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Versmessen N, Van Simaey L, Negash AA, Vandekerckhove M, Hulpiau P, Vaneechoutte M, Cools P. Comparison of DeNovix, NanoDrop and Qubit for DNA quantification and impurity detection of bacterial DNA extracts. PLoS One 2024; 19:e0305650. [PMID: 38885212 PMCID: PMC11182499 DOI: 10.1371/journal.pone.0305650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
Accurate DNA quantification is key for downstream application including library preparations for whole genome sequencing (WGS) and the quantification of standards for quantitative PCR. Two commonly used technologies for nucleic acid quantification are based on spectrometry, such as NanoDrop, and fluorometry, such as Qubit. The DS-11+ Series spectrophotometer/fluorometer (DeNovix) is a UV spectrophotometry-based instrument and is a relatively new spectrophotometric method but has not yet been compared to established platforms. Here, we compared three DNA quantification platforms, including two UV spectrophotometry-based techniques (DeNovix and NanoDrop) and one fluorometry-based approach (Qubit). We used genomic prokaryotic DNA extracted from Streptococcus pneumoniae using a Roche DNA extraction kit. We also evaluated purity assessment and effect of a single freeze-thaw cycle. Spectrophotometry-based methods reported 3 to 4-fold higher mean DNA concentrations compared to Qubit, both before and after freezing. The ratio of DNA concentrations assessed by spectrophotometry on the one hand, and Qubit on the other hand, was function of the A260/280. In case DNA was pure (A260/280 between 1.7 and 2.0), the ratio DeNovix or Nanodrop vs. Qubit was close or equal to 2, while this ratio showed an incline for DNA with increasing A260/280 values > 2.0. The A260/280 and A260/230 purity ratios exhibited negligible variation across spectrophotometric methods and freezing conditions. The comparison of DNA concentrations from before and after freezing revealed no statistically significant disparities for each technique. DeNovix exhibited the highest Spearman correlation coefficient (0.999), followed by NanoDrop (0.81), and Qubit (0.77). In summary, there is no difference between DeNovix and NanoDrop in estimated gDNA concentrations of S. pneumoniae, and the spectrophotometry methods estimated close or equal to 2 times higher concentrations compared to Qubit for pure DNA.
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Affiliation(s)
- Nick Versmessen
- 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
| | - Abel Abera Negash
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Paco Hulpiau
- HOWEST University of Applied Sciences, Bruges, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Piet Cools
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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Abdulqader HA, Abood ZH. Effect of Salicylic Acid on the gene expression of FnbA and FnbB genes in Staphylococcus hominis. Hum Antibodies 2024:HAB240023. [PMID: 38875028 DOI: 10.3233/hab-240023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
BACKGROUND Staphylococcus hominis is an opportunistic pathogen that expresses surface proteins, which are adhesive proteins that play a major role in biofilm formation. Biofilm is a protective layer that provides S. hominis bacteria with greater antibiotic resistance and promotes its adherence to biomedical surfaces, facilitating its entry into the bloodstream. OBJECTIVE This research aimed to investigate the activity of Salicylic Acid (SA) and its effect on the gene expression of biofilm genes (FnbA and FnbB genes). METHODS A total of 150 blood specimens were collected from patients. The specimens were cultured in broth media of the BacT/ALERT® system and subcultured on blood and chocolate agar. Bacteria were detected using the VITEK2 system. FnbA and FnbB genes were detected using PCR. The broth microdilution method performed the minimum inhibitory concentration (MIC) of Salicylic acid (SA) on S. hominis isolates with both genes. Detection of the gene expression levels of FnbA and FnbB genes was assessed using Real-Time PCR(RT-PCR). RESULTS The results showed that out of the 150 specimens collected, 35 were S. hominis. The detection of S. hominis bacteria was performed by PCR amplification of two genes FnbA and FnbB and showed 100% and 17.14% of isolates were positive for genes FnbA and FnbB, respectively. The expression of FnbA and FnbB genes was decreased in samples treated with SA compared with untreated ones. CONCLUSION In conclusion, there is a significant impact of SA on the prevention of biofilm formation of S. hominis through the suppression of gene expression, specifically FnbA and FnbB. This could enhance susceptibility to antimicrobial treatments. However, more research is required to determine whether SA leads to the selection of resistant bacteria.
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Nath S, VanSlambrouck JT, Yao JW, Gullapalli A, Razi F, Lu Y. DNA barcoding of terrestrial invasive plant species in Southwest Michigan. PLANT DIRECT 2024; 8:e615. [PMID: 38895104 PMCID: PMC11185875 DOI: 10.1002/pld3.615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Because of the detrimental effects of terrestrial invasive plant species (TIPS) on native species, ecosystems, public health, and the economy, many countries have been actively looking for strategies to prevent the introduction and minimize the spread of TIPS. Fast and accurate detection of TIPS is essential to achieving these goals. Conventionally, invasive species monitoring has relied on morphological attributes. Recently, DNA-based species identification (i.e., DNA barcoding) has become more attractive. To investigate whether DNA barcoding can aid in the detection and management of TIPS, we visited multiple nature areas in Southwest Michigan and collected a small piece of leaf tissue from 91 representative terrestrial plant species, most of which are invasive. We extracted DNA from the leaf samples, amplified four genomic loci (ITS, rbcL, matK, and trnH-psbA) with PCR, and then purified and sequenced the PCR products. After careful examination of the sequencing data, we were able to identify reliable DNA barcode regions for most species and had an average PCR-and-sequencing success rate of 87.9%. We found that the species discrimination rate of a DNA barcode region is inversely related to the ease of PCR amplification and sequencing. Compared with rbcL and matK, ITS and trnH-psbA have better species discrimination rates (80.6% and 63.2%, respectively). When ITS and trnH-psbA are simultaneously used, the species discrimination rate increases to 97.1%. The high species/genus/family discrimination rates of DNA barcoding indicate that DNA barcoding can be successfully employed in TIPS identification. Further increases in the number of DNA barcode regions show little or no additional increases in the species discrimination rate, suggesting that dual-barcode approaches (e.g., ITS + trnH-psbA) might be the efficient and cost-effective method in DNA-based TIPS identification. Close inspection of nucleotide sequences at the four DNA barcode regions among related species demonstrates that DNA barcoding is especially useful in identifying TIPS that are morphologically similar to other species.
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Affiliation(s)
- Sneha Nath
- Department of Biological SciencesWestern Michigan UniversityKalamazooMichiganUSA
| | | | - Janelle W. Yao
- Kalamazoo Area Math and Science CenterKalamazooMichiganUSA
- Portage Central High SchoolPortageMichiganUSA
| | - Ashika Gullapalli
- Kalamazoo Area Math and Science CenterKalamazooMichiganUSA
- Portage Northern High SchoolPortageMichiganUSA
| | - Fayyaz Razi
- Kalamazoo Area Math and Science CenterKalamazooMichiganUSA
- Portage Central High SchoolPortageMichiganUSA
| | - Yan Lu
- Department of Biological SciencesWestern Michigan UniversityKalamazooMichiganUSA
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Kofanova O, Paul S, Pexaras A, Bellora C, Petersons A, Schmitt M, Baker Berjaoui M, Qaoud Y, Kenk M, Wagner H, Fleshner N, Betsou F. Biospecimen Qualification in a Clinical Biobank of Urological Diseases. Biopreserv Biobank 2024; 22:257-267. [PMID: 37878356 DOI: 10.1089/bio.2022.0190] [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: 10/26/2023] Open
Abstract
Development of novel biomarkers for diagnosis of disease and assessment of treatment efficacy utilizes a wide range of biospecimens for discovery research. The fitness of biospecimens for the purpose of biomarker development depends on the clinical characteristics of the donor and on a number of critical and potentially uncontrolled pre-analytical variables. Pre-analytical factors influence the reliability of the biomarkers to be analyzed and can seriously impact analytic outcomes. Sample quality stratification assays and tools can be utilized by biorepositories to minimize bias resulting from samples' inconsistent quality. In this study, we evaluated the quality of biobanked specimens by comparing analytical outcomes at 1, 5, and 10 years after collection. Our results demonstrate that currently available assays and tools can be used by biobank laboratories to support objective biospecimen qualification. We have established a workflow to monitor the quality of different types of biospecimens and, in this study, present the results of a qualification exercise applied to fluid samples and their derivatives in the context of urological diseases.
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Affiliation(s)
- Olga Kofanova
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Sangita Paul
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Achilleas Pexaras
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Camille Bellora
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Ala Petersons
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Margaux Schmitt
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
| | - Mohamad Baker Berjaoui
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Yazan Qaoud
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Miran Kenk
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Heidi Wagner
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Neil Fleshner
- McCain GU BioBank (MGB), University Health Network-Princess Margaret Cancer Centre, Toronto, Canada
| | - Fay Betsou
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), Dudelange, Luxembourg
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Ousset MJ, Pianciola LA, Mazzeo M, Oteiza JM, Jaureguiberry MS, Venturino A, Barril PA. Improved SARS-CoV-2 RNA recovery in wastewater matrices using a CTAB-based extraction method. J Virol Methods 2024; 327:114918. [PMID: 38556176 DOI: 10.1016/j.jviromet.2024.114918] [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: 02/01/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Wastewater-based epidemiology has allowed tracking the magnitude and distribution of SARS-CoV-2 in communities, allowing public health officials to prepare for impending outbreaks. While many factors influence recovery of SARS-CoV-2 from wastewater, proper extraction, concentration, and purification of RNA are key steps to ensure accurate detection of viral particles. The aim of this study was to compare the efficiency of four commonly used RNA extraction methods for detection of the SARS-CoV-2 RNA genome in sewage samples artificially inoculated with the virus, in order to identify a protocol that improves viral recovery. These methods included CTAB-based, TRIzol-based, and guanidinium thiocyanate (GTC)-based extraction procedures coupled with silica spin column-based purification, and an automated extraction/purification protocol using paramagnetic particles. Following RNA extraction, virus recovery rates were compared using RT-qPCR-based detection. The CTAB-based approach yielded the highest recovery rates and was the only method to consistently demonstrate stable virus recovery percentages regardless of the specific physicochemical characteristics of the samples tested. The TRIzol method proved to be the second most effective, yielding significantly higher recovery rates compared to both the GTC-based and the automated extraction methods. These results suggest that the CTAB-based approach could be a useful tool for the recovery of viral RNA from complex wastewater matrices.
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Affiliation(s)
- María Julia Ousset
- Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue (CITAAC), CONICET- Universidad Nacional del Comahue, Buenos Aires 1400, Neuquén 8300, Argentina.
| | - Luis Alfredo Pianciola
- Laboratorio Central "Mg. Luis Alfredo Pianciola", Ministerio de Salud de la Provincia de Neuquén, Gregorio Martinez 65, Neuquén 8300, Argentina
| | - Melina Mazzeo
- Laboratorio Central "Mg. Luis Alfredo Pianciola", Ministerio de Salud de la Provincia de Neuquén, Gregorio Martinez 65, Neuquén 8300, Argentina
| | - Juan Martín Oteiza
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Laboratorio de Microbiología de los Alimentos, Centro de Investigación y Asistencia Técnica a la Industria (CIATI), Expedicionarios del Desierto 1310, Centenario, Neuquén 8309, Argentina
| | - María Soledad Jaureguiberry
- Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue (CITAAC), CONICET- Universidad Nacional del Comahue, Buenos Aires 1400, Neuquén 8300, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Andrés Venturino
- Centro de Investigaciones en Toxicología Ambiental y Agrobiotecnología del Comahue (CITAAC), CONICET- Universidad Nacional del Comahue, Buenos Aires 1400, Neuquén 8300, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Patricia Angélica Barril
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Laboratorio de Microbiología de los Alimentos, Centro de Investigación y Asistencia Técnica a la Industria (CIATI), Expedicionarios del Desierto 1310, Centenario, Neuquén 8309, Argentina
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Encinas M, Ferrara Muñiz X, Sammarruco RA, Ruiz Menna V, Garro CJ, Delgado F, Macías A, Magnano G, Zumárraga MJ, Garbaccio SG, Eirin ME. Limited usefulness of the IS 6110 touchdown-PCR in blood for tuberculin skin test false-negative cattle with serological response to Mycobacterium bovis. Front Vet Sci 2024; 11:1359205. [PMID: 38835898 PMCID: PMC11149419 DOI: 10.3389/fvets.2024.1359205] [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: 12/21/2023] [Accepted: 04/23/2024] [Indexed: 06/06/2024] Open
Abstract
Ante-mortem diagnosis of bovine tuberculosis (bTB) is based mainly on the tuberculin skin test (TST) and the ɣ-IFN release assay (IGRA). Some infected animals escape screening tests, thus, limit herd sanitation. Previous reports have suggested a predominant pattern of multi-organ lesions attributable to Mycobacterium bovis (the causative agent of bTB) bacteraemia. A case-control study was conducted to investigate blood PCR as an alternative tool for improving ante-mortem detection of TST false-negative bovines. Cases comprised 70 TST false-negative bovines (cases), which were serology positive, and controls included 81 TST positive bovines; all of them confirmed as infected with M. bovis. Detection of the IS6110 target through touchdown blood-PCR (IS6110 TD-PCR) was performed. The positivity of the blood-PCR was 27.2% in the control group. This performance was similar to the 15% obtained among cases (p = 0.134). Most cases identified by the IS6110 TD-PCR exhibited focalized lesions (p = 0.002). Results demonstrated that blood-PCR could detect TST false-negative cattle, even if they are negative for IGRA. Considering that cases exhibited humoral response to M. bovis, further studies conducted in a pre-serological stage could provide evidence about the real contribution of the technique in herds.
