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Costa-Ribeiro A, Lamas A, Garrido-Maestu A. Evaluating Commercial Loop-Mediated Isothermal Amplification Master Mixes for Enhanced Detection of Foodborne Pathogens. Foods 2024; 13:1635. [PMID: 38890864 PMCID: PMC11172173 DOI: 10.3390/foods13111635] [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: 04/15/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
Loop-mediated isothermal amplification, LAMP, is nowadays the most popular isothermal nucleic acid amplification technique, and as such, several commercial, ready-to-use master mixes have flourished. Unfortunately, independent studies to determine their performance are limited. The current study performed an independent evaluation of the existing ready-to-use commercial LAMP master mixes WarmStart® LAMP Kit, LavaLAMP™ DNA Master Mix, Saphir Bst Turbo GreenMaster, OptiGene Fast Master Mix ISO-004, and SynLAMP Mix. To reduce bias, three different genes, namely ttr (Salmonella spp.), rfbE (E. coli O157), and hly (Listeria monocytogenes), were targeted. The comparison was based on amplification speed, performance with decreasing DNA concentrations, and the effect of five typical LAMP reaction additives (betaine, DMSO, pullulan, TMAC, and GuHCl). Significant differences were observed among the different master mixes. OptiGene provided the fastest amplification and showed less detrimental effects associated with the supplements evaluated. Out of the chemicals tested, pullulan provided the best results in terms of amplification speed. It is noteworthy that the different additives impacted the master mixes differently. Overall, the current study provides insights into the performance of commercial LAMP master mixes, which can be of value for the scientific community to better select appropriate reagents when developing new methods.
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Affiliation(s)
- Ana Costa-Ribeiro
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal;
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Campus Terra, University of Santiago de Compostela (USC), 27002 Lugo, Spain;
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal;
- Laboratory of Microbiology and Technology of Marine Products (MicroTEC), Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain
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Lago JC, Ganzerla MD, Dias ALA, Savietto JP. The Influence of Blue Light Exposure on Reconstructed 3-Dimensional Skin Model: Molecular Changes and Gene Expression Profile. JID INNOVATIONS 2024; 4:100252. [PMID: 38328595 PMCID: PMC10848142 DOI: 10.1016/j.xjidi.2023.100252] [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: 12/13/2021] [Revised: 11/09/2023] [Accepted: 11/16/2023] [Indexed: 02/09/2024] Open
Abstract
Recent studies have provided information about digital eye strain and the potential damage that blue light from digital devices can cause to the eyes. In this study, we analyzed the influence of blue light exposure on reconstructed 3-dimensional skin model using RNA sequencing to identify the expression of transcripts and abnormal events. Three-dimensional skin was exposed to visible light spectrum and isolated blue wavelength for 1, 2, and 4 hours to represent acute exposure and 1 hour over 4 sequential days to represent repeated exposure, respectively, in this in vitro model. We compared gene expression levels with those of unexposed control. Samples submitted to repeated exposure showed reduced AK2 and DDX47, whereas they showed increased PABPC3 gene expression, revealing a significantly negative impact. RT-PCR validation assay with exposed 3-dimensional skin compared with unexposed control regarding 1 and 4 days of incubation showed increased IL-6 signaling mechanism activation and signal transducer and activator of transcription 3 gene STAT3 gene expression, whereas it showed decreased peroxisome proliferator-activated receptor signaling mechanism activation, suggesting an influence on inflammatory pathways. We also demonstrate upregulated gene expression of KIT, MAPK2, and PI3KC in samples from exposed condition, corroborating previous findings related to pigmentation signaling stimuli. These results reveal, to our knowledge, previously unreported data that enable studies on molecular response correlation of in vitro digital blue light exposure and human skin studies.
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Encinas-García T, Mendoza-Cano F, Muhlia-Almazán A, Vega-Peralta J, Sánchez-Paz A. Comparison of five commercial kits for isolation of total RNA in samples of WSSV-infected shrimp. DISEASES OF AQUATIC ORGANISMS 2023; 156:59-70. [PMID: 38032039 DOI: 10.3354/dao03762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Viral diseases are the most serious threat to the expansion and development of shrimp aquaculture. Rapid diagnosis of the white spot syndrome virus (WSSV), a lethal shrimp pathogen, is essential to restrict its spread and reduce the mortality of infected shrimp. This virus has globally affected the shrimp farming industry, with a devastating economic impact. Several studies have focused on the expression of WSSV transcripts to understand the molecular mechanisms governing the pathological development of the disease. Since gene expression studies and molecular diagnostics at the early stages of infection depend on the efficient isolation of high-quality RNA, the extraction methods should be carefully selected. However, previous comparisons of the performance of RNA isolation kits have yet to be systematically investigated. In this study, 5 commercial RNA extraction methods were compared in WSSV-infected shrimp. The highest total RNA yield (ng mg-1 tissue) was obtained using TRIzol. Even though the 260/280 nm absorption ratios showed significant differences, the methods showed good purity values (>2.0). RNA integrity was evaluated in a denaturing agarose gel electrophoresis, and degradation was observed after the total RNA samples were treated with DNase I. Finally, the method that allowed the earlier detection of WSSV transcripts by qRT-PCR was the Zymo Direct-zol RNA MiniPrep kit. This study shows that the amount of observed (or estimated) WSSV transcripts might be affected because of the RNA isolation method. In addition, these results may contribute to improve the accuracy of the results obtained in gene expression studies, for more sensitive and robust detection of WSSV.
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Affiliation(s)
- Trinidad Encinas-García
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Campus Hermosillo, Hermosillo, Sonora, CP 83106, México
| | - Fernando Mendoza-Cano
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Campus Hermosillo, Hermosillo, Sonora, CP 83106, México
| | - Adriana Muhlia-Almazán
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD) Unidad Hermosillo, Carretera Gustavo Enrique Astiazaran Rosas, No. 46, Col. La Victoria, Hermosillo, Sonora 83304, México
| | - Juan Vega-Peralta
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Campus Hermosillo, Hermosillo, Sonora, CP 83106, México
| | - Arturo Sánchez-Paz
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Campus Hermosillo, Hermosillo, Sonora, CP 83106, México
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4
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Balpınar Ö, Nadaroğlu H, Hacımüftüoğlu A. Green synthesis, characterization of melatonin-like drug bioconjugated CoS quantum dots and its antiproliferative effect on different cancer cells. Mol Biol Rep 2023; 50:9143-9151. [PMID: 37768465 DOI: 10.1007/s11033-023-08817-3] [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: 07/10/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
BACKGROUND Quantum dots are usually particles smaller than 100 nm and have a low toxic effect. This study aimed to bioconjugate the anticancer effective melatonin agonist to quantum dots and demonstrate its effects in two cancer lines. This is the first study that aims to examine the anticancer activity of ramelteon bioconjugation to quantum dots, providing a new perspective on the use of Melatonin and its derivatives in cancer. METHODS AND RESULTS For this purpose, first of all, cobalt sulfide (CoS) quantum dots were synthesized, bioconjugated and characterized with Punica granatum extract by green synthesis method. The effects of synthesized nanomaterials on neuroblastoma and prostate cancer cells were investigated. It was noted that nanomaterials reduced cell viability by 50% in neuroblastoma and prostate cancer lines at a dose of 50 µg/mL. Ramelteon bioconjugated nanomaterials reduced cancer cell viability by 1.4 times more than free melatonin. CoS quantum dots were determined to double the oxidative stress in the neuroblastoma cell line compared to the control, while no change was observed in prostate cancer. In the gene expression findings, it was observed that CoS nanoparticles caused an increase in the expression levels of apoptosis-related genes in the neuroblastoma cell line and induced key protein expression levels of pathways such as ROR-alpha in the prostate cancer cell line. CONCLUSION As a result, it was observed that the viability of the neuroblastoma cell line decreased with apoptosis induced by oxidative stress, while this effect was observed in the DU-145 cell line via the ROR-alpha pathway.
