1
|
Park JW, Bae SJ, Yun JH, Kim S, Park M. Assessment of Genetic Stability in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes by Using Droplet Digital PCR. Int J Mol Sci 2024; 25:1101. [PMID: 38256178 PMCID: PMC10815998 DOI: 10.3390/ijms25021101] [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: 12/19/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Unintended genetic modifications that occur during the differentiation and proliferation of human induced pluripotent stem cells (hiPSCs) can lead to tumorigenicity. This is a crucial concern in the development of stem cell-based therapies to ensure the safety and efficacy of the final product. Moreover, conventional genetic stability testing methods are limited by low sensitivity, which is an issue that remains unsolved. In this study, we assessed the genetic stability of hiPSCs and hiPSC-derived cardiomyocytes using various testing methods, including karyotyping, CytoScanHD chip analysis, whole-exome sequencing, and targeted sequencing. Two specific genetic mutations in KMT2C and BCOR were selected from the 17 gene variants identified by whole-exome and targeted sequencing methods, which were validated using droplet digital PCR. The applicability of this approach to stem cell-based therapeutic products was further demonstrated with associated validation according to the International Council for Harmonisation (ICH) guidelines, including specificity, precision, robustness, and limit of detection. Our droplet digital PCR results showed high sensitivity and accuracy for quantitatively detecting gene mutations, whereas conventional qPCR could not avoid false positives. In conclusion, droplet digital PCR is a highly sensitive and precise method for assessing the expression of mutations with tumorigenic potential for the development of stem cell-based therapeutics.
Collapse
Affiliation(s)
| | | | | | | | - Misun Park
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (J.W.P.); (S.J.B.); (J.H.Y.); (S.K.)
| |
Collapse
|
2
|
Kim E, Yang SM, Choi CH, Shin MK, Kim HY. Droplet digital PCR method for the absolute quantitative detection and monitoring of Lacticaseibacillus casei. Food Microbiol 2023; 113:104265. [PMID: 37098421 DOI: 10.1016/j.fm.2023.104265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
Droplet digital polymerase chain reaction (ddPCR) is an emerging molecular detection assay that provides an absolute quantification of targets. Despite its emerging applications in the detection of food microorganisms, there are limited reports of its use for the monitoring of microorganisms utilized as starters in the dairy industry. This study investigated the applicability of ddPCR as a detection platform for Lacticaseibacillus casei, a probiotic found in fermented foods and exerts beneficial effects on human health. In addition, this study compared the performance of ddPCR with that of real-time PCR. The ddPCR targeting the haloacid dehalogenase-like hydrolase (LBCZ_1793) exhibited high specificity against 102 nontarget bacteria, including Lacticaseibacillus species that is very closely related to L. casei. The ddPCR exhibited high linearity and efficiency within the quantitation range (105-100 CFU/ml), with the limit of detection being 100 CFU/ml. The ddPCR also demonstrated a higher sensitivity than real-time PCR in detecting low bacterial concentration in spiked milk samples. Furthermore, it provided an accurate absolute quantification of the concentration of L. casei, without the need for standard calibration curves. This study demonstrated that ddPCR is a useful method for monitoring starter cultures in dairy fermentations and detecting L. casei in foods.
Collapse
|
3
|
Baettig CG, Zirngibl M, Smith KF, Lear G, Tremblay LA. Comparison between droplet digital PCR and reverse transcription-quantitative PCR methods to measure ecotoxicology biomarkers. MARINE POLLUTION BULLETIN 2023; 190:114829. [PMID: 36958116 DOI: 10.1016/j.marpolbul.2023.114829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is currently the gold-standard technique for detecting and quantifying messenger RNA. However, without proper validation, the method may produce artefactual and non-reproducible cycle threshold values generating poor-quality data. The newer droplet digital PCR (ddPCR) method allows for the absolute quantification of targeted nucleic acids providing more sensitive and accurate measurements without requiring external standards. This study compared these two PCR-based methods to measure the expression of well-documented genes used in ecotoxicology studies. We exposed Mediterranean mussels (Mytilus galloprovincialis) to copper and analyzed gene expression in gills and digestive glands using RT-qPCR and ddPCR assays. A step-by-step methodology to optimize and compare the two technologies is described. After ten-fold serial complementary DNA dilution, both RT-qPCR and ddPCR exhibited comparable linearity and efficiency and produced statistically similar results. We conclude that ddPCR is a suitable method to assess gene expression in an ecotoxicological context. However, RT-qPCR has a shorter processing time and remains more cost-effective.
