step method for rapid isolation of genomic DNA and validation of R81T insecticide resistance mutation in Myzus persicae. Saudi J Biol Sci 2023; 30:103791. [PMID: 37711971 PMCID: PMC10497781 DOI: 10.1016/j.sjbs.2023.103791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 09/16/2023] Open
Abstract
Isolation and amplification of nucleic acid (DNA) is considered a vital and potent instrument in molecular biological research. However, its functioning outside of a laboratory setting is difficult because of complex procedures that demand expert personnel and expensive equipment in addition to the fulfillment of several additional requirements. DNA isolation from minute insects is sometimes difficult, making diagnostic and genotyping procedures problematic. Thus, the current work offers a high-throughput, cost-effective, straightforward, and faster approach for isolating DNA from the aphid Myzus persicae. Intriguingly, two-step DNA extraction process yielded a high yield of extremely pure genomic DNA and required only 10 s to complete. PCR investigation aiming at amplifying the non-synonymous R81T region on the loop D site of the nAChR gene of M. persicae was subsequently utilized to successfully validate the recovered DNA. Moreover, the proposed method was compared in terms of yield and purity with conventionally used DNA isolation methods including, phenol:chloroform, salt out, and commercially available kits. In conclusion, this newly developed method would enable researchers to quickly process many biological samples used to analyze genetic diversity, mutant screening, and large spectrum diagnosis both in laboratory and field conditions.
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Affiliation(s)
- Muhammad Umair Sial
- Department of Entomology, University of Agriculture, Faisalabad 38000, Pakistan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Tahir Farooq
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Luaay Kahtan Khalaf
- Department of Plant Protection, College of Agricultural Engineering Science, University of Baghdad, Baghdad, Iraq
| | - Saqib Rahman
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Muhammad Asad
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Bilal Ahamad Paray
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
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9
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Ranasinghe P, Addison ML, Dear JW, Webb DJ. Small interfering RNA: Discovery, pharmacology and clinical development-An introductory review. Br J Pharmacol 2023; 180:2697-2720. [PMID: 36250252 DOI: 10.1111/bph.15972] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/23/2022] [Accepted: 09/29/2022] [Indexed: 11/28/2022] Open
Abstract
Post-transcriptional gene silencing targets and degrades mRNA transcripts, silencing the expression of specific genes. RNA interference technology, using synthetic structurally well-defined short double-stranded RNA (small interfering RNA [siRNA]), has advanced rapidly in recent years. This introductory review describes the utility of siRNA, by exploring the underpinning biology, pharmacology, recent advances and clinical developments, alongside potential limitations and ongoing challenges. Mediated by the RNA-induced silencing complex, siRNAs bind to specific complementary mRNAs, which are subsequently degraded. siRNA therapy offers advantages over other therapeutic approaches, including ability of specifically designed siRNAs to potentially target any mRNA and improved patient adherence through infrequent administration associated with a very long duration of action. Key pharmacokinetic and pharmacodynamic challenges include targeted administration, poor tissue penetration, nuclease inactivation, rapid renal elimination, immune activation and off-target effects. These have been overcome by chemical modification of siRNA and/or by utilising a range of delivery systems, increasing bioavailability and stability to allow successful clinical translation. Patisiran (hereditary transthyretin-mediated amyloidosis) was the first licensed siRNA, followed by givosiran (acute hepatic porphyria), lumasiran (primary hyperoxaluria type 1) and inclisiran (familial hypercholesterolaemia), which all use N-acetylgalactosamine (GalNAc) linkage for effective liver-directed delivery. Others are currently under development for indications varying from rare genetic diseases to common chronic non-communicable diseases (hypertension, cancer). Technological advances are paving the way for broader clinical use. Ongoing challenges remain in targeting organs beyond the liver and reaching special sites (e.g., brain). By overcoming these barriers, siRNA therapy has the potential to substantially widen its therapeutic impact.
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Affiliation(s)
- Priyanga Ranasinghe
- Department of Pharmacology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - Melisande L Addison
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - James W Dear
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - David J Webb
- University/British Heart Foundation Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
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10
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Kaunitz JD, Bejjani A. Very Unstable Genetics: How the Confluence of Microsatellite Instability and Immunotherapy Revolutionized the Treatment of Colon Cancer. Dig Dis Sci 2023; 68:3494-3503. [PMID: 37402981 DOI: 10.1007/s10620-023-08007-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 07/06/2023]
Affiliation(s)
- Jonathan D Kaunitz
- Medical Service, Section of Gastroenterology, Greater Los Angeles VAMC, Los Angeles, CA, USA.
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
| | - Anthony Bejjani
- Medical Service, Section of Hematology Oncology, Greater Los Angeles VAMC, Los Angeles, CA, USA
- Division of Hematology-Oncology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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11
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de la Iglesia A, Jodar M, Oliva R, Castillo J. Insights into the sperm chromatin and implications for male infertility from a protein perspective. WIREs Mech Dis 2023; 15:e1588. [PMID: 36181449 DOI: 10.1002/wsbm.1588] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022]
Abstract
Male germ cells undergo an extreme but fascinating process of chromatin remodeling that begins in the testis during the last phase of spermatogenesis and continues through epididymal sperm maturation. Most of the histones are replaced by small proteins named protamines, whose high basicity leads to a tight genomic compaction. This process is epigenetically regulated at many levels, not only by posttranslational modifications, but also by readers, writers, and erasers, in a context of a highly coordinated postmeiotic gene expression program. Protamines are key proteins for acquiring this highly specialized chromatin conformation, needed for sperm functionality. Interestingly, and contrary to what could be inferred from its very specific DNA-packaging function across protamine-containing species, human sperm chromatin contains a wide spectrum of protamine proteoforms, including truncated and posttranslationally modified proteoforms. The generation of protamine knock-out models revealed not only chromatin compaction defects, but also collateral sperm alterations contributing to infertile phenotypes, evidencing the importance of sperm chromatin protamination toward the generation of a new individual. The unique features of sperm chromatin have motivated its study, applying from conventional to the most ground-breaking techniques to disentangle its peculiarities and the cellular mechanisms governing its successful conferment, especially relevant from the protein point of view due to the important epigenetic role of sperm nuclear proteins. Gathering and contextualizing the most striking discoveries will provide a global understanding of the importance and complexity of achieving a proper chromatin compaction and exploring its implications on postfertilization events and beyond. This article is categorized under: Reproductive System Diseases > Genetics/Genomics/Epigenetics Reproductive System Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Alberto de la Iglesia
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain
| | - Meritxell Jodar
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain.,Biochemistry and Molecular Genetics Service, Hospital Clinic, Barcelona, Spain
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain.,Biochemistry and Molecular Genetics Service, Hospital Clinic, Barcelona, Spain
| | - Judit Castillo
- Molecular Biology of Reproduction and Development Research Group, Fundació Clínic per a la Recerca Biomèdica, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Barcelona, Spain
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12
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Wang R, Wang X, Xie S, Zhang Y, Ji D, Zhang X, Cui C, Jiang J, Tan W. Molecular elements: novel approaches for molecular building. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220024. [PMID: 36633277 PMCID: PMC9835600 DOI: 10.1098/rstb.2022.0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Ruowen Wang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Xueqiang Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Sitao Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Yanyan Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Dingkun Ji
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
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Karlsson J, Eichner H, Loh E. Total Bacterial RNA Isolation and Northern Blotting Analysis. Methods Mol Biol 2023; 2674:73-85. [PMID: 37258961 DOI: 10.1007/978-1-0716-3243-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The study of bacterial gene expression during infection provides vital information for researchers to understand bacterial pathogenesis and infection. The ability to obtain clean and undegraded RNA could be challenging and daunting and remains the most crucial experimental step prior to downstream analyses, such as Northern blotting, quantitative PCR (qPCR), and RNA-seq.This chapter describe two methods (acid guanidinium thiocyanate (TRIzol) phenol-chloroform and hot phenol) commonly used to isolate total bacterial RNA and are suitable for both Gram-positive and Gram-negative bacteria. Procedures such as RNA quantification and DNase treatment are also included to ensure amount and quality of the RNA samples. The second part of the chapter includes a method used to analyze bacterial gene expression (Northern blotting), two methods to generate radioactive probes, as well as target detection using a phosphorimager.