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Affiliation(s)
- Micaela Encinas
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo) UEDD CONICET-INTA, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-CNIA, Hurlingham, Argentina
| | - Ximena Ferrara Muñiz
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo) UEDD CONICET-INTA, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-CNIA, Hurlingham, Argentina
| | - Romina Ayelén Sammarruco
- Instituto de Patobiología Veterinaria (IPVET), UEDD CONICET-INTA, Instituto Nacional de Tecnología Agropecuaria (INTA), INTA-CONICET, Hurlingham, Argentina
| | - Victoria Ruiz Menna
- Instituto de Patobiología Veterinaria (IPVET), UEDD CONICET-INTA, Instituto Nacional de Tecnología Agropecuaria (INTA), INTA-CONICET, Hurlingham, Argentina
| | - Carlos Javier Garro
- Instituto de Patobiología Veterinaria (IPVET), UEDD CONICET-INTA, Instituto Nacional de Tecnología Agropecuaria (INTA), INTA-CONICET, Hurlingham, Argentina
| | - Fernando Delgado
- Instituto de Patobiología Veterinaria (IPVET), UEDD CONICET-INTA, Instituto Nacional de Tecnología Agropecuaria (INTA), INTA-CONICET, Hurlingham, Argentina
| | - Analía Macías
- Departamento de Patología Animal, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
| | - Gabriel Magnano
- Departamento de Patología Animal, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
| | - Martín José Zumárraga
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo) UEDD CONICET-INTA, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-CNIA, Hurlingham, Argentina
| | - Sergio Gabriel Garbaccio
- Instituto de Patobiología Veterinaria (IPVET), UEDD CONICET-INTA, Instituto Nacional de Tecnología Agropecuaria (INTA), INTA-CONICET, Hurlingham, Argentina
| | - María Emilia Eirin
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo) UEDD CONICET-INTA, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-CNIA, Hurlingham, Argentina
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Pearce DL, Edson JE, Jennelle CS, Walter WD. Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels. Sci Rep 2024; 14:11340. [PMID: 38760358 PMCID: PMC11101418 DOI: 10.1038/s41598-024-56128-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/01/2024] [Indexed: 05/19/2024] Open
Abstract
Genetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, microsatellites have been the primary method; however, there currently is a shift from microsatellites to single nucleotide polymorphisms (SNPs). With the different DNA requirements between microsatellites and SNPs, an investigation into which samples can provide adequate DNA yield is warranted. Using samples that were collected from previous genetic projects from regions in the USA from 2014 to 2021, we investigated the DNA yield of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed high- or medium-density SNP panels. We found seven sample categories that met the DNA requirements for use in all three panels, and one sample category that did not meet any of the three panels requirements; however, DNA integrity was highly variable and not all sample categories that met panel DNA requirements could be considered high quality DNA. Additionally, we used linear random-effects models to determine which covariates would have the greatest influence on DNA yield. We determined that all covariates (tissue type, storage method, preservative, DNA quality, time until DNA extraction and time after DNA extraction) could influence DNA yield.
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Affiliation(s)
- David L Pearce
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
- Department of Rangeland, Wildlife and Fisheries Management, Texas A&M University, College Station, TX, 77843, USA
| | - Jessie E Edson
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 413 Forest Resources Building, University Park, PA, 16802, USA
| | - Chris S Jennelle
- Minnesota Department of Natural Resources, 5463 West Broadway Ave., Forest Lake, MN, 55025, USA
- Minnesota Department of Natural Resources, Division of Ecological and Water Resources, Nongame Wildlife Program, St Paul, MN, 55155, USA
| | - W David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, 403 Forest Resources Building, University Park, PA, 16802, USA.
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Dabrowski P, Rasmus M, Jundzill A, Drewa T, Pokrywczynska M. A comparison of five methods to maximize RNA and DNA isolation yield from adipose tissue. PeerJ 2024; 12:e17071. [PMID: 38711623 PMCID: PMC11073010 DOI: 10.7717/peerj.17071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/18/2024] [Indexed: 05/08/2024] Open
Abstract
Adipose tissue in the human body occurs in various forms with different functions. It is an energy store, a complex endocrine organ, and a source of cells used in medicine. Many molecular analyses require the isolation of nucleic acids, which can cause some difficulties connected with the large amount of lipids in adipocytes. Ribonucleic acid isolation is particularly challenging due to its low stability and easy degradation by ribonucleases. The study aimed to compare and evaluate five RNA and DNA isolation methods from adipose tissue. The tested material was subcutaneous porcine adipose tissue subjected to different homogenization methods and RNA or DNA purification. A mortar and liquid nitrogen or ceramic beads were used for homogenization. The organic extraction (TriPure Reagent), spin columns with silica-membrane (RNeasy Mini Kit or High Pure PCR Template Preparation Kit), and the automatic MagNA Pure system were used for the purification. Five combinations were compared for RNA and DNA isolation. Obtained samples were evaluated for quantity and quality. The methods were compared in terms of yield (according to tissue mass), purity (A260/280 and A260/230), and nucleic acid degradation (RNA Integrity Number, RIN; DNA Integrity Number, DIN). The results were analyzed statistically. The average RNA yield was highest in method I, which used homogenization with ceramic beads and organic extraction. Low RNA concentration didn't allow us to measure degradation for all samples in method III (homogenization with ceramic beads and spin-column purification). The highest RNA quality was achieved with method IV using homogenization in liquid nitrogen and spin column purification, which makes it the most effective for RNA isolation from adipose tissue. Required values of DNA yield, purity, and integrity were achieved only with spin column-based methods (III and IV). The most effective method for DNA isolation from adipose tissue is method III, using spin-columns without additional homogenization.
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Affiliation(s)
- Pawel Dabrowski
- Chair of Urology and Andrology, Department of Regenerative Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Marta Rasmus
- Chair of Urology and Andrology, Department of Regenerative Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Arkadiusz Jundzill
- Chair of Urology and Andrology, Department of Regenerative Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- Department of Plastic, Reconstructive and Aesthetic Surgery, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Tomasz Drewa
- Chair of Urology and Andrology, Department of Regenerative Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Marta Pokrywczynska
- Chair of Urology and Andrology, Department of Regenerative Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
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Okojie J, O’Neal N, Burr M, Worley P, Packer I, Anderson D, Davis J, Kearns B, Fatema K, Dixon K, Barrott JJ. DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples. Curr Oncol 2024; 31:2441-2452. [PMID: 38785464 PMCID: PMC11119490 DOI: 10.3390/curroncol31050183] [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: 03/18/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024] Open
Abstract
Personalized cancer care requires molecular characterization of neoplasms. While the research community accepts frozen tissues as the gold standard analyte for molecular assays, the source of tissue for testing in clinical cancer care comes almost universally from formalin-fixed, paraffin-embedded tissue (FFPE). As newer technologies emerge for DNA characterization that requires higher molecular weight DNA, it was necessary to compare the quality of DNA in terms of DNA length between FFPE and cryopreserved samples. We hypothesized that cryopreserved samples would yield higher quantity and superior quality DNA compared to FFPE samples. We analyzed DNA metrics by performing a head-to-head comparison between FFPE and cryopreserved samples from 38 human tumors representing various cancer types. DNA quantity and purity were measured by UV spectrophotometry, and DNA from cryopreserved tissue demonstrated a 4.2-fold increase in DNA yield per mg of tissue (p-value < 0.001). DNA quality was measured on a fragment microelectrophoresis analyzer, and again, DNA from cryopreserved tissue demonstrated a 223% increase in the DNA quality number and a 9-fold increase in DNA fragments > 40,000 bp (p-value < 0.0001). DNA from the cryopreserved tissues was superior to the DNA from FFPE samples in terms of DNA yield and quality.
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Affiliation(s)
- Jeffrey Okojie
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
| | - Nikole O’Neal
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
| | - Mackenzie Burr
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Peyton Worley
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Isaac Packer
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - DeLaney Anderson
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Jack Davis
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Bridger Kearns
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Kaniz Fatema
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
| | - Ken Dixon
- Specicare, 690 Medical Park Ln, Gainesville, GA 30501, USA
| | - Jared J. Barrott
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
- Specicare, 690 Medical Park Ln, Gainesville, GA 30501, USA
- Simmons Center for Cancer Research, Brigham Young University, Provo, UT 84602, USA
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10
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Shim SM, Lee M, Jeon JP. Assessment of the Impact of Preanalytical DNA Integrity on the Genome Data Quality. Biopreserv Biobank 2024. [PMID: 38563611 DOI: 10.1089/bio.2023.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Many molecular approaches have been employed for the quality control (QC) of biobanked DNA samples. Since 2003, the National Biobank of Korea (NBK) has provided various studies with over half a million quality-controlled genomic DNA samples using conventional agarose gel electrophoresis and spectrophotometry. We assessed the postanalytical genomic data quality of DNA samples (n = 41) with a different range of the DNA quality index such as genomic quality number (GQN) for developing an evidence-based best practice for DNA quality criteria. We examined the quality indices of three different platforms, including single nucleotide polymorphism arrays, methylation arrays, and next-generation sequencing, using the same DNA samples (n = 41) of different quality, ranging from 4.0 to 10.0 values of the GQN. Our data analysis revealed that higher GQN value and/or double-stranded DNA concentration resulted in higher quality genomic data. In addition, all the analyzed DNA samples successfully generated good-quality genomic data. This study provides a guide for the QC of biobanked DNA samples for genomic analysis platforms.
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Affiliation(s)
- Sung-Mi Shim
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Meehee Lee
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Jae-Pil Jeon
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
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11
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Xie Y, Butler M. N-glycomic profiling of capsid proteins from Adeno-Associated Virus serotypes. Glycobiology 2024; 34:cwad074. [PMID: 37774344 PMCID: PMC10950483 DOI: 10.1093/glycob/cwad074] [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: 05/01/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023] Open
Abstract
Adeno-associated virus (AAV) vector has become the leading platform for gene delivery. Each serotype exhibits a different tissue tropism, immunogenicity, and in vivo transduction performance. Therefore, selecting the most suitable AAV serotype is critical for efficient gene delivery to target cells or tissues. Genome divergence among different serotypes is due mainly to the hypervariable regions of the AAV capsid proteins. However, the heterogeneity of capsid glycosylation is largely unexplored. In the present study, the N-glycosylation profiles of capsid proteins of AAV serotypes 1 to 9 have been systemically characterized and compared using a previously developed high-throughput and high-sensitivity N-glycan profiling platform. The results showed that all 9 investigated AAV serotypes were glycosylated, with comparable profiles. The most conspicuous feature was the high abundance mannosylated N-glycans, including FM3, M5, M6, M7, M8, and M9, that dominated the chromatograms within a range of 74 to 83%. Another feature was the relatively lower abundance of fucosylated and sialylated N-glycan structures, in the range of 23%-40% and 10%-17%, respectively. However, the exact N-glycan composition differed. These differences may be utilized to identify potential structural relationships between the 9 AAV serotypes. The current research lays the foundation for gaining better understanding of the importance of N-glycans on the AAV capsid surface that may play a significant role in tissue tropism, interaction with cell surface receptors, cellular uptake, and intracellular processing.
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Affiliation(s)
- Yongjing Xie
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
| | - Michael Butler
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin (UCD), Belfield, Dublin 4, D04 V1W8, Ireland
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12
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Wolf SE, Hastings WJ, Ye Q, Etzel L, Apsley AT, Chiaro C, Heim CC, Heller T, Noll JG, Schreier HMC, Shenk CE, Shalev I. Cross-tissue comparison of telomere length and quality metrics of DNA among individuals aged 8 to 70 years. PLoS One 2024; 19:e0290918. [PMID: 38386656 PMCID: PMC10883573 DOI: 10.1371/journal.pone.0290918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/03/2024] [Indexed: 02/24/2024] Open
Abstract
Telomere length (TL) is an important biomarker of cellular aging, yet its links with health outcomes may be complicated by use of different tissues. We evaluated within- and between-individual variability in TL and quality metrics of DNA across five tissues using a cross-sectional dataset ranging from 8 to 70 years (N = 197). DNA was extracted from all tissue cells using the Gentra Puregene DNA Extraction Kit. Absolute TL (aTL) in kilobase pairs was measured in buccal epithelial cells, saliva, dried blood spots (DBS), buffy coat, and peripheral blood mononuclear cells (PBMCs) using qPCR. aTL significantly shortened with age for all tissues except saliva and buffy coat, although buffy coat was available for a restricted age range (8 to 15 years). aTL did not significantly differ across blood-based tissues (DBS, buffy coat, PBMC), which had significantly longer aTL than buccal cells and saliva. Additionally, aTL was significantly correlated for the majority of tissue pairs, with partial Spearman's correlations controlling for age and sex ranging from ⍴ = 0.18 to 0.51. We also measured quality metrics of DNA including integrity, purity, and quantity of extracted DNA from all tissues and explored whether controlling for DNA metrics improved predictions of aTL. We found significant tissue variation: DNA from blood-based tissues had high DNA integrity, more acceptable A260/280 and A260/230 values, and greater extracted DNA concentrations compared to buccal cells and saliva. Longer aTL was associated with lower DNA integrity, higher extracted DNA concentrations, and higher A260/230, particularly for saliva. Model comparisons suggested that incorporation of quality DNA metrics improves models of TL, although relevant metrics vary by tissue. These findings highlight the merits of using blood-based tissues and suggest that incorporation of quality DNA metrics as control variables in population-based studies can improve TL predictions, especially for more variable tissues like buccal and saliva.