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Affiliation(s)
- Özge Balpınar
- Hemp Research Institute, Ondokuz Mayıs University, 55200, Samsun, Turkey.
| | - Hayrunnisa Nadaroğlu
- Department of Nano-Science and Nano-Engineering, Faculty of Engineering, Ataturk University, 25240, Erzurum, Turkey
| | - Ahmet Hacımüftüoğlu
- Department of Medical Pharmacology, Faculty of Medicine, Ataturk University, 25240, Erzurum, Turkey
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5
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Sakyi SA, Effah A, Naturinda E, Senu E, Opoku S, Amoani B, Agordzo SK, Mensah OSO, Grant J, Abban E, Buckman TA, Kwarteng A, Ephraim RKD, Danquah KO. Comparison of Modified Manual Acid-Phenol Chloroform Method and Commercial RNA Extraction Kits for Resource Limited Laboratories. Int J Clin Pract 2023; 2023:9593796. [PMID: 37333947 PMCID: PMC10275685 DOI: 10.1155/2023/9593796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/11/2023] [Accepted: 05/30/2023] [Indexed: 06/20/2023] Open
Abstract
Method In a comparative experimental cross-sectional study, RNA was extracted from oral swabs and blood samples from 25 healthy individuals at the Department of Molecular Medicine, KNUST. RNA was extracted by the manual AGPC extraction method and commercial RNA extraction kits. The quantity (ng/μl) and purities (260/280 nm) of the extracted RNA were measured spectrophotometrically using the IMPLEN NanoPhotometer® N60. The presence of RNA in the extracts was confirmed using 2% agarose gel electrophoresis. Statistical analyses were conducted using R language. Results The yield of RNA extracted from blood and oral swab samples using modified AGPC was significantly higher compared to the commercial methods (p < 0.0001). However, the purity of RNA extracted by the manual AGPC method from blood was significantly lower than the commercial methods (p < 0.0001). Moreover, the purity from oral swabs using the manual AGPC method was significantly lower compared to QIAamp (p < 0.0001) and the OxGEn kits method (p < 0.001). Conclusion The modified manual AGPC method has a very high yield of RNA extracts using blood samples, which could serve as an alternate cost-effective method for RNA extraction in resource-limited laboratories; however, its purity may not be suitable for downstream processes. Moreover, the manual AGPC method may not be suitable for extracting RNA from oral swab samples. Future investigation is needed to improve the purity of the manual AGPC RNA extraction method and also confirmation of the obtained results by PCR amplification and RNA purity verification by sequencing.
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Affiliation(s)
- Samuel Asamoah Sakyi
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alfred Effah
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Department of Medical Diagnostics, Faculty of Allied Health Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emmanuel Naturinda
- Department of Medical Diagnostics, Faculty of Allied Health Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ebenezer Senu
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Stephen Opoku
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, UK
| | - Benjamin Amoani
- Department of Biomedical Science, School of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Samuel Kekeli Agordzo
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Oscar Simon Olympio Mensah
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - James Grant
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Elizabeth Abban
- Department of Medical Diagnostics, Faculty of Allied Health Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Department of Medical Laboratory Technology, Garden City University College, Kumasi, Ghana
| | - Tonnies Abeku Buckman
- Department of Molecular Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richard K. Dadzie Ephraim
- Department of Medical Laboratory Sciences, Faculty of Allied Health, University of Cape Coast, Cape Coast, Ghana
| | - Kwabena Owusu Danquah
- Department of Clinical Pathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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Moitra P, Chaichi A, Abid Hasan SM, Dighe K, Alafeef M, Prasad A, Gartia MR, Pan D. Probing the mutation independent interaction of DNA probes with SARS-CoV-2 variants through a combination of surface-enhanced Raman scattering and machine learning. Biosens Bioelectron 2022; 208:114200. [PMID: 35367703 PMCID: PMC8938299 DOI: 10.1016/j.bios.2022.114200] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/06/2022] [Accepted: 03/17/2022] [Indexed: 12/01/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has been characterized by the emergence of sets of mutations impacting the virus characteristics, such as transmissibility and antigenicity, presumably in response to the changing immune profile of the human population. The presence of mutations in the SARS-CoV-2 virus can potentially impact therapeutic and diagnostic test performances. We design and develop here a unique set of DNA probes i.e., antisense oligonucleotides (ASOs) which can interact with genetic sequences of the virus irrespective of its ongoing mutations. The probes, developed herein, target a specific segment of the nucleocapsid phosphoprotein (N) gene of SARS-CoV-2 with high binding efficiency which do not mutate among the known variants. Further probing into the interaction profile of the ASOs reveals that the ASO-RNA hybridization remains unaltered even for a hypothetical single point mutation at the target RNA site and diminished only in case of the hypothetical double or triple point mutations. The mechanism of interaction among the ASOs and SARS-CoV-2 RNA is then explored with a combination of surface-enhanced Raman scattering (SERS) and machine learning techniques. It has been observed that the technique, described herein, could efficiently discriminate between clinically positive and negative samples with ∼100% sensitivity and ∼90% specificity up to 63 copies/mL of SARS-CoV-2 RNA concentration. Thus, this study establishes N gene targeted ASOs as the fundamental machinery to efficiently detect all the current SARS-CoV-2 variants regardless of their mutations.
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Affiliation(s)
- Parikshit Moitra
- Department of Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, United States
| | - Ardalan Chaichi
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Syed Mohammad Abid Hasan
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Ketan Dighe
- Department of Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, United States; Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, United States
| | - Maha Alafeef
- Department of Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, United States; Bioengineering Department, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, United States; Biomedical Engineering Department, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Alisha Prasad
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Manas Ranjan Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, United States.
| | - Dipanjan Pan
- Department of Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, United States; Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, United States; Bioengineering Department, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, United States.