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Affiliation(s)
- Jens Karlsson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
- Clinical Microbiology, Karolinska University Hospital, Solna, Sweden.
| | - Hannes Eichner
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- Clinical Microbiology, Karolinska University Hospital, Solna, Sweden
- Department of Microbiology, New York University, New York, NY, USA
| | - Edmund Loh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
- Clinical Microbiology, Karolinska University Hospital, Solna, Sweden.
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
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14
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Onur S, Çeşme M, Köse M, Tümer F. New imino-methoxy derivatives: design, synthesis, characterization, antimicrobial activity, DNA interaction and molecular docking studies. J Biomol Struct Dyn 2022; 40:11082-11094. [PMID: 34355663 DOI: 10.1080/07391102.2021.1955741] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Four new diarylmethylamine imine compounds (5a-5d) were prepared in order to examine their DNA binding properties, antimicrobial activity and molecular docking. The compounds were characterized by the common spectroscopic and analytic methods. Furthermore, solid-state structure of compounds 5a and 5c were determined by single-crystal X-ray diffraction studies. The compounds were then investigated for their DNA binding properties employing UV absorption, fluorescence spectroscopy under the physiological pH condition Tris-HCl buffer at pH 7.4. The compounds 5a-5d showed moderate binding constants with Kb values of 3.56 ± 0.3 × 104, 2.18 ± 0.2 × 105, 1.44 ± 0.3 × 105 and 2.56 ± 0.3 × 104 M-1, respectively. The molecular dockings were performed to investigate the ligand-DNA interactions. The in-silico DNA-compound interaction studies showed that the compounds interact with DNA in groove binding mode. Antimicrobial activity studies of imine compounds were tested against E. coli as bacteria, S. typhimurium, S. aureus, B. cereus, B. subtilis, and C. albicans as fungi. While all compounds show moderate activity against bacteria, no activity against fungi has been investigated.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sultan Onur
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaraş Sütçü İmam University, Kahramanmaraş, Turkey
| | - Mustafa Çeşme
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaraş Sütçü İmam University, Kahramanmaraş, Turkey
| | - Muhammet Köse
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaraş Sütçü İmam University, Kahramanmaraş, Turkey
| | - Ferhan Tümer
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaraş Sütçü İmam University, Kahramanmaraş, Turkey
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Zhang A, Kondhare D, Leonard P, Seela F. Purine–Purine Base Pairs in Parallel DNA: β-D Anomeric 8-Aza-7-deazaisoguanine and 7-Functionalized Conjugates Form Stable Base Pairs with α-D 5-Aza-7-deaza-2′-deoxyguanosine. Bioconjug Chem 2022; 33:1796-1802. [DOI: 10.1021/acs.bioconjchem.2c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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16
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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17
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Zuccarini M, Giuliani P, Ronci M, Caciagli F, Caruso V, Ciccarelli R, Di Iorio P. Purinergic Signaling in Oral Tissues. Int J Mol Sci 2022; 23:ijms23147790. [PMID: 35887132 PMCID: PMC9318746 DOI: 10.3390/ijms23147790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023] Open
Abstract
The role of the purinergic signal has been extensively investigated in many tissues and related organs, including the central and peripheral nervous systems as well as the gastrointestinal, cardiovascular, respiratory, renal, and immune systems. Less attention has been paid to the influence of purines in the oral cavity, which is the first part of the digestive apparatus and also acts as the body’s first antimicrobial barrier. In this review, evidence is provided of the presence and possible physiological role of the purinergic system in the different structures forming the oral cavity including teeth, tongue, hard palate, and soft palate with their annexes such as taste buds, salivary glands, and nervous fibers innervating the oral structures. We also report findings on the involvement of the purinergic signal in pathological conditions affecting the oral apparatus such as Sjögren’s syndrome or following irradiation for the treatment of head and neck cancer, and the use of experimental drugs interfering with the purine system to improve bone healing after damage. Further investigations are required to translate the results obtained so far into the clinical setting in order to pave the way for a wider application of purine-based treatments in oral diseases.
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Affiliation(s)
- Mariachiara Zuccarini
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti-Pescara, Via dei Vestini 29, 66100 Chieti, Italy; (M.Z.); (P.G.); (P.D.I.)
- Center for Advanced Studies and Technologies (CAST), University of Chieti-Pescara, Via L. Polacchi, 66100 Chieti, Italy; (M.R.); (F.C.)
| | - Patricia Giuliani
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti-Pescara, Via dei Vestini 29, 66100 Chieti, Italy; (M.Z.); (P.G.); (P.D.I.)
- Center for Advanced Studies and Technologies (CAST), University of Chieti-Pescara, Via L. Polacchi, 66100 Chieti, Italy; (M.R.); (F.C.)
| | - Maurizio Ronci
- Center for Advanced Studies and Technologies (CAST), University of Chieti-Pescara, Via L. Polacchi, 66100 Chieti, Italy; (M.R.); (F.C.)
- Department of Pharmacy, University of Chieti-Pescara, Via dei Vestini 29, 66100 Chieti, Italy
| | - Francesco Caciagli
- Center for Advanced Studies and Technologies (CAST), University of Chieti-Pescara, Via L. Polacchi, 66100 Chieti, Italy; (M.R.); (F.C.)
| | - Vanni Caruso
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart, TAS 7005, Australia;
| | - Renata Ciccarelli
- Center for Advanced Studies and Technologies (CAST), University of Chieti-Pescara, Via L. Polacchi, 66100 Chieti, Italy; (M.R.); (F.C.)
- Stem TeCh Group, Via L. Polacchi, 66100 Chieti, Italy
- Correspondence:
| | - Patrizia Di Iorio
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti-Pescara, Via dei Vestini 29, 66100 Chieti, Italy; (M.Z.); (P.G.); (P.D.I.)
- Center for Advanced Studies and Technologies (CAST), University of Chieti-Pescara, Via L. Polacchi, 66100 Chieti, Italy; (M.R.); (F.C.)
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18
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Benga G, Cox G. Light and Scanning Electron Microscopy of Red Blood Cells From Humans and Animal Species Providing Insights into Molecular Cell Biology. Front Physiol 2022; 13:838071. [PMID: 35845990 PMCID: PMC9283769 DOI: 10.3389/fphys.2022.838071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
We reviewed the many discoveries in cell biology, made since the 17th century, which have been based on red blood cells (RBCs). The advances in molecular and structural biology in the past 40 years have enabled the discovery with these cells, most notably, of the first water channel protein (WCP) called today aquaporin1 (AQP1). The main aim of our work reviewed was to examine by light and electron microscopy a very wide range of RBCs from reptiles, birds, monotremes, marsupials and placentals, in order to estimate from these images the RBC cell volume and surface area. The diffusional water permeability of the RBC membrane from these species has further been measured with a nuclear magnetic resonance (NMR) spectroscopy technique. The significance of the observed permeability of RBCs to water and possible influences on the whole body are discussed.