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Affiliation(s)
- Sarah E. Wolf
- Department of Biobehavioral Health, Penn State University, University Park, Pennsylvania, United States of America
| | - Waylon J. Hastings
- Department of Biobehavioral Health, Penn State University, University Park, Pennsylvania, United States of America
- Department of Psychiatry and Behavioral Science, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Qiaofeng Ye
- Department of Biobehavioral Health, Penn State University, University Park, Pennsylvania, United States of America
| | - Laura Etzel
- Department of Biobehavioral Health, Penn State University, University Park, Pennsylvania, United States of America
| | - Abner T. Apsley
- Department of Biobehavioral Health, Penn State University, University Park, Pennsylvania, United States of America
| | - Christopher Chiaro
- Department of Biobehavioral Health, Penn State University, University Park, Pennsylvania, United States of America
| | - Christine C. Heim
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin Institute of Health, Institute of Medical Psychology, Berlin, Germany
| | - Thomas Heller
- Department of Biobehavioral Health, Penn State University, University Park, Pennsylvania, United States of America
| | - Jennie G. Noll
- Department of Psychology, University of Rochester, Rochester, NY, United States of America
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, United States of America
| | - Hannah M. C. Schreier
- Department of Biobehavioral Health, Penn State University, University Park, Pennsylvania, United States of America
| | - Chad E. Shenk
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, United States of America
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, United States of America
| | - Idan Shalev
- Department of Biobehavioral Health, Penn State University, University Park, Pennsylvania, United States of America
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13
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Garg R, Maurya A, Mani NK, Prasad D. Thread-powered cell lysis and isotachophoresis: unlocking microbial DNA for diverse molecular applications. World J Microbiol Biotechnol 2024; 40:97. [PMID: 38349426 DOI: 10.1007/s11274-024-03906-2] [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: 10/07/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024]
Abstract
Central to the domain of molecular biology resides the foundational process of DNA extraction and purification, a cornerstone underpinning a myriad of pivotal applications. In this research, we introduce a DNA extraction and purification technique leveraging polypropylene (PP) threads. The process commences with robust cell lysis achieved through the vigorous agitation of interwoven PP threads. The friction between the threads facilitates cell lysis especially those microbes having tough cell wall. For purification of DNA, thread-based isotachophoresis was employed which makes the whole process swift and cost-effective. Lysed cell-laden threads were submerged in a trailing electrolyte which separated DNA from other cellular contents. The process was performed with a tailored ITP device. An electric field directs DNA, cell debris, trailing electrolyte, and leading electrolyte toward the anode. Distinct ion migration resulted in DNA concentrating on the PP thread's anode-proximal region. The SYBR green dye is used to visualize DNA as a prominent green zone under blue light. The purified DNA exhibits high purity levels of 1.82 ± 0.1 (A260/A280), making it suitable for various applications aiming at nucleic acid detection.
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Affiliation(s)
- Rishabh Garg
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Jharkhand, 835215, India
| | - Aharnish Maurya
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Jharkhand, 835215, India
| | - Naresh Kumar Mani
- Microfluidics, Sensors and Diagnostics (μSenD) Laboratory, Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Jharkhand, 835215, India.
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14
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Mishra G, Meena RK, Kant R, Pandey S, Ginwal HS, Bhandari MS. An improved Shorea robusta genomic DNA extraction protocol with high PCR fidelity. Biol Methods Protoc 2023; 8:bpad039. [PMID: 38116323 PMCID: PMC10728041 DOI: 10.1093/biomethods/bpad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023] Open
Abstract
Shorea robusta (Dipterocarpaceae), commonly known as Sal, is an economically and culturally important timber species, known to contain a wide spectrum of polyphenols, polysaccharides, and other secondary metabolites in the tissues, which can interfere with the extraction of high-quality genomic DNA. In order to screen simple sequence repeat (SSR) markers and carry out other DNA-based analyses for this species in our laboratory, a high-throughput DNA extraction methodology was needed. Hence, we have optimized a simple, rapid, safe, and reliable high-throughput protocol for DNA extraction suitable for both fresh and dry leaves. The standardized protocol delivered good DNA yield of ∼1500 µg from 1 g of leaf tissue, with purity indicated by a 260 nm/280 nm absorbance ratio ranging from 1.70 to 1.91, which validated the suitability of extracted DNA and revealed reduced levels of contaminants. Additionally, the protocol that we developed was found to be suitable for polymerase chain reaction (PCR) amplification using microsatellite markers. Genome-wide characterization with SSR markers has been established in S. robusta, which further validates the protocol and its usefulness in DNA-based studies across the genus and/or family.
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Affiliation(s)
- Garima Mishra
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun 248 195, Uttarakhand, India
| | - Rajendra K Meena
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun 248 195, Uttarakhand, India
| | - Rama Kant
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun 248 195, Uttarakhand, India
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, ICFRE-Forest Research Institute, Dehradun 248 006, Uttarakhand, India
| | - Harish S Ginwal
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun 248 195, Uttarakhand, India
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun 248 195, Uttarakhand, India
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15
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Ortega-Pinazo J, Pacheco-Rodríguez MJ, Serrano-Castro PJ, Martínez B, Pinto-Medel MJ, Gómez-Zumaquero JM, Lago-Sampedro A, García-Díaz B, Estivill-Torrús G, Emilio Ferro Gallego P. Comparing RNA extraction methods to face the variations in RNA quality using two human biological matrices. Mol Biol Rep 2023; 50:9263-9271. [PMID: 37812354 DOI: 10.1007/s11033-023-08761-2] [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: 12/27/2022] [Accepted: 08/16/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Nucleic acids, RNA among them, are widely used in biomedicine and Biotechnology. Because of their susceptibility to degradation by RNases, the handling and extraction process of RNA from cells and tissues require specialized personnel and standardized methods to guarantee high purity and integrity. Due to the diversity of techniques found in the market, a comparative study between different RNA extraction methods is useful to facilitate the best choice for the researcher or in research service platforms such as biobanks to see the traceability of the samples. METHODS AND RESULTS In this study, we have compared seven different RNA extraction methods: manual (TRIzol™), semiautomated (QIAGEN™, Bio-Rad, Monarch®, and Canvax™), and fully automated (QIAcube™ and Maxwell®) processes, from two biological matrices: human Jurkat T cells and peripheral blood mononuclear cells (PBMC). Results showed marked differences in the RNA quality and functionality according to the method employed for RNA extraction and the matrix used. DISCUSSION QIAcube™ and semi-automated extraction methods were perceived as the best options because of their lower variability, good functionality, and lower cost (P < 0.001). These data contribute to facilitating researchers or research service platforms (Biobanks) in decision-making practices and emphasize the relevance of the selection of the RNA extraction method in each experimental procedure or traceability study to guarantee both quality standards and its reproducibility.
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Affiliation(s)
- J Ortega-Pinazo
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - M J Pacheco-Rodríguez
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - P J Serrano-Castro
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - B Martínez
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Intercentros de Oncología Médica, Hospitales Universitarios Regional de Málaga y Virgen de la Victoria, Málaga, Spain
| | - M J Pinto-Medel
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- ECAI de Genómica, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | - J M Gómez-Zumaquero
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- ECAI de Genómica, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | - A Lago-Sampedro
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- ECAI de Genómica, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
| | - B García-Díaz
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Guillermo Estivill-Torrús
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain.
- Unidad Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain.
| | - Pedro Emilio Ferro Gallego
- Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain.
- Biobank ECAI, Instituto de Investigación Biomédica de Málaga y Plataforma de Nanomedicina (IBIMA Plataforma BIONAND), Málaga, Spain.
- Unidad Clínica de Endocrinología y Nutrición, Hospital Universitario Virgen de la Victoria, Málaga, Spain.
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16
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Boboltz A, Yang S, Duncan GA. Engineering in vitro models of cystic fibrosis lung disease using neutrophil extracellular trap inspired biomaterials. J Mater Chem B 2023; 11:9419-9430. [PMID: 37701932 PMCID: PMC10591795 DOI: 10.1039/d3tb01489d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Cystic fibrosis (CF) is a muco-obstructive lung disease where inflammatory responses due to chronic infection result in the accumulation of neutrophil extracellular traps (NETs) in the airways. NETs are web-like complexes comprised mainly of decondensed chromatin that function to capture and kill bacteria. Prior studies have established excess release of NETs in CF airways increases viscoelasticity of mucus secretions and reduces mucociliary clearance. Despite the pivotal role of NETs in CF disease pathogenesis, current in vitro models of this disease do not account for their contribution. Motivated by this, we developed a new approach to study the pathobiological effects of NETs in CF by combining synthetic NET-like biomaterials, composed of DNA and histones, with an in vitro human airway epithelial cell culture model. To determine the impact of synthetic NETs on airway clearance function, we incorporated synthetic NETs into mucin hydrogels and cell culture derived airway mucus to assess their rheological and transport properties. We found that the addition of synthetic NETs significantly increases mucin hydrogel viscoelasticity. As a result, mucociliary transport in vitro was significantly reduced with the addition of mucus containing synthetic NETs. Given the prevalence of bacterial infection in the CF lung, we also evaluated the growth of Pseudomonas aeruginosa in mucus with or without synthetic NETs. We found mucus containing synthetic NETs promoted microcolony growth and prolonged bacterial survival. Together, this work establishes a new biomaterial enabled approach to study innate immunity mediated airway dysfunction in CF.
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Affiliation(s)
- Allison Boboltz
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA.
| | - Sydney Yang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA.
| | - Gregg A Duncan
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA.
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17
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Ignatavičienė I, Ragauskas A, Rakauskas V, Butkauskas D. Quality of DNA extracted from freshwater fish scales and mucus and its application in genetic diversity studies of Perca fluviatilis and Rutilus rutilus. Biol Methods Protoc 2023; 8:bpad022. [PMID: 37817807 PMCID: PMC10561993 DOI: 10.1093/biomethods/bpad022] [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: 07/19/2023] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023] Open
Abstract
Studies on genetic diversity require biological material containing a reliable source of DNA that can be extracted and analyzed. Recently, non-invasive sampling has become a preferred sampling method of biological material. The suitability of a less invasive approach that involves obtaining samples by swabbing the fish skin (including live, non-anesthetized fish) should be considered. In this study, we compared the efficiency of DNA extraction, amplification, and sequencing of mtDNA fragments of two fish species Perca fluviatilis and Rutilus rutilus based on DNA collected from the scales and mucus using the modified Aljanabi and Martinez method. The results revealed a higher quality of DNA extracted from the mucus; however, the mean DNA concentration obtained from the scales of both fish species was higher. We verified the method suitable for amplification and sequencing of mtDNA fragments of both fish species using newly designed markers (D-loop, ATP6) and examined the potential risk of intraspecific cross-contamination. The DNA sequence alignment analysis revealed identical sequences attributed to the same individual when DNA, extracted from two different sources (scales and mucus), was used. We demonstrated that the quantity and quality of DNA extracted from the scales and mucus using the proposed method were high enough to carry out genetic diversity studies based on sampling of live fish with the possibility to release it after collecting samples.