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Ng NS, Maksour S, Lum JS, Newbery M, Shephard V, Ooi L. An Optimized Direct Lysis Gene Expression Microplate Assay and Applications for Disease, Differentiation, and Pharmacological Cell-Based Studies. BIOSENSORS 2022; 12:364. [PMID: 35735512 PMCID: PMC9221485 DOI: 10.3390/bios12060364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Routine cell culture reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) gene expression analysis is limited in scalability due to minimum sample requirement and multistep isolation procedures. In this study, we aimed to optimize and apply a cost-effective and rapid protocol for directly sampling gene expression data from microplate cell cultures. The optimized protocol involves direct lysis of microplate well population followed by a reduced thermocycler reaction time one-step RT-qPCR assay. In applications for inflammation and stress-induced cell-based models, the direct lysis RT-qPCR microplate assay was utilized to detect IFN1 and PPP1R15A expression by poly(I:C) treated primary fibroblast cultures, IL6 expression by poly(I:C) iPSC-derived astrocytes, and differential PPP1R15A expression by ER-stressed vanishing white-matter disease patient induced pluripotent stem cell (iPSC)-derived astrocytes. In application for neural differentiation medium recipe optimizations, conditions were screened for SYN1 and VGLUT1 in neuronal cultures, and S100B, GFAP and EAAT1 in astrocyte cultures. The protocol provides microplate gene expression results from cell lysate to readout within ~35 min, with comparable cost to routine RT-qPCR, and it may be utilized to support laboratory cell-based assays in basic and applied scientific and medical fields of research including stem-cell differentiation, cell physiology, and drug mechanism studies.
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Affiliation(s)
- Neville S. Ng
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia; (S.M.); (J.S.L.); (M.N.); (V.S.)
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Simon Maksour
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia; (S.M.); (J.S.L.); (M.N.); (V.S.)
- School of Medical, Indigenous and Health Sciences, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Jeremy S. Lum
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia; (S.M.); (J.S.L.); (M.N.); (V.S.)
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Michelle Newbery
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia; (S.M.); (J.S.L.); (M.N.); (V.S.)
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Victoria Shephard
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia; (S.M.); (J.S.L.); (M.N.); (V.S.)
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, Northfields Avenue, Wollongong, NSW 2522, Australia; (S.M.); (J.S.L.); (M.N.); (V.S.)
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
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Shirai Y, Miura K, Kaneko N, Ishizuka K, Endo A, Hashimoto T, Kanda S, Harita Y, Hattori M. A novel de novo truncating TRIM8 variant associated with childhood-onset focal segmental glomerulosclerosis without epileptic encephalopathy: a case report. BMC Nephrol 2021; 22:417. [PMID: 34930159 PMCID: PMC8686241 DOI: 10.1186/s12882-021-02626-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/05/2021] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Heterozygous truncating variants in the Tripartite motif containing 8 (TRIM8) gene have been reported to cause epileptic encephalopathy, both with and without proteinuria. A recent study showed a lack of TRIM8 protein expression, with suppressor of cytokine signaling 1 (SOCS1) overexpression, in podocytes and tubules from a patient with a TRIM8 variant, who presented with epileptic encephalopathy and focal segmental glomerulosclerosis (FSGS). To date, no patients with TRIM8 variants who presented with nephrotic syndrome but without neurological manifestations have been described. CASE PRESENTATION An 8-year-old girl presented with nephrotic syndrome, without epilepsy or developmental delay. Her kidney biopsy specimens showed FSGS and cystic dilatations of the distal tubules. Whole-exome sequencing identified a novel de novo heterozygous variant in the C-terminal encoding portion of TRIM8 (c.1461C > A), resulting in a premature stop codon (p.Tyr487*). Reverse transcription-polymerase chain reaction using peripheral blood mononuclear cells identified the mRNA sequence of the mutant allele, which confirmed an escape from nonsense-mediated mRNA decay. Immunofluorescence studies showed a lack of TRIM8 expression in glomerular and tubular cells and cystic dilatation of distal tubules. Immunohistochemical studies showed overexpression of SOCS1 in glomerular and tubular cells. CONCLUSIONS We reported a patient with FSGS, associated with a de novo heterozygous TRIM8 variant, without any neurological manifestations. Our results expanded the clinical phenotypic spectrum of TRIM8 variants.
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Affiliation(s)
- Yoko Shirai
- Department of Pediatric Nephrology, Tokyo Women's Medical University, Tokyo, Japan
| | - Kenichiro Miura
- Department of Pediatric Nephrology, Tokyo Women's Medical University, Tokyo, Japan
| | - Naoto Kaneko
- Department of Pediatric Nephrology, Tokyo Women's Medical University, Tokyo, Japan
| | - Kiyonobu Ishizuka
- Department of Pediatric Nephrology, Tokyo Women's Medical University, Tokyo, Japan
| | - Amane Endo
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Taeko Hashimoto
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Shoichiro Kanda
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Harita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Motoshi Hattori
- Department of Pediatric Nephrology, Tokyo Women's Medical University, Tokyo, Japan.
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9
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Alafeef M, Moitra P, Dighe K, Pan D. RNA-extraction-free nano-amplified colorimetric test for point-of-care clinical diagnosis of COVID-19. Nat Protoc 2021; 16:3141-3162. [PMID: 33931780 DOI: 10.1038/s41596-021-00546-w] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
The global pandemic of coronavirus disease 2019 (COVID-19) highlights the shortcomings of the current testing paradigm for viral disease diagnostics. Here, we report a stepwise protocol for an RNA-extraction-free nano-amplified colorimetric test for rapid and naked-eye molecular diagnosis of COVID-19. The test employs a unique dual-prong approach that integrates nucleic acid (NA) amplification and plasmonic sensing for point-of-care detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with a sample-to-assay response time of <1 h. The RNA-extraction-free nano-amplified colorimetric test utilizes plasmonic gold nanoparticles capped with antisense oligonucleotides (ASOs) as a colorimetric reporter to detect the amplified nucleic acid from the COVID-19 causative virus, SARS-CoV-2. The ASOs are specific for the SARS-CoV-2 N-gene, and binding of the ASOs to their target sequence results in the aggregation of the plasmonic gold nanoparticles. This highly specific agglomeration step leads to a change in the plasmonic response of the nanoparticles. Furthermore, when tested using clinical samples, the accuracy, sensitivity and specificity of the test were found to be >98.4%, >96.6% and 100%, respectively, with a detection limit of 10 copies/μL. The test can easily be adapted to diagnose other viral infections with a simple modification of the ASOs and primer sequences. It also provides a low-cost, rapid approach requiring minimal instrumentation that can be used as a screening tool for the diagnosis of COVID-19 at point-of-care settings in resource-poor situations. The colorimetric readout of the test can even be monitored using a handheld optical reader to obtain a quantitative response. Therefore, we anticipate that this protocol will be widely useful for the development of biosensors for the molecular diagnostics of COVID-19 and other infectious diseases.
