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Silva-Santos AR, Sousa Rosa S, Marques MPC, Azevedo AM, Prazeres DMF. Quantification of ssDNA Scaffold Production by Ion-Pair Reverse Phase Chromatography. ACS OMEGA 2024; 9:22619-22624. [PMID: 38826531 PMCID: PMC11137683 DOI: 10.1021/acsomega.3c10533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 06/04/2024]
Abstract
DNA origami is an emerging technology that can be used as a nanoscale platform in numerous applications ranging from drug delivery systems to biosensors. The DNA nanostructures are assembled from large single-stranded DNA (ssDNA) scaffolds, ranging from hundreds to thousands of nucleotides and from short staple strands. Scaffolds are usually obtained by asymmetric PCR (aPCR) or Escherichia coli infection/transformation with phages or phagemids. Scaffold quantification is typically based on agarose gel electrophoresis densitometry for molecules obtained by aPCR, or by UV absorbance, in the case of scaffolds obtained by infection or transformation. Although these methods are well-established and easy-to-apply, the results obtained are often inaccurate due to the lack of selectivity and sensitivity in the presence of impurities. Herein, we present an HPLC method based on ion-pair reversed-phase (IP-RP) chromatography to quantify DNA scaffolds. Using IP-RP chromatography, ssDNA products (449 and 1000 nt) prepared by aPCR were separated from impurities and from the double stranded (ds) DNA byproduct. Additionally, both ss and dsDNA were quantified with high accuracy. The method was used to guide the optimization of the production of ssDNA by aPCR, which targeted the maximization of the ratio of ssDNA to dsDNA obtained. Moreover, ssDNA produced from phage infection of E. coli cells was also quantified by IP-RP using commercial ssDNA from the M13mp18 phage as a standard.
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Affiliation(s)
- A. Rita Silva-Santos
- iBB—Institute for Bioengineering
and Biosciences, Department of Bioengineering, Instituto Superior
Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
- Associate
Laboratory i4HB−Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sara Sousa Rosa
- iBB—Institute for Bioengineering
and Biosciences, Department of Bioengineering, Instituto Superior
Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
- Associate
Laboratory i4HB−Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Marco P. C. Marques
- Department
of Biochemical Engineering, University College
London, Bernard Katz Building, Gordon Street, London WC1H 0AH, U.K.
| | - Ana M. Azevedo
- iBB—Institute for Bioengineering
and Biosciences, Department of Bioengineering, Instituto Superior
Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
- Associate
Laboratory i4HB−Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Duarte Miguel F. Prazeres
- iBB—Institute for Bioengineering
and Biosciences, Department of Bioengineering, Instituto Superior
Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
- Associate
Laboratory i4HB−Institute for Health and Bioeconomy at Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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Farahmand S, SamadiAfshar S, Hosseini L. TA-Cloning for Diabetes Treatment: Expressing Corynebacterium Malic Enzyme Gene in E. coli. Curr Microbiol 2024; 81:167. [PMID: 38727744 DOI: 10.1007/s00284-024-03686-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/02/2024] [Indexed: 05/16/2024]
Abstract
Diabetes mellitus represents a persistent metabolic condition marked by heightened levels of blood glucose, presenting a considerable worldwide health concern, and finding targeted treatment for it is a crucial priority for global health. Gram-positive aerobic bacteria, predominantly inhabiting water and soil, are known carriers of various enzyme-encoding genetic material, which includes the malic enzyme gene that plays a role in insulin secretion. Corynebacterium glutamicum bacteria (ATCC 21799) were acquired from the Pasteur Institute and confirmed using microbiological and molecular tests, including DNA extraction. After identification, gene purification and cloning of the maeB gene were performed using the TA Cloning method. Additionally, the enhancement of enzyme expression was assessed using the expression vector pET-28a, and validation of simulation results was monitored through a real-time PCR analysis. Based on previous studies, the malic enzyme plays a pivotal role in maintaining glucose homeostasis, and increased expression of this enzyme has been associated with enhanced insulin sensitivity. However, the production of malic enzyme has encountered numerous challenges and difficulties. This study successfully isolated the malic enzyme genes via Corynebacterium glutamicum and introduced them into Escherichia coli for high-yield production. According to the results, the optimum temperature for the activity of enzymes has been identified as 39 °C.
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Affiliation(s)
| | - Saber SamadiAfshar
- Pediatric Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ladan Hosseini
- Department of Biology, Payame Noor University (PNU), Tehran, Iran
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3
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Lee SY, Oh SW. Point-of-Care Diagnostic System for Viable Salmonella Species via Improved Propidium Monoazide and Recombinase Polymerase Amplification Based Nucleic Acid Lateral Flow. Diagnostics (Basel) 2024; 14:831. [PMID: 38667476 PMCID: PMC11049151 DOI: 10.3390/diagnostics14080831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Salmonella species are prominent foodborne microbial pathogens transmitted through contaminated food or water and pose a significant threat to human health. Accurate and rapid point-of-care (POC) diagnosis is gaining attention in effectively preventing outbreaks of foodborne disease. However, the presence of dead bacteria can interfere with an accurate diagnosis, necessitating the development of methods for the rapid, simple, and efficient detection of viable bacteria only. Herein, we used an improved propidium monoazide (PMAxx) to develop a nucleic acid lateral flow (NALF) assay based on recombinase polymerase amplification (RPA) to differentiate viable Salmonella Typhimurium. We selected an RPA primer set targeting the invA gene and designed a probe for NALF. RPA-based NALF was optimized for temperature (30-43 °C), time (1-25 min), and endonuclease IV concentration (0.025-0.15 unit/µL). PMAxx successfully eliminated false-positive results from dead S. Typhimurium, enabling the accurate detection of viable S. Typhimurium with a detection limit of 1.11 × 102 CFU/mL in pure culture. The developed method was evaluated with spiked raw chicken breast and milk with analysis completed within 25 min at 39 °C. This study has potential as a tool for the POC diagnostics of viable foodborne pathogens with high specificity, sensitivity, rapidity, and cost-effectiveness.