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18
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Raj A, Thomas RK, Vidya L, Neelima S, Aparna VM, Sudarsanakumar C. A Minor Groove Binder with Significant Cytotoxicity on Human Lung Cancer Cells: The Potential of Hesperetin Functionalised Silver Nanoparticles. J Fluoresc 2023:10.1007/s10895-023-03409-7. [PMID: 37721707 DOI: 10.1007/s10895-023-03409-7] [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: 07/16/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023]
Abstract
Natural drug functionalised silver (Ag) nanoparticles (NPs) have gained significant interest in pharmacology related applications due to their therapeutic efficiency. We have synthesised silver nanoparticle using hesperetin as a reducing and capping agent. This work aims to discuss the relevance of the hesperetin functionalised silver nanoparticles (H-AgNPs) in the field of nano-medicine. The article primarily investigates the anticancer activity of H-AgNPs and then their interactions with calf thymus DNA (ctDNA) through spectroscopic and thermodynamic techniques. The green synthesised H-AgNPs are stable, spherical in shape and size of 10 ± 3 nm average diameter. The complex formation of H-AgNPs with ctDNA was established by UV-Visible absorption, fluorescent dye displacement assay, isothermal calorimetry and viscosity measurements. The binding constants obtained from these experiments were consistently in the order of 104 Mol-1. The melting temperature analysis and FTIR measurements confirmed that the structural alterations of ctDNA by the presence of H-AgNPs are minimal. All the thermodynamic variables and the endothermic binding nature were acquired from ITC experiments. All these experimental outcomes reveal the formation of H-AgNPs-ctDNA complex, and the results consistently verify the minor groove binding mode of H-AgNPs. The binding constant and limit of detection of 1.8 μM found from the interaction studies imply the DNA detection efficiency of H-AgNPs. The cytotoxicity of H-AgNPs against A549 and L929 cell lines were determined by in vitro MTT cell viability assay and lactate dehydrogenase (LDH) assay. The cell viability and LDH enzyme release are confirmed that the H-AgNPs has high anticancer activity. Moreover, the calculated LD50 value for H-AgNPs against lung cancer cells is 118.49 µl/ml, which is a low value comparing with the value for fibroblast cells (269.35 µl/ml). In short, the results of in vitro cytotoxicity assays revealed that the synthesised nanoparticles can be considered in applications related to cancer treatments. Also, we have found that, H-AgNPs is a minor groove binder, and having high DNA detection efficiency.
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Affiliation(s)
- Aparna Raj
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - Riju K Thomas
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
- Bharata Mata College, Thrikkakara, Ernakulam, Kerala, 682032, India
| | - L Vidya
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - S Neelima
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - V M Aparna
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - C Sudarsanakumar
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India.
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19
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Ilosvai ÁM, Gerzsenyi TB, Sikora E, Harasztosi L, Kristály F, Viskolcz B, Váradi C, Szőri-Dorogházi E, Vanyorek L. Simplified Synthesis of the Amine-Functionalized Magnesium Ferrite Magnetic Nanoparticles and Their Application in DNA Purification Method. Int J Mol Sci 2023; 24:14190. [PMID: 37762494 PMCID: PMC10532358 DOI: 10.3390/ijms241814190] [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: 08/21/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
For pathogens identification, the PCR test is a widely used method, which requires the isolation of nucleic acids from different samples. This extraction can be based on the principle of magnetic separation. In our work, amine-functionalized magnesium ferrite nanoparticles were synthesized for this application by the coprecipitation of ethanolamine in ethylene glycol from Mg(II) and Fe(II) precursors. The conventional synthesis method involves a reaction time of 12 h (MgFe2O4-H&R MNP); however, in our modified method, the reaction time could be significantly reduced to only 4 min by microwave-assisted synthesis (MgFe2O4-MW MNP). A comparison was made between the amine-functionalized MgFe2O4 samples prepared by two methods in terms of the DNA-binding capacity. The experimental results showed that the two types of amine-functionalized magnesium ferrite magnetic nanoparticles (MNPs) were equally effective in terms of their DNA extraction yield. Moreover, by using a few minutes-long microwave synthesis, we obtained the same quality magnesium ferrite particles as those made through the long and energy-intensive 12-h production method. This advancement has the potential to improve and expedite pathogen identification processes, helping to better prevent the spread of epidemics.
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Affiliation(s)
- Ágnes M. Ilosvai
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary; (Á.M.I.); (E.S.); (B.V.)
| | - Tímea B. Gerzsenyi
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary; (T.B.G.); (C.V.)
| | - Emőke Sikora
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary; (Á.M.I.); (E.S.); (B.V.)
| | - Lajos Harasztosi
- Department of Solid-State Physics, Faculty of Science and Technology, University of Debrecen, 4010 Debrecen, Hungary;
| | - Ferenc Kristály
- Institute of Mineralogy and Geology, Faculty of Earth and Environmental Sciences and Engineering, University of Miskolc, 3515 Miskolc, Hungary;
| | - Béla Viskolcz
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary; (Á.M.I.); (E.S.); (B.V.)
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary; (T.B.G.); (C.V.)
| | - Csaba Váradi
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary; (T.B.G.); (C.V.)
| | - Emma Szőri-Dorogházi
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary; (T.B.G.); (C.V.)
| | - László Vanyorek
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary; (Á.M.I.); (E.S.); (B.V.)
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20
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Jarrar Y, Abudahab S, Abdul-Wahab G, Zaiter D, Madani A, Abaalkhail SJ, Abulebdah D, Alhawari H, Musleh R, Lee SJ. Clinical Significance of NAT2 Genetic Variations in Type II Diabetes Mellitus and Lipid Regulation. Pharmgenomics Pers Med 2023; 16:847-857. [PMID: 37724295 PMCID: PMC10505377 DOI: 10.2147/pgpm.s422495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023] Open
Abstract
Background N-acetyltransferase 2 (NAT2) enzyme is a Phase II drug-metabolizing enzyme that metabolizes different compounds. Genetic variations in NAT2 can influence the enzyme's activity and potentially lead to the development of certain diseases. Aim This study aimed to investigate the association of NAT2 variants with the risk of Type II diabetes mellitus (T2DM) and the lipid profile among Jordanian patients. Methods We sequenced the whole protein-coding region in NAT2 using Sanger's method among a sample of 45 Jordanian T2DM patients and 50 control subjects. Moreover, we analyzed the lipid profiles of the patients and examined any potential associations with NAT2 variants. Results This study revealed that the heterozygous NAT2*13 C/T genotype is significantly (P = 0.03) more common among T2DM (44%) than non-T2DM subjects (23.5%). Furthermore, the frequency of homozygous NAT2*13 T/T genotype was found to be significantly higher (P = 0.03) among T2DM patients (26.7%) compared to that of non-T2DM subjects (11%). The heterozygous NAT2*7 G/A genotype was exclusively observed in T2DM patients (11.1%) and absent in the control non-T2DM group. Moreover, among T2DM patients, those with a homozygous NAT2*11 T/T genotype exhibited significantly higher levels of triglycerides (381.50 ± 9.19 ng/dL) with a P value of 0.01 compared to those with heterozygous NAT2*11 C/T (136.23 ± 51.12 ng/dL) or wild-type NAT2*11 C/C (193.65 ± 109.89 ng/dL) genotypes. T2DM patients with homozygous NAT2*12 G/G genotype had a significantly (P = 0.04) higher triglyceride levels (275.67 ± 183.42 ng/dL) than the heterozygous NAT2*12 A/G (140.02 ± 49.53 ng/dL) and the wild NAT2*12 A/A (193.65 ± 109.89 ng/dL). Conclusion The finding in this study suggests that the NAT2 gene is a potential biomarker for the development of T2DM and changes in triglyceride levels among Jordanians. However, it is important to note that our sample size was limited; therefore, further clinical studies with a larger cohort are necessary to validate these findings.
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Affiliation(s)
- Yazun Jarrar
- Department of Basic Medical Sciences, Faculty of Medicine, Al-Balqa Applied University, Al-Salt, Jordan
| | - Sara Abudahab
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Ghasaq Abdul-Wahab
- Department of Oral Surgery and Periodontology, College of Dentistry, Al-Mustansiriya University, Baghdad, Iraq
| | - Dana Zaiter
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Abdalla Madani
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Sara J Abaalkhail
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Dina Abulebdah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Hussam Alhawari
- Department of Internal Medicine, School of Medicine, The University of Jordan, Amman, Jordan
| | - Rami Musleh
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Su-Jun Lee
- Department of Pharmacology, Pharmacogenomics Research Center, College of Medicine, Inje University, Busan, Korea
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21
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Shi X, Hu Z, Gan B, He Y, Zhang L, Chen M, Wang Y, Li X. Multivariate Evaluation of DNA Quality Differences in Different Preanalytical Procedures in Mouse Livers. Biopreserv Biobank 2023; 21:378-387. [PMID: 36067273 DOI: 10.1089/bio.2022.0027] [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: 11/13/2022] Open
Abstract
Successful histogenetic research relies on proper handling of tissue samples to maximize DNA quality. As the largest gland in the body, the liver is particularly sensitive to sample mishandling owing to its enzymatic and transcriptional activity. However, the impact of preanalytical procedures on the quality of extracted liver DNA remains poorly understood. In this study, we assessed the impact of extraction methods, duration of ex vivo liver ischemia, liver storage time, and temperature on extracted DNA quality. Comprehensive parameters such as DNA yields, purity, DNA integrity number, the percentage of double-stranded DNA (%dsDNA), and PCR amplification of the GAPDH gene fragment were assessed to identify the quality of extracted DNA. Our results revealed that these preanalytical processes had little effect on DIN values and PCR efficiency of GAPDH gene fragments for each sample, whereas the DNA yields, purity, and %dsDNAs varied widely across different processes. For liver DNA extraction, RNase is necessary to isolate "pure" DNA, and the presence of RNase could significantly increase the %dsDNA. In addition, significant increases in the yields, purity, and %dsDNA of extracted DNA were observed in the TissueLyser-processed livers compared with the mortar and pestle or shear cell disruption methods. Further investigation revealed that livers experiencing longer periods of ex vivo ischemia resulted in significantly compromised DNA yields, and to obtain sufficient DNA, the ex vivo liver ischemia should be limited to within 30 minutes. Moreover, compared with storage of livers at -80°C, storage of livers in the vapor phase of liquid nitrogen yielded a higher quality of the extracted DNA. Our findings exhibited significant implications for liver-derived DNA quality assessment and management.
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Affiliation(s)
- Xue Shi
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Baoyu Gan
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yinlin He
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Linpei Zhang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Min Chen
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Xiaojiao Li
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
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22
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Vitošević K, Todorović D, Slović Ž, Varljen T, Radaković I, Radojević D, Čanović V, Todorović M. The quality of DNA isolated from autopsy formalin-fixed and formalin-fixed paraffin-embedded tissues: study of 1662 samples. Mol Biol Rep 2023; 50:6323-6336. [PMID: 37310548 DOI: 10.1007/s11033-023-08491-5] [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: 01/05/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND There are enormous formalin-fixed paraffin-embedded tissue archives and a constantly growing number of methods for molecular analyses but, the isolation of DNA from this tissue is still challenging due to the damaging effect of formalin on DNA. To determine the extent to which DNA purity, yield and integrity depend on the process of fixation in formalin, and to what extent on the process of tissue paraffin embedding, we compared the quality of DNA isolated from fixed tissues and DNA isolated from tissues embedded in paraffin blocks after fixation. METHODS AND RESULTS Heart, liver and brain tissues obtained from healthy people who suddenly died a violent death were fixed in 10% buffered formalin as well as in 4% unbuffered formalin for 6 h, 1-7 days (every 24 h), 10, 14, 28 days and 2 months. Additionally, the same tissues were fixed in 4% unbuffered formalin embedded in a paraffin block and stored from a few months to 30 years. The yield and purity of the DNA samples isolated from these tissues were measured using spectrophotometry. PCR amplification of the hTERT gene was performed to evaluate the degree of DNA fragmentation. Although the purity of the DNA isolated from almost all tissue samples was satisfactory, the DNA yields changed significantly. There was a decrease in successful PCR amplification of the hTERT gene in DNA samples isolated from tissue fixed in buffered and unbuffered formalin for up to 2 months from 100% to 8.3%. Archiving the tissue in paraffin blocks for up to 30 years also impacts the integrity of DNA, so there was a decrease in PCR amplification of the hTERT gene from 91% success to 3%. CONCLUSION The largest decrease in DNA yield was observed after tissue formalin fixation after 14 days of fixation in buffered and unbuffered formalin. DNA integrity depends on the time of tissue formalin fixation, especially after 6 days for tissue fixed in unbuffered formalin, while for tissue fixed in buffered formalin the time is prolonged up to 28 days. The age of paraffin blocks also impacted DNA integrity, after 1 year and 16 years of archiving the paraffin blocks of tissues, there was a decrease in the success of PCR amplification.
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Affiliation(s)
- Katarina Vitošević
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia.
