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Tang R, Zhu L, Zhu P, Yin R, Zheng C. The Effect of Blood Clots on the Quality of RNA Extracted from PAXgene Blood RNA Tubes. Biopreserv Biobank 2024; 22:174-178. [PMID: 37540078 DOI: 10.1089/bio.2023.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Background: PAXgene® Blood RNA tubes are routinely used in clinical research and molecular biology applications to preserve the stability of RNA in whole blood. However, in practice, blood clots are occasionally observed after blood collection and are often ignored. Currently, there are few studies on whether blood clots affect the quality of RNA extracted from these tubes. Materials and Methods: Fifteen pairs of non-clot and clot PAXgene Blood RNA tube samples (n = 30) were collected to form two matched groups from 15 patients. According to the maximum diameter (d) of the blood clot observed visually at the time of sample reception, the clot groups were divided into a small-clot group (0 cm < d < 0.5 cm) and a large-clot group (d ≥ 0.5 cm). RNA was extracted by the PAXgene Blood RNA Kit. To analyze the quality of RNA, its yield and purity were assessed by spectrophotometry, and integrity was measured by microfluidic electrophoresis. An A260/280 ratio between 1.8 and 2.2 indicated purified RNA, and RNA integrity number (RIN) values ≥7.0 were considered to represent qualified integrity. Results: The median yields of RNA from the non-clot and clot groups were 3.84 (2.80-6.38) μg and 4.87 (2.77-8.30) μg, respectively. The median A260/280 ratios were 2.08 (2.06-2.09) and 2.09 (2.07-2.11), whereas the median A260/230 ratios were 1.77 (1.31-1.91) and 1.67 (1.21-1.94) in the two groups. In addition, the median RINs were 8.20 (8.00-8.40) and 7.20 (6.60-7.70), respectively. There were no significant differences in RNA yields, A260/280, or A260/230 between the two groups. However, the RIN value of the clot group was significantly lower compared with the non-clot group (p < 0.05), with RIN ≥7.0 found in all non-clot samples and 60% of clot samples (p < 0.05). Furthermore, in the clot groups, the small-clot samples had higher RIN values than large-clot samples (8.25 [7.75-8.75] vs. 6.90 [6.60-7.30], p < 0.001). Conclusions: The formation of large blood clots in PAXgene Blood RNA tubes will reduce the integrity of extracted RNA.
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Affiliation(s)
- Rong Tang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ling Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ping Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ru Yin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chunxia Zheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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Lynch CE, Brandt AR, Vincenty CS, Robbins E, Skiles C, Minchev K, Chambers TL, Belangee A, Trappe TA, Trappe SW. Adipose biopsy techniques for studies in human exercise physiology. Am J Physiol Regul Integr Comp Physiol 2024; 326:R220-R229. [PMID: 38223939 DOI: 10.1152/ajpregu.00266.2023] [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: 11/28/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/16/2024]
Abstract
Adipose biopsy techniques are relatively undefined for exercise physiology research in individuals at or near normal weight. The purpose of this study was to compare the influence of two adipose biopsy techniques on tissue quality through measurements of adipocyte cell size, as well as mRNA and protein levels of select pro- and anti-inflammatory cytokines and adipokines. Thirteen participants (9 M, 4 W; 28 ± 4 yr; 27 ± 3 kg·m-2; V̇o2max: 3.3 ± 0.7 L·min-1) underwent subcutaneous adipose biopsies on either side of the umbilicus (incision: ∼8 cm lateral, sampling area: ∼5 cm lateral) using 1) a 6-mm Bergström biopsy needle and 2) a mini-liposuction approach with a 4-mm Mercedes biopsy needle that used prebiopsy tumescent delivery (∼30 mL 0.9% NaCl solution) into the sampling area (i.e., 'wet' technique). Tissue obtained was processed identically for analysis and both techniques returned high-quality tissue for histology (similar % intact adipocytes), mRNA (RNA integrity numbers >7.0), and protein. Adipocyte size was similar (P > 0.05) between both techniques (Bergström: 6,116 ± 1,652 μm2, 554-23,522 µm2; Mercedes: 6,517 ± 952 μm2, 926-21,969 µm2). There were also no differences (P > 0.05) between the two techniques for the measured cytokines (pro- and anti-inflammatory) and adipokines at the mRNA and protein levels. Adipocyte size was positively correlated with body mass index and body fat percentage, and negatively correlated with V̇o2max (P < 0.05). These results suggest both adipose biopsy techniques used in the current investigation are appropriate for histological, transcriptional, and translational level measurements in exercise physiology studies of nonobese women and men.NEW & NOTEWORTHY This study provides investigators with useful information related to adipose biopsy sampling approaches that can be used when planning studies that use measurements of adipose histology, as well as measurements at the mRNA and protein level. Adipose periumbilical sampling with the Bergström biopsy needle and the Mercedes wet mini-liposuction technique are both appropriate options for studies in exercise physiology and in nonobese individuals.