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Affiliation(s)
| | - Se-Wook Oh
- Department of Food and Nutrition, Kookmin University, Seoul 136-702, Republic of Korea;
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4
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Talaat R, Abu El-Naga MN, El-Bialy HAA, El-Fouly MZ, Abouzeid MA. Quenching of quorum sensing in multi-drug resistant Pseudomonas aeruginosa: insights on halo-bacterial metabolites and gamma irradiation as channels inhibitors. Ann Clin Microbiol Antimicrob 2024; 23:31. [PMID: 38600513 PMCID: PMC11007959 DOI: 10.1186/s12941-024-00684-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/03/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Anti-virulence therapy is a promising strategy to treat multi-drug resistant (MDR) pathogens. Pseudomonas aeruginosa is a potent opportunistic pathogen because of an array of virulence factors that are regulated by quorum sensing systems. METHODS The virulence features of four multi-drug resistant P. aeruginosa strains were investigated upon exposure to the sub-lethal dose of gamma rays (1 kGy), and sub-inhibitory concentrations of bioactive metabolites recovered from local halophilic strains in comparison to control. Then, the gene expression of AHL-mediated quorum sensing systems (las/rhl) was quantitatively determined in treated and untreated groups by real-time PCR. RESULTS The bioactive metabolites recovered from halophilic strains previously isolated from saline ecosystems were identified as Halomonas cupida (Halo-Rt1), H. elongate (Halo-Rt2), Vigibacillus natechei (Halo-Rt3), Sediminibacillus terrae (Halo-Rt4) and H. almeriensis (Halo-Rt5). Results revealed that both gamma irradiation and bioactive metabolites significantly reduced the virulence factors of the tested MDR strains. The bioactive metabolites showed a maximum efficiency for inhibiting biofilm formation and rhamnolipids production whereas the gamma irradiation succeeded in decreasing other virulence factors to lower levels in comparison to control. Quantitative-PCR results showed that AHL-mediated quorum sensing systems (las/rhl) in P. aeruginosa strains were downregulated either by halo-bacterial metabolites or gamma irradiation in all treatments except the upregulation of both lasI internal gene and rhlR intact gene in P. aeruginosa NCR-RT3 and both rhlI internal gene and rhlR intact gene in P. aeruginosa U3 by nearly two folds or more upon exposure to gamma irradiation. The most potent result was observed in the expression of lasI internal gene that was downregulated by more than ninety folds in P. aeruginosa NCR-RT2 after treatment with metabolites of S. terrae (Halo-Rt4). Analyzing metabolites recovered from H. cupida (Halo-Rt1) and H. elongate (Halo-Rt2) using LC-ESI-MS/MS revealed many chemical compounds that have quorum quenching properties including glabrol, 5,8-dimethoxyquinoline-2-carbaldehyde, linoleoyl ethanolamide, agelasine, penigequinolones derivatives, berberine, tetracosanoic acid, and liquidambaric lactone in the former halophile and phloretin, lycoctonine, fucoxanthin, and crassicauline A in the latter one. CONCLUSION QS inhibitors can significantly reduce the pathogenicity of MDR P. aeruginosa strains; and thus can be an effective and successful strategy for treating antibiotic resistant traits.
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Affiliation(s)
- Reham Talaat
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Mohamed N Abu El-Naga
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Heba Abd Alla El-Bialy
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt.
| | - Mohie Z El-Fouly
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Mohamed A Abouzeid
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
- Faculty of Science, Galala University, Suez, Egypt
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Wang L, Wang J, Feng D, Wang B, Jahan-Mihan Y, Wang Y, Bi Y, Lim D, Ji B. A simple and effective genotyping workflow for rapid detection of CRISPR genome editing. Am J Physiol Gastrointest Liver Physiol 2024; 326:G473-G481. [PMID: 38410866 PMCID: PMC11216750 DOI: 10.1152/ajpgi.00013.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/28/2024]
Abstract
Genetically engineered mouse models play a pivotal role in the modeling of diseases, exploration of gene functions, and the development of novel therapies. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated genome editing technology has revolutionized the process of developing such models by enabling precise genome modifications of the multiple interested genes simultaneously. Following genome editing, an efficient genotyping methodology is crucial for subsequent characterization. However, current genotyping methods are laborious, time-consuming, and costly. Here, using targeting the mouse trypsinogen genes as an example, we introduced common applications of CRISPR-Cas9 editing and a streamlined cost-effective genotyping workflow for CRISPR-edited mouse models, in which Sanger sequencing is required only at the initial steps. In the F0 mice, we focused on identifying the presence of positive editing by PCR followed by Sanger sequencing without the need to know the exact sequences, simplifying the initial screening. In the F1 mice, Sanger sequencing and algorithms decoding were used to identify the precise editing. Once the edited sequence was established, a simple and effective genotyping strategy was established to distinguish homozygous and heterozygous status by PCR from tail DNA. The genotyping workflow applies to deletions as small as one nucleotide, multiple-gene knockout, and knockin studies. This simplified, efficient, and cost-effective genotyping shall be instructive to new investigators who are unfamiliar with characterizing CRISPR-Cas9-edited mouse strains.NEW & NOTEWORTHY This study presents a streamlined, cost-effective genotyping workflow for clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) edited mouse models, focusing on trypsinogen genes. It simplifies initial F0 mouse screening using PCR and Sanger sequencing without needing exact sequences. For F1 mice, precise editing is identified through Sanger sequencing and algorithm decoding. The workflow includes a novel PCR strategy for distinguishing homozygous and heterozygous statuses in subsequent generations, effective for small deletions, multiple-gene knockouts, and knockins.