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Affiliation(s)
- Maha Alafeef
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Biomedical Engineering Department, Jordan University of Science and Technology, Irbid, Jordan.,Departments of Diagnostic Radiology and Nuclear Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA.,Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Parikshit Moitra
- Departments of Diagnostic Radiology and Nuclear Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA
| | - Ketan Dighe
- Departments of Diagnostic Radiology and Nuclear Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA.,Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Dipanjan Pan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Departments of Diagnostic Radiology and Nuclear Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, USA. .,Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, USA.
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10
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Rodríguez A, Duyvejonck H, Van Belleghem JD, Gryp T, Van Simaey L, Vermeulen S, Van Mechelen E, Vaneechoutte M. Comparison of procedures for RNA-extraction from peripheral blood mononuclear cells. PLoS One 2020; 15:e0229423. [PMID: 32084228 PMCID: PMC7034890 DOI: 10.1371/journal.pone.0229423] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
RNA quality and quantity are important factors for ensuring the accuracy of gene expression analysis and other RNA-based downstream applications. Thus far, only a limited number of methodological studies have compared sample storage and RNA extraction procedures for human cells. We compared three commercially available RNA extraction kits, i.e., (NucliSENS) easyMAG, RNeasy (Mini Kit) and RiboPure (RNA Purification Kit–blood). In addition, additional conditions, such as storage medium and storage temperature of human peripheral blood mononuclear cells were evaluated, i.e., 4 °C for RNAlater or -80 °C for QIAzol and for the respective cognate lysis buffers; easyMAG, RNeasy or RiboPure. RNA was extracted from aliquots that had been stored for one day (Run 1) or 83 days (Run 2). After DNase treatment, quantity and quality of RNA were assessed by means of a NanoDrop spectrophotometer, 2100 Bioanalyzer and RT-qPCR for the ACTB reference gene. We observed that high-quality RNA can be obtained using RNeasy and RiboPure, regardless of the storage medium, whereas samples stored in RNAlater resulted in the least amount of RNA extracted. In addition, RiboPure combined with storage of samples in its cognate lysis buffer yielded twice as much RNA as all other procedures. These results were supported by RT-qPCR and by the reproducibility observed for two independent extraction runs.
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Affiliation(s)
- Antonio Rodríguez
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- * E-mail:
| | - Hans Duyvejonck
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Jonas D. Van Belleghem
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Tessa Gryp
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Stefan Vermeulen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Els Van Mechelen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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Cortés-Maldonado L, Marcial-Quino J, Gómez-Manzo S, Fierro F, Tomasini A. A method for the extraction of high quality fungal RNA suitable for RNA-seq. J Microbiol Methods 2020; 170:105855. [PMID: 32004552 DOI: 10.1016/j.mimet.2020.105855] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 11/16/2022]
Abstract
Transcriptomic analysis is an OMICs technology that is becoming indispensable to understand and get a complete picture of cell functioning and adaptation to the environmental cues the cell is continuously receiving. Among the techniques available to perform transcriptomics, RNA-seq is becoming the method of choice. The quality of the RNA used for the generation of cDNA libraries and subsequent sequencing is crucial for the success of the process. Good RNA-seq performance is often limited by problems such as low RNA yield and/or integrity, RNA stability, and contamination with DNA, salts or chemicals. RNA isolation from fungi usually faces these problems and is particularly sensitive to degradation due to the high RNase activity content present in many species. Here we describe the development of a robust, highly reproducible and simple RNA purification method for filamentous fungi, which combines various strategies to get fully DNA-free RNA samples of high purity and integrity without the need to use a DNase I digestion step. The obtained RNA samples complied with all required standards to be used for RNA-seq and showed an excellent performance when subjected to Illumina-HiSeq 2500.
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Affiliation(s)
- Leyda Cortés-Maldonado
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Mexico City 09340, Mexico
| | - Jaime Marcial-Quino
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico.
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico.
| | - Francisco Fierro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Mexico City 09340, Mexico
| | - Araceli Tomasini
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Mexico City 09340, Mexico.
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RNA-based qPCR as a tool to quantify and to characterize dual-species biofilms. Sci Rep 2019; 9:13639. [PMID: 31541147 PMCID: PMC6754382 DOI: 10.1038/s41598-019-50094-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022] Open
Abstract
While considerable research has focused on studying individual-species, we now face the challenge of determining how interspecies interactions alter bacterial behaviours and pathogenesis. Pseudomonas aeruginosa and Staphylococcus aureus are often found to co-infect cystic-fibrosis patients. Curiously, their interaction is reported as competitive under laboratory conditions. Selecting appropriate methodologies is therefore critical to analyse multi-species communities. Herein, we demonstrated the major biases associated with qPCR quantification of bacterial populations and optimized a RNA-based qPCR able not only to quantify but also to characterize microbial interactions within dual-species biofilms composed by P. aeruginosa and S. aureus, as assessed by gene expression quantification. qPCR quantification was compared with flow-cytometry and culture-based quantification. Discrepancies between culture independent and culture dependent methods could be the result of the presence of viable but not-cultivable bacteria within the biofilm. Fluorescence microscopy confirmed this. A higher sensitivity to detect viable cells further highlights the potentialities of qPCR approach to quantify biofilm communities. By using bacterial RNA and an exogenous mRNA control, it was also possible to characterize bacterial transcriptomic profile, being this a major advantage of this method.
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mRNA extraction of Xanthomonas fragariae in strawberry and validation of reference genes for the RT-qPCR for study of bacterial gene expression. Mol Biol Rep 2019; 46:5723-5733. [PMID: 31368022 DOI: 10.1007/s11033-019-05006-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/26/2019] [Indexed: 01/11/2023]
Abstract
This is the first study which describes a unique procedure of isolating of high-quality, intact RNA from strawberry leaves of Xanthomonas fragariae, three most suitable reference genes, crucial for the normalization of RT-qPCR data for this pathogen and accurate expression analysis of target genes. In our study, various mathematic algorithms: NormFinder geNorm, BestKeeper, the delta CT method, RefFinder were adopted for validation of most stable reference genes from nine candidate genes (ffh, glyA, gyrA, gyrB, proC, pykA, recA, rpoB, rpoD). The analyses allowing to select three most suitable pioneer reference genes, gyrB, ffh, and pykA, that we recommend for the normalization of RT-qPCR data and for the study of the expression of target genes in Xf. Moreover, their combination as references allowed for an accurate expression analysis and computation of the fold change of the flhF and iroN2 genes in Xf. These two genes are important for the success of the colonization of plant tissue and pathogenicity and sequences of primers designed to study these genes, are presented.