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia.
| | - Danijela Todorović
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Živana Slović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
| | - Tatjana Varljen
- Institute of Legal Medicine, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Radaković
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Dušan Radojević
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Vanja Čanović
- Faculty of Medical Sciences, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Miloš Todorović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
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23
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Ring N, Low AS, Wee B, Paterson GK, Nuttall T, Gally D, Mellanby R, Fitzgerald JR. Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections. Microb Genom 2023; 9:mgen001066. [PMID: 37471128 PMCID: PMC10438823 DOI: 10.1099/mgen.0.001066] [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: 02/16/2023] [Accepted: 06/18/2023] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing typically requires 48-72 h to identify appropriate antibiotics for treatment. In the meantime, broad-spectrum antimicrobials are often used, which may be ineffective or impact non-target commensal bacteria. Here, we present a rapid, culture-free, diagnostics pipeline, involving metagenomic nanopore sequencing directly from clinical urine and skin samples of dogs. We have planned this pipeline to be versatile and easily implementable in a clinical setting, with the potential for future adaptation to different sample types and animals. Using our approach, we can identify the bacterial pathogen present within 5 h, in some cases detecting species which are difficult to culture. For urine samples, we can predict antibiotic sensitivity with up to 95 % accuracy. Skin swabs usually have lower bacterial abundance and higher host DNA, confounding antibiotic sensitivity prediction; an additional host depletion step will likely be required during the processing of these, and other types of samples with high levels of host cell contamination. In summary, our pipeline represents an important step towards the design of individually tailored veterinary treatment plans on the same day as presentation, facilitating the effective use of antibiotics and promoting better antimicrobial stewardship.
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Affiliation(s)
- Natalie Ring
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Alison S. Low
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bryan Wee
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Gavin K. Paterson
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Tim Nuttall
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - David Gally
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Richard Mellanby
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
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24
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Boboltz AM, Yang S, Duncan GA. Engineering in vitro models of cystic fibrosis lung disease using neutrophil extracellular trap inspired biomaterials. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546583. [PMID: 37425779 PMCID: PMC10327088 DOI: 10.1101/2023.06.26.546583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cystic fibrosis (CF) is a muco-obstructive lung disease where inflammatory responses due to chronic infection result in the accumulation of neutrophil extracellular traps (NETs) in the airways. NETs are web-like complexes comprised mainly of decondensed chromatin that function to capture and kill bacteria. Prior studies have established excess release of NETs in CF airways increases viscoelasticity of mucus secretions and reduces mucociliary clearance. Despite the pivotal role of NETs in CF disease pathogenesis, current in vitro models of this disease do not account for their contribution. Motivated by this, we developed a new approach to study the pathobiological effects of NETs in CF by combining synthetic NET-like biomaterials, composed of DNA and histones, with an in vitro human airway epithelial cell culture model. To determine the impact of synthetic NETs on airway clearance function, we incorporated synthetic NETs into mucin hydrogels and cell culture derived airway mucus to assess their rheological and transport properties. We found that the addition of synthetic NETs significantly increases mucin hydrogel and native mucus viscoelasticity. As a result, mucociliary transport in vitro was significantly reduced with the addition of mucus containing synthetic NETs. Given the prevalence of bacterial infection in the CF lung, we also evaluated the growth of Pseudomonas aeruginosa in mucus with or without synthetic NETs. We found mucus containing synthetic NETs promoted microcolony growth and prolonged bacterial survival. Together, this work establishes a new biomaterial enabled approach to study innate immunity mediated airway dysfunction in CF.
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Affiliation(s)
- Allison M Boboltz
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Sydney Yang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Gregg A Duncan
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
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25
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El-Ryalat S, Irshaid Y, Abujbara M, El-Khateeb M, Ajlouni K. Adipocyte "Fatty Acid Binding Protein" Gene Polymorphisms ( rs1054135, rs16909196 and rs16909187) in Jordanians with Obesity and Type 2 Diabetes Mellitus. Balkan J Med Genet 2023; 25:63-70. [PMID: 37265971 PMCID: PMC10230837 DOI: 10.2478/bjmg-2022-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
Background Obesity, type 2 diabetes mellitus (T2DM), and dyslipidemia may result from the interactions of genetic and environmental factors. There are controversial reports concerning the association of polymorphisms (rs1054135, rs16909196 and rs16909187) in the gene of adipocyte fatty acid binding protein (FABP4) with obesity and T2DM. Therefore, we designed this study to determine the association of these polymorphisms with obesity, T2DM, and dyslipidemia among Jordanian subjects. Methods The study was approved by the National Center for Diabetes, Endocrinology, and Genetics (NCDEG) Institutional Review Board (IRB). A total of 397 subjects were enrolled in the study and divided into four groups as described in materials and methods section. The fatty acid binding protein 4 (FABP4) gene containing (rs1054135, rs16909196 and rs16909187) single nucleotide polymorphisms (SNP) was amplified by polymerase chain reaction (PCR) followed by Sanger DNA sequencing of the PCR product. Results None of the three SNPs were associated with T2DM (p > 0.05). The rs16909187 and rs16909196 were significantly associated with obesity. The wild type (CC) of rs16909187 was significantly higher among the overweight and obese group compared with normal weight controls (OD = 2.17, 95% CI = 1.18 - 3.96, p =0.01). The wild type of rs16909196 (AA) was significantly higher among the overweight and obese group compared to controls, (OD = 2.26, 95% CI = 1.24 - 4.14, p = 0.01). These results may indicate that the wild-type may be a risk factor for obesity.Only the rs1054135 SNP was significantly associated with increased low density lipoprotein (LDL) levels in the overweight and obese group compared with the controls (p = 0.03). Conclusions The wild-type genotypes of rs16909196 and rs16909187 may be risk factors for obesity but not T2DM. None of the three SNPs was associated with T2DM.
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Affiliation(s)
- S.W. El-Ryalat
- Department of Pharmacology, College of Medicine, the University of Jordan, AmmanJordan
| | - Y.M. Irshaid
- Department of Pharmacology, College of Medicine, the University of Jordan, AmmanJordan
| | - M. Abujbara
- The National Center for Diabetes, Endocrinology, and Genetics, Amman11942, Jordan
| | - M. El-Khateeb
- The National Center for Diabetes, Endocrinology, and Genetics, Amman11942, Jordan
| | - K.M. Ajlouni
- The National Center for Diabetes, Endocrinology, and Genetics, Amman11942, Jordan
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26
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Pardo Z, Mateos I, Saro C, Campos R, Argüello H, Lachica M, Ranilla MJ, Fernández-Fígares I. The Effect of Supplementation with Betaine and Zinc on In Vitro Large Intestinal Fermentation in Iberian Pigs under Heat Stress. Animals (Basel) 2023; 13:ani13061102. [PMID: 36978642 PMCID: PMC10044697 DOI: 10.3390/ani13061102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/03/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
We investigated the effects of betaine and zinc on the in vitro fermentation of pigs under heat stress (HS). Twenty-four Iberian pigs (43.4 ± 1.2 kg) under HS (30 °C) were assigned to treatments for 4 weeks: control (unsupplemented), betaine (5 g/kg), and zinc (0.120 g/kg) supplemented diet. Rectal content was used as the inoculum in 24-hincubations with pure substrates (starch, pectin, inulin, cellulose). Total gas, short-chain fatty acid (SCFA), and methane production and ammonia concentration were measured. The abundance of total bacteria and several bacterial groups was assessed. Betaine increased the acetate production with pectin and inulin, butyrate production with starch and inulin, and ammonia concentration, and decreased propionate production with pectin and inulin. The abundance of Bifidobacterium and two groups of Clostridium decreased with betaine supplementation. Zinc decreased the production of SCFA and gas with starch and inulin, associated with diminished bacterial activity. Propionate production decreased with starch, pectin, and inulin while butyrate production increased with inulin, and isoacid production increased with cellulose and inulin in pigs supplemented with zinc. The ammonia concentration increased for all substrates. The Clostridium cluster XIV abundance decreased in pigs fed zinc supplemented diets. The results reported were dependent on the substrate fermented, but the augmented butyrate production with both betaine and zinc could be of benefit for the host.
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Affiliation(s)
- Zaira Pardo
- Departamento de Nutrición y Producción Animal Sostenible, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, (CSIC) Profesor Albareda 1, 18008 Granada, Spain
| | - Iván Mateos
- Departamento de Producción Animal, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
- Instituto de Ganadería de Montaña, CSIC-Universidad de León, Finca Marzanas s/n, Grulleros, 24346 León, Spain
| | - Cristina Saro
- Departamento de Producción Animal, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
- Instituto de Ganadería de Montaña, CSIC-Universidad de León, Finca Marzanas s/n, Grulleros, 24346 León, Spain
| | - Rómulo Campos
- Departamento de Producción Animal, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
- Departamento de Ciencia Animal, Universidad Nacional de Colombia, Carrera 32 # 12-00, Palmira 76531, Colombia
| | - Héctor Argüello
- Departamento de Sanidad Animal, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Manuel Lachica
- Departamento de Nutrición y Producción Animal Sostenible, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, (CSIC) Profesor Albareda 1, 18008 Granada, Spain
| | - María José Ranilla
- Departamento de Producción Animal, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
- Instituto de Ganadería de Montaña, CSIC-Universidad de León, Finca Marzanas s/n, Grulleros, 24346 León, Spain
| | - Ignacio Fernández-Fígares
- Departamento de Nutrición y Producción Animal Sostenible, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, (CSIC) Profesor Albareda 1, 18008 Granada, Spain
- Correspondence: or
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27
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Ortiz-Alvarez L, Acosta FM, Xu H, Sanchez-Delgado G, Vilchez-Vargas R, Link A, Plaza-Díaz J, Llamas JM, Gil A, Labayen I, Rensen PCN, Ruiz JR, Martinez-Tellez B. Fecal microbiota composition is related to brown adipose tissue 18F-fluorodeoxyglucose uptake in young adults. J Endocrinol Invest 2023; 46:567-576. [PMID: 36242744 PMCID: PMC9938059 DOI: 10.1007/s40618-022-01936-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/07/2022] [Indexed: 10/17/2022]
Abstract
OBJECTIVE Human brown adipose tissue (BAT) has gained considerable attention as a potential therapeutic target for obesity and its related cardiometabolic diseases; however, whether the gut microbiota might be an efficient stimulus to activate BAT metabolism remains to be ascertained. We aimed to investigate the association of fecal microbiota composition with BAT volume and activity and mean radiodensity in young adults. METHODS 82 young adults (58 women, 21.8 ± 2.2 years old) participated in this cross-sectional study. DNA was extracted from fecal samples and 16S rRNA sequencing was performed to analyse the fecal microbiota composition. BAT was determined via a static 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography-computed tomography scan (PET/CT) after a 2 h personalized cooling protocol. 18F-FDG uptake was also quantified in white adipose tissue (WAT) and skeletal muscles. RESULTS The relative abundance of Akkermansia, Lachnospiraceae sp. and Ruminococcus genera was negatively correlated with BAT volume, BAT SUVmean and BAT SUVpeak (all rho ≤ - 0.232, P ≤ 0.027), whereas the relative abundance of Bifidobacterium genus was positively correlated with BAT SUVmean and BAT SUVpeak (all rho ≥ 0.262, P ≤ 0.012). On the other hand, the relative abundance of Sutterellaceae and Bifidobacteriaceae families was positively correlated with 18F-FDG uptake by WAT and skeletal muscles (all rho ≥ 0.213, P ≤ 0.042). All the analyses were adjusted for the PET/CT scan date as a proxy of seasonality. CONCLUSION Our results suggest that fecal microbiota composition is involved in the regulation of BAT and glucose uptake by other tissues in young adults. Further studies are needed to confirm these findings. CLINICAL TRIAL INFORMATION ClinicalTrials.gov no. NCT02365129 (registered 18 February 2015).
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Affiliation(s)
- L Ortiz-Alvarez
- PROFITH (PROmoting FITness and Health Through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain.
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain.
| | - F M Acosta
- PROFITH (PROmoting FITness and Health Through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain
- Turku PET Centre, University of Turku, Turku, Finland
- Turku PET Centre, Turku University Hospital, Turku, Finland
- InFLAMES Research Flagship Centre, University of Turku, Turku, Finland
- Department of Physical and Sports Education, School of Sports Science, University of Granada, Granada, Spain
| | - H Xu
- PROFITH (PROmoting FITness and Health Through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
| | - G Sanchez-Delgado
- Department of Physical and Sports Education, School of Sports Science, University of Granada, Granada, Spain
- Pennington Biomedical Research Center, Baton Rouge, LA, 70808, USA
| | - R Vilchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke-University Magdeburg, Magdeburg, Germany
| | - A Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-Von-Guericke-University Magdeburg, Magdeburg, Germany
| | - J Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - J M Llamas
- Instituto de Investigación Biosanitaria Ibs Granada, 18014, Granada, Spain
- Servicio de Medicina Nuclear, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - A Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs Granada, 18014, Granada, Spain
- Centro de Investigación Biomédica En Red (CIBER) Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Málaga, Spain
- Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center, Parque Tecnológico Ciencias de la Salud, University of Granada, Armilla, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs.Granada, Granada, Spain
| | - I Labayen
- Institute for Innovation and Sustainable Development in Food Chain (IS-FOOD), Public University of Navarra, Campus de Arrosadía, Pamplona, Spain
| | - P C N Rensen
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - J R Ruiz
- PROFITH (PROmoting FITness and Health Through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain
- Department of Physical and Sports Education, School of Sports Science, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria, Ibs.Granada, Granada, Spain
| | - B Martinez-Tellez
- PROFITH (PROmoting FITness and Health Through Physical Activity) Research Group, Sport and Health University Research Institute (iMUDS), University of Granada, Granada, Spain.