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Affiliation(s)
- Gheorghe Benga
- Romanian Academy, Cluj-Napoca, Romania
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Darlington, NSW, Australia
- *Correspondence: Gheorghe Benga, ; Guy Cox,
| | - Guy Cox
- Australian Centre for Microscopy & Microanalysis, University of Sydney, Darlington, NSW, Australia
- *Correspondence: Gheorghe Benga, ; Guy Cox,
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19
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Budharaju H, Zennifer A, Sethuraman S, Paul A, Sundaramurthi D. Designer DNA biomolecules as a defined biomaterial for 3D bioprinting applications. MATERIALS HORIZONS 2022; 9:1141-1166. [PMID: 35006214 DOI: 10.1039/d1mh01632f] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA has excellent features such as the presence of functional and targeted molecular recognition motifs, tailorability, multifunctionality, high-precision molecular self-assembly, hydrophilicity, and outstanding biocompatibility. Due to these remarkable features, DNA has emerged as a leading next-generation biomaterial of choice to make hydrogels by self-assembly. In recent times, novel routes for the chemical synthesis of DNA, advances in tailorable designs, and affordable production ways have made DNA as a building block material for various applications. These advanced features have made researchers continuously explore the interesting properties of pure and hybrid DNA for 3D bioprinting and other biomedical applications. This review article highlights the topical advancements in the use of DNA as an ideal bioink for the bioprinting of cell-laden three-dimensional tissue constructs for regenerative medicine applications. Various bioprinting techniques and emerging design approaches such as self-assembly, nucleotide sequence, enzymes, and production cost to use DNA as a bioink for bioprinting applications are described. In addition, various types and properties of DNA hydrogels such as stimuli responsiveness and mechanical properties are discussed. Further, recent progress in the applications of DNA in 3D bioprinting are emphasized. Finally, the current challenges and future perspectives of DNA hydrogels in 3D bioprinting and other biomedical applications are discussed.
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Affiliation(s)
- Harshavardhan Budharaju
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613 401, Tamil Nadu, India.
| | - Allen Zennifer
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613 401, Tamil Nadu, India.
| | - Swaminathan Sethuraman
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613 401, Tamil Nadu, India.
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
- School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Dhakshinamoorthy Sundaramurthi
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613 401, Tamil Nadu, India.
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20
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Rekvig OP. The Anti-DNA Antibodies: Their Specificities for Unique DNA Structures and Their Unresolved Clinical Impact-A System Criticism and a Hypothesis. Front Immunol 2022; 12:808008. [PMID: 35087528 PMCID: PMC8786728 DOI: 10.3389/fimmu.2021.808008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is diagnosed and classified by criteria, or by experience, intuition and traditions, and not by scientifically well-defined etiology(ies) or pathogenicity(ies). One central criterion and diagnostic factor is founded on theoretical and analytical approaches based on our imperfect definition of the term “The anti-dsDNA antibody”. “The anti-dsDNA antibody” holds an archaic position in SLE as a unique classification criterium and pathogenic factor. In a wider sense, antibodies to unique transcriptionally active or silent DNA structures and chromatin components may have individual and profound nephritogenic impact although not considered yet – not in theoretical nor in descriptive or experimental contexts. This hypothesis is contemplated here. In this analysis, our state-of-the-art conception of these antibodies is probed and found too deficient with respect to their origin, structural DNA specificities and clinical/pathogenic impact. Discoveries of DNA structures and functions started with Miescher’s Nuclein (1871), via Chargaff, Franklin, Watson and Crick, and continues today. The discoveries have left us with a DNA helix that presents distinct structures expressing unique operations of DNA. All structures are proven immunogenic! Unique autoimmune antibodies are described against e.g. ssDNA, elongated B DNA, bent B DNA, Z DNA, cruciform DNA, or individual components of chromatin. In light of the massive scientific interest in anti-DNA antibodies over decades, it is an unexpected observation that the spectrum of DNA structures has been known for decades without being implemented in clinical immunology. This leads consequently to a critical analysis of historical and contemporary evidence-based data and of ignored and one-dimensional contexts and hypotheses: i.e. “one antibody - one disease”. In this study radical viewpoints on the impact of DNA and chromatin immunity/autoimmunity are considered and discussed in context of the pathogenesis of lupus nephritis.
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Affiliation(s)
- Ole Petter Rekvig
- Section of Autoimmunity, Fürst Medical Laboratory, Oslo, Norway.,Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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21
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Richardson MK, Keuck G. The revolutionary developmental biology of Wilhelm His, Sr. Biol Rev Camb Philos Soc 2022; 97:1131-1160. [PMID: 35106889 PMCID: PMC9304566 DOI: 10.1111/brv.12834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/21/2022]
Abstract
Swiss‐born embryologist Wilhelm His, Sr. (1831–1904) was the first scientist to study embryos using paraffin histology, serial sectioning and three‐dimensional modelling. With these techniques, His made many important discoveries in vertebrate embryology and developmental neurobiology, earning him two Nobel Prize nominations. He also developed several theories of mechanical and evolutionary developmental biology. His argued that adult form is determined by the differential growth of developmental primordia. Furthermore, he suggested that changes in the growth parameters of those primordia are responsible for generating new phenotypes during evolution. His developed these theories in his book ‘Our Bodily Form’ (Unsere Körperform). Here, we review His's work with special emphasis on its potential importance to the disciplines of evolutionary developmental biology (evo‐devo) and mechanobiology.
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Affiliation(s)
- Michael K Richardson
- Institute of Biology, University of Leiden, Sylvius Laboratory, Sylviusweg 72, Leiden, 2333 BE, The Netherlands
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23
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Zhou L, Hayden A, Chandrasekaran AR, Vilcapoma J, Cavaliere C, Dey P, Mao S, Sheng J, Dey BK, Rangan P, Halvorsen K. Sequence-selective purification of biological RNAs using DNA nanoswitches. CELL REPORTS METHODS 2021; 1:100126. [PMID: 35072148 PMCID: PMC8782281 DOI: 10.1016/j.crmeth.2021.100126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/07/2021] [Accepted: 11/12/2021] [Indexed: 12/24/2022]
Abstract
Nucleic acid purification is a critical aspect of biomedical research and a multibillion-dollar industry. Here we establish sequence-selective RNA capture, release, and isolation using conformationally responsive DNA nanoswitches. We validate purification of specific RNAs ranging in size from 22 to 401 nt with up to 75% recovery and 99.98% purity in a benchtop process with minimal expense and equipment. Our method compared favorably with bead-based extraction of an endogenous microRNA from cellular total RNA, and can be programmed for multiplexed purification of multiple individual RNA targets from one sample. Coupling our approach with downstream LC/MS, we analyzed RNA modifications in 5.8S ribosomal RNA, and found 2'-O-methylguanosine, 2'-O-methyluridine, and pseudouridine in a ratio of ~1:7:22. The simplicity, low cost, and low sample requirements of our method make it suitable for easy adoption, and the versatility of the approach provides opportunities to expand the strategy to other biomolecules.