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Human uterine leiomyoma contains low levels of 1, 25 dihdroxyvitamin D3, and shows dysregulated expression of vitamin D metabolizing enzymes. Eur J Obstet Gynecol Reprod Biol 2018; 229:117-122. [PMID: 30172168 DOI: 10.1016/j.ejogrb.2018.08.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/11/2018] [Accepted: 08/12/2018] [Indexed: 01/08/2023]
Abstract
OBJECTIVES To evaluate tissue concentration of 1, 25 dihydroxyvitamin D3, and gene expression level of CYP27B1 that codes for 1-α hydroxylase (vitamin D activating enzyme), and CYP24A1 that codes for 24-hydroxylase (vitamin D catabolizing enzyme) in human uterine leiomyoma (ULM), its adjacent myometrium (Myo-F), and normal myometrium (Myo-N). STUDY DESIGN Levels of 1, 25 dihydroxyvitamin D3 were measured using HPLC and Diode detectors whereas CYP27B1, and CYP24A1 expressions were assessed using Real-Time PCR in ULM, Myo-F, and Myo-N. Non-parametric statistics were used. RESULTS ULMs contained significantly less 1, 25 dihydroxy vitamin D3 compared to Myo-F (3.0, IQR: 1.0-9.0 versus 6.0, IQR: 3.0-13.0 μg/ kg, P value is 0.03). No significant difference was detected between ULM and Myo-N, or Myo-F and Myo-N. Intratumoral level of the active form of vitamin D did not differ according to the type of ULM (submucous or interstitial/subserous), or to the ULM volume. CYP27B1 was expressed in ULM (2.17, IQR: 0.65-4.9), Myo-F (4.94, IQR: 1.04-22.59), and Myo-N (0.99, IQR: 0.49-1.71) to a comparable level. CYP24A1 expression was significantly higher in ULM compared to Myo-N (2.00, IQR: 0.69-10.77 versus 0.22, IQR: 00- 0.96, respectively, P value is 0.04). CONCLUSIONS Human ULMs contain significantly lower 1, 25 dihydroxyvitamin D3 than its adjacent myometrium. ULM, Myo-F, and Myo-N express CYP27B1 and CYP24A1. ULMs express significantly higher level of CYP24A1 than normal myometrium indicating that over expression of 24-hydroxylase is a mechanism by which ULMs sustain a relative state of hypovitaminosis D.
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Mishra A, Reddy IJ, Gupta PSP, Mondal S. Total RNA content in sheep oocytes and developing embryos produced in vitro, a comparative study between spectrophotometric and fluorometric assay. CYTOL GENET+ 2018. [DOI: 10.3103/s0095452718010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Beedle AM. Cryosectioning of Contiguous Regions of a Single Mouse Skeletal Muscle for Gene Expression and Histological Analyses. J Vis Exp 2016. [PMID: 28060301 DOI: 10.3791/55058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
With this method, consecutive cryosections are collected to enable both microscopy applications for tissue histology and enrichment of RNA for gene expression using adjacent regions from a single mouse skeletal muscle. Typically, it is challenging to achieve adequate homogenization of small skeletal muscle samples because buffer volumes may be too low for efficient grinding applications, yet without sufficient mechanical disruption, the dense tissue architecture of muscle limits penetration of buffer reagents, ultimately causing low RNA yield. By following the protocol reported here, 30 μm sections are collected and pooled allowing cryosectioning and subsequent needle homogenization to mechanically disrupt the muscle, increasing the surface area exposed for buffer penetration. The primary limitations of the technique are that it requires a cryostat, and it is relatively low throughput. However, high-quality RNA can be obtained from small samples of pooled muscle cryosections, making this method accessible for many different skeletal muscles and other tissues. Furthermore, this technique enables matched analyses (e.g., tissue histopathology and gene expression) from adjacent regions of a single skeletal muscle so that measurements can be directly compared across applications to reduce experimental uncertainty and to reduce replicative animal experiments necessary to source a small tissue for multiple applications.
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Affiliation(s)
- Aaron M Beedle
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia;
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17
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Changes in Bacillus Spore Small Molecules, rRNA, Germination, and Outgrowth after Extended Sublethal Exposure to Various Temperatures: Evidence that Protein Synthesis Is Not Essential for Spore Germination. J Bacteriol 2016; 198:3254-3264. [PMID: 27645383 DOI: 10.1128/jb.00583-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/08/2016] [Indexed: 11/20/2022] Open
Abstract
rRNAs of dormant spores of Bacillus subtilis were >95% degraded during extended incubation at 50°C, as reported previously (E. Segev, Y. Smith, and S. Ben-Yehuda, Cell 148:139-114, 2012, doi:http://dx.doi.org/10.1016/j.cell.2011.11.059), and this was also true of spores of Bacillus megaterium Incubation of spores of these two species for ∼20 h at 75 to 80°C also resulted in the degradation of all or the great majority of the 23S and 16S rRNAs, although this rRNA degradation was slower than nonenzymatic hydrolysis of purified rRNAs at these temperatures. This rRNA degradation at high temperature generated almost exclusively oligonucleotides with minimal levels of mononucleotides. RNase Y, suggested to be involved in rRNA hydrolysis during B. subtilis spore incubation at 50°C, did not play a role in B. subtilis spore rRNA breakdown at 80°C. Twenty hours of incubation of Bacillus spores at 70°C also decreased the already minimal levels of ATP in dormant spores 10- to 30-fold, to ≤0.01% of the total free adenine nucleotide levels. Spores depleted of rRNA were viable and germinated relatively normally, often even faster than starting spores. Their return to vegetative growth was also similar to that of untreated spores for B. megaterium spores and slower for heat-treated B. subtilis spores; accumulation of rRNA took place only after completion of spore germination. These findings thus strongly suggest that protein synthesis is not essential for Bacillus spore germination.IMPORTANCE A recent report (L. Sinai, A. Rosenberg, Y. Smith, E. Segev, and S. Ben-Yehuda, Mol Cell 57:3486-3495, 2015, doi:http://dx.doi.org/10.1016/j.molcel.2014.12.019) suggested that protein synthesis is essential for early steps in the germination of dormant spores of Bacillus subtilis If true, this would be a paradigm shift in our understanding of spore germination. We now show that essentially all of the rRNA can be eliminated from spores of Bacillus megaterium or B. subtilis, and these rRNA-depleted spores are viable and germinate as well as or better than spores with normal rRNA levels. Thus, protein synthesis is not required in the process of spore germination.