- Department of Medicine, Division of Endocrinology, and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands.
- Department of Education, Faculty of Education Sciences, SPORT Research Group (CTS-1024), CERNEP Research Center, University of Almería, Almería, Spain.
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28
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Gerzsenyi TB, Ilosvai ÁM, Szilágyi G, Szőri M, Váradi C, Viskolcz B, Vanyorek L, Szőri-Dorogházi E. A Simplified and Efficient Method for Production of Manganese Ferrite Magnetic Nanoparticles and Their Application in DNA Isolation. Int J Mol Sci 2023; 24:ijms24032156. [PMID: 36768483 PMCID: PMC9917137 DOI: 10.3390/ijms24032156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/25/2023] Open
Abstract
A simplified, fast, and effective production method has been developed for the synthesis of manganese ferrite (MnFe2O4) magnetic nanoparticles (MNPs). In addition to the wide applicability of MnFe2O4 MNPs, this work also reports their application in DNA isolation for the first time. An ultrasonic-cavitation-assisted combustion method was applied in the synthesis of MnFe2O4 MNPs at different furnace temperatures (573 K, 623 K, 673 K, and 773 K) to optimize the particles' properties. It was shown that MnFe2O4 nanoparticles synthesized at 573 K consist of a spinel phase only with adequate size and zeta potential distributions and superparamagnetic properties. It was also demonstrated that superparamagnetic manganese ferrite nanoparticles bind DNA in buffer with a high NaCl concentration (2.5 M), and the DNA desorbs from the MNPs by decreasing the NaCl concentration of the elution buffer. This resulted in a DNA yield comparable to that of commercial DNA extraction products. Both the DNA concentration measurements and electrophoresis confirmed that a high amount of isolated bacterial plasmid DNA (pDNA) with adequate purity can be extracted with MnFe2O4 (573 K) nanoparticles by applying the DNA extraction method proposed in this article.
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Affiliation(s)
- Tímea B. Gerzsenyi
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary
| | - Ágnes M. Ilosvai
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary
| | - Gergely Szilágyi
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary
| | - Milán Szőri
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary
| | - Csaba Váradi
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary
| | - Béla Viskolcz
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary
| | - László Vanyorek
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary
- Correspondence: (L.V.); (E.S.-D.)
| | - Emma Szőri-Dorogházi
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary
- Correspondence: (L.V.); (E.S.-D.)
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29
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Khalaf QA, Rasool KH, Naji EN. Evaluation of IL-6 and IL-17A gene polymorphisms in Iraqi patients infected with COVID-19 and type 2 diabetes mellitus. Hum Antibodies 2023; 31:35-44. [PMID: 37458031 DOI: 10.3233/hab-230007] [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: 07/18/2023]
Abstract
BACKGROUND In patients with COVID-19, diabetes mellitus type 2 (T2DM) increases the risk of hospitalization and death. Patients who have IL-6 and IL-17A single nucleotide polymorphisms (SNPs) are more likely to have severe COVID-19. This study aims to determine whether SNPs of the IL-6 gene at rs1800795 (G > C) and the IL-17A gene at rs2275913 (G > A) are associated with COVID-19 and T2DM in the Iraqi population. PATIENTS AND METHODS Twenty-four people were divided into 4 groups as follows: six patients with severe COVID-19 and T2DM were placed in Group 1 as "G1", six patients with COVID-19 but no T2DM were placed in Group 2 as "G2", and six patients with T2DM were placed in Group 3 as "G3". There were also six healthy controls included in each group. Polymerase chain reaction (PCR) was used to amplify the target genes after genomic DNA from the blood samples was extracted. Sanger sequencing was used to find the SNPs in both the forward and reverse directions for each sample. RESULTS In the case of IL-6 SNP at rs1800795, the GG genotype was more common in "G3", the CC genotype was less common in all patient groups than in controls, and the GC allele was more common in "G2" than in the control group. In comparison to the controls, the three patient groups showed lower frequencies of the C allele and higher frequencies of the G allele. Regarding IL-17A gene polymorphism, the AA and GA genotypes were more prevalent in "G2" and "G3", respectively. The GG genotype and G allele frequency dropped in all patient groups compared to the control group, whereas the A allele frequency increased in all patient groups. CONCLUSIONS The IL-6 gene at rs1800795 (G/C) and the IL-17A gene at rs2275913 (G/A) loci were associated with COVID-19 and T2DM in Iraqi population.
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30
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Servais MD, Galtier F, Nouvel A, Rebuffat S, Laget J, Géan A, Provost N, Lorcy F, Rigau V, Couderc G, Géraud P, Nocca D, Builles N, De Préville N, Lajoix AD. Addressing the quality challenge of a human biospecimen biobank through the creation of a quality management system. PLoS One 2022; 17:e0278780. [PMID: 36584180 PMCID: PMC9803146 DOI: 10.1371/journal.pone.0278780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/22/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The objective of the COMET (COllection of MEtabolic Tissues) biobank project is to create a high-quality collection of insulin-sensitive tissues (liver, muscle, adipose tissues, and epiploic artery) and blood sample derivatives (plasma, serum, DNA and RNA), collected from 270 grade 2-3 obese patients undergoing bariatric surgery. Relevant data on patient such as clinical/biological characteristics and sample handling are also collected. For this, our aim was to establish a Quality Management System (QMS) to meet the reliability and quality requirements necessary for its scientific exploitation. MATERIALS AND METHODS The COMET QMS includes: (1) Quality Assurance to standardize all stages of the biobanking process, (2) Quality Controls on samples from the first patients included in order to validate the sample management process and ensure reproducible quality; and 3) "in process" Quality Controls to ensure the reliability of the storage procedures and the stability of the samples over time. RESULTS For serum and plasma, several corrective actions, such as temperature handling and centrifugation conditions, were made to the protocol and led to improvement of the volume and quality of samples. Regarding DNA, all samples evaluated achieved a satisfactory level of purity and integrity and most of them yielded the required DNA quantity. All frozen tissue samples had RNAs of good purity. RNA quality was confirmed by RIN, achieving values in most cases over 7 and efficient amplification of housekeeping genes by RT-qPCR, with no significant differences among samples from the same tissue type. In the "in process" Quality Controls, DNA, RNA, and histological integrity of tissues showed no differences among samples after different preservation times. CONCLUSION Quality Control results have made it possible to validate the entire biobank process and confirm the utility of implementing QMS to guarantee the quality of a biospecimen collection.
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Affiliation(s)
| | - Florence Galtier
- INSERM, Clinical Investigation Center 1411, St Eloi Hospital, University Hospital of Montpellier, Montpellier, France
- Department of Endocrinology, Lapeyronie Hospital, University Hospital of Montpellier, Montpellier, France
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Agathe Nouvel
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Sandra Rebuffat
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Jonas Laget
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | | | | | - Frédéric Lorcy
- Biological Resources Center, Anatomy and Cytology Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Valérie Rigau
- Biological Resources Center, Anatomy and Cytology Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Guilhem Couderc
- Biological Resources Center, Tissue Bank, University Hospital of Montpellier, Montpellier, France
| | - Philippe Géraud
- INSERM, Clinical Investigation Center 1411, St Eloi Hospital, University Hospital of Montpellier, Montpellier, France
| | - David Nocca
- Department of Digestive Surgery, University Hospital of Montpellier, Montpellier, France
| | - Nicolas Builles
- Biological Resources Center, Tissue Bank, University Hospital of Montpellier, Montpellier, France
| | | | - Anne-Dominique Lajoix
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
- * E-mail:
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31
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El Gazzar WB, Allam MM, Shaltout SA, Mohammed LA, Sadek AM, Nasr HE. Pioglitazone modulates immune activation and ameliorates inflammation induced by injured renal tubular epithelial cells via PPARγ/miRNA‑124/STAT3 signaling. Biomed Rep 2022; 18:2. [PMID: 36544854 PMCID: PMC9756109 DOI: 10.3892/br.2022.1584] [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: 09/06/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Acute kidney injury (AKI) is commonly a result of renal ischemia reperfusion injury (IRI), which produces clinical complications characterized by the rapid deterioration of renal function, leading to chronic kidney disease and increases the risk of morbidity and mortality. Currently, only supportive treatment is available. AKI, which is accompanied by immune activation and inflammation, is caused by proximal tubular injury. The present study investigated the role of tubular epithelial cells as drivers of inflammation in renal IRI and their potential function as antigen-presenting cells, as well as the molecular mechanisms by which peroxisome proliferator-activated receptor-γ (PPARγ) agonists [such as pioglitazone (Pio)] exert reno-protective action in renal IRI. A total of 50 Wistar male albino rats were divided into five groups: Sham + DMSO, Sham + Pio, IRI + DMSO, IRI + prophylactic preoperative (pre) Pio and IRI + postoperative Pio. The histopathological changes in renal tissue samples and the renal epithelial cell expression of CD86, miRNA-124, STAT3, pro-inflammatory cytokines, inducible nitric oxide synthase (iNOS) and Arginase-II were analyzed by immunohistochemistry, reverse transcription-quantitative PCR, western blotting and ELISA respectively. IRI was a potent inducer for CD86 immunoexpression. An ameliorative action of Pio was demonstrated via decreased CD86 immunoexpression, upregulation of miRNA-124, decreased STAT3 expression and beneficial anti-inflammatory effects. The tubular epithelium served a notable role in the inflammatory response in renal IRI. Pio exerted its anti-inflammatory effects via PPARγ/miRNA-124/STAT3 signaling.
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Affiliation(s)
- Walaa Bayoumie El Gazzar
- Department of Anatomy, Physiology and Biochemistry, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan,Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Benha University, Benha 13518, Egypt,Correspondence to: Dr Walaa Bayoumie El Gazzar, Department of Anatomy, Physiology and Biochemistry, Faculty of Medicine, Hashemite University, Zarqa 13133, Jordan
| | - Mona Maher Allam
- Department of Physiology, Faculty of Medicine, Benha University, Benha 13518, Egypt
| | - Sherif Ahmed Shaltout
- Department of Pharmacology, Public Health and Clinical Skills, Faculty of Medicine, Hashemite University, Zarqa 13133, Jordan,Department of Pharmacology, Faculty of Medicine, Benha University, Benha 13518, Egypt
| | - Lina Abdelhady Mohammed
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Benha University, Benha 13518, Egypt
| | - Ashraf Mohamed Sadek
- Department of Anatomy, Physiology and Biochemistry, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan,Department of Anatomy and Embryology, Faculty of Medicine, Ain Shams University, Cairo 1181, Egypt
| | - Hend Elsayed Nasr
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Benha University, Benha 13518, Egypt
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32
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Iannarelli NJ, Wade TJ, Dempster KS, Moore J, MacNeil AJ, O'Leary DD. No Mediation Effect of Telomere Length or Mitochondrial DNA Copy Number on the Association Between Adverse Childhood Experiences (ACEs) and Central Arterial Stiffness. J Am Heart Assoc 2022; 11:e026619. [DOI: 10.1161/jaha.122.026619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background
Adverse childhood experiences (ACEs) have been linked to increased cardiovascular disease (CVD) risk. Previous reports have suggested that accelerated biological aging—indexed by telomere length (TL) and mitochondrial DNA copy number (mtDNAcn)—may contribute to associations between ACEs and cardiovascular health outcomes. Here, we examine the potential mediating effects of TL and mtDNAcn on the association between ACEs and central arterial stiffness—an intermediate cardiovascular health outcome—as a novel pathway linking ACEs to CVD risk among young adults.
Methods and Results
One hundred and eighty‐five (n=102 women; mean age, 22.5±1.5 years) individuals provided information on ACEs. TL (kb per diploid cell) and mtDNAcn (copies per diploid cell) were quantified using quantitative polymerase chain reaction techniques. Central arterial stiffness was measured as carotid‐femoral pulse wave velocity (cfPWV; m/s). Multiple linear regression analyses were used to examine the associations between ACEs, TL, mtDNAcn, and cfPWV. ACEs were positively associated with cfPWV (
β
=0.147,
P
=0.035). TL (
β
=−0.170,
P
=0.011) and mtDNAcn (
β
=−0.159,
P
=0.019) were inversely associated with cfPWV. Neither TL (
β
=−0.027,
P
=0.726) nor mtDNAcn (
β
=0.038,
P
=0.620) was associated with ACEs. Neither marker mediated the association between ACEs and cfPWV.
Conclusions
An increasing number of ACEs were associated with a faster cfPWV and thus, a greater degree of central arterial stiffness. ACEs were not associated with either TL or mtDNAcn, suggesting that these markers do not represent a mediating pathway linking ACEs to central arterial stiffness.