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Affiliation(s)
- Colleen E Lynch
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Anna R Brandt
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Caroline S Vincenty
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Ethan Robbins
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Chad Skiles
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Kiril Minchev
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Toby L Chambers
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Alicia Belangee
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Todd A Trappe
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Scott W Trappe
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
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3
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Liu Z, Liu J, Geng J, Wu E, Zhu J, Cong B, Wu R, Sun H. Metatranscriptomic characterization of six types of forensic samples and its potential application to body fluid/tissue identification: A pilot study. Forensic Sci Int Genet 2024; 68:102978. [PMID: 37995518 DOI: 10.1016/j.fsigen.2023.102978] [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: 06/02/2023] [Revised: 10/21/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Microorganisms are potential markers for identifying body fluids (venous and menstrual blood, semen, saliva, and vaginal secretion) and skin tissue in forensic genetics. Existing published studies have mainly focused on investigating microbial DNA by 16 S rRNA gene sequencing or metagenome shotgun sequencing. We rarely find microbial RNA level investigations on common forensic body fluid/tissue. Therefore, the use of metatranscriptomics to characterize common forensic body fluids/tissue has not been explored in detail, and the potential application of metatranscriptomics in forensic science remains unknown. Here, we performed 30 metatranscriptome analyses on six types of common forensic sample from healthy volunteers by massively parallel sequencing. After quality control and host RNA filtering, a total of 345,300 unigenes were assembled from clean reads. Four kingdoms, 137 phyla, 267 classes, 488 orders, 985 families, 2052 genera, and 4690 species were annotated across all samples. Alpha- and beta-diversity and differential analysis were also performed. As a result, the saliva and skin groups demonstrated high alpha diversity (Simpson index), while the venous blood group exhibited the lowest diversity despite a high Chao1 index. Specifically, we discussed potential microorganism contamination and the "core microbiome," which may be of special interest to forensic researchers. In addition, we implemented and evaluated artificial neural network (ANN), random forest (RF), and support vector machine (SVM) models for forensic body fluid/tissue identification (BFID) using genus- and species-level metatranscriptome profiles. The ANN and RF prediction models discriminated six forensic body fluids/tissue, demonstrating that the microbial RNA-based method could be applied to BFID. Unlike metagenomic research, metatranscriptomic analysis can provide information about active microbial communities; thus, it may have greater potential to become a powerful tool in forensic science for microbial-based individual identification. This study represents the first attempt to explore the application potential of metatranscriptome profiles in forensic science. Our findings help deepen our understanding of the microorganism community structure at the RNA level and are beneficial for other forensic applications of metatranscriptomics.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Enlin Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jianzhang Zhu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510080, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China.
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4
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Hernandez-Morato I, Kemfack AM. Next-Generation Sequencing Application: A Systematic Approach for High-Quality RNA Isolation from Skeletal Muscles. Methods Mol Biol 2024; 2822:13-24. [PMID: 38907908 DOI: 10.1007/978-1-0716-3918-4_2] [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: 06/24/2024]
Abstract
RNA extraction and analyses from tissues using bulk RNA-Sequencing (RNA-Seq) provide a more accurate picture of the gene expression compared to other molecular biology techniques for RNA quantification. Challenges associated with high-quality RNA extraction from skeletal muscles require a modification of standard protocols. Here, we describe a procedure for high-quality RNA isolation from intrinsic laryngeal muscles transferable to skeletal muscles with comparable technical and biological difficulties. Standard protocols for RNA isolation were optimized by maximizing the pooling strategy, determining the sample weight, applying cryogenic muscle disruption, and incorporating RNase-inhibiting reagents during the tissue preparation steps.