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18
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Beltrame CO, Côrtes MF, Bandeira PT, Figueiredo AMS. Optimization of the RNeasy Mini Kit to obtain high-quality total RNA from sessile cells of Staphylococcus aureus. ACTA ACUST UNITED AC 2016; 48:1071-6. [PMID: 26517334 PMCID: PMC4661022 DOI: 10.1590/1414-431x20154734] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 07/23/2015] [Indexed: 12/20/2022]
Abstract
Biofilm formed by Staphylococcus aureus is considered an important
virulence trait in the pathogenesis of infections associated with implantable medical
devices. Gene expression analyses are important strategies for determining the
mechanisms involved in production and regulation of biofilm. Obtaining intact RNA
preparations is the first and most critical step for these studies. In this article,
we describe an optimized protocol for obtaining total RNA from sessile cells of
S. aureus using the RNeasy Mini Kit. This method essentially
consists of a few steps, as follows: 1) addition of acetone-ethanol to sessile cells,
2) lysis with lysostaphin at 37°C/10 min, 3) vigorous mixing, 4) three cycles of
freezing and thawing, and 5) purification of the lysate in the RNeasy column. This
simple pre-kit procedure yields high-quality total RNA from planktonic and sessile
cells of S. aureus.
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Affiliation(s)
- C O Beltrame
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - M F Côrtes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - P T Bandeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - A M S Figueiredo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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Kolijn K, van Leenders GJLH. Comparison of RNA extraction kits and histological stains for laser capture microdissected prostate tissue. BMC Res Notes 2016; 9:17. [PMID: 26744212 PMCID: PMC4705748 DOI: 10.1186/s13104-015-1813-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 12/17/2015] [Indexed: 12/02/2022] Open
Abstract
Background Laser capture microdissection offers unique possibilities for the isolation of specific cell populations or histological structures. However, isolation of RNA from microdissected tissue is challenging due to degradation and minimal yield of RNA during laser capture microdissection (LCM). Our aim was to optimize the isolation of high-quality RNA from laser capture microdissected fresh frozen prostate tissue on the level of staining and RNA extraction. Results Cresyl violet and haematoxylin were compared as histological stains for LCM. While RNA quality was similar for cresyl violet (median RIN 7.4) and haematoxylin (median RIN 7.6), tissue morphology was more detailed with cresyl violet as compared to haematoxylin. RNA quality from the following kits was compared: RNeasy® Micro (median RIN 7.2), miRNeasy Mini (median RIN 6.6), Picopure® (median RIN 6.0), mirVana™ miRNA (median RIN 6.5) and RNAqueous®-Micro (median RIN 6.3). RNA quality from microdissected samples with either the RNeasy Micro or miRNeasy Mini kit, was comparable to RNA isolated directly from whole tissue slices (median RIN 7.5, p = 0.09). Isolated RNA from benign and prostate cancer microdissected tissue demonstrated that RNA quality can vary between regions from the same clinical sample. Additionally, RNA quality (r = 0.89), but not quantity (r = 0.69) could be precisely measured with the Agilent Bioanalyzer. Conclusions We demonstrate that staining with cresyl violet results in the isolation of high quality RNA from laser capture microdissected tissue with high discriminative morphology. The RNeasy Micro and miRNeasy Mini RNA extraction kits generated the highest quality RNA compared to Picopure, mirVana and RNAqueous with minimal loss of RNA quality during LCM. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1813-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kimberley Kolijn
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands.
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20
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Heera R, Sivachandran P, Chinni SV, Mason J, Croft L, Ravichandran M, Yin LS. Efficient extraction of small and large RNAs in bacteria for excellent total RNA sequencing and comprehensive transcriptome analysis. BMC Res Notes 2015; 8:754. [PMID: 26645211 PMCID: PMC4673735 DOI: 10.1186/s13104-015-1726-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 11/20/2015] [Indexed: 11/13/2022] Open
Abstract
Background Next-generation transcriptome sequencing (RNA-Seq) has become the standard practice for studying gene splicing, mutations and changes in gene expression to obtain valuable, accurate biological conclusions. However, obtaining good sequencing coverage and depth to study these is impeded by the difficulties of obtaining high quality total RNA with minimal genomic DNA contamination. With this in mind, we evaluated the performance of Phenol-free total RNA purification kit (Amresco) in comparison with TRI Reagent (MRC) and RNeasy Mini (Qiagen) for the extraction of total RNA of Pseudomonas aeruginosa which was grown in glucose-supplemented (control) and polyethylene-supplemented (growth-limiting condition) minimal medium. All three extraction methods were coupled with an in-house DNase I treatment before the yield, integrity and size distribution of the purified RNA were assessed. RNA samples extracted with the best extraction kit were then sequenced using the Illumina HiSeq 2000 platform. Results TRI Reagent gave the lowest yield enriched with small RNAs (sRNAs), while RNeasy gave moderate yield of good quality RNA with trace amounts of sRNAs. The Phenol-free kit, on the other hand, gave the highest yield and the best quality RNA (RIN value of 9.85 ± 0.3) with good amounts of sRNAs. Subsequent bioinformatic analysis of the sequencing data revealed that 5435 coding genes, 452 sRNAs and 7 potential novel intergenic sRNAs were detected, indicating excellent sequencing coverage across RNA size ranges. In addition, detection of low abundance transcripts and consistency of their expression profiles across replicates from the same conditions demonstrated the reproducibility of the RNA extraction technique. Conclusions Amresco’s Phenol-free Total RNA purification kit coupled with DNase I treatment yielded the highest quality RNAs containing good ratios of high and low molecular weight transcripts with minimal genomic DNA. These RNA extracts gave excellent non-biased sequencing coverage useful for comprehensive total transcriptome sequencing and analysis. Furthermore, our findings would be useful for those interested in studying both coding and non-coding RNAs from precious bacterial samples cultivated in growth-limiting condition, in a single sequencing run. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1726-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rajandas Heera
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling, 08100, Bedong, Kedah, Malaysia. .,Unit of Biochemistry, Faculty of Medicine, AIMST University, Semeling, 08100, Bedong, Kedah, Malaysia.
| | - Parimannan Sivachandran
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling, 08100, Bedong, Kedah, Malaysia.
| | - Suresh V Chinni
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling, 08100, Bedong, Kedah, Malaysia.
| | - Joanne Mason
- Malaysian Genomics Resource Centre, 27-9, Level 9 Boulevard Signature Offices, 59200, Mid Valley City, Malaysia. .,Oxford Biomedical Research Centre, Old Road Headington Oxford, Oxfordshire, OX3 7LE, UK.
| | - Larry Croft
- Malaysian Genomics Resource Centre, 27-9, Level 9 Boulevard Signature Offices, 59200, Mid Valley City, Malaysia.
| | - Manickam Ravichandran
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling, 08100, Bedong, Kedah, Malaysia.
| | - Lee Su Yin
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Semeling, 08100, Bedong, Kedah, Malaysia.