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Affiliation(s)
- Lingxiang Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Jiale Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Dongfeng Feng
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Bin Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Yasmin Jahan-Mihan
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Ying Wang
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Yan Bi
- Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, United States
| | - DoYoung Lim
- The Transgenic and Knockout Core, Mayo Clinic, Rochester, Minnesota, United States
| | - Baoan Ji
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
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Aditya S, Aggarwal R, Bashyal BM, Gurjar MS, Saharan MS, Aggarwal S. Unraveling the dynamics of wheat leaf blight complex: isolation, characterization, and insights into pathogen population under Indian conditions. Front Microbiol 2024; 15:1287721. [PMID: 38450160 PMCID: PMC10915091 DOI: 10.3389/fmicb.2024.1287721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024] Open
Abstract
Wheat, a staple food crop for 35% of the global population, faces a threat from Helminthosporium leaf blight (HLB), a complex of spot blotch (Bipolaris sorokiniana) and tan spot (Pyrenophora-tritici-repentis) diseases under warm and humid conditions. However, in Indian conditions, the knowledge of existing pathogen populations associated with the HLB complex is limited and largely dominated by only B. sorokiniana (spot blotch). To address this, diseased samples were collected from all six wheat growing zones during 2020-2022. The pathogenic species were identified through in-depth morphological characterization, supplemented with ITS-rDNA and GAPDH sequence analysis, a diagnostic SCAR marker, and pathogenicity studies on two wheat varieties: Sonalika and HD2733. The 32 isolates collected from 10 different states consist of B. spicifera (12.5% of all isolates), Exserohilum rostratum (9.3%), Bipolaris oryzae (3.1%), and B. sorokiniana (75%). B. sorokiniana exhibited the highest disease severity on both varieties. Other lesser-known pathogenic species also produced comparable disease severity as B. sorokiniana isolates and, therefore are economically important. Unraveling pathogen composition and biology aids in disease control and resistance breeding. Our study highlights economically impactful and lesser-known pathogenic species causing wheat leaf blight/spot blotch in India, guiding both current management and future resistance breeding strategies in plant pathology.
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Affiliation(s)
- Sanghmitra Aditya
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rashmi Aggarwal
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Shahbaz F, Muccee F, Shahab A, Safi SZ, Alomar SY, Qadeer A. Isolation and in vitro assessment of chicken gut microbes for probiotic potential. Front Microbiol 2024; 15:1278439. [PMID: 38348194 PMCID: PMC10860760 DOI: 10.3389/fmicb.2024.1278439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Poultry production occupies an important place in the economy of any country. High broiler production in recent years has badly affected its profitability due to bad feed quality, excessive use of chemotherapeutic agents, emergence of diverse pathogens, and the deficiencies in management practices during rearing cycle. Microbiological improvement of the meat quality using potential probiotics can be beneficial for broiler farming. Present study was initiated to isolate chicken gastrointestinal tract (GIT) bacteria with probiotic potential. To isolate probiotics from chicken gut, alimentary canal of chickens of known sizes and ages was suspended in ringers soln. Under shaking conditions for overnight followed by serial dilutions of ringers soln. Bacterial isolates were analyzed via growth curve analysis, biochemical testing using RapID™ NF Plus Panel kit, molecular characterization, antimicrobial activity assay, antibiotic sensitivity assay, GIT adherence assay, bile salt and gastric acid resistant assay, and cholesterol assimilation assay. Four bacteria isolated in present study were identified as Limosilactobacillus antri strain PUPro1, Lactobacillus delbrueckii strain PUPro2, Lacticaseibacillus casei strain PUPro3, and Ligilactobacillus salivarius strain PUPro4. L. delbrueckii strain PUPro2 grew extremely fast. All isolates exhibited exceptional resistance to increasing concentrations of NaCl and bile salts with value of p >0.5. L. delbrueckii strain PUPro2 adhered to chicken ileum epithelial cells and demonstrated the highest viable counts of 320 colony forming units (CFUs). Antagonistic action was found in all isolates against P. aeruginosa, B. subtilis, B. proteus, and S. aureus, with value of p >0.5. Antibiotic susceptibility testing showed sensitivity to all the antibiotics used. Cholesterol assimilation was detected in all bacteria, with values ranging from 216.12 to 192.2 mg/dL. All isolates exhibited γ-hemolysis. In future, these bacteria might be tested for their impact on broilers meat quality and growth and can be recommended for their use as supplements for broilers diet with positive impact on poultry production.