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Affiliation(s)
- Ignacio Hernandez-Morato
- Department of Anatomy and Embryology, School of Medicine, Complutense University of Madrid, Madrid, Spain.
| | - Angela M Kemfack
- The Center for Voice and Swallowing, Department of Otolaryngology-Head & Neck Surgery, Columbia University Irving Medical Center/New York Presbyterian, New York, NY, USA
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5
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Arihisa W, Kondo T, Yamaguchi K, Matsumoto J, Nakanishi H, Kunii Y, Akatsu H, Hino M, Hashizume Y, Sato S, Sato S, Niwa S, Yabe H, Sasaki T, Shigenobu S, Setou M. Lipid-correlated alterations in the transcriptome are enriched in several specific pathways in the postmortem prefrontal cortex of Japanese patients with schizophrenia. Neuropsychopharmacol Rep 2023; 43:403-413. [PMID: 37498306 PMCID: PMC10496066 DOI: 10.1002/npr2.12368] [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: 03/09/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
AIMS Schizophrenia is a chronic relapsing psychiatric disorder that is characterized by many symptoms and has a high heritability. There were studies showing that the phospholipid abnormalities in subjects with schizophrenia (Front Biosci, S3, 2011, 153; Schizophr Bull, 48, 2022, 1125; Sci Rep, 7, 2017, 6; Anal Bioanal Chem, 400, 2011, 1933). Disturbances in prefrontal cortex phospholipid and fatty acid composition have been reported in subjects with schizophrenia (Sci Rep, 7, 2017, 6; Anal Bioanal Chem, 400, 2011, 1933; Schizophr Res, 215, 2020, 493; J Psychiatr Res, 47, 2013, 636; Int J Mol Sci, 22, 2021). For exploring the signaling pathways contributing to the lipid changes in previous study (Sci Rep, 7, 2017, 6), we performed two types of transcriptome analyses in subjects with schizophrenia: an unbiased transcriptome analysis solely based on RNA-seq data and a correlation analysis between levels of gene expression and lipids. METHODS RNA-Seq analysis was performed in the postmortem prefrontal cortex from 10 subjects with schizophrenia and 5 controls. Correlation analysis between the transcriptome and lipidome from 9 subjects, which are the same samples in the previous lipidomics study (Sci Rep, 7, 2017, 6). RESULTS Extraction of differentially expressed genes (DEGs) and further sequence and functional group analysis revealed changes in gene expression levels in phosphoinositide 3-kinase (PI3K)-Akt signaling and the complement system. In addition, a correlation analysis clarified alterations in ether lipid metabolism pathway, which is not found as DEGs in transcriptome analysis alone. CONCLUSIONS This study provided results of the integrated analysis of the schizophrenia-associated transcriptome and lipidome within the PFC and revealed that lipid-correlated alterations in the transcriptome are enriched in specific pathways including ether lipid metabolism pathway.