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Affiliation(s)
- Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | | | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Cassandra Cavaliere
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Paromita Dey
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Song Mao
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Bijan K. Dey
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Prashanth Rangan
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
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24
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Sirtuin1 and Sirtuin3 gene polymorphisms and acute myocardial infarction susceptibility. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Thachil J. Protamine-The Journey from DNA to Heparin Neutralization to Gene therapy. Semin Thromb Hemost 2021; 48:240-243. [PMID: 34729729 DOI: 10.1055/s-0041-1736574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Protamine is now well recognized as a key heparin neutralizing agent. However, protamine was discovered over a century ago, during experiments performed to uncover the secrets behind heritability. Although protamine was discovered as a highly charged protein, it did not receive the attention it deserved until the dawn of insulin era, when it was used to create the neutral protamine Hagedorn formulation. Based on the same principles, protamine was identified to neutralize heparin and has since been used successfully for many years in cardiothoracic surgery. More recently, its clinical applications have extended to gene therapy. In this historical sketch, the journey from the discovery of protamine, onwards to heparin neutralization, and up to its utilization in genetic modulatory treatments is detailed.
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Affiliation(s)
- Jecko Thachil
- Department of Haematology, Manchester University Hospitals, Manchester, United Kingdom
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26
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Thess A, Hoerr I, Panah BY, Jung G, Dahm R. Historic nucleic acids isolated by Friedrich Miescher contain RNA besides DNA. Biol Chem 2021; 402:1179-1185. [PMID: 34523295 DOI: 10.1515/hsz-2021-0226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/22/2021] [Indexed: 11/15/2022]
Abstract
One hundred fifty years ago, Friedrich Miescher discovered DNA when he isolated "Nuclein"-as he named it-from nuclei of human pus cells. Miescher recognized his isolate as a new type of molecule equal in importance to proteins. He realised that it is an acid of large molecular weight and high phosphorus content. Subsequently, he discovered Nuclein also in the nuclei of other cell types, realised that it chemically defines the nucleus, and speculated on its role in proliferation, heredity and fertilisation. While now universally recognised as the discoverer of DNA, whether Miescher also discovered RNA has not yet been addressed. To determine whether his isolation also yielded RNA, we first reproduced his historic protocols. Our resulting modern Nuclein contained a significant percentage of RNA. Encouraged by this result, we then analysed a sample of Nuclein isolated by Miescher from salmon sperm. Assuming that the RNA present in this sample had degraded to nucleobases, we tested for the presence of uracil in the historic Nuclein. Detection of significant levels of uracil by LC-UV-MS demonstrates that Miescher isolated both forms of nucleic acid-DNA and RNA-and underlines the fundamental nature of his discovery for the field of molecular genetics.
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Affiliation(s)
- Andreas Thess
- CureVac AG, Friedrich-Miescher-Str. 15, D-72076 Tübingen, Germany
| | - Ingmar Hoerr
- CureVac AG, Friedrich-Miescher-Str. 15, D-72076 Tübingen, Germany
| | | | - Günther Jung
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Ralf Dahm
- Department of Biology, University of Padova, I-35131 Padua, Italy
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Alshaer W, Zureigat H, Al Karaki A, Al-Kadash A, Gharaibeh L, Hatmal MM, Aljabali AAA, Awidi A. siRNA: Mechanism of action, challenges, and therapeutic approaches. Eur J Pharmacol 2021; 905:174178. [PMID: 34044011 DOI: 10.1016/j.ejphar.2021.174178] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 11/19/2022]
Abstract
Owing to specific and compelling gene silencing, RNA interference (RNAi) is expected to become an essential approach in treating a variety of infectious, hemato-oncological, cardiovascular, and neurodegenerative conditions. The mechanism of action of small interfering RNA (siRNA) is based on post-transcriptional gene silencing. siRNA molecules are usually specific and efficient in the knockdown of disease-related genes. However, they are characterized by low cellular uptake and are susceptible to nuclease-mediated degradation. Therefore, siRNAs require a carrier for their protection and efficient delivery into target cells. The current review highlights the siRNA-based mechanism of action, challanges, and recent advances in clinical applications.
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Affiliation(s)
- Walhan Alshaer
- Cell Therapy Center, The University of Jordan, Amman, 11942, Jordan.
| | - Hadil Zureigat
- Faculty of Medicine, The University of Jordan, Amman, 11942, Jordan
| | - Arwa Al Karaki
- Faculty of Medicine, The University of Jordan, Amman, 11942, Jordan
| | | | - Lobna Gharaibeh
- Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, 19328, Jordan
| | - Ma'mon M Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, Zarqa 13133, Jordan
| | - Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman, 11942, Jordan; Faculty of Medicine, The University of Jordan, Amman, 11942, Jordan; Department of Hematology and Oncology, Jordan University Hospital, The University of Jordan, Amman, 11942, Jordan.
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28
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Abstract
Nanozymes have the potential to replace natural enzymes, so they are widely used in energy conversion technologies such as biosensors and signal transduction (converting biological signals of a target into optical, electrical, or metabolic signals). The participation of nucleic acids leads nanozymes to produce richer interface effects and gives energy conversion events more attractive characteristics, creating what are called “functional nanozymes”. Since different nanozymes have different internal structures and external morphological characteristics, functional modulation needs to be compatible with these properties, and attention needs to be paid to the influence of nucleic acids on nanozyme activity. In this review, “functional nanozymes” are divided into three categories, (nanozyme precursor ion)/ (nucleic acid) self-assembly, nanozyme-nucleic acid irreversible binding, and nanozyme-nucleic acid reversible binding, and the effects of nucleic acids on modulation principles are summarized. Then, the latest developments of nucleic acid-modulated nanozymes are reviewed in terms of their use in energy conversion technology, and their conversion mechanisms are critically discussed. Finally, we outline the advantages and limitations of “functional nanozymes” and discuss the future development prospects and challenges in this field.
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Abstract
Hypertrophic cardiomyopathy (HCM) is a genetic disease of the myocardium characterized by a hypertrophic left ventricle with a preserved or increased ejection fraction. Cardiac hypertrophy is often asymmetrical, which is associated with left ventricular outflow tract obstruction. Myocyte hypertrophy, disarray, and myocardial fibrosis constitute the histological features of HCM. HCM is a relatively benign disease but an important cause of sudden cardiac death in the young and heart failure in the elderly. Pathogenic variants (PVs) in genes encoding protein constituents of the sarcomeres are the main causes of HCM. PVs exhibit a gradient of effect sizes, as reflected in their penetrance and variable phenotypic expression of HCM. MYH7 and MYBPC3, encoding β-myosin heavy chain and myosin binding protein C, respectively, are the two most common causal genes and responsible for ≈40% of all HCM cases but a higher percentage of HCM in large families. PVs in genes encoding protein components of the thin filaments are responsible for ≈5% of the HCM cases. Whereas pathogenicity of the genetic variants in large families has been firmly established, ascertainment causality of the PVs in small families and sporadic cases is challenging. In the latter category, PVs are best considered as probabilistic determinants of HCM. Deciphering the genetic basis of HCM has enabled routine genetic testing and has partially elucidated the underpinning mechanism of HCM as increased number of the myosin molecules that are strongly bound to actin. The discoveries have led to the development of mavacamten that targets binding of the myosin molecule to actin filaments and imparts beneficial clinical effects. In the coming years, the yield of the genetic testing is expected to be improved and the so-called missing causal gene be identified. The advances are also expected to enable development of additional specific therapies and editing of the mutations in HCM.