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Affiliation(s)
- Fatima Shahbaz
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Fatima Muccee
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Aansa Shahab
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Sher Zaman Safi
- Faculty of Medicine, MAHSA University, Kuala Lumpur, Malaysia
| | - Suliman Yousef Alomar
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdul Qadeer
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
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Jimenez-Bueno I, Garcia-Contreras R, Aranda-Herrera B, Sakagami H, Lopez-Ayuso CA, Nakajima H, Jurado CA, Nurrohman H. Cytotoxicity, Differentiation, and Biocompatibility of Root-End Filling: A Comprehensive Study. Biomimetics (Basel) 2023; 8:514. [PMID: 37999155 PMCID: PMC10669418 DOI: 10.3390/biomimetics8070514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
Assessing the biocompatibility of endodontic root-end filling materials through cell line responses is both essential and of utmost importance. This study aimed to the cytotoxicity of the type of cell death through apoptosis and autophagy, and odontoblast cell-like differentiation effects of MTA, zinc oxide-eugenol, and two experimental Portland cements modified with bismuth (Portland Bi) and barium (Portland Ba) on primary cell cultures. Material and methods: The cells corresponded to human periodontal ligament and gingival fibroblasts (HPLF, HGF), human pulp cells (HPC), and human squamous carcinoma cells from three different patients (HSC-2, -3, -4). The cements were inoculcated in different concentrations for cytotoxicity evaluation, DNA fragmentation in electrophoresis, apoptosis caspase activation, and autophagy antigen reaction, odontoblast-like cells were differentiated and tested for mineral deposition. The data were subject to a non-parametric test. Results: All cements caused a dose-dependent reduction in cell viability. Contact with zinc oxide-eugenol induced neither DNA fragmentation nor apoptotic caspase-3 activation and autophagy inhibitors (3-methyladenine, bafilomycin). Portland Bi accelerated significantly (p < 0.05) the differentiation of odontoblast-like cells. Within the limitation of this study, it was concluded that Portland cement with bismuth exhibits cytocompatibility and promotes odontoblast-like cell differentiation. This research contributes valuable insights into biocompatibility, suggesting its potential use in endodontic repair and biomimetic remineralization.
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Affiliation(s)
- Ignacio Jimenez-Bueno
- Department of Endodontics, Faculty of Dentistry, Autonomous University State of Mexico (UAEMex), Toluca 50130, State of Mexico, Mexico;
| | - Rene Garcia-Contreras
- Interdisciplinary Research Laboratory, Nanostructures and Biomaterials Area, National School of Higher Studies (ENES) Leon, National Autonomous University of Mexico (UNAM), Leon 37684, Guanajuato, Mexico; (R.G.-C.); (C.A.L.-A.)
| | - Benjamin Aranda-Herrera
- Interdisciplinary Research Laboratory, Nanostructures and Biomaterials Area, National School of Higher Studies (ENES) Leon, National Autonomous University of Mexico (UNAM), Leon 37684, Guanajuato, Mexico; (R.G.-C.); (C.A.L.-A.)
| | - Hiroshi Sakagami
- Meikai University Research Institute of Odontology (M-RIO), Meikai University School of Dentistry, Sakado 350-0283, Saitama, Japan;
| | - Christian Andrea Lopez-Ayuso
- Interdisciplinary Research Laboratory, Nanostructures and Biomaterials Area, National School of Higher Studies (ENES) Leon, National Autonomous University of Mexico (UNAM), Leon 37684, Guanajuato, Mexico; (R.G.-C.); (C.A.L.-A.)
| | - Hiroshi Nakajima
- Division of Dental Biomaterials Science, Department of Restorative and Biomaterials Sciences, Meikai University School of Dentistry, Sakado 350-0283, Saitama, Japan
| | - Carlos A. Jurado
- Department of Prosthodontics, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, IA 52242, USA
| | - Hamid Nurrohman
- Department of Restorative Dentistry & Prosthodontics, University of Texas School of Dentistry, Houston, TX 77054, USA
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Durgo K, Orešić S, Rinčić Mlinarić M, Fiket Ž, Jurešić GČ. Toxicity of Metal Ions Released from a Fixed Orthodontic Appliance to Gastrointestinal Tract Cell Lines. Int J Mol Sci 2023; 24:9940. [PMID: 37373088 DOI: 10.3390/ijms24129940] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The mechanism of toxicity and cellular response to metal ions present in the environment is still a very current area of research. In this work, which is a continuation of the study of the toxicity of metal ions released by fixed orthodontic appliances, eluates of archwires, brackets, ligatures, and bands are used to test the prooxidant effect, cytotoxicity, and genotoxicity on cell lines of the gastrointestinal tract. Eluates obtained after three immersion periods (3, 7, and 14 days) and with known amounts and types of metal ions were used. Four cell lines-CAL 27 (human tongue), Hep-G2 (liver), AGS (stomach) and CaCo-2 (colon)-were treated with each type of eluate at four concentrations (0.1×, 0.5×, 1.0×, and 2.0×) for 24 h. Most eluates had toxic effects on CAL 27 cells over the entire concentration range regardless of exposure time, while CaCo-2 proved to be the most resistant. In AGS and Hep-G2 cells, all samples tested induced free radical formation, with the highest concentration (2×) causing a decrease in free radicals formed compared to the lowest concentrations. Eluates containing Cr, Mn, and Al showed a slight pro-oxidant effect on DNA (on plasmid φX-174 RF I) and slight genotoxicity (comet assay), but these effects are not so great that the human body could not "resist" them. Statistical analysis of data on chemical composition, cytotoxicity, ROS, genotoxicity, and prooxidative DNA damage shows the influence of metal ions present in some eluates on the toxicity obtained. Fe and Ni are responsible for the production of ROS, while Mn and Cr have a great influence on hydroxyl radicals, which cause single-strand breaks in supercoiled plasmid DNA in addition to the production of ROS. On the other hand, Fe, Cr, Mn, and Al are responsible for the cytotoxic effect of the studied eluates. The obtained results confirm that this type of research is useful and brings us closer to more accurate in vivo conditions.