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Affiliation(s)
- Wataru Arihisa
- Department of Cellular and Molecular AnatomyHamamatsu University School of MedicineShizuokaJapan
| | - Takeshi Kondo
- Department of Cellular and Molecular AnatomyHamamatsu University School of MedicineShizuokaJapan
- International Mass Imaging CenterHamamatsu University School of MedicineShizuokaJapan
- Department of Biochemistry, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | | | - Junya Matsumoto
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | | | - Yasuto Kunii
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
- Department of Disaster PsychiatryInternational Research Institute of Disaster Science, Tohoku UniversitySendaiJapan
| | - Hiroyasu Akatsu
- Choju Medical Institute, Fukushimura HospitalToyohashiJapan
- Department of Community‐based Medical Education/Department of Community‐based MedicineNagoya City University Graduate School of Medical ScienceNagoyaJapan
| | - Mizuki Hino
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
- Department of Disaster PsychiatryInternational Research Institute of Disaster Science, Tohoku UniversitySendaiJapan
| | | | - Shumpei Sato
- RIKEN Center for Biosystems Dynamics ResearchOsakaJapan
| | - Shinji Sato
- Business Development, Otsuka Pharmaceutical Co., Ltd. Shinagawa Grand Central TowerTokyoJapan
| | - Shin‐Ichi Niwa
- Department of Psychiatry, Aizu Medical CenterFukushima Medical UniversityFukushimaJapan
| | - Hirooki Yabe
- Department of Neuropsychiatry, School of MedicineFukushima Medical UniversityFukushimaJapan
| | - Takehiko Sasaki
- Department of Biochemical PathophysiologyMedical Research Institute, Tokyo Medical and Dental UniversityTokyoJapan
| | | | - Mitsutoshi Setou
- Department of Cellular and Molecular AnatomyHamamatsu University School of MedicineShizuokaJapan
- International Mass Imaging CenterHamamatsu University School of MedicineShizuokaJapan
- Preeminent Medical Photonics Education & Research CenterHamamatsu University School of MedicineShizuokaJapan
- Department of AnatomyThe University of Hong KongHong KongChina
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6
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Kowalik S, Groszyk J. Profiling of Barley, Wheat, and Rye FPG and OGG1 Genes during Grain Germination. Int J Mol Sci 2023; 24:12354. [PMID: 37569728 PMCID: PMC10418959 DOI: 10.3390/ijms241512354] [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: 06/30/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
This research is about the profiling of barley (Hordeum vulgare L.), wheat (Triticum aestivum L.), and rye (Secale cereale L.) FPG and OGG1 genes during grain germination. During seed germination, reactive oxygen species accumulate, which leads to DNA damage. In the base excision repair (BER) system, the enzymes formamidopyrimidine DNA glycosylase (FPG) and 8-oxoguanine DNA glycosylase (OGG1), among others, are responsible for repairing such damage. We decided to check how the expression of genes encoding these two enzymes changes in germinating grains. Spring varieties of barley, wheat, and rye from the previous growing season were used in the study. Expression level changes were checked using Real-Time PCR. After analyzing the obtained results, the maximum expression levels of FPG and OGG1 genes during germination were determined for barley, wheat, and rye. The results of the study show differences in expression levels specific to each species. The highest expression was observed at different time points for each of them. There were no differences in the highest expression for FPG and OGG1 within one species. In conclusion, the research provides information on how the level of FPG and OGG1 gene expression changes during the germination process in cereals. This is the first study looking at the expression levels of these two genes in cereals.
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Affiliation(s)
| | - Jolanta Groszyk
- Plant Breeding and Acclimatization Institute–National Research Institute, Radzików, 05-870 Błonie, Poland;
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Chambers TL, Stroh AM, Chavez C, Brandt AR, Claiborne A, Fountain WA, Gries KJ, Jones AM, Kuszmaul DJ, Lee GA, Lester BE, Lynch CE, Minchev K, Montenegro CF, Naruse M, Raue U, Trappe TA, Trappe S. Multitissue responses to exercise: a MoTrPAC feasibility study. J Appl Physiol (1985) 2023; 135:302-315. [PMID: 37318985 PMCID: PMC10393343 DOI: 10.1152/japplphysiol.00210.2023] [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: 04/03/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023] Open
Abstract