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Affiliation(s)
- A J Marian
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine, University of Texas Health Sciences Center at Houston
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30
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Wang X, Zhao L, Wu X, Luo H, Wu D, Zhang M, Zhang J, Pakvasa M, Wagstaff W, He F, Mao Y, Zhang Y, Niu C, Wu M, Zhao X, Wang H, Huang L, Shi D, Liu Q, Ni N, Fu K, Hynes K, Strelzow J, El Dafrawy M, He TC, Qi H, Zeng Z. Development of a simplified and inexpensive RNA depletion method for plasmid DNA purification using size selection magnetic beads (SSMBs). Genes Dis 2021; 8:298-306. [PMID: 33997177 PMCID: PMC8093646 DOI: 10.1016/j.gendis.2020.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/03/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023] Open
Abstract
Plasmid DNA (pDNA) isolation from bacterial cells is one of the most common and critical steps in molecular cloning and biomedical research. Almost all pDNA purification involves disruption of bacteria, removal of membrane lipids, proteins and genomic DNA, purification of pDNA from bulk lysate, and concentration of pDNA for downstream applications. While many liquid-phase and solid-phase pDNA purification methods are used, the final pDNA preparations are usually contaminated with varied degrees of host RNA, which cannot be completely digested by RNase A. To develop a simple, cost-effective, and yet effective method for RNA depletion, we investigated whether commercially available size selection magnetic beads (SSMBs), such as Mag-Bind® TotalPure NGS Kit (or Mag-Bind), can completely deplete bacterial RNA in pDNA preparations. In this proof-of-principle study, we demonstrated that, compared with RNase A digestion and two commercial plasmid affinity purification kits, the SSMB method was highly efficient in depleting contaminating RNA from pDNA minipreps. Gene transfection and bacterial colony formation assays revealed that pDNA purified from SSMB method had superior quality and integrity to pDNA samples cleaned up by RNase A digestion and/or commercial plasmid purification kits. We further demonstrated that the SSMB method completely depleted contaminating RNA in large-scale pDNA samples. Furthermore, the Mag-bind-based SSMB method costs only 5-10% of most commercial plasmid purification kits on a per sample basis. Thus, the reported SSMB method can be a valuable and inexpensive tool for the removal of bacterial RNA for routine pDNA preparations.
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Affiliation(s)
- Xi Wang
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Ling Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Xiaoxing Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Huaxiu Luo
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan Province, 610041, PR China
| | - Di Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Meng Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510405, PR China
| | - Jing Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Mikhail Pakvasa
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - William Wagstaff
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Fang He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Yukun Mao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Orthopaedic Surgery and Neurosurgery, The Affiliated Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
| | - Yongtao Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, 266061, PR China
| | - Changchun Niu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Laboratory Diagnostic Medicine, Chongqing General Hospital, Chongqing, 400021, PR China
| | - Meng Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Institute of Bone and Joint Research, The departments of Orthopaedic Surgery and Obstetrics and Gynecology, The First and Second Hospitals of Lanzhou University, Lanzhou, Gansu Province, 730030, PR China
| | - Xia Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, 266061, PR China
| | - Hao Wang
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Linjuan Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Deyao Shi
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430022, PR China
| | - Qing Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Department of Spine Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan Province, 410011, PR China
| | - Na Ni
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Kai Fu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
- Departments of Orthopaedic Surgery and Neurosurgery, The Affiliated Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, 430072, PR China
| | - Kelly Hynes
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Jason Strelzow
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Mostafa El Dafrawy
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
| | - Hongbo Qi
- Departments of Gastrointestinal Surgery, Obstetrics and Gynecology, and Nephrology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Zongyue Zeng
- Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory and Diagnostic Medicine, Chongqing Medical University, Chongqing, 400016, PR China
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL, 60637, USA
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Abstract
The discovery of hemoglobin allosteric properties is briefly summarized and contextualized in the frame of the main biochemical revelations that characterized the first half of the XX century. In particular, the historical background of DNA, RNA, and protein structure research is recalled and the new role that protein-protein interaction may have on allosteric regulation is discussed.
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Hall K, Sankaran N. DNA translated: Friedrich Miescher's discovery of nuclein in its original context. BRITISH JOURNAL FOR THE HISTORY OF SCIENCE 2021; 54:99-107. [PMID: 33602346 DOI: 10.1017/s000708742000062x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In 1871, the Swiss physiological chemist Friedrich Miescher published the results of a detailed chemical analysis of pus cells, in which he showed that the nuclei of these cells contained a hitherto unknown phosphorus-rich chemical which he named 'nuclein' for its specific localisation. Published in German, 'Ueber Die Chemische Zusammensetzung Der Eiterzellen', [On the Chemical Composition of Pus Cells] Medicinisch-Chemische Untersuchungen (1871) 4: 441-60, was the first publication to describe DNA, and yet remains relatively obscure. We therefore undertook a translation of the paper into English, which, together with the original article, can be accessed via the following link https://doi.org/10.1017/S000708742000062X. In this paper, we offer some intellectual context for its publication and immediate reception.
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Zell J, Rota Sperti F, Britton S, Monchaud D. DNA folds threaten genetic stability and can be leveraged for chemotherapy. RSC Chem Biol 2021; 2:47-76. [PMID: 35340894 PMCID: PMC8885165 DOI: 10.1039/d0cb00151a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022] Open
Abstract
Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an anticancer target, and the manipulation of DDR pathways as a valuable anticancer strategy. We describe in detail the DDR signalling and repair pathways activated in response to DNA damage. We then summarise the current understanding of non-B DNA folds, such as G-quadruplexes and DNA junctions, when they are formed and why they can offer a more specific therapeutic target compared to that of canonical B-DNA. Finally, we merge these subjects to depict the new and highly promising chemotherapeutic strategy which combines enhanced-specificity DNA damaging and DDR targeting agents. This review thus highlights how chemical biology has given rise to significant scientific advances thanks to resolutely multidisciplinary research efforts combining molecular and cell biology, chemistry and biophysics. We aim to provide the non-specialist reader a gateway into this exciting field and the specialist reader with a new perspective on the latest results achieved and strategies devised.
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Affiliation(s)
- Joanna Zell
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS Toulouse France
- Équipe Labellisée la Ligue Contre le Cancer 2018 Toulouse France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
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Leguia M, Vila-Sanjurjo A, Chain PSG, Berry IM, Jarman RG, Pollett S. Precision Medicine and Precision Public Health in the Era of Pathogen Next-Generation Sequencing. J Infect Dis 2021; 221:S289-S291. [PMID: 31751454 DOI: 10.1093/infdis/jiz424] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This brief report serves as an introduction to a supplement of the Journal of Infectious Diseases entitled "Next-Generation Sequencing (NGS) Technologies to Advance Global Infectious Disease Research." We briefly discuss the history of NGS technologies and describe how the techniques developed during the past 40 years have impacted our understanding of infectious diseases. Our focus is on the application of NGS in the context of pathogen genomics. Beyond obvious clinical and public health applications, we also discuss the challenges that still remain within this rapidly evolving field.