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Affiliation(s)
- Ksenija Durgo
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Universtiy of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | - Sunčana Orešić
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Universtiy of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | | | - Željka Fiket
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Gordana Čanadi Jurešić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, Universtiy of Rijeka, B. Branchetta 20, 51000 Rijeka, Croatia
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Asad N, Cregg S, Shakya S, Stegman S, Timmons L. Sustainable and Cost-Effective Gel Documentation. Methods Protoc 2023; 6:mps6020021. [PMID: 36961041 PMCID: PMC10037652 DOI: 10.3390/mps6020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
A common laboratory method involves gel electrophoresis followed by photographic documentation of the results, a procedure which is performed worldwide by students and experienced scientists alike. Proprietary Gel Documentation Systems are convenient and useful for documentation of electrophoresis results, but the systems can be prohibitively expensive to purchase and repair, they contain features that are not necessary for everyday documentation, and some users may not find the systems intuitive to operate. We describe our gel documentation setup that meets the everyday needs for documentation in our lab. The setup is inexpensive, modular, user friendly, and increases sustainability through extending the working life of obsolete cell phones, iPads, or other electronic devices containing a camera. More importantly, the setup completely shields users from potentially damaging ultraviolet radiation.
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Affiliation(s)
- Nadeem Asad
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
- Department of Biochemistry and Molecular Medicine, University of West Virginia Health Science Center, 64 Medical Center Drive, Morgantown, WV 26506, USA
| | - Scott Cregg
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Sudeep Shakya
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Sutton Stegman
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
| | - Lisa Timmons
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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Kee PS, Karunanathie H, Maggo SDS, Kennedy MA, Chua EW. Long-Range Polymerase Chain Reaction. Methods Mol Biol 2023; 2967:181-192. [PMID: 37608112 DOI: 10.1007/978-1-0716-3358-8_15] [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: 08/24/2023]
Abstract
Polymerase chain reaction (PCR) is a laboratory technique used to amplify a targeted region of DNA, demarcated by a set of oligonucleotide primers. Long-range PCR is a form of PCR optimized to facilitate the amplification of large fragments. Using the adapted long-range PCR protocol described in this chapter, we were able to generate PCR products of 6.6, 7.2, 13, and 20 kb from human genomic DNA samples. For some of the long PCRs, successful amplification was not possible without the use of PCR enhancers. Thus, we also evaluated the impact of some enhancers on long-range PCR and included the findings as part of this updated chapter.
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Affiliation(s)
- Ping Siu Kee
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Harsheni Karunanathie
- Centre for Drug and Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Simran D S Maggo
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
- Department of Pathology, Center for Personalized Medicine, Children's Hospital Los Angeles, California, LA, USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Eng Wee Chua
- Centre for Drug and Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
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Green MR, Sambrook J. Alkaline Agarose Gel Electrophoresis. Cold Spring Harb Protoc 2021; 2021:2021/11/pdb.prot100438. [PMID: 34725171 DOI: 10.1101/pdb.prot100438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Alkaline agarose gels are run at high pH, which causes each thymine and guanine residue to lose a proton and thus prevents the formation of hydrogen bonds with their adenine and cytosine partners. The denatured DNA is maintained in a single-stranded state and migrates through an alkaline agarose gel as a function of its size. Other denaturants such as formamide and urea do not work well because they cause the agarose to become rubbery.