Collapse
Affiliation(s)
- Camille G Baettig
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Cawthron Institute, Nelson, New Zealand.
| | | | - Kirsty F Smith
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Cawthron Institute, Nelson, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Louis A Tremblay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Cawthron Institute, Nelson, New Zealand
| |
Collapse
|
4
|
Hu G, Huang K, Zhou W, Wang R, Zhao W, Zou H, Li W, Wu S, Li M, Wang G. Comparison of droplet digital PCR and real-time quantitative PCR for quantitative detection of the parasitic ciliate Ichthyophthirius multifiliis in the water environment. JOURNAL OF FISH DISEASES 2023; 46:357-367. [PMID: 36606558 DOI: 10.1111/jfd.13749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Ichthyophthiriasis, caused by the parasitic ciliate Ichthyophthirius multifiliis (Ich), is considered one of the most harmful diseases affecting freshwater fish globally. It can cause mass mortalities of fish in intensive farming systems. In such systems, it is thus necessary to detect and quantify the number of Ich in the water so that control measures can be implemented before Ichthyophthiriasis breaks out. In recent years, molecular diagnostic methods have become increasingly important in aquaculture. Real-time quantitative polymerase chain reaction (qPCR) and droplet digital polymerase chain reaction (ddPCR) have become robust assays for detecting pathogens. In this study, a set of specific primers and a TaqMan-minor groove binder probe targeting the small-subunit rDNA (SSU rDNA) of Ich were developed. They were used in qPCR and ddPCR assays to compare the performance of these two different methods in quantitatively detecting Ich. After optimizing the reaction conditions, both qPCR and ddPCR assays were found to have high linearity and quantitative correlations for standard plasmid DNA. When used for the detection of Ich eDNA in water samples, the qPCR assay had a wider detection range, making it a suitable method to screen for the prevalence of Ichthyophthiriasis. However, the ddPCR approach had higher sensitivity, which would help provide advance notice of the disease in complex water environmental samples.
Collapse
Affiliation(s)
- Guangran Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weitian Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Runqiu Wang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Weishan Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wenxiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shangong Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guitang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
5
|
Teng F, Wang L, Hu M, Tao Y. Cell-free regeneration of ATP based on polyphosphate kinase 2 facilitates cytidine 5'-monophosphate production. Enzyme Microb Technol 2023; 165:110211. [PMID: 36804179 DOI: 10.1016/j.enzmictec.2023.110211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Cytidine 5'-monophosphate (5'-CMP), a key intermediate for the production of nucleotide derivatives, has been extensively used in food, agriculture, and medicine industries. Compared to RNA degradation and chemical synthesis, the biosynthesis of 5'-CMP has attracted wide attention due to its relatively low cost and eco-friendliness. In this study, we developed a cell-free regeneration of ATP based on polyphosphate kinase 2 (PPK2) to manufacture 5'-CMP from cytidine (CR). McPPK2 from Meiothermus cerbereus exhibited high specific activity (128.5 U/mg) and was used to accomplish ATP regeneration. McPPK2 and LhUCK (a uridine-cytidine kinase from Lactobacillus helveticus) were combined to convert CR to 5'-CMP. Further, the degradation of CR was inhibited by knocking out cdd from the Escherichia coli genome to enhance 5'-CMP production. Finally, the cell-free system based on ATP regeneration maximized the titer of 5'-CMP up to 143.5 mM. The wider applicability of this cell-free system was demonstrated in the synthesis of deoxycytidine 5'-monophosphate (5'-dCMP) from deoxycytidine (dCR) by incorporating McPPK2 and BsdCK (a deoxycytidine kinase from Bacillus subtilis). This study suggests that the cell-free regeneration of ATP based on PPK2 has the advantage of great flexibility for producing 5'-(d)CMP and other (deoxy)nucleotides.
Collapse
Affiliation(s)
- Fei Teng
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Meirong Hu
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Tao
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
6
|
McNeil CJ, Araujo K, Godfrey K, Slupsky CM. Metabolite Signature and Differential Expression of Genes in Washington Navel Oranges ( Citrus sinensis) Infected by Spiroplasma citri. PHYTOPATHOLOGY 2023; 113:299-308. [PMID: 35984373 DOI: 10.1094/phyto-05-22-0177-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Spiroplasma citri is the pathogen that causes citrus stubborn disease (CSD). Infection of citrus with S. citri has been shown to cause leaf mottling, reduce fruit yield, and stunt tree growth. Fruit from trees exhibiting symptoms of CSD are misshapen and discolored. The symptoms of CSD are easily confused with nutrient deficiencies or symptoms of citrus greening disease. In this study, young Washington navel oranges (Citrus sinensis) were graft-inoculated with budwood originating from trees confirmed to be infected with S. citri. Leaf samples were collected monthly for 10 months for metabolomics and differential gene expression analyses. Significant differences in the concentration of metabolites and expressed genes were observed between control and S. citri-infected trees throughout the experiment. Metabolites and genes associated with important defense and stress pathways, including jasmonic acid signaling, cell wall modification, amino acid biosynthesis, and the production of antioxidant and antimicrobial secondary metabolites, were impacted by S. citri throughout the study, and even prior to symptom development. This work fills a current gap in knowledge surrounding the pathogenicity of S. citri and provides an updated mechanistic explanation for the development of CSD symptoms in S. citri-infected plants.