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Affiliation(s)
- Nathaniel J. Iannarelli
- Department of Health Sciences Faculty of Applied Health Sciences Brock University St. Catharines Ontario Canada
- Brock‐Niagara Centre for Health and Well‐Being Brock University St. Catharines Ontario Canada
| | - Terrance J. Wade
- Department of Health Sciences Faculty of Applied Health Sciences Brock University St. Catharines Ontario Canada
- Brock‐Niagara Centre for Health and Well‐Being Brock University St. Catharines Ontario Canada
| | - Kylie S. Dempster
- Department of Health Sciences Faculty of Applied Health Sciences Brock University St. Catharines Ontario Canada
- Brock‐Niagara Centre for Health and Well‐Being Brock University St. Catharines Ontario Canada
| | - Jessy Moore
- Department of Health Sciences Faculty of Applied Health Sciences Brock University St. Catharines Ontario Canada
| | - Adam J. MacNeil
- Department of Health Sciences Faculty of Applied Health Sciences Brock University St. Catharines Ontario Canada
| | - Deborah D. O'Leary
- Department of Health Sciences Faculty of Applied Health Sciences Brock University St. Catharines Ontario Canada
- Brock‐Niagara Centre for Health and Well‐Being Brock University St. Catharines Ontario Canada
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33
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Díaz T, Ortega-Pinazo J, Martínez B, Jiménez A, Gómez-Zumaquero JM, Caracuel Z, Hortas ML, Ferro P. Measurement of yield and quality of DNA in human buffy coat is extraction method dependent. Prep Biochem Biotechnol 2022:1-8. [PMID: 36121058 DOI: 10.1080/10826068.2022.2119574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
During the last few years, an important element in the improvement of the molecular biology techniques has been the necessity for availability of high quality and functionality DNA. Several DNA extraction procedures with different results in both performance and quality, have been proposed. In this study our objective was to determine the most reliable extraction method that balances DNA quantity, and to assess the sample quantification of the fluorometric DNA quantification methods. For this, blood extracted by venopunction from 20 healthy volunteers was used to obtain DNA from buffy coat, and 4 commercial DNA extraction kits were assessed as well as two fluorometric DNA quantification methods with protocols of different complexity. Results suggest that manual methods achieve higher quality and larger yields of DNA. DNA purity obtained with the 4 extraction kits evaluated through the 260/280 and 260/230 ratio showed that the Qiacube kit fulfilled the criteria established in this work, followed very close by the Flexigene kit. On the other hand, the fluorometric DNA methods used in the samples quantification showed a higher variability when using QuantiFlour method, obtaining better results probably due to the simplicity of this protocol.
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Affiliation(s)
- T Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - J Ortega-Pinazo
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga-IBIMA, UGC Neurociencias, Hospital Regional Universitario de Málaga, Malaga, Spain
| | - B Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - A Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - J M Gómez-Zumaquero
- Genomic ECAI, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - Z Caracuel
- Costa del Sol Sanitary Agency, Sanitary District of Málaga, Malaga, Spain
| | - M L Hortas
- Costa del Sol Sanitary Agency, Sanitary District of Málaga, Malaga, Spain
| | - P Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain.,Unidad Clínica de Endocrinología y Nutrición, Hospital Universitario Virgen de la Victoria, Málaga, Spain
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34
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The suitability of using spectrophotometry to determine the concentration and purity of DNA extracted from processed food matrices. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Brandão WQ, da Silva RJ, Mojica-Sánchez LC, Maciel BG, Ratkovski GP, de Melo CP. Use of polypyrrole-polystyrene membranes for extracting DNA from plant tissues. BIOMATERIALS AND BIOSYSTEMS 2022; 7:100060. [PMID: 36824490 PMCID: PMC9934434 DOI: 10.1016/j.bbiosy.2022.100060] [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: 04/29/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 10/16/2022] Open
Abstract
We describe the preparation of a membrane composed of polypyrrole-polystyrene (PPy-PS) and its application in DNA extraction. We adopted the electrospinning technique to prepare polystyrene (PS) membranes, which we used as substrates for incorporating polypyrrole chains through an in situ chemical procedure. As a model system, we initially investigated the use of PPy-PS membranes for the extraction of salmon sperm DNA from aqueous solutions. These studies have shown that the PPy-PS membrane has a maximum adsorption capacity of 236.0 mg of DNA per gram of PPy after 30 min of exposure to a DNA solution (100 mg/L). We incorporated the PPy-PS membranes into centrifugation columns, which we used to carry out experiments for extracting and purification of DNA from curly lettuce leaves. The protocol was initially optimized by first examining the most appropriate concentration of the three components of the lysis buffer (Tris/HCl, NaCl, and EDTA-Na). We then investigated the most adequate volumes of the concentrated surfactant solution (SDS 20%) and that used in the protein and polysaccharide precipitation step (5 M potassium acetate, pH 6.3), factors that directly influence the quality and quantity of the fraction of DNA obtained. For curly lettuce leaves, both in their mature and young stages, the yield and purity of the DNA purified using the PPy-PS membrane were comparable to those obtained using a commercial kit. In both cases, the collected DNA samples presented excellent integrity and quality. These results are suggestive that these composite membranes are competitive with the commercial kits available for the extraction and purification of DNA from plants.
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Affiliation(s)
| | - Romário J. da Silva
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | | | | | - Gabriela P. Ratkovski
- Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Celso P. de Melo
- Pós-Graduação em Ciência de Materiais, Brazil,Departamento de Física, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil,Corresponding author at: Pós-Graduação em Ciência de Materiais, Brazil.
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36
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Yuan Q, Liang Z, Wang S, Zuo P, Wang Y, Luo Y. Size-controlled mesoporous magnetic silica beads effectively extract extracellular DNA in the absence of chaotropic solutions. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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37
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Mordenti M, Capicchioni V, Corsini S, Locatelli M, Abelli E, Banchelli F, Boarini M, Sangiorgi L. Preanalytical DNA assessment for downstream applications: How to optimize the management of human biospecimens to support molecular diagnosis-An experimental study. J Clin Lab Anal 2022; 36:e24531. [PMID: 35666551 PMCID: PMC9279999 DOI: 10.1002/jcla.24531] [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: 02/11/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Background The development of next‐generation sequencing approaches has accelerated the diagnostic process, although at present, there is a lack of a clear consensus on efficient management of human samples for downstream applications. This study aims to investigate timeframe (in terms of short preservation), temperature, and additional preservation procedures (i.e., freeze and thaw cycles) for human biospecimens to implement the reliability and reproducibility of molecular investigations. Methods Overall, 45 whole peripheral bloods, 22 peripheral blood mononuclear cells samples, 15 saliva, and 15 buccal swab biospecimens (through the extracted DNA) were investigated, assessing yield, integrity, amplifiability, and sizing accuracy via the most common molecular techniques. Results Based on the overall evaluation criteria, the results indicate that DNA extracted from all samples, shortly preserved, have suitable quality and reliable reproducibility to be used in diagnostic activities and biomedical research, even if DNA from peripheral blood mononuclear cells is more affected by the experimental conditions. Conclusion Our findings confirm the reliability of peripheral blood samples in almost all the experimental conditions. Saliva and buccal swabs are efficient almost as well, while peripheral blood mononuclear cells, albeit remain a primary source of DNA for molecular screenings, represent a less efficient source.
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Affiliation(s)
- Marina Mordenti
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Valentina Capicchioni
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.,Ministry of Education, San Marino, Repubic of San Marino
| | - Serena Corsini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manuela Locatelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Elisabetta Abelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Federico Banchelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manila Boarini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Luca Sangiorgi
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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38
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Lourenco JM, Welch CB. Using microbiome information to understand and improve animal performance. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2077147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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39
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Talukdar FR, Abramović I, Cuenin C, Carreira C, Gangane N, Sincic N, Herceg Z. A protocol for good quality genomic DNA isolation from formalin-fixed paraffin-embedded tissues without using commercial kits. Mol Biol Rep 2022; 49:4115-4121. [PMID: 35359238 DOI: 10.1007/s11033-022-07394-1] [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: 10/28/2021] [Accepted: 03/16/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND DNA isolation from formalin-fixed paraffin-embedded (FFPE) tissues for molecular analysis has become a frequent procedure in cancer research. However, the yield or quality of the isolated DNA is often compromised, and commercial kits are used to overcome this to some extent. METHODS We developed a new protocol (IARCp) to improve the quality and yield of DNA from FFPE tissues without using any commercial kit. To evaluate the IARCp's performance, we compared the quality and yield of DNA with two commercial kits, namely NucleoSpin® DNA FFPE XS (MN) and QIAamp DNA Micro (QG) isolation kit. RESULTS Total DNA yield for QG ranged from 120.0 to 282.0 ng (mean 216.5 ng), for MN: 213.6-394.2 ng (mean 319.1 ng), and with IARCp the yield was much higher ranging from 775.5 to 1896.9 ng (mean 1517.8 ng). Moreover, IARCp has also performed well in qualitative assessments by spectrophotometer, fluorometer, and real-time PCR assay. CONCLUSION Overall, IARCp represents a novel approach to DNA isolation from FFPE which results in good quality and significant amounts of DNA suitable for many downstream genome-wide and targeted molecular analyses. This protocol does not require the use of any commercial kits or phenol for isolating DNA from FFPE tissues, making it suitable to implement in low-resource settings such as low and middle-income countries.
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Affiliation(s)
- Fazlur Rahman Talukdar
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008, Lyon Cedex 08, France.
| | - Irena Abramović
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008, Lyon Cedex 08, France
| | - Christine Carreira
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008, Lyon Cedex 08, France
| | - Nitin Gangane
- Mahatma Gandhi Institute of Medical Sciences, Sevagram, India
| | - Nino Sincic
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Medical Biology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), 150 Cours Albert-Thomas, 69008, Lyon Cedex 08, France
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Nkuna R, Ijoma GN, Matambo TS. Applying EDTA in Chelating Excess Metal Ions to Improve Downstream DNA Recovery from Mine Tailings for Long-Read Amplicon Sequencing of Acidophilic Fungi Communities. J Fungi (Basel) 2022; 8:jof8050419. [PMID: 35628675 PMCID: PMC9143545 DOI: 10.3390/jof8050419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 12/10/2022] Open
Abstract
The hostile environment of mine tailings contains unique microbial life capable of bioleaching. The metagenomic analysis of such an environment provides an in-depth understanding of the microbial life and its potential, especially in biomining operations. However, DNA recovery from samples collected in those environments is challenging due to the presence of metal ions that interfere with the DNA analysis. A varied concentration of EDTA (4–13 µg/µL) to chelate the metal ions of enriched tailing samples prior to DNA extraction was performed. The results show that 9 µg/µL of EDTA was effective in most samples. However, the increasing concentration of EDTA negatively affected the DNA recovery. The sequencing of the successfully extracted DNA revealed a diverse range of fungal genera, some of which have not been previously reported in tailing or bioleaching applications. The dominant genera include Fodinomyces, Penicillium, Recurvomuces, Trichoderma, and Xenoacremonium; their traits were determined using the FungalTraits database. This study demonstrates the need to include a preliminary metal-chelating step using EDTA before DNA extractions for samples collected from metal-rich environments. It further showed the need for optimization but provided a benchmark range, particularly for tailings. However, we caution that a further EDTA removal step from the extracted DNA should be included to avoid its interferences in downstream applications.
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Zeinalzadeh S, Kheradmand N, Rasouli G, Esmaeilzadeh E, Pakzad B, Behroozi J, Chamanara M, Zoshk MY, Ehtesham N, Sabet MN. Association of a miRNA-binding site polymorphism in IL-16 gene with disease risk and clinical characteristics of rheumatoid arthritis and systemic lupus erythematosus. Clin Rheumatol 2022; 41:2189-2196. [PMID: 35332405 DOI: 10.1007/s10067-022-06131-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/16/2022] [Accepted: 03/13/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION /objectives. Single nucleotide polymorphisms (SNPs) located at the 3'-UTR region of the target genes of microRNAs (miRNAs) can dysregulate their expression via disrupting the binding site of miRNAs. Interleukin-16 (IL-16) is involved in the pathogenesis of rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). In the current study, we assessed the possible association between rs1131445 polymorphism in IL-16 gene with risk and clinical characteristics of RA and SLE in the Iranian population. METHODS In this case-control study, 120 patients with RA, 120 patients with SLE, and 120 unrelated healthy subjects were collected to estimate rs1131445 (T > C) polymorphism in IL-16 gene using real-time PCR high-resolution melting (HRM) method. RESULTS Our results demonstrated considerable associations between TC genotype and C allele of rs1131445 with enhanced risk of RA (ORfor TC genotype = 3.01; 95%CI [1.667-5.526], P < 0.001; ORfor C allele = 1.96; 95%CI [1.314-2.941], P < 0.001). Besides, there was a marginal association between CC genotype and increased risk of RA (P: 0.031). However, there was an insignificant correlation between genotypes and allele frequencies of rs1131445 with incidence risk of SLE (P > 0.05). Moreover, stratification analysis indicated that the C allele in rs1131445 was linked with disease activity-associated laboratory parameters such as CRP and ESR in both RA and SLE patients, as well as the higher incidence of neurological symptoms in SLE subjects (P < 0.05). CONCLUSION These results proposed a significant association between IL-16 polymorphism and augmented risk of RA and clinical characteristics of RA and SLE.