We assessed the feasibility of the Molecular Transducers of Physical Activity Consortium (MoTrPAC) human adult clinical exercise protocols, while also documenting select cardiovascular, metabolic, and molecular responses to these protocols. After phenotyping and familiarization sessions, 20 subjects (25 ± 2 yr, 12 M, 8 W) completed an endurance exercise bout (n = 8, 40 min cycling at 70% V̇o2max), a resistance exercise bout (n = 6, ∼45 min, 3 sets of ∼10 repetition maximum, 8 exercises), or a resting control period (n = 6, 40 min rest). Blood samples were taken before, during, and after (10 min, 2 h, and 3.5 h) exercise or rest for levels of catecholamines, cortisol, glucagon, insulin, glucose, free fatty acids, and lactate. Heart rate was recorded throughout exercise (or rest). Skeletal muscle (vastus lateralis) and adipose (periumbilical) biopsies were taken before and ∼4 h following exercise or rest for mRNA levels of genes related to energy metabolism, growth, angiogenesis, and circadian processes. Coordination of the timing of procedural components (e.g., local anesthetic delivery, biopsy incisions, tumescent delivery, intravenous line flushes, sample collection and processing, exercise transitions, and team dynamics) was reasonable to orchestrate while considering subject burden and scientific objectives. The cardiovascular and metabolic alterations reflected a dynamic and unique response to endurance and resistance exercise, whereas skeletal muscle was transcriptionally more responsive than adipose 4 h postexercise. In summary, the current report provides the first evidence of protocol execution and feasibility of key components of the MoTrPAC human adult clinical exercise protocols. Scientists should consider designing exercise studies in various populations to interface with the MoTrPAC protocols and DataHub.NEW & NOTEWORTHY This study highlights the feasibility of key aspects of the MoTrPAC adult human clinical protocols. This initial preview of what can be expected from acute exercise trial data from MoTrPAC provides an impetus for scientists to design exercise studies to interlace with the rich phenotypic and -omics data that will populate the MoTrPAC DataHub at the completion of the parent protocol.
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Affiliation(s)
- Toby L Chambers
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Andrew M Stroh
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Clarisa Chavez
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Anna R Brandt
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Alex Claiborne
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - William A Fountain
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Kevin J Gries
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Andrew M Jones
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Dillon J Kuszmaul
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Gary A Lee
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Bridget E Lester
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Colleen E Lynch
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Kiril Minchev
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | | | - Masatoshi Naruse
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Ulrika Raue
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Todd A Trappe
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
| | - Scott Trappe
- Human Performance Laboratory, Ball State University, Muncie, Indiana, United States
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8
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Trusiak M, Plitta-Michalak BP, Michalak M. Choosing the Right Path for the Successful Storage of Seeds. PLANTS (BASEL, SWITZERLAND) 2022; 12:72. [PMID: 36616200 PMCID: PMC9823941 DOI: 10.3390/plants12010072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Seeds are the most commonly used source of storage material to preserve the genetic diversity of plants. However, prior to the deposition of seeds in gene banks, several questions need to be addressed. Here, we illustrate the scheme that can be used to ensure that the most optimal conditions are identified to enable the long-term storage of seeds. The main questions that need to be answered pertain to the production of viable seeds by plants, the availability of proper protocols for dormancy alleviation and germination, seed tolerance to desiccation and cold storage at -20 °C. Finally, it is very important to fully understand the capability or lack thereof for seeds or their explants to tolerate cryogenic conditions. The proper storage regimes for orthodox, intermediate and recalcitrant seeds are discussed.
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Affiliation(s)
- Magdalena Trusiak
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego 1A, 10-721 Olsztyn, Poland
| | | | - Marcin Michalak
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego 1A, 10-721 Olsztyn, Poland
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9
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Verbeelen T, Van Houdt R, Leys N, Ganigué R, Mastroleo F. Optimization of RNA extraction for bacterial whole transcriptome studies of low-biomass samples. iScience 2022; 25:105311. [PMID: 36345334 PMCID: PMC9636042 DOI: 10.1016/j.isci.2022.105311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/22/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