Collapse
Affiliation(s)
- Christopher J McNeil
- Department of Food Science & Technology, University of California-Davis, Davis, CA 95616
| | - Karla Araujo
- Contained Research Facility, University of California-Davis, Davis, CA 95616
| | - Kristine Godfrey
- Contained Research Facility, University of California-Davis, Davis, CA 95616
| | - Carolyn M Slupsky
- Department of Food Science & Technology, University of California-Davis, Davis, CA 95616
- Department of Nutrition, University of California-Davis, Davis, CA 95616
| |
Collapse
|
7
|
Tian H, Zhao L, Li H, Huang Y, Wang Y. Circular RNA in Retina: A Potential Biomarker and Therapeutic Target. Ophthalmic Res 2023; 66:516-528. [PMID: 36689924 DOI: 10.1159/000529207] [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: 05/12/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023]
Abstract
Circular RNA (circRNA) is a newly discovered noncoding RNA, which forms a closed ring with more than 200 bases in length. CircRNA is formed by back splicing of precursor RNA, and its expression abundance in body fluid is up to 10 times that of homologous linear transcripts. Recently, novel activities for circRNA in various diseases have emerged, ranging from cancer therapy and neurodegenerative diseases. Here, we reviewed the literature on the biogenesis of circRNA and its relationship with retinal diseases in recent years. We first described the mechanism, existing form and main function of circRNA. Next, we also pinpoint that circRNA has great value in the diagnosis and treatment of retinal diseases represented by retinoblastoma, retinal degeneration, and diabetic retinopathy. By this review, we hope to explore more possibilities of circRNA in clinical diagnosis and treatment.
Collapse
Affiliation(s)
- Huiwen Tian
- Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, China,
| | - Lu Zhao
- Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hongyang Li
- Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yingxiang Huang
- Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yanling Wang
- Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
8
|
Chen Y, Tournayre O, Tian H, Lougheed SC. Assessing the breeding phenology of a threatened frog species using eDNA and automatic acoustic monitoring. PeerJ 2023; 11:e14679. [PMID: 36710869 PMCID: PMC9879156 DOI: 10.7717/peerj.14679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/13/2022] [Indexed: 01/25/2023] Open
Abstract
Background Climate change has driven shifts in breeding phenology of many amphibians, causing phenological mismatches (e.g., predator-prey interactions), and potentially population declines. Collecting data with high spatiotemporal sensitivity on hibernation emergence and breeding times can inform conservation best practices. However, monitoring the phenology of amphibians can be challenging because of their cryptic nature over much of their life cycle. Moreover, most salamanders and caecilians do not produce conspicuous breeding calls like frogs and toads do, presenting additional monitoring challenges. Methods In this study, we designed and evaluated the performance of an environmental DNA (eDNA) droplet digital PCR (ddPCR) assay as a non-invasive tool to assess the breeding phenology of a Western Chorus Frog population (Pseudacris maculata mitotype) in Eastern Ontario and compared eDNA detection patterns to hourly automatic acoustic monitoring. For two eDNA samples with strong PCR inhibition, we tested three methods to diminish the effect of inhibitors: diluting eDNA samples, adding bovine serum albumin to PCR reactions, and purifying eDNA using a commercial clean-up kit. Results We recorded the first male calling when the focal marsh was still largely frozen. Chorus frog eDNA was detected on April 6th, 6 days after acoustic monitoring revealed this first calling male, but only 2 days after males attained higher chorus activity. eDNA signals were detected at more sampling locales within the marsh and eDNA concentrations increased as more males participated in the chorus, suggesting that eDNA may be a reasonable proxy for calling assemblage size. Internal positive control revealed strong inhibition in some samples, limiting detection probability and quantification accuracy in ddPCR. We found diluting samples was the most effective in reducing inhibition and improving eDNA quantification. Conclusions Altogether, our results showed that eDNA ddPCR signals lagged behind male chorusing by a few days; thus, acoustic monitoring is preferable if the desire is to document the onset of male chorusing. However, eDNA may be an effective, non-invasive monitoring tool for amphibians that do not call and may provide a useful complement to automated acoustic recording. We found inhibition patterns were heterogeneous across time and space and we demonstrate that an internal positive control should always be included to assess inhibition for eDNA ddPCR signal interpretations.
Collapse
|
9
|
Wang D, Liu E, Liu H, Jin X, Niu C, Gao Y, Su X. A droplet digital PCR assay for detection and quantification of Verticillium nonalfalfae and V. albo-atrum. Front Cell Infect Microbiol 2023; 12:1110684. [PMID: 36710974 PMCID: PMC9874294 DOI: 10.3389/fcimb.2022.1110684] [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: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Verticillium nonalfalfae and V. albo-atrum are notorious pathogenic fungi that cause a destructive vascular disease called Verticillium wilt worldwide. Thus, timely and quantitative monitoring of fungal progression is highly desirable for early diagnosis and risk assessment. In this study, we developed a droplet digital polymerase chain reaction (ddPCR) assay to detect and quantify V. nonalfalfae and V. albo-atrum. The performance of this assay was validated in comparison with that of a quantitative real-time polymerase chain reaction (qPCR) assay. The standard curve analysis of the ddPCR assay showed good linearity. The ddPCR assay indicated similar detection sensitivity to that of qPCR on pure genomic DNA, while it enhanced the positive rate for low-abundance fungi, especially in alfalfa stems. Receiver operating characteristic analysis revealed that ddPCR provided superior diagnostic performance on field tissues compared to qPCR, and the area under curve values were 0.94 and 0.90 for alfalfa roots and stems, respectively. Additionally, the quantitative results of the two methods were highly concordant (roots: R2 = 0.91; stems: R2 = 0.76); however, the concentrations determined by ddPCR were generally higher than those determined by qPCR. This discrepancy was potentially caused by differing amplification efficiencies for qPCR between cultured and field samples. Furthermore, the ddPCR assays appreciably improved quantitative precision, as reflected by lower coefficients of variation. Overall, the ddPCR method enables sensitive detection and accurate quantification of V. nonalfalfae and V. albo-atrum, providing a valuable tool for evaluating disease progression and enacting effective disease control.