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Maurye P, Basu A, Kumari K, Dey P, Sen S, Devi MS. A unified quartet DNA gel electrophoresis instrument with integrated agarose gel casting, electrophoresis, staining, and imaging facilities. SEPARATION SCIENCE PLUS 2021. [DOI: 10.1002/sscp.202100012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Praveen Maurye
- Aquatic Environmental Biotechnology and Nanotechnology Division ICAR‐Central Inland Fisheries Research Institute (Indian Council of Agricultural Research) Barrackpore Kolkata West Bengal India
| | - Arpita Basu
- Biotechnology Kendriya Vidyalaya Ministry of Human Resource Development Bhubaneswar Orissa India
| | - Kavita Kumari
- Aquatic Environmental Biotechnology and Nanotechnology Division ICAR‐Central Inland Fisheries Research Institute (Indian Council of Agricultural Research) Barrackpore Kolkata West Bengal India
| | | | - Sohini Sen
- School of Bioscience and Engineering Jadavpur Universty Kolkata West Bengal India
| | - Manoharmayum Shaya Devi
- Aquatic Environmental Biotechnology and Nanotechnology Division ICAR‐Central Inland Fisheries Research Institute (Indian Council of Agricultural Research) Barrackpore Kolkata West Bengal India
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Silva RFD, Lacchini R, Pinheiro LC, Ferezin LP, Tanus-Santos JE, Luizon MR, Dionísio TJ, Santos CF, Reia TA, Jacomini AM, Moreno AMG, Zago AS. Association between endothelial nitric oxide synthase and the renin-angiotensin-aldosterone system polymorphisms, blood pressure and training status in normotensive/pre-hypertension and hypertensive older adults: a pilot study. Clin Exp Hypertens 2021; 43:661-670. [PMID: 34156316 DOI: 10.1080/10641963.2021.1937202] [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] [Indexed: 10/21/2022]
Abstract
Introduction:Variations in blood pressure (BP) are, in part, genetically determined and some polymorphisms of renin-angiotensin- aldosterone system (RAAS) and synthase of endothelial nitric oxide (eNOS) have been related to hypertension (HT). Conversely, physical exercise is considered a non-pharmacological tool for HT control, treatment, and prevention.Objective: The purpose of this study is to investigate the relationship between eNOS and RAAS polymorphisms, their epistatic interaction, and the respective humoral factors in the BP control in normotensive/pre-hypertension and hypertensive older adults and how this relationship can be modulated by training status (TS) level.Methods:A total of 155 older adults (66.94 ± 6.83 years old) performed the following evaluations: AAHPERD battery test to determine the general functional fitness index (GFFI), systolic and diastolic blood pressure (SBP and DBP), blood collection for DNA extraction, analysis of eNOS gene polymorphisms rs2070744; rs61722009 and rs1799983 and RAAS polymorphisms rs699; rs1799752 and rs5186, and quantification of ACE activity (Fluorimetric Assay) and nitrite concentration (Chemiluminescence Method).Results and Conclusion:Good TS level appears to exert greater influence on SBP for G2 and G3 (G1: 125.79 ± 14.03/ G2: 119.91 ± 11.72/G3: 119.71 ± 10.85) and on NO2 for G3 (G1: 0.42 ± 0.25/ G2: 0.54 ± 0.45/ G3: 0.71 ± 0.52). No associations were observed between eNOS and RAAS polymorphisms, but the epistasis was identified between eNOS polymorphism, rs2070744, and RAAS polymorphism, rs699, revealing a statistically significant interaction (p = .0235) with training score of 0.63, a training test accuracy of 0.61 and a cross-validation consistency of 10/10. This result suggests an increased risk of hypertension.
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Affiliation(s)
- Roberta Fernanda da Silva
- Department of Physical Education, Post-Graduate Program in Movement Sciences, School of Sciences, Sao Paulo State University (Unesp), Bauru, Brazil
| | - Riccardo Lacchini
- Department of Psychiatric Nursing and Human Sciences, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Lucas Cezar Pinheiro
- Department of Psychiatric Nursing and Human Sciences, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Letícia Perticarrara Ferezin
- Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - José Eduardo Tanus-Santos
- Department of Pharmacology, Faculty of Medicine of Ribeirão, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Marcelo Rizzatti Luizon
- Institute of Biological Sciences, Department of Genetics, Ecology and Evolution, University of Minas Gerais Federal, Belo Horizonte, MG, Brazil
| | - Thiago José Dionísio
- Department of Pharmacology, Bauru School of Dentistry, University of São Paulo (USP), Bauru, SP, Brazil
| | - Carlos Ferreira Santos
- Department of Pharmacology, Bauru School of Dentistry, University of São Paulo (USP), Bauru, SP, Brazil
| | - Thaís Amanda Reia
- Department of Physical Education, Post-Graduate Program in Movement Sciences, School of Sciences, Sao Paulo State University (Unesp), Bauru, Brazil
| | - André Mourão Jacomini
- Department of Physical Education, Post-Graduate Program in Movement Sciences, School of Sciences, Sao Paulo State University (Unesp), Bauru, Brazil
| | - Ana Maria Guilmo Moreno
- Department of Physical Education, Post-Graduate Program in Movement Sciences, School of Sciences, Sao Paulo State University (Unesp), Bauru, Brazil
| | - Anderson Saranz Zago
- Department of Physical Education, Post-Graduate Program in Movement Sciences, School of Sciences, Sao Paulo State University (Unesp), Bauru, Brazil.,Department of Physical Education, Center for Noncommunicable Diseases, Aging and Exercise Studies (CEDEE), School of Sciences, Sao Paulo State University (Unesp), Bauru, Brazil
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15
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The Chemical Compounds from Degradation of Profenofos and Malathion by Indigenous Bacterial Consortium. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Indonesian Pesticide Regulations state that Malathion and Profenofos have been restricted in their use for agriculture because of is bioaccumulative in ecological systems. Cleaning technology using microorganisms is an effective solution for cleaning pesticide residues. This study aims to identify the bacteria that degrade and the degradation process of Malathion and Profenophos into non-toxic compounds. The research method was experimental, identification of bacteria by 16S-rRNA gene analysis, degradation ability by GC MS. The results of phylogenetic tree analysis showed that the tested bacteria were closely related to Oceanobacillus iheyenis (RPL1) and Exiquobacterium profundum (RPL5) with a similarity level of 87% and 99%. The two bacteria are used as a consortium of test bacteria. The results of degradation based on the observation chromatogram T = 0 showed that the Malathion compound C10H19O6PS2 or butanedioic acid [(dimethoxyphosphinothioyl) thio]) was detected at peak 4, real-time = 19,675, area% = 7.37 and Profenofos compound C11H15BrClO3PSO-(4-Bromo-2-chlorophenyl)o-ethyl s-propyl thiophosphate, peak 8, real-time = 23,957, area% = 6.91. Likewise, the chromatogram results at T = 96 were still detected Malathion ((dimethoxyphosphinothioyl) thio) at peak 14, real-time = 19,675, area% = 2.25, and Profenofos (o- (4-Bromo-2-chlorophenyl)) o – ethyl. s – propyl thiophosphate) peak = 22 real-time = 23,951, area% = 2,2. However, the observation of T = 192 hours, Malathion and Profenofos compounds were not detected. The conclusion showed that the consortium bacteria were able to completely degrade Malathion and Profenophos within 192 hours.