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Danckert L, Hoppe S, Bier FF, von Nickisch-Rosenegk M. Rapid identification of novel antigens of Salmonella Enteritidis by microarray-based immunoscreening. Mikrochim Acta 2014; 181:1707-1714. [PMID: 25253911 PMCID: PMC4167438 DOI: 10.1007/s00604-014-1197-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/30/2014] [Indexed: 01/13/2023]
Abstract
We report on an approach to rapidly screen thousands of Salmonella Enteritidis proteins with the goal of identifying novel immunodominant proteins. We used a microarray-based system that warrants high throughput and easy handling. Seven immunogenic candidates were selected after screening. Comparative analyses by ELISA and microarrays manifested their immunodominant character. The large repetitive protein (SEN4030) that plays a role as a putative adhesin in initial cell surface interaction and is highly specific to Salmonella is considered to be the most suitable protein for a diagnostic approach. The results further demonstrate that the strategy applied herein is convenient for specifically identifying immunogenic proteins of pathogenic microorganisms. Consequently, it enables a sound assessment of promising candidates for diagnostic applications and vaccine development. Moreover, the elucidation of immunogenic proteins may assist in unveiling unknown virulence-associated factors, thus furthering the understanding of the underlying pathogenicity of Salmonella in general, and of S. Enteritidis, one of the most frequently detected serovars of this pathogen, in particular. The microarray-based approach was aimed at identifying novel immunodominant proteins of S. Enteritidis. Seven antigens were revealed by screening a cDNA expression library. SEN4030, a large repetitive protein specific for salmonella, is considered an optimal candidate for future applications. ![]()
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Affiliation(s)
- Lena Danckert
- Fraunhofer IBMT, Am Mühlenberg 13., 14476 Potsdam, Germany
| | | | - Frank F Bier
- Fraunhofer IBMT, Am Mühlenberg 13., 14476 Potsdam, Germany
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Bergkvist KS, Nyegaard M, Bøgsted M, Schmitz A, Bødker JS, Rasmussen SM, Perez-Andres M, Falgreen S, Bilgrau AE, Kjeldsen MK, Gaihede M, Nørgaard MA, Bæch J, Grønholdt ML, Jensen FS, Johansen P, Dybkær K, Johnsen HE. Validation and implementation of a method for microarray gene expression profiling of minor B-cell subpopulations in man. BMC Immunol 2014; 15:3. [PMID: 24483235 PMCID: PMC3937209 DOI: 10.1186/1471-2172-15-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/28/2014] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND This report describes a method for the generation of global gene expression profiles from low frequent B-cell subsets by using fluorescence-activated cell sorting and RNA amplification. However, some of the differentiating compartments involve a low number of cells and therefore it is important to optimize and validate each step in the procedure. METHODS Normal lymphoid tissues from blood, tonsils, thymus and bone marrow were immunophenotyped by the 8-colour Euroflow panel using multiparametric flow cytometry. Subsets of B-cells containing cell numbers ranging from 800 to 33,000 and with frequencies varying between 0.1 and 10 percent were sorted, subjected to mRNA purification, amplified by the NuGEN protocol and finally analysed by the Affymetrix platform. RESULTS Following a step by step strategy, each step in the workflow was validated and the sorting/storage conditions optimized as described in this report. First, an analysis of four cancer cell lines on Affymetrix arrays, using either 100 ng RNA labelled with the Ambion standard protocol or 1 ng RNA amplified and labelled by the NuGEN protocol, revealed a significant correlation of gene expressions (r ≥ 0.9 for all). Comparison of qPCR data in samples with or without amplification for 8 genes showed that a relative difference between six cell lines was preserved (r ≥ 0.9). Second, a comparison of cells sorted into PrepProtect, RNAlater or directly into lysis/binding buffer showed a higher yield of purified mRNA following storage in lysis/binding buffer (p < 0.001). Third, the identity of the B-cell subsets validated by the cluster of differentiation (CD) membrane profile was highly concordant with the transcriptional gene expression (p-values <0.001). Finally, in normal bone marrow and tonsil samples, eight evaluated genes were expressed in accordance with the biology of lymphopoiesis (p-values < 0.001), which enabled the generation of a gene-specific B-cell atlas. CONCLUSION A description of the implementation and validation of commercially available kits in the laboratory has been examined. This included steps for cell sorting, cell lysis/stabilization, RNA isolation, RNA concentration and amplification for microarray analysis. The workflow described in this report will enable the generation of microarray data from minor sorted B-cell subsets.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital Science and Innovation Center, Sdr Skovvej 15, DK-9000 Aalborg, Denmark.
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Gadkar VJ, Filion M. Development of a versatile TaqMan™ real-time quantitative PCR (RT-qPCR) compliant anchor sequence to quantify bacterial gene transcripts from RNA samples containing carryover genomic DNA. BMC Biotechnol 2013; 13:7. [PMID: 23369378 PMCID: PMC3689636 DOI: 10.1186/1472-6750-13-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/22/2013] [Indexed: 12/23/2022] Open
Abstract
Background In bacterial systems, the sequence congruence of genomic DNA (gDNA) and cDNA obtained following reverse transcription of RNA, makes gDNA an automatic target for qPCR primers. This could lead to aberrant gene expression quantification. This is why a rigorous treatment of bacterial RNA with DNase I is usually required to remove any traces of carryover gDNA. As bacterial RNA is known to be extremely labile, any procedure that affects RNA yield, such as DNase I treatment, can be logically assumed to also influence detection and quantification of gene transcripts, leading to either an underestimation or no detection at all. To address such problems, we have developed a novel and versatile TaqMan RT-qPCR compliant anchor sequence (MYT4) for quantifying bacterial gene transcripts without the need for DNase I treatment. Results A non-genomic anchor sequence, henceforth referred to as MYT4 was designed using a synthetic DNA sequence called myIC, previously shown to share no significant homology to any known accession in the GenBank database. The sequence characteristic of MYT4 was kept within the design parameters required for the TaqMan RT-qPCR platform. The specificity and robustness of the novel MYT4 sequence was validated on RNA extracted from the bacterium Pseudomonas sp. LBUM300, grown under liquid culture and spiked soil conditions. Two transcripts, namely hcnC and phlD, were quantified from these two experimental systems. Using the MYT4 anchor, no RT-qPCR signal was detected from non-DNase I treated RNA, while strong signals were obtained using conventional reverse primers and RT-qPCR, indicating the presence of carryover gDNA in the RNA, extracted from either liquid culture or soil. Serial treatment of the RNA samples with DNase I (required to achieve absolute gDNA elimination) resulted in 50-70% loss of RNA which, when submitted to conventional RT-qPCR, significantly altered the transcript numbers detected when compared to the MYT4-based approach. Conclusions Implementation of the versatile approach described in this study, which can be “retrofitted” to any existing TaqMan RT-qPCR system, should contribute to reducing the time and lowering the costs required to perform adequate bacterial RNA purification for downstream quantification of gene transcripts.