Collapse
Affiliation(s)
- Di Wang
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Enliang Liu
- 2Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haiyang Liu
- 3Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xi Jin
- 4Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Hebei, China
| | - Chunyan Niu
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yunhua Gao
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
| | - Xiaofeng Su
- 5Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
| |
Collapse
|
10
|
Skin microbiota analysis in patients with anorexia nervosa and healthy-weight controls reveals microbial indicators of healthy weight and associations with the antimicrobial peptide psoriasin. Sci Rep 2022; 12:15515. [PMID: 36109548 PMCID: PMC9477808 DOI: 10.1038/s41598-022-19676-6] [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: 05/20/2022] [Accepted: 09/01/2022] [Indexed: 12/29/2022] Open
Abstract
Anorexia nervosa (AN), a psychiatric condition defined by low body weight for age and height, is associated with numerous dermatological conditions. Yet, clinical observations report that patients with AN do not suffer from infectious skin diseases like those associated with primary malnutrition. Cell-mediated immunity appears to be amplified in AN; however, this proinflammatory state does not sufficiently explain the lower incidence of infections. Antimicrobial peptides (AMPs) are important components of the innate immune system protecting from pathogens and shaping the microbiota. In Drosophila melanogaster starvation precedes increased AMP gene expression. Here, we analyzed skin microbiota in patients with AN and age-matched, healthy-weight controls and investigated the influence of weight gain on microbial community structure. We then correlated features of the skin microbial community with psoriasin and RNase 7, two highly abundant AMPs in human skin, to clarify whether an association between AMPs and skin microbiota exists and whether such a relationship might contribute to the resistance to cutaneous infections observed in AN. We find significant statistical correlations between Shannon diversity and the highly abundant skin AMP psoriasin and bacterial load, respectively. Moreover, we reveal psoriasin significantly associates with Abiotrophia, an indicator for the healthy-weight control group. Additionally, we observe a significant correlation between an individual's body mass index and Lactobacillus, a microbial indicator of health. Future investigation may help clarify physiological mechanisms that link nutritional intake with skin physiology.
Collapse
|
11
|
Wang D, Jiao X, Jia H, Cheng S, Jin X, Wang Y, Gao Y, Su X. Detection and quantification of Verticillium dahliae and V. longisporum by droplet digital PCR versus quantitative real-time PCR. Front Cell Infect Microbiol 2022; 12:995705. [PMID: 36072220 PMCID: PMC9441566 DOI: 10.3389/fcimb.2022.995705] [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: 07/19/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Vascular wilt, caused by Verticillium dahliae and V. longisporum, limits the quality and yield of agricultural crops. Although quantitative real-time PCR (qPCR) has greatly improved the diagnosis of these two pathogens over traditional, time-consuming isolation methods, the relatively poor detection sensitivity and high measurement bias for traceable matrix-rich samples need to be improved. Here, we thus developed a droplet digital PCR (ddPCR) assay for accurate, sensitive detection and quantification of V. dahliae and V. longisporum. We compared the analytical and diagnostic performance in detail of ddPCR and the corresponding qPCR assay against the genomic DNA (gDNA) of the two fungi from cultures and field samples. In our study, the species specificity, quantification linearity, analytical sensitivity, and measurement viability of the two methods were analyzed. The results indicated that ddPCR using field samples enhanced diagnostic sensitivity, decreased quantification bias, and indicated less susceptibility to inhibitors compared with qPCR. Although ddPCR was as sensitive as qPCR when using gDNA from cultures of V. dahliae and V. longisporum, its detection rates using field samples were much higher than those of qPCR, potentially due to the inhibition from residual matrix in the extracts. The results showed that digital PCR is more sensitive and accurate than qPCR for quantifying trace amounts of V. dahliae and V. longisporum and can facilitate management practices to limit or prevent their prevalence.