We developed a procedure for extracting maximal amounts of high-quality RNA from low-biomass producing (autotrophic) bacteria for experiments where sample volume is limited. Large amounts of high-quality RNA for downstream analyses cannot be obtained using larger quantities of culture volume. The performance of standard commercial silica-column based kit protocols and these procedures amended by ultrasonication or enzymatic lysis were assessed. The ammonium-oxidizing Nitrosomonas europaea and nitrite-oxidizing Nitrobacter winogradskyi were used as model organisms for optimization of the RNA isolation protocol. Enzymatic lysis through lysozyme digestion generated high-quality, high-yield RNA samples. Subsequent RNA-seq analysis resulted in qualitative data for both strains. The RNA extraction procedure is suitable for experiments with volume and/or biomass limitations, e.g., as encountered during space flight experiments. Furthermore, it will also result in higher RNA yields for whole transcriptome experiments where sample volume and/or biomass was increased to compensate the low-biomass characteristic of autotrophs. Lysis through ultrasonication results in a high RNA yield but in a low RNA quality Enzymatic lysis using lysozyme provides high-yield, high-quality RNA samples RNA from low-biomass bacterial samples is suitable for downstream RNA-seq
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10
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Sarathkumara YD, Browne DJ, Kelly AM, Pattinson DJ, Rush CM, Warner J, Proietti C, Doolan DL. The Effect of Tropical Temperatures on the Quality of RNA Extracted from Stabilized Whole-Blood Samples. Int J Mol Sci 2022; 23:ijms231810609. [PMID: 36142559 PMCID: PMC9503649 DOI: 10.3390/ijms231810609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/26/2022] Open
Abstract
Whole-blood-derived transcriptional profiling is widely used in biomarker discovery, immunological research, and therapeutic development. Traditional molecular and high-throughput transcriptomic platforms, including molecular assays with quantitative PCR (qPCR) and RNA-sequencing (RNA-seq), are dependent upon high-quality and intact RNA. However, collecting high-quality RNA from field studies in remote tropical locations can be challenging due to resource restrictions and logistics of post-collection processing. The current study tested the relative performance of the two most widely used whole-blood RNA collection systems, PAXgene® and Tempus™, in optimal laboratory conditions as well as suboptimal conditions in tropical field sites, including the effects of extended storage times and high storage temperatures. We found that Tempus™ tubes maintained a slightly higher RNA quantity and integrity relative to PAXgene® tubes at suboptimal tropical conditions. Both PAXgene® and Tempus™ tubes gave similar RNA purity (A260/A280). Additionally, Tempus™ tubes preferentially maintained the stability of mRNA transcripts for two reference genes tested, Succinate dehydrogenase complex, subunit A (SDHA) and TATA-box-binding protein (TBP), even when RNA quality decreased with storage length and temperature. Both tube types preserved the rRNA transcript 18S ribosomal RNA (18S) equally. Our results suggest that Tempus™ blood RNA collection tubes are preferable to PAXgene® for whole-blood collection in suboptimal tropical conditions for RNA-based studies in resource-limited settings.
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Affiliation(s)
- Yomani D. Sarathkumara
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Daniel J. Browne
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Ashton M. Kelly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - David J. Pattinson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Catherine M. Rush
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| | - Jeffrey Warner
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| | - Carla Proietti
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Denise L. Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- Correspondence:
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Applications of transcriptomics in support of drug development for osteoarthritis. OSTEOARTHRITIS AND CARTILAGE OPEN 2021; 3:100221. [DOI: 10.1016/j.ocarto.2021.100221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/31/2021] [Accepted: 11/16/2021] [Indexed: 11/22/2022] Open
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Barley Seeds miRNome Stability during Long-Term Storage and Aging. Int J Mol Sci 2021; 22:ijms22094315. [PMID: 33919202 PMCID: PMC8122619 DOI: 10.3390/ijms22094315] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/27/2021] [Accepted: 04/18/2021] [Indexed: 12/18/2022] Open
Abstract
Seed aging is a complex biological process that has been attracting scientists’ attention for many years. High-throughput small RNA sequencing was applied to examine microRNAs contribution in barley seeds senescence. Unique samples of seeds that, despite having the same genetic makeup, differed in viability after over 45 years of storage in a dry state were investigated. In total, 61 known and 81 novel miRNA were identified in dry seeds. The highest level of expression was found in four conserved miRNA families, i.e., miR159, miR156, miR166, and miR168. However, the most astonishing result was the lack of significant differences in the level of almost all miRNAs in seed samples with significantly different viability. This result reveals that miRNAs in dry seeds are extremely stable. This is also the first identified RNA fraction that is not deteriorating along with the loss of seed viability. Moreover, the novel miRNA hvu-new41, with higher expression in seeds with the lowest viability as detected by RT-qPCR, has the potential to become an indicator of the decreasing viability of seeds during storage in a dry state.
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