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Lu H, Liu R, Liu P, Lin W, Huang Y, Xiao R, Li Z, Ma J, Wang W, Li J, Sun LP, Guan BO. Au-NPs signal amplification ultra-sensitivity optical microfiber interferometric biosensor. OPTICS EXPRESS 2021; 29:13937-13948. [PMID: 33985120 DOI: 10.1364/oe.424878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
Abstract
An optical microfiber interferometric biosensor for the low concentration detection of sequence-specific deoxyribonucleic acid (DNA) based on signal amplification technology via oligonucleotides linked to gold nanoparticles (Au-NPs) is proposed and experimentally analyzed. The sensor uses a "sandwich" detection strategy, in which capture probe DNA (DNA-c) is immobilized on the surface of the optical microfiber interferometer, the reporter probe DNA (DNA-r) is immobilized on the surface of Au-NPs, and the DNA-c and DNA-r are hybridized to the target probe DNA (DNA-t) in a sandwich arrangement. The dynamic detection of the DNA-t was found to range from 1.0×10-15 M to 1.0×10-8 M, and the limit of detection (LOD) concentration was 1.32 fM. This sensor exhibited not only a low LOD but also excellent selectivity against mismatched DNA-t, and it can be further developed for application in various sensing platforms.
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Abstract
This chapter details the techniques used to detect transposon-induced genome rearrangements. Here, we describe a rapid DNA isolation technique, PCR amplification, and a novel High Efficiency Agarose Gel Electrophoresis Method (HEA-GEM).
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Affiliation(s)
- Sharu Paul Sharma
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Thomas Peterson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA. .,Department of Agronomy, Iowa State University, Ames, IA, USA.
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Motohashi K. A Simple and Fast Manual Centrifuge to Spin Solutions in 96-Well PCR Plates. Methods Protoc 2020; 3:E41. [PMID: 32466310 PMCID: PMC7359706 DOI: 10.3390/mps3020041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/21/2020] [Accepted: 05/24/2020] [Indexed: 11/19/2022] Open
Abstract
A simple and fast manual centrifuge was developed to spin down solutions in 96-well polymerase chain reaction (PCR) plates. A commercially available salad spinner was utilized for this purpose. Acceleration and deceleration of the centrifuge were faster than those of a conventional electric centrifuge using 96-well PCR plates. Solutions in a 96-well PCR plate settled quickly after centrifuging for only 3 s. This lightweight centrifuge can be stored under a laboratory bench or on a shelf and can be put on the bench only when required, whereas the electric centrifuge is immobile due to its weight and the requirement of electric cables. This simple centrifuge is inexpensive, requires minimal effort for making, and can be used anywhere.
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Affiliation(s)
- Ken Motohashi
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama, Kita-ku, Kyoto 603-8047, Japan; ; Fax: +81-75-705-1914
- Center for Plant Sciences, Kyoto Sangyo University, Kamigamo Motoyama, Kita-Ku, Kyoto 603-8047, Japan
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Green MR, Sambrook J. Recovery of DNA from Low-Melting-Temperature Agarose Gels: Organic Extraction. Cold Spring Harb Protoc 2020; 2020:100461. [PMID: 32123015 DOI: 10.1101/pdb.prot100461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this protocol, DNA fragments are separated according to size by electrophoresis through low-melting-temperature agarose, and then recovered by melting the agarose and extracting with phenol:chloroform. The protocol works best for DNA fragments ranging in size from 0.5 to 5.0 kb. Yields of DNA fragments outside this range are usually lower, but often are sufficient for many purposes.