Collapse
Affiliation(s)
- Di Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xinya Jiao
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Haijiang Jia
- Raw Material Technology Center of Guangxi Tobacco, Nanning, China
| | - Shumei Cheng
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xi Jin
- Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Hebei, China
| | - Youhua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
- *Correspondence: Xiaofeng Su, ; Yunhua Gao,
| | - Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Xiaofeng Su, ; Yunhua Gao,
| |
Collapse
|
12
|
Development of Droplet Digital PCR Assay for Detection of Seed-Borne Burkholderia glumae and B. gladioli Causing Bacterial Panicle Blight Disease of Rice. Microorganisms 2022; 10:microorganisms10061223. [PMID: 35744741 PMCID: PMC9227566 DOI: 10.3390/microorganisms10061223] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial panicle blight of rice or bacterial grain rot of rice is a worldwide rice disease. Burkholderia glumae and B. gladioli are the causal agents. The early and accurate detection of seed-borne B. glumae and B. gladioli is critical for domestic and international quarantine and effective control of the disease. Here, genomic analyses revealed that B. gladioli contains five phylogroups and the BG1 primer pair designed to target the 3’-end sequence of a gene encoding a Rhs family protein is specific to B. glumae and two phylogroups within B. gladioli. Using the BG1 primer pair, a 138-bp DNA fragment was amplified only from the tested panicle blight pathogens B. glumae and B. gladioli. An EvaGreen droplet digital PCR (dPCR) assay on detection and quantification of the two pathogens was developed from a SYBR Green real-time quantitative PCR (qPCR). The detection limits of the EvaGreen droplet dPCR on the two pathogens were identical at 2 × 103 colony forming units (CFU)∙mL−1 from bacterial suspensions and 2 × 102 CFU∙seed−1 from rice seeds. The EvaGreen droplet dPCR assay showed 10-fold detection sensitivity of the SYBR Green qPCR and could detect a single copy of the target gene in a 20-μL assay. Together, the SYBR Green qPCR assay allows for routine high-throughput detection of the panicle blight pathogens and the EvaGreen droplet dPCR assay provides a high-sensitive and high-accurate diagnostic method for quarantine of the pathogens.
Collapse
|
13
|
Rotondo JC, Martini F, Maritati M, Caselli E, Gallenga CE, Guarino M, De Giorgio R, Mazziotta C, Tramarin ML, Badiale G, Tognon M, Contini C. Advanced Molecular and Immunological Diagnostic Methods to Detect SARS-CoV-2 Infection. Microorganisms 2022; 10:1193. [PMID: 35744711 PMCID: PMC9231257 DOI: 10.3390/microorganisms10061193] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 emerged in late 2019 in China and quickly spread across the globe, causing over 521 million cases of infection and 6.26 million deaths to date. After 2 years, numerous advances have been made. First of all, the preventive vaccine, which has been implemented in record time, is effective in more than 95% of cases. Additionally, in the diagnostic field, there are numerous molecular and antigenic diagnostic kits that are equipped with high sensitivity and specificity. Real Time-PCR-based assays for the detection of viral RNA are currently considered the gold-standard method for SARS-CoV-2 diagnosis and can be used efficiently on pooled nasopharyngeal, or oropharyngeal samples for widespread screening. Moreover, additional, and more advanced molecular methods such as droplet-digital PCR (ddPCR), clustered regularly interspaced short palindromic repeats (CRISPR) and next-generation sequencing (NGS), are currently under development to detect the SARS-CoV-2 RNA. However, as the number of subjects infected with SARS-CoV-2 continuously increases globally, health care systems are being placed under increased stress. Thus, the clinical laboratory plays an important role, helping to select especially asymptomatic individuals who are actively carrying the live replicating virus, with fast and non-invasive molecular technologies. Recent diagnostic strategies, other than molecular methods, have been adopted to either detect viral antigens, i.e., antigen-based immunoassays, or human anti-SARS-CoV-2 antibodies, i.e., antibody-based immunoassays, in nasal or oropharyngeal swabs, as well as in blood or saliva samples. However, the role of mucosal sIgAs, which are essential in the control of viruses entering the body through mucosal surfaces, remains to be elucidated, and in particular the role of the immune response in counteracting SARS-CoV-2 infection, primarily at the site(s) of virus entry that appears to be promising.
Collapse
Affiliation(s)
- John Charles Rotondo
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Martina Maritati
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Orthopaedic Ward, Casa di Cura Santa Maria Maddalena, 45030 Occhiobello, Italy
| | - Elisabetta Caselli
- Section of Microbiology, CIAS Research Center and LTTA, Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Carla Enrica Gallenga
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Matteo Guarino
- Department of Translational Medicine, St. Anna University Hospital of Ferrara, University of Ferrara, 44124 Ferrara, Italy; (M.G.); (R.D.G.)
| | - Roberto De Giorgio
- Department of Translational Medicine, St. Anna University Hospital of Ferrara, University of Ferrara, 44124 Ferrara, Italy; (M.G.); (R.D.G.)