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Affiliation(s)
| | - Nahid Kheradmand
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ghazal Rasouli
- Faculty of Basic Sciences, Central Tehran Branch, Islamic Azad University, Isfahan, Iran
| | | | - Bahram Pakzad
- Division of Rheumatology, Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Javad Behroozi
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran, Iran.,Department of Genetics and Advanced Medical Technology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Mohsen Chamanara
- Toxicology Research Center, Aja University of Medical Sciences, Tehran, Iran.,Department of Pharmacology, School of Medicine, Aja University of Medical Sciences, Tehran, Iran
| | | | - Naeim Ehtesham
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
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Genetic Analysis of Forty MLPA-Negative Duchenne Muscular Dystrophy Patients by Whole-Exome Sequencing. J Mol Neurosci 2022; 72:1098-1107. [PMID: 35218518 DOI: 10.1007/s12031-022-01980-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/26/2022] [Indexed: 10/19/2022]
Abstract
This manuscript aimed to determine the underlying point mutations causing Duchenne muscular dystrophy (DMD) in a heterogeneous group of Iranian patients, who are clinically suspected. Whole-exome sequencing was utilized to detect disease-causing variants in 40 MLPA-negative DMD patients. Disease-causing variants were detected in the DMD gene in 36/40 of the patients (90%), and 4/40 of them (10%) remained undiagnosed. WES analysis revealed that nonsense variant was the most common type in our study (23/36 of the cases). Besides, 12/36 of the cases had frameshift variant, and one of the patients had a likely pathogenic splice variant in the DMD gene. Carrier testing revealed that 21/40 of the mothers had the identified variant. Therefore, most variants were inherited (58.3%), while 19/40 were de novo (41. 7%). The present study has demonstrated the importance of performing WES to detect disease-causing point mutations in MLPA-negative DMD patients and to identify carrier females. Due to regulatory challenges, the clinical development of therapeutic approaches is time-consuming and may not be available to all patients shortly. Therefore, it appears that the techniques used to accurately detect disease-causing variants in carrier mothers are a more efficient solution to prevent the increased prevalence of DMD.
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Recombinase polymerase amplification combined with fast DNA extraction for on–spot identification of Deinagkistrodon acutus, a threatened species. ANIMAL BIODIVERSITY AND CONSERVATION 2022. [DOI: 10.32800/abc.2022.45.0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This study addresses the use of recombinase polymerase amplification combined with fast DNA extraction for on–spot identification of Deinagkistrodon acutus, a snake species threatened
due to over–exploitation and habitat destruction. For its conservation, an efficient species identification method is urgently neededto fight against illegal capture and trade. Fourteen individuals representing 12 snake species (including D. acutus and other snake species) were collected from mountainous regions in Southern China. Genomic DNA was extracted within five minutes by a modified alkaline lysis method. Species–specific primers for recombinase polymerase amplification (RPA) were designed based on the sequences of cytochrome C oxidase subunit I (COI) barcode region, and an optimized RPA assay system was set up. Specificity and sensitivity of the assay were checked, and the assay was validated by identifying 10 commercial Qi She crude drug samples derived from D. acutus. Under optimized RPA conditions, a distinct single band of 354 bp was amplified only for D. acutus but not for the related snake species. The entire procedure can be completed in 30 min at room temperature. Commercial Qi She crude drug identification validated effectiveness of the established assay system. Using a recombinase polymerase amplification (RPA) assay with rapid DNA extraction, we established an on–spot D. acutus identification method with good specificity and sensitivity. This method could become an efficient tool for rigorous supervision of illegal D. acutus capture and trade.
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Nur I. Molecular Identification of Lobster Species Based on Cytochrome Oxidase Subunit I Gene characters. Pak J Biol Sci 2022; 25:501-508. [PMID: 36098185 DOI: 10.3923/pjbs.2022.501.508] [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: 06/15/2023]
Abstract
<b>Background and Objective:</b> In the puerulus phase, which is not pigmented, identification of lobster species based on morphological characteristics is still difficult identity, so it is necessary to identify based on molecular characters. This study aimed to analyze the mitochondrial subunit I cytochrome oxidase (COI) gene characters of the puerulus of lobster species. <b>Materials and Methods:</b> The data can be useful for developing lobster seed identification methods based on DNA characteristics. Location of lobster sampling in Staring Bay, coastal waters of Moramo District, South Konawe Regency, Indonesia. The molecular characterization method is carried out in several stages, namely specific primer design, DNA preparation, PCR with specific primers, DNA sequencing and DNA sequence analysis. Characteristics of COI gene fragments were analyzed using BLAST analysis, restriction enzyme analysis and phylogenetic tree analysis. <b>Results:</b> The results showed that DNA was successfully isolated with a high level of purity. The results of the amplification of the COI gene fragment showed thick and firm bands and formed a single band measuring 751 bp with 249 amino acids. Based on the BLAST analysis shows that the COI gene fragment has 99% similarity with <i>Panulirus homarus</i>. Based restriction enzyme analysis shows that the site of recognition and restriction enzyme cutting position in the <i>Panulirus</i> COI gene fragment is the same as <i>Panulirus homarus</i> in Genebank, the <i>Ase</i>I enzyme in position 392 and <i>Psi </i>I in positions 47 and 106. <b>Conclusion:</b> Based on phylogenetic tree analysis, the COI gene fragment is in one group with <i>Panulirus homarus</i> and has a bootstrap value of 100% which shows that the nucleotide sequence is stable. The three analyzes show that the DNA source organism is the same species as <i>Panulirus homarus</i>.
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Naveed M, Tianying H, Wang F, Yin X, Chan MWH, Ullah A, Xu B, Aslam S, Ali N, Abbas Q, Hussain I, Khan A, Khan AM. Isolation of lysozyme producing Bacillus subtilis Strains, identification of the new strain Bacillus subtilis BSN314 with the highest enzyme production capacity and optimization of culture conditions for maximum lysozyme production. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Bischof H, Burgstaller S, Graier WF, Lukowski R, Malli R. Unveiling the K +-sensitivity of cell metabolism using genetically encoded, FRET-based K +, glucose, and ATP biosensors. STAR Protoc 2021; 2:100843. [PMID: 34589717 PMCID: PMC8458979 DOI: 10.1016/j.xpro.2021.100843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Investigating dynamic changes of mitochondrial ATP and cytosolic glucose levels of single living cells over time by genetically encoded biosensors provides an informative readout of their metabolic activities. Here, we describe how to monitor the metabolic K+-sensitivity of HEK293 cells exploiting ATP-, glucose-, and K+ probes. Fluorescence live-cell imaging of these Förster resonance energy transfer-based biosensors over time in response to gramicidin, an ionophoric peptide, indicated an absolute dependency of cellular ATP homeostasis on high intracellular K+ levels. For complete information on the generation and use of this protocol please refer to Bischof et al. (2021).
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Affiliation(s)
- Helmut Bischof
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany.,Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Sandra Burgstaller
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany.,Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.,Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
| | - Wolfgang F Graier
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.,BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Robert Lukowski
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Roland Malli
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.,BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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La TM, Kim JH, Kim T, Lee HJ, Lee Y, Shin H, Song Y, Ahn G, Hur W, Lee JB, Park SY, Choi IS, Lee SW. The optimal standard protocols for whole-genome sequencing of antibiotic-resistant pathogenic bacteria using third-generation sequencing platforms. Mol Cell Toxicol 2021. [DOI: 10.1007/s13273-021-00157-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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A modified approach for high-quality RNA extraction of spore-forming Bacillus subtilis at varied physiological stages. Mol Biol Rep 2021; 48:6757-6768. [PMID: 34455533 DOI: 10.1007/s11033-021-06673-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND High quality RNA is required for the molecular study. Sample preparation of the spore-forming, Gram-positive bacteria like Bacillus sp., remains challenging although several methods have been proposed. Those techniques were simply developed using cell samples at certain growth stages despite some molecular studies like transcriptomic analyses require RNA samples from different physiological stages. METHODS AND RESULTS We developed the rapid, simple yet effective cell-lysis technique with limit use of harsh reagents by modifying the kit-based protocols. Appropriate lysozyme loading (20 mg/mL), incubation time (30 min), and temperature (37 °C) enabled cell lysis and enhanced RNA extraction from both vegetative cells and endospores of Bacillus subtilis TL7-3. High RNA Integrity Numbers and ratios of A260/A280 and A260/A230 of all RNA products collected during the batch cultivation confirmed that invert mixing with absolute ethanol prevented RNA damage during protein denaturation. With the process modification of the major steps in cell lysis and RNA extraction compared with the kit-based protocols that are typically used in laboratory work, interestingly, our modified protocol, simple-yet-effective, yielded higher concentration, purity, and integrity of RNA products from all cell samples collected at different physiological stages. While the kit-based protocols either failed to provide high RNA concentration or RNA purity and integrity for all cell samples particularly during the late-log, stationary, or sporulation. CONCLUSIONS Therefore, we can claim the significance of this modified protocol to be applicable for RNA extraction to those spore-forming Gram-positive bacteria not limited to B. subtilis growing at varied physiological stages.
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Bjedov D, Mikuška A, Lackmann C, Begović L, Mikuška T, Velki M. Application of Non-Destructive Methods: Biomarker Assays in Blood of White Stork ( Ciconia ciconia) Nestlings. Animals (Basel) 2021; 11:2341. [PMID: 34438798 PMCID: PMC8388685 DOI: 10.3390/ani11082341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/06/2021] [Indexed: 01/31/2023] Open
Abstract
White stork (Ciconia ciconia) nestlings can provide quantitative information on the quality of the surrounding environment by indicating the presence of pollutants, as they depend on locally foraged food. This study represents the first comparison of biomarkers in two fractions of white stork nestling blood: plasma and S9 (the post-mitochondrial fraction). The aim of this study was to evaluate acetylcholinesterase (AChE), carboxylesterase (CES), glutathione S-transferase (GST), and glutathione reductase (GR), as well as to establish a novel fluorescence-based method for glutathione (GSH) and reactive oxygen species (ROS) detection in plasma and S9. Considering the enzymatic biomarkers, lower variability in plasma was detected only for AChE, as CES, GST, and GR had lower variability in S9. Enzyme activity was higher in plasma for AChE, CES, and GST, while GR had higher activity in S9. Regarding the fluorescence-based method, lower variability was detected in plasma for GSH and ROS, although higher GSH detection was reported in S9, and higher ROS was detected in plasma. The present study indicated valuable differences by successfully establishing protocols for biomarker measurement in plasma and S9 based on variability, enzyme activity, and fluorescence. For a better understanding of the environmental effects on nestlings' physiological condition, biomarkers can be measured in plasma and S9.
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Affiliation(s)
- Dora Bjedov
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (D.B.); (A.M.); (L.B.)
| | - Alma Mikuška
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (D.B.); (A.M.); (L.B.)
| | - Carina Lackmann
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany;
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Lidija Begović
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (D.B.); (A.M.); (L.B.)
| | - Tibor Mikuška
- Croatian Society for Birds and Nature Protection, 31000 Osijek, Croatia;
| | - Mirna Velki
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (D.B.); (A.M.); (L.B.)
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Nag M, Lahiri D, Dutta B, Jadav G, Ray RR. Biodegradation of used polyethylene bags by a new marine strain of Alcaligenes faecalis LNDR-1. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:41365-41379. [PMID: 33786758 DOI: 10.1007/s11356-021-13704-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Disposable plastic bags of two different chemical compositions and colors were remediated by the application of novel mesophilic group of bacteria isolated from the banks of sea water, using a 10 week soil burial method. The new strain, LNDR-1, was identified as Alcaligens faecalis by its morphological features and 16S rRNA sequencing. LNDR-1 was able to produce extracellular enzymes such as lipase, CMCase, xylanase, and protease, having PET surface degrading activity. It was found that LNDR-1 had a better decay rate of 15.25 ± 1% and 21.72 ± 2.1% for black and white plastic bags respectively in 10 weeks without prior oxidation as compared to S. marcescens. Polyethylene degradation was confirmed by substantial weight loss, alterations in surface topology, and hydrophobicity index and was found to be directly proportional to the ability to form biofilm on the plastic surface. FTIR results suggest presence of different metabolites in the bags treated with bacterial biofilm in comparison to the control setup inferring various types of metabolic pathways. Present study also reveals the ability of the strain to utilize the used polyethylene bag as the carbon source, without any prior treatment, and as per the literature survey, the working strain is with the capacity to biodegrade plastic at a considerably appreciable rate. This study suggests effectual method for the mechanism of biodegradation of plastic mediated by extracellular enzymes and formation of biofilm.
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Affiliation(s)
- Moupriya Nag
- Department of Biotechnology, University of Engineering & Management, Kolkata, Kolkata, India
| | - Dibyajit Lahiri
- Department of Biotechnology, University of Engineering & Management, Kolkata, Kolkata, India
| | - Bandita Dutta
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, India
| | - Gaurav Jadav
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, India
| | - Rina Rani Ray
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, India.
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