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Motohashi K. Development of highly sensitive and low-cost DNA agarose gel electrophoresis detection systems, and evaluation of non-mutagenic and loading dye-type DNA-staining reagents. PLoS One 2019; 14:e0222209. [PMID: 31498824 PMCID: PMC6733488 DOI: 10.1371/journal.pone.0222209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/23/2019] [Indexed: 11/18/2022] Open
Abstract
Highly sensitive and low-cost DNA agarose gel detection systems were developed using non-mutagenic and loading dye-type DNA-staining reagents. The DNA detection system that used Midori Green Direct and Safelook Load-Green, both with an optimum excitation wavelength at ~490 nm, could detect DNA-fragments at the same sensitivity to that of the UV (312 nm)-transilluminator system combined with ethidium bromide, after it was excited by a combination of cyan LED light and a shortpass filter (510 nm). The cyan LED system can be also applied to SYBR Safe that is widely used as a non-toxic dye for post-DNA-staining. Another DNA-detection system excited by black light was also developed. Black light used in this system had a peak emission at 360 nm and caused less damage to DNA due to lower energy of UV rays with longer wavelength when compared to those of short UV rays. Moreover, hardware costs of the black light system were ~$100, less than 1/10 of the commercially available UV (365 nm) transilluminator (>$1,000). EZ-Vision and Safelook Load-White can be used as non-mutagenic and loading dye-type DNA-staining reagents in this system. The black light system had a greater detection sensitivity for DNA fragments stained by EZ-Vision and Safelook Load-White compared with the commercially available imaging system using UV (365 nm) transilluminator.
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Affiliation(s)
- Ken Motohashi
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo Motoyama, Kita-ku, Kyoto, Japan
- Center for Ecological Evolutionary Developmental Biology, Kyoto Sangyo University, Kamigamo Motoyama, Kita-Ku, Kyoto, Japan
- * E-mail:
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Filizola PRB, Luna MAC, de Souza AF, Coelho IL, Laranjeira D, Campos-Takaki GM. Biodiversity and phylogeny of novel Trichoderma isolates from mangrove sediments and potential of biocontrol against Fusarium strains. Microb Cell Fact 2019; 18:89. [PMID: 31122261 PMCID: PMC6532204 DOI: 10.1186/s12934-019-1108-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 03/18/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Studies carried out with novel 13 strains of Trichoderma, isolated from mangrove sediments (PE, Brazil) using morphophysiological and molecular characterization, followed evaluation of biocontrol using Fusarium strains isolated from Caatinga soil (PE, Brazil). Trichoderma strains were characterized by polyphasic taxonomic approach, and the extracted DNA was amplified with primers ITS 1 and 4, and sequenced. The biocontrol evaluation was conducted at 24 and 48 h of growth intervals by Tukey test, with a significance of 5%. Antibiosis tests were assessed in vitro by dual plate and partition plate techniques against Fusarium strains. RESULTS Trichoderma molecular identification, sequences of 500 bp were amplified, deposited into GenBank, and used for phylogenetic analyses. The strains were identified as T. asperellum (10), as T. harzianum (2) and one as T. longibrachiatum. Growth rate presented an average of 0.1207 cm h-1 for Trichoderma and lower growth rate of 0.031 cm h-1 for Fusarium spp., respectively. Antibiosis tests presented the best antagonist level of efficiency for T. asperellum UCP 0149 against F. solani UCP 1395 (82.2%) and F. solani UCP 1075 (70.0%), followed by T. asperellum UCP 0319 against F. solani UCP1083 (73.4%) and T. asperellum UCP 0168 against F. solani UCP1098 (71.5%), respectively. CONCLUSIONS The data obtained in this study as tool for identification of novel Trichoderma strains serve as basis for development of several sustainable use for biotechnological processes. Those Trichoderma strains found promising for the management antagonistic potential and interaction could aid the conduct of biotechnological biocontrol of contaminants, and improve environmental conditions for the health of plants.
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Affiliation(s)
- Patrícia Rego Barros Filizola
- Northeast Network for Biotechnology Post-graduation Program, Federal Rural University of Pernambuco, Recife, Pernambuco 52171-900 Brazil
- Nucleus of Research in Environmental Sciences and Biotechnology, Catholic University of Pernambuco, Recife, Pernambuco 50050-590 Brazil
| | - Marcos Antônio Cavalcanti Luna
- Northeast Network for Biotechnology Post-graduation Program, Federal Rural University of Pernambuco, Recife, Pernambuco 52171-900 Brazil
- Nucleus of Research in Environmental Sciences and Biotechnology, Catholic University of Pernambuco, Recife, Pernambuco 50050-590 Brazil
| | - Adriana Ferreira de Souza
- Northeast Network for Biotechnology Post-graduation Program, Federal Rural University of Pernambuco, Recife, Pernambuco 52171-900 Brazil
- Nucleus of Research in Environmental Sciences and Biotechnology, Catholic University of Pernambuco, Recife, Pernambuco 50050-590 Brazil
| | - Iwanne Lima Coelho
- Federal Rural University of Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, Pernambuco 52171-900 Brazil
| | - Delson Laranjeira
- Federal Rural University of Pernambuco, Rua Dom Manoel de Medeiros, s/n, Dois Irmãos, Recife, Pernambuco 52171-900 Brazil
| | - Galba Maria Campos-Takaki
- Nucleus of Research in Environmental Sciences and Biotechnology, Catholic University of Pernambuco, Recife, Pernambuco 50050-590 Brazil
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Abstract
This protocol describes steps for the preparation and running of agarose gels and for staining and visualization of DNA in gels using three dyes: ethidium bromide, SYBR Gold, and SYBR Green 1.
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