| | - Chiara Mazziotta
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Maria Letizia Tramarin
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Giada Badiale
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Carlo Contini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| |
Collapse
|
14
|
D’Alessandra Y, Valerio V, Moschetta D, Massaiu I, Bozzi M, Conte M, Parisi V, Ciccarelli M, Leosco D, Myasoedova VA, Poggio P. Extraction-Free Absolute Quantification of Circulating miRNAs by Chip-Based Digital PCR. Biomedicines 2022; 10:biomedicines10061354. [PMID: 35740375 PMCID: PMC9220272 DOI: 10.3390/biomedicines10061354] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022] Open
Abstract
Circulating microRNAs (miRNA) have been proposed as specific biomarkers for several diseases. Quantitative Real-Time PCR (RT-qPCR) is the gold standard technique currently used to evaluate miRNAs expression from different sources. In the last few years, digital PCR (dPCR) emerged as a complementary and accurate detection method. When dealing with gene expression, the first and most delicate step is nucleic-acid isolation. However, all currently available protocols for RNA extraction suffer from the variable loss of RNA species due to the chemicals and number of steps involved, from sample lysis to nucleic acid elution. Here, we evaluated a new process for the detection of circulating miRNAs, consisting of sample lysis followed by direct evaluation by dPCR in plasma from healthy donors and in the cardiovascular setting. Our results showed that dPCR is able to detect, with high accuracy, low-copy-number as well as highly expressed miRNAs in human plasma samples without the need for RNA extraction. Moreover, we assessed a known myocardial infarction-related miR-133a in acute myocardial infarct patients vs. healthy subjects. In conclusion, our results show the suitability of the extraction-free quantification of circulating miRNAs as disease markers by direct dPCR.
Collapse
Affiliation(s)
- Yuri D’Alessandra
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
| | - Vincenza Valerio
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
| | - Donato Moschetta
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20122 Milan, Italy
| | - Ilaria Massaiu
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
| | - Michele Bozzi
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
| | - Maddalena Conte
- Department of Translational Medical Sciences, University of Naples Federico II, 80138 Naples, Italy; (M.C.); (V.P.); (D.L.)
- Casa di Cura San Michele, 81024 Maddaloni, Italy
| | - Valentina Parisi
- Department of Translational Medical Sciences, University of Naples Federico II, 80138 Naples, Italy; (M.C.); (V.P.); (D.L.)
| | - Michele Ciccarelli
- Department of Medicine, Surgery and Dentistry, University of Salerno, 84084 Fisciano, Italy;
| | - Dario Leosco
- Department of Translational Medical Sciences, University of Naples Federico II, 80138 Naples, Italy; (M.C.); (V.P.); (D.L.)
| | - Veronika A. Myasoedova
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
| | - Paolo Poggio
- Centro Cardiologico Monzino IRCCS, 20138 Milan, Italy; (Y.D.); (V.V.); (D.M.); (I.M.); (M.B.); (V.A.M.)
- Correspondence: ; Tel.: +39-02-5800-2853
| |
Collapse
|
15
|
Cao J, Wu Q, Wan F, Guo J, Wang R. Reliable and rapid identification of glyphosate-resistance in the invasive weed Amaranthus palmeri in China. PEST MANAGEMENT SCIENCE 2022; 78:2173-2182. [PMID: 35191163 DOI: 10.1002/ps.6843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/30/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Glyphosate-resistant invasive plants, including Amaranthus palmeri S. Watson, have greatly challenged management of new invasions. Elucidating their glyphosate resistance levels rapidly and accurately will better inform management strategies. Quantitative real-time PCR (qPCR) has been used to identify glyphosate resistance in A. palmeri by detecting gene copy numbers of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an enzyme inhibited by glyphosate. However, qPCR can only indirectly determine copy numbers because it requires a calibrator sample; it also lacks standardization, thus limiting its usefulness. Droplet digital PCR (ddPCR) is a new method to detect copy number directly and precisely. We evaluated ddPCR as a tool to determine glyphosate-resistance level while using qPCR and glyphosate dose response (GDR) assays as reference technologies to compare performance and efficiency between methods. RESULTS We identified seven susceptible and seven resistant populations of A. palmeri using the GDR assay. Resistant levels detected by qPCR and ddPCR were generally consistent with the GDR results. Although detected values obtained by qPCR and ddPCR were highly correlated (R2 = 0.94), ddPCR results had a lower proportion of non-ideal values (36%) with better accuracy (100%) and specificity (100%) than those of qPCR results. CONCLUSIONS Our findings demonstrate that ddPCR offers improved accuracy and specificity in detecting EPSPS gene copy numbers and is a robust and rapid method for glyphosate-resistance identification in A. palmeri. Our research is the first to measure glyphosate resistance in A. palmeri by ddPCR assay and will shed light on future applications of ddPCR in identifying herbicide resistance in other invasive weeds. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Jingjing Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qianmei Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Fanghao Wan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jianying Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Rui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| |
Collapse
|
16
|
Gao P, Wu C, Zhang J, Wang S, Huang Y, Dong Y, Liu T, Ye C, Xu X, Xin W. Evaluation and Optimization of Microdrop Digital PCR for Detection of Serotype A and B Clostridium botulinum. Front Microbiol 2022; 13:860992. [PMID: 35615503 PMCID: PMC9125207 DOI: 10.3389/fmicb.2022.860992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/11/2022] [Indexed: 12/02/2022] Open
Abstract
Clostridium botulinum is the causative pathogen of botulism. Laboratory detection of C. botulinum is essential for clinical therapy treatment of botulism due to the difficulty in diagnosis, especially in infant botulism. The extreme toxicity of botulinum neurotoxin (BoNT) requires a sensitive detection method. Due to the detection limit of real-time quantitative PCR (q-PCR), a more sensitive detection method, micro-drop digital PCR (ddPCR) was applied in C. botulinum main serotypes A and B. The following performance criteria were evaluated by ddPCR: analytical sensitivity; repeatability; and diagnostic specificity. The limit of detection (LOD) was 0.84 and 0.88 copies/μl for BoNT A and B genes, respectively, by ddPCR with high specificity, compared to 5.04×102 and 6.91×102 copies/μl by q-PCR. It was increased 10 times compared with q-PCR in spiked stool samples. This improvement in sensitivity was especially important in clinical samples as more positive samples were detected by digital PCR compared with q-PCR. Meanwhile, enrichment time for low bacteria content samples was shortened by four hours both in serotypes A and B C. botulinum by ddPCR compared with q-PCR, which are important for laboratory diagnosis and epidemiology work.