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Affiliation(s)
- Vijay J Gadkar
- Department of Biology, Université de Moncton, 18 Antonine-Maillet, Moncton, NB E1A 3E9, Canada
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See MJ, Staggs SE, Dubey J, Villegas EN. Evaluation of four RNA extraction methods for gene expression analyses of Cryptosporidium parvum and Toxoplasma gondii oocysts. J Microbiol Methods 2012; 89:185-92. [DOI: 10.1016/j.mimet.2012.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/05/2012] [Accepted: 03/09/2012] [Indexed: 11/16/2022]
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Optimizing a qPCR gene expression quantification assay for S. epidermidis biofilms: a comparison between commercial kits and a customized protocol. PLoS One 2012; 7:e37480. [PMID: 22629403 PMCID: PMC3357405 DOI: 10.1371/journal.pone.0037480] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 04/24/2012] [Indexed: 01/02/2023] Open
Abstract
Staphylococcus epidermidis biofilm-related infections are a current concern within the medical community due to their high incidence and prevalence, particularly in patients with indwelling medical devices. Biofilm gene expression analysis by quantitative real-time PCR (qPCR) has been increasingly used to understand the role of biofilm formation in the pathogenesis of S. epidermidis infections. However, depending on the RNA extraction procedure, and cDNA synthesis and qPCR master mixes used, gene expression quantification can be suboptimal. We recently showed that some RNA extraction kits are not suitable for S. epidermidis biofilms, due to sample composition, in particular the presence of the extracellular matrix. In this work, we describe a custom RNA extraction assay followed by the evaluation of gene expression using different commercial reverse transcriptase kits and qPCR master mixes. Our custom RNA extraction assay was able to produce good quality RNA with reproducible gene expression quantification, reducing the time and the costs associated. We also tested the effect of reducing cDNA and qPCR reaction volumes and, in most of the cases tested, no significant differences were found. Finally, we titered the SYBR Green I concentrations in standard PCR master mixes and compared the normalized expression of the genes icaA, bhp, aap, psmβ1 and agrB using 4 distinct biofilm forming S. epidermidis strains to the results obtained with commercially available kits. The overall results demonstrated that despite some statistically, but not biologically significant differences observed, the customized qPCR protocol resulted in the same gene expression trend presented by the commercially available kits used.
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França A, Bento JC, Cerca N. Variability of RNA Quality Extracted from Biofilms of Foodborne Pathogens Using Different Kits Impacts mRNA Quantification by qPCR. Curr Microbiol 2012; 65:54-9. [DOI: 10.1007/s00284-012-0124-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Accepted: 03/27/2012] [Indexed: 10/28/2022]
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Cheung PY, Kam KM. Salmonella in food surveillance: PCR, immunoassays, and other rapid detection and quantification methods. Food Res Int 2012. [DOI: 10.1016/j.foodres.2011.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Atshan SS, Shamsudin MN, Lung LTT, Ling KH, Sekawi Z, Pei CP, Ghaznavi-Rad E. Improved method for the isolation of RNA from bacteria refractory to disruption, including S. aureus producing biofilm. Gene 2012; 494:219-24. [DOI: 10.1016/j.gene.2011.12.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/24/2011] [Accepted: 12/06/2011] [Indexed: 11/24/2022]
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França A, Melo LD, Cerca N. Comparison of RNA extraction methods from biofilm samples of Staphylococcus epidermidis. BMC Res Notes 2011; 4:572. [PMID: 22208502 PMCID: PMC3260333 DOI: 10.1186/1756-0500-4-572] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 12/30/2011] [Indexed: 11/30/2022] Open
Abstract
Background Microbial biofilms are communities of bacteria adhered to a surface and surrounded by an extracellular polymeric matrix. Biofilms have been associated with increased antibiotic resistance and tolerance to the immune system. Staphylococcus epidermidis is the major bacterial species found in biofilm-related infections on indwelling medical devices. Obtaining high quality mRNA from biofilms is crucial to validate the transcriptional measurements associated with the switching to the biofilm mode of growth. Therefore, we selected three commercially available RNA extraction kits with distinct characteristics, including those using silica membrane or organic extraction methods, and enzymatic or mechanical cell lysis, and evaluated the RNA quality obtained from two distinct S. epidermidis bacterial biofilms. Results RNA extracted using the different kits was evaluated for quantity, purity, integrity, and functionally. All kits were able to extract intact and functional total RNA from the biofilms generated from each S. epidermidis strain. The results demonstrated that the kit based on mechanical lysis and organic extraction (FastRNA® Pro Blue) was the only one that was able to isolate pure and large quantities of RNA. Normalized expression of the icaA virulence gene showed that RNA extracted with PureLink™ had a significant lower concentration of icaA mRNA transcripts than the other kits tested. Conclusions When working with complex samples, such as biofilms, that contain a high content extracellular polysaccharide and proteins, special care should be taken when selecting the appropriate RNA extraction system, in order to obtain accurate, reproducible, and biologically significant results. Among the RNA extraction kits tested, FastRNA® Pro Blue was the best option for both S. epidermidis biofilms used.
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Affiliation(s)
- Angela França
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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Comparison of real-time PCR, reverse transcriptase real-time PCR, loop-mediated isothermal amplification, and the FDA conventional microbiological method for the detection of Salmonella spp. in produce. Appl Environ Microbiol 2011; 77:6495-501. [PMID: 21803916 DOI: 10.1128/aem.00520-11] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Contamination of foods, especially produce, with Salmonella spp. is a major concern for public health. Several methods are available for the detection of Salmonella in produce, but their relative efficiency for detecting Salmonella in commonly consumed vegetables, often associated with outbreaks of food poisoning, needs to be confirmed. In this study, the effectiveness of three molecular methods for detection of Salmonella in six produce matrices was evaluated and compared to the FDA microbiological detection method. Samples of cilantro (coriander leaves), lettuce, parsley, spinach, tomato, and jalapeno pepper were inoculated with Salmonella serovars at two different levels (10(5) and <10(1) CFU/25 g of produce). The inoculated produce was assayed by the FDA Salmonella culture method (Bacteriological Analytical Manual) and by three molecular methods: quantitative real-time PCR (qPCR), quantitative reverse transcriptase real-time PCR (RT-qPCR), and loop-mediated isothermal amplification (LAMP). Comparable results were obtained by these four methods, which all detected as little as 2 CFU of Salmonella cells/25 g of produce. All control samples (not inoculated) were negative by the four methods. RT-qPCR detects only live Salmonella cells, obviating the danger of false-positive results from nonviable cells. False negatives (inhibition of either qPCR or RT-qPCR) were avoided by the use of either a DNA or an RNA amplification internal control (IAC). Compared to the conventional culture method, the qPCR, RT-qPCR, and LAMP assays allowed faster and equally accurate detection of Salmonella spp. in six high-risk produce commodities.
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