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Affiliation(s)
- Mariana Leguia
- Laboratorio de Genómica, Pontificia Universidad Católica del Perú, Lima
| | - Anton Vila-Sanjurjo
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade de A Coruña, Spain
| | | | | | | | - Simon Pollett
- Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics (Uniformed Services University of the Health Sciences), Bethesda, Maryland
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Muñoz ADO, Escobedo-Morales A, Skakerzadeh E, Anota EC. Effect of homonuclear boron bonds in the adsorption of DNA nucleobases on boron nitride nanosheets. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114951] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Danylova TV, Komisarenko SV. Standing on the shoulders of giants: James Watson, Francis Crick, Maurice Wilkins, Rosalind Franklin and the birth of molecular biology. UKRAINIAN BIOCHEMICAL JOURNAL 2020. [DOI: 10.15407/ubj92.04.154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Veigl SJ, Harman O, Lamm E. Friedrich Miescher's Discovery in the Historiography of Genetics: From Contamination to Confusion, from Nuclein to DNA. JOURNAL OF THE HISTORY OF BIOLOGY 2020; 53:451-484. [PMID: 32524311 DOI: 10.1007/s10739-020-09608-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In 1869, Johann Friedrich Miescher discovered a new substance in the nucleus of living cells. The substance, which he called nuclein, is now known as DNA, yet both Miescher's name and his theoretical ideas about nuclein are all but forgotten. This paper traces the trajectory of Miescher's reception in the historiography of genetics. To his critics, Miescher was a "contaminator," whose preparations were impure. Modern historians portrayed him as a "confuser," whose misunderstandings delayed the development of molecular biology. Each of these portrayals reflects the disciplinary context in which Miescher's work was evaluated. Using archival sources to unearth Miescher's unpublished speculations-including an analogy between the hereditary material and language, and a speculation that a series of asymmetric carbon atoms could account for hereditary variation-this paper clarifies the ways in which the past was judged through the lens of contemporary concerns. It also shows how organization, structure, function, and information were already being considered when nuclein was first discovered nearly 150 years ago.
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Affiliation(s)
| | - Oren Harman
- Graduate Program in Science, Technology and Society, Bar Ilan University, Ramat Gan, Israel
| | - Ehud Lamm
- The Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.
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Abstract
Our understanding of the human genome has continuously expanded since its draft publication in 2001. Over the years, novel assays have allowed us to progressively overlay layers of knowledge above the raw sequence of A's, T's, G's, and C's. The reference human genome sequence is now a complex knowledge base maintained under the shared stewardship of multiple specialist communities. Its complexity stems from the fact that it is simultaneously a template for transcription, a record of evolution, a vehicle for genetics, and a functional molecule. In short, the human genome serves as a frame of reference at the intersection of a diversity of scientific fields. In recent years, the progressive fall in sequencing costs has given increasing importance to the quality of the human reference genome, as hundreds of thousands of individuals are being sequenced yearly, often for clinical applications. Also, novel sequencing-based assays shed light on novel functions of the genome, especially with respect to gene expression regulation. Keeping the human genome annotation up to date and accurate is therefore an ongoing partnership between reference annotation projects and the greater community worldwide.
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Affiliation(s)
- Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom; , ,
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom; , ,
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom; , ,
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Adkar-Purushothama CR, Perreault JP. Impact of Nucleic Acid Sequencing on Viroid Biology. Int J Mol Sci 2020; 21:ijms21155532. [PMID: 32752288 PMCID: PMC7432327 DOI: 10.3390/ijms21155532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022] Open
Abstract
The early 1970s marked two breakthroughs in the field of biology: (i) The development of nucleotide sequencing technology; and, (ii) the discovery of the viroids. The first DNA sequences were obtained by two-dimensional chromatography which was later replaced by sequencing using electrophoresis technique. The subsequent development of fluorescence-based sequencing method which made DNA sequencing not only easier, but many orders of magnitude faster. The knowledge of DNA sequences has become an indispensable tool for both basic and applied research. It has shed light biology of viroids, the highly structured, circular, single-stranded non-coding RNA molecules that infect numerous economically important plants. Our understanding of viroid molecular biology and biochemistry has been intimately associated with the evolution of nucleic acid sequencing technologies. With the development of the next-generation sequence method, viroid research exponentially progressed, notably in the areas of the molecular mechanisms of viroids and viroid diseases, viroid pathogenesis, viroid quasi-species, viroid adaptability, and viroid–host interactions, to name a few examples. In this review, the progress in the understanding of viroid biology in conjunction with the improvements in nucleotide sequencing technology is summarized. The future of viroid research with respect to the use of third-generation sequencing technology is also briefly envisaged.
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Lamm E, Harman O, Veigl SJ. Before Watson and Crick in 1953 Came Friedrich Miescher in 1869. Genetics 2020; 215:291-296. [PMID: 32487691 PMCID: PMC7268995 DOI: 10.1534/genetics.120.303195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/25/2020] [Indexed: 11/18/2022] Open
Abstract
In 1869, the young Swiss biochemist Friedrich Miescher discovered the molecule we now refer to as DNA, developing techniques for its extraction. In this paper we explain why his name is all but forgotten, and his role in the history of genetics is mostly overlooked. We focus on the role of national rivalries and disciplinary turf wars in shaping historical memory, and on how the story we tell shapes our understanding of the science. We highlight that Miescher could just as correctly be portrayed as the person who understood the chemical nature of chromatin (before the term existed), and the first to suggest how stereochemistry might serve as the basis for the transmission of hereditary variation.
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Affiliation(s)
- Ehud Lamm
- The Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv, Israel 6997801
| | - Oren Harman
- Science, Technology and Society, Bar Ilan University, Israel 5290002
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Löffler M, Carrey EA, Knecht W. The pathway to pyrimidines: The essential focus on dihydroorotate dehydrogenase, the mitochondrial enzyme coupled to the respiratory chain. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1281-1305. [PMID: 32043431 DOI: 10.1080/15257770.2020.1723625] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This paper is based on the Anne Simmonds Memorial Lecture, given by Monika Löffler at the International Symposium on Purine and Pyrimidine Metabolism in Man, Lyon 2019. It is dedicated to H. Anne Simmonds (died 2010) - a founding member of the ESSPPMM, since 2003 Purine and Pyrimidine Society - and her outstanding contributions to the identification and study of inborn errors of purine and pyrimidine metabolism. The distinctive intracellular arrangement of pyrimidine de novo synthesis in higher eukaryotes is important to cells with a high demand for nucleic acid synthesis. The proximity of the enzyme active sites and the resulting channeling in CAD and UMP synthase is of kinetic benefit. The intervening enzyme dihydroorotate dehydrogenase (DHODH) is located in the mitochondrion with access to the ubiquinone pool, thus ensuring efficient removal of redox equivalents through the constitutive activity of the respiratory chain, also a mechanism through which the input of 2 ATP for carbamylphosphate synthesis is balanced by Oxphos. The obligatory contribution of O2 to de novo UMP synthesis means that DHODH has a pivotal role in adapting the proliferative capacity of cells to different conditions of oxygenation, such as hypoxia in growing tumors. DHODH also is a validated drug target in inflammatory diseases. This survey of selected topics of personal interest and reflection spans some 40 years of our studies from tumor cell cultures under hypoxia to in vitro assays including purification from mitochondria, localization, cloning, expression, biochemical characterization, crystallisation, kinetics and inhibition patterns of eukaryotic DHODH enzymes.