Collapse
Affiliation(s)
- Pengya Gao
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Changde Wu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jin Zhang
- Criminal Investigation School, People's Public Security University of China, Beijing, China
| | - Shuping Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ying Huang
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tingting Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuefang Xu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- *Correspondence: Xuefang Xu
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- Wenwen Xin
| |
Collapse
|
17
|
Sagouti T, Belabess Z, Rhallabi N, Barka EA, Tahiri A, Lahlali R. Citrus Stubborn Disease: Current Insights on an Enigmatic Problem Prevailing in Citrus Orchards. Microorganisms 2022; 10:183. [PMID: 35056632 PMCID: PMC8779666 DOI: 10.3390/microorganisms10010183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 12/29/2022] Open
Abstract
Citrus stubborn was initially observed in California in 1915 and was later proven as a graft-transmissible disease in 1942. In the field, diseased citrus trees have compressed and stunted appearances, and yield poor-quality fruits with little market value. The disease is caused by Spiroplasma citri, a phloem-restricted pathogenic mollicute, which belongs to the Spiroplasmataceae family (Mollicutes). S. citri has the largest genome of any Mollicutes investigated, with a genome size of roughly 1780 Kbp. It is a helical, motile mollicute that lacks a cell wall and peptidoglycan. Several quick and sensitive molecular-based and immuno-enzymatic pathogen detection technologies are available. Infected weeds are the primary source of transmission to citrus, with only a minor percentage of transmission from infected citrus to citrus. Several phloem-feeding leafhopper species (Cicadellidae, Hemiptera) support the natural spread of S. citri in a persistent, propagative manner. S. citri-free buds are used in new orchard plantings and bud certification, and indexing initiatives have been launched. Further, a quarantine system for newly introduced types has been implemented to limit citrus stubborn disease (CSD). The present state of knowledge about CSD around the world is summarized in this overview, where recent advances in S. citri detection, characterization, control and eradication were highlighted to prevent or limit disease spread through the adoption of best practices.
Collapse
Affiliation(s)
- Tourya Sagouti
- Laboratoire de Virologie, Microbiologie et Qualité/Ecotoxicologie et Biodiversité, Faculté des Sciences et Techniques de Mohammedia, Mohammedia 20650, Morocco; (T.S.); (N.R.)
| | - Zineb Belabess
- Plant Protection Laboratory, Regional Center of Agricultural Research of Oujda, National Institute of Agricultural Research, Avenue Mohamed VI, BP428 Oujda, Oujda 60000, Morocco;
| | - Naima Rhallabi
- Laboratoire de Virologie, Microbiologie et Qualité/Ecotoxicologie et Biodiversité, Faculté des Sciences et Techniques de Mohammedia, Mohammedia 20650, Morocco; (T.S.); (N.R.)