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Affiliation(s)
- Monika Löffler
- Institute of Physiological Chemistry, Faculty of Medicine, Philipps-University Marburg, Marburg, Germany
| | | | - Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform, Lund University, Lund, Sweden
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Zanetti BF, Braga DPDAF, Setti AS, Iaconelli A, Borges E. Effect of GnRH analogues for pituitary suppression on oocyte morphology in repeated ovarian stimulation cycles. JBRA Assist Reprod 2020; 24:24-29. [PMID: 31436072 PMCID: PMC6993161 DOI: 10.5935/1518-0557.20190050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE To compare the effect of pituitary suppression regimens on oocyte morphology in consecutive ICSI cycles of the same patients. METHODS Data was obtained from 200 matched consecutive intracytoplasmic sperm injection (ICSI) cycles performed in 100 couples undergoing the first cycle with the GnRH agonist and the following cycle with the GnRH antagonist regimen, from January 2010 to August 2016, in a private university-affiliated IVF centre. The effects of the pituitary suppression type on oocyte morphology were assessed by multivariate General Linear Models. RESULTS Mean interval between cycles was 185.32±192.85 days. Maternal age, body mass index, and total FSH dose administered were similar in both patients' cycles. Antagonist cycles presented lower incidence of dark cytoplasm (0.69±3.28% vs. 4.40±17.70%, p=0.047), Smooth endoplasmic reticulum (SER cluster (4.37±11.62% vs. 7.36±17.17%, p=0.046), and ZP defects (6.05±14.76% vs. 11.84±25.13%, p=0.049). Similar numbers of follicles retrieved oocytes, and mature oocytes were observed between the GnRH groups, as well as the fertilisation rate, number of obtained embryos, high-quality embryo rates, and the clinical outcomes. CONCLUSION GnRH antagonist's inhibitory effect on the ovaries in consecutive ICSI cycles results in improved oocyte maturity and morphology, despite similar laboratory and clinical outcomes, compared to the GnRH agonist treatment.
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Affiliation(s)
- Bianca Ferrarini Zanetti
- Fertility Medical Group, São Paulo, SP - Brazil.,Instituto Sapientiae - Centro de Estudos e Pesquisa em Reprodução Humana Assistida, São Paulo, SP - Brazil
| | - Daniela Paes de Almeida Ferreira Braga
- Fertility Medical Group, São Paulo, SP - Brazil.,Instituto Sapientiae - Centro de Estudos e Pesquisa em Reprodução Humana Assistida, São Paulo, SP - Brazil
| | - Amanda Souza Setti
- Fertility Medical Group, São Paulo, SP - Brazil.,Instituto Sapientiae - Centro de Estudos e Pesquisa em Reprodução Humana Assistida, São Paulo, SP - Brazil
| | - Assumpto Iaconelli
- Fertility Medical Group, São Paulo, SP - Brazil.,Instituto Sapientiae - Centro de Estudos e Pesquisa em Reprodução Humana Assistida, São Paulo, SP - Brazil
| | - Edson Borges
- Fertility Medical Group, São Paulo, SP - Brazil.,Instituto Sapientiae - Centro de Estudos e Pesquisa em Reprodução Humana Assistida, São Paulo, SP - Brazil
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Maes L, Massana Roqeuro D, Pitet LM, Adriaensens P, Junkers T. Sequence-defined nucleobase containing oligomers via reversible addition–fragmentation chain transfer single monomer addition. Polym Chem 2020. [DOI: 10.1039/c9py01853k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nucleobase acrylate monomers have been synthesized and monodisperse tetramers with any order of bases are created via single monomer insertion reactions in a RAFT process.
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Affiliation(s)
- Lowie Maes
- Polymer Reaction Design group
- Hasselt University – Institute for Materials Research
- B-3590 Diepenbeek
- Belgium
| | - Daniel Massana Roqeuro
- Polymer Reaction Design group
- Hasselt University – Institute for Materials Research
- B-3590 Diepenbeek
- Belgium
| | - Louis M. Pitet
- Advanced Polymer Functionalization group
- Hasselt University – Institute for Materials Research
- B-3590 Diepenbeek
- Belgium
| | - Peter Adriaensens
- Nuclear Magnetic Resonance Spectroscopy Group
- Institute for Materials Research (IMO-IMOMEC)
- B-3590 Diepenbeek
- Belgium
- IMEC vzw–Division IMOMEC
| | - Tanja Junkers
- Polymer Reaction Design group
- Hasselt University – Institute for Materials Research
- B-3590 Diepenbeek
- Belgium
- School of Chemistry
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Clark DJ, Moore CM, Flanagan M, Bocxlaer KV, Piperaki ET, Yardley V, Croft SL, Tyson J, Whitehouse SP, O'Halloran J, Krishna S, Staines HM. An efficient and novel technology for the extraction of parasite genomic DNA from whole blood or culture. Biotechniques 2019; 68:79-84. [PMID: 31774301 PMCID: PMC7115988 DOI: 10.2144/btn-2019-0086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to assess pathogen DNA extraction with a new spin column-based method (DNA-XT). DNA from either whole-blood samples spiked with Plasmodium falciparum or Leishmania donovani amastigote culture was extracted with DNA-XT and compared with that produced by a commercial extraction kit (DNeasy®). Eluates from large and small sample volumes were assessed by PCR and spectroscopy. Using a small volume (5 μl) of blood, the DNA-XT and DNeasy methods produced eluates with similar DNA concentrations (0.63 vs 1.06 ng/μl, respectively). The DNA-XT method produced DNA with lower PCR inhibition than DNeasy. The new technique was also twice as fast and required fewer plastics and manipulations but had reduced total recovered DNA compared with DNeasy. DNA-XT, which is designed for small sample volumes, uses a 5-min detergent and enzymatic lysis step to release DNA from cells. Contaminating proteins and lipids are then bound to a matrix within a spin column during a 1-min centrifugation step while DNA passes directly through.
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Affiliation(s)
- David J Clark
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Catherine M Moore
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | | | - Katrien Van Bocxlaer
- Infection & Immunity Department, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Evangelia-Theophano Piperaki
- Infection & Immunity Department, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Vanessa Yardley
- Infection & Immunity Department, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Simon L Croft
- Infection & Immunity Department, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - John Tyson
- QuantuMDx, Newcastle upon Tyne, NE1 2JQ, UK
| | | | | | - Sanjeev Krishna
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Henry M Staines
- Centre for Diagnostics & Antimicrobial Resistance, Institute for Infection & Immunity, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
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Mohajeri N, Imani M, Akbarzadeh A, Sadighi A, Zarghami N. An update on advances in new developing DNA conjugation diagnostics and ultra-resolution imaging technologies: Possible applications in medical and biotechnological utilities. Biosens Bioelectron 2019; 144:111633. [DOI: 10.1016/j.bios.2019.111633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
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Prokopov IA, Kovaleva EL, Minaeva ED, Pryakhina EA, Savin EV, Gamayunova AV, Pozharitskaya ON, Makarov VG, Shikov AN. Animal-derived medicinal products in Russia: Current nomenclature and specific aspects of quality control. JOURNAL OF ETHNOPHARMACOLOGY 2019; 240:111933. [PMID: 31116966 DOI: 10.1016/j.jep.2019.111933] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Animal-derived medicinal products (ADMP) had been extensively used in Russia and became a part of officinal medicine in 1778. AIM OF THE STUDY The aim of the current review was to analyse the ADMPs authorised in the Russian Federation and to identify specific aspects of quality evaluation of these medicinal products. MATERIALS AND METHODS Information of ADMPs was extracted from the online State Register of Medicinal Products of the Russian Federation. At the next stage, we systematically searched library catalogues, E-library.ru, Medline/PubMed, Scopus, Web of Science and Google Scholar databases to find data related to ADMP quality evaluation, clinically proven efficacy and safety. RESULTS For classification of ADMP, we propose an approach based on the raw material used: ADMPs derived from marine organisms, ADMPs from cattle and pigs and ADMPs from other terrestrial animals. The majority of ADMPs authorised in Russia are produced by local manufacturers. ADMPs are available in dosage forms of solution for parenteral administration (35% of all products) and lyophilisates for parenteral use (19%), tablets and capsules (17% and 11%, respectively), ointments (5%) and powders (3%). ADMPs belong to the following pharmacotherapeutic groups: medicines for tissue regeneration and repair stimulators (30%), digestive enzyme products (22%), anticoagulants (17%), proteolytic agents (6%) and medicines for the treatment of chronic prostatitis (5%). The most important approaches to standardisation of ADMPs are implementation of modern requirements for registration dossiers, development of risk-oriented approaches for evaluation of impurities, elaboration of advanced instrumental and in vitro test methods capable of replacing in vivo methods and harmonisation of the potency units used for standardisation. CONCLUSIONS The key features of ADMPs that help them retain their leading position in the pharmaceutical market are as follows: (i) their unique composition usually represented by a complex of biologically active substances; (ii) a high degree of affinity of the active ingredient of an ADMP to the human body and (iii) proved safety and clinical efficiency. Variability in the quality of raw ingredients, epidemiological situation and other conditions pose additional challenges for the development of ADMPs and for the standardisation.
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Affiliation(s)
- Ilya A Prokopov
- Federal State Budgetary Institution "Scientific Centre for Expert Evaluation of Medicinal Products" of the Ministry of Health of the Russian Federation, 8/2 Petrovsky Blvd, Moscow, 127051, Russia.
| | - Elena L Kovaleva
- Federal State Budgetary Institution "Scientific Centre for Expert Evaluation of Medicinal Products" of the Ministry of Health of the Russian Federation, 8/2 Petrovsky Blvd, Moscow, 127051, Russia
| | - Elena D Minaeva
- Federal State Budgetary Institution "Scientific Centre for Expert Evaluation of Medicinal Products" of the Ministry of Health of the Russian Federation, 8/2 Petrovsky Blvd, Moscow, 127051, Russia
| | - Ekaterina A Pryakhina
- Federal State Budgetary Institution "Scientific Centre for Expert Evaluation of Medicinal Products" of the Ministry of Health of the Russian Federation, 8/2 Petrovsky Blvd, Moscow, 127051, Russia
| | - Evgenyi V Savin
- Federal State Budgetary Institution "Scientific Centre for Expert Evaluation of Medicinal Products" of the Ministry of Health of the Russian Federation, 8/2 Petrovsky Blvd, Moscow, 127051, Russia
| | - Alexandra V Gamayunova
- Federal State Budgetary Institution "Scientific Centre for Expert Evaluation of Medicinal Products" of the Ministry of Health of the Russian Federation, 8/2 Petrovsky Blvd, Moscow, 127051, Russia
| | - Olga N Pozharitskaya
- Saint-Petersburg Institute of Pharmacy, Leningrad Region, Vsevolozhsky District, Kuzmolovo 245, 188663, Russia
| | - Valery G Makarov
- Saint-Petersburg Institute of Pharmacy, Leningrad Region, Vsevolozhsky District, Kuzmolovo 245, 188663, Russia
| | - Alexander N Shikov
- Saint-Petersburg Institute of Pharmacy, Leningrad Region, Vsevolozhsky District, Kuzmolovo 245, 188663, Russia
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Huo S, Li H, Boersma AJ, Herrmann A. DNA Nanotechnology Enters Cell Membranes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900043. [PMID: 31131200 PMCID: PMC6523375 DOI: 10.1002/advs.201900043] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/16/2019] [Indexed: 05/19/2023]
Abstract
DNA is more than a carrier of genetic information: It is a highly versatile structural motif for the assembly of nanostructures, giving rise to a wide range of functionalities. In this regard, the structure programmability is the main advantage of DNA over peptides, proteins, and small molecules. DNA amphiphiles, in which DNA is covalently bound to synthetic hydrophobic moieties, allow interactions of DNA nanostructures with artificial lipid bilayers and cell membranes. These structures have seen rapid growth with great potential for medical applications. In this Review, the current state of the art of the synthesis of DNA amphiphiles and their assembly into nanostructures are first summarized. Next, an overview on the interaction of these DNA amphiphiles with membranes is provided, detailing on the driving forces and the stability of the interaction. Moreover, the interaction with cell surfaces in respect to therapeutics, biological sensing, and cell membrane engineering is highlighted. Finally, the challenges and an outlook on this promising class of DNA hybrid materials are discussed.
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Affiliation(s)
- Shuaidong Huo
- DWI‐Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AG GroningenThe Netherlands
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
| | - Hongyan Li
- DWI‐Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AG GroningenThe Netherlands
| | - Arnold J. Boersma
- DWI‐Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
| | - Andreas Herrmann
- DWI‐Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AG GroningenThe Netherlands
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
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Rekvig OP. The dsDNA, Anti-dsDNA Antibody, and Lupus Nephritis: What We Agree on, What Must Be Done, and What the Best Strategy Forward Could Be. Front Immunol 2019; 10:1104. [PMID: 31156647 PMCID: PMC6529578 DOI: 10.3389/fimmu.2019.01104] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/30/2019] [Indexed: 12/19/2022] Open
Abstract
This study aims to understand what lupus nephritis is, its origin, clinical context, and its pathogenesis. Truly, we encounter many conceptual and immanent tribulations in our attempts to search for the pathogenesis of this disease—and how to explain its assumed link to SLE. Central in the present landscape stay a short history of the early studies that substantiated the structures of isolated or chromatin-assembled mammalian dsDNA, and its assumed, highly controversial role in induction of anti-dsDNA antibodies. Arguments discussed here may provoke the view that anti-dsDNA antibodies are not what we think they are, as they may be antibodies operational in quite different biological contexts, although they bind dsDNA by chance. This may not mean that these antibodies are not pathogenic but they do not inform how they are so. This theoretical study centers the content around the origin and impact of extra-cellular DNA, and if dsDNA has an effect on the adaptive immune system. The pathogenic potential of chromatin-anti-dsDNA antibody interactions is limited to incite lupus nephritis and dermatitis which may be linked in a common pathogenic process. These are major criteria in SLE classification systems but are not shared with other defined manifestations in SLE, which may mean that they are their own disease entities, and not integrated in SLE. Today, the models thought to explain lupus nephritis are divergent and inconsistent. We miss a comprehensive perspective to try the different models against each other. To do this, we need to take all elements of the syndrome SLE into account. This can only be achieved by concentrating on the interactions between autoimmunity, immunopathology, deviant cell death and necrotic chromatin in context of elements of system science. System science provides a framework where data generated by experts can be compared, and tested against each other. This approach open for consensus on central elements making up “lupus nephritis” to separate what we agree on and how to understand the basis for conflicting models. This has not been done yet in a systematic context.
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Affiliation(s)
- Ole Petter Rekvig
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
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Dovrolis N, Filidou E, Kolios G. Systems biology in inflammatory bowel diseases: on the way to precision medicine. Ann Gastroenterol 2019; 32:233-246. [PMID: 31040620 PMCID: PMC6479645 DOI: 10.20524/aog.2019.0373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining data from different scientific sources. In combination with bioinformatics and network medicine, it uses principles from computer science, mathematics, physics, chemistry, biology, medicine and computational tools to achieve its purposes. Systems biology utilizes scientific sources that provide data from omics studies (e.g., genomics, transcriptomics, etc.) and clinical observations, whose combined analysis leads to network formation and ultimately to a more integrative image of disease etiopathogenesis. In this review, we analyze the current literature on the methods and the tools utilized by systems biology in order to cover an innovative and exciting field: IBD-omics.
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Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eirini Filidou
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Correspondence to: Prof. George Kolios, MD PhD, Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Dragana, Alexandroupolis, 68100, Greece, e-mail:
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