| | - Essaid Ait Barka
- Unité de Recherche Résistance Induite et Bio-Protection des Plantes-EA 4707, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Abdessalem Tahiri
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Meknes 50001, Morocco;
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Meknes 50001, Morocco;
| |
Collapse
|
18
|
Development and evaluation of a molecular based protocol for detection and quantification of Cryptosporidium spp. In wastewater. Exp Parasitol 2022; 234:108216. [DOI: 10.1016/j.exppara.2022.108216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 01/13/2022] [Accepted: 01/21/2022] [Indexed: 12/19/2022]
|
19
|
Raguseo C, Gerin D, Pollastro S, Rotolo C, Rotondo PR, Faretra F, De Miccolis Angelini RM. A Duplex-Droplet Digital PCR Assay for Simultaneous Quantitative Detection of Monilinia fructicola and Monilinia laxa on Stone Fruits. Front Microbiol 2021; 12:747560. [PMID: 34912308 PMCID: PMC8667764 DOI: 10.3389/fmicb.2021.747560] [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: 11/04/2021] [Indexed: 11/28/2022] Open
Abstract
Brown rot, caused by different Monilinia species, is a most economically important disease of pome and stone fruits worldwide. In Europe and in Italy, the quarantine pathogen M. fructicola was recently introduced and rapidly spread and, by competing with the main indigenous species Monilinia fructigena and Monilinia laxa, caused relevant changes in Monilinia populations. As a result, in most areas, the pathogen almost replaced M. fructigena and now coexists with M. laxa. The availability of specific and easy-of-use quantification methods is essential to study the population dynamics, and in this work, a new method for the simultaneous quantification of M. fructicola and M. laxa based on droplet digital PCR (ddPCR) technique was established. Under the optimized reaction conditions, consisting of 250/500 nM of primers/probe sets concentration, 58°C as annealing temperature and 50 PCR cycles, the duplex-ddPCR assay was 200-fold more sensitive than duplex-real-time quantitative PCR (qPCR) assay, quantifying < 1 copy μL–1 of target DNA in the PCR mixture. The results obtained with the validation assay performed on apricot and peach fruits, artificially inoculated with conidial suspensions containing different ratios of M. fructicola and M. laxa, showed a high correlation (R2 = 0.98) between the relative quantity of DNA of the two species quantified by ddPCR and qPCR and a more accurate quantification by ddPCR compared to qPCR at higher concentrations of M. fructicola. The herein described method represents a useful tool for the early detection of Monilinia spp. on stone fruits and for the improving knowledge on the epidemiology of brow rot and interactions between the two prevalent Monilinia species.
Collapse
Affiliation(s)
- Celeste Raguseo
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | - Donato Gerin
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | - Stefania Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | - Caterina Rotolo
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | - Palma Rosa Rotondo
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | | |
Collapse
|
20
|
Keremane ML, McCollum TG, Roose ML, Lee RF, Ramadugu C. An Improved Reference Gene for Detection of " Candidatus Liberibacter asiaticus" Associated with Citrus Huanglongbing by qPCR and Digital Droplet PCR Assays. PLANTS 2021; 10:plants10102111. [PMID: 34685920 PMCID: PMC8540500 DOI: 10.3390/plants10102111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022]
Abstract
Citrus huanglongbing (HLB) disease associated with the 'Candidatus Liberibacter asiaticus' (CLas) bacterium has caused significant financial damage to many citrus industries. Large-scale pathogen surveys are routinely conducted in California to detect CLas early in the disease cycle by lab-based qPCR assays. We have developed an improved reference gene for the sensitive detection of CLas from plants in diagnostic duplex qPCR and analytical digital droplet PCR (ddPCR) assays. The mitochondrial cytochrome oxidase gene (COX), widely used as a reference, is not ideal because its high copy number can inhibit amplification of small quantities of target genes. In ddPCRs, oversaturation of droplets complicates data normalization and quantification. The variable copy numbers of COX gene in metabolically active young tissue, greenhouse plants, and citrus relatives suggest the need for a non-variable, nuclear, low copy, universal reference gene for analysis of HLB hosts. The single-copy nuclear gene, malate dehydrogenase (MDH), developed here as a reference gene, is amenable to data normalization, suitable for duplex qPCR and ddPCR assays. The sequence of MDH fragment selected is conserved in most HLB hosts in the taxonomic group Aurantioideae. This study emphasizes the need to develop standard guidelines for reference genes in DNA-based PCR assays.
Collapse
Affiliation(s)
- Manjunath L. Keremane
- USDA ARS National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507, USA; (M.L.K.); (R.F.L.)
| | | | - Mikeal L. Roose
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Richard F. Lee
- USDA ARS National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA 92507, USA; (M.L.K.); (R.F.L.)
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
- Correspondence:
| |
Collapse
|
21
|
Widmer TL, Costa JM. Impact of the United States Department of Agriculture, Agricultural Research Service on Plant Pathology: 2015-2020. PHYTOPATHOLOGY 2021; 111:1265-1276. [PMID: 33507089 DOI: 10.1094/phyto-09-20-0393-ia] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
There is an increasing need to supply the world with more food as the population continues to grow. Research on mitigating the effects of plant diseases to improve crop yield and quality can help provide more food without increasing the land area devoted to farming. National Program 303 (NP 303) within the U.S. Department of Agriculture, Agricultural Research Service is dedicated to research across multiple fields in plant pathology. This review article highlights the research impact within NP 303 between 2015 and 2020, including case studies on wheat and citrus diseases and the National Plant Disease Recovery System, which provide specific examples of this impact.
Collapse
Affiliation(s)
- Timothy L Widmer
- United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
| | - José M Costa
- United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
| |
Collapse
|
22
|
Barrett-Manako K, Andersen M, Martínez-Sánchez M, Jenkins H, Hunter S, Reese-George J, Montefiori M, Wohlers M, Rikkerink E, Templeton M, Nardozza S. Real-Time PCR and Droplet Digital PCR Are Accurate and Reliable Methods To Quantify Pseudomonas syringae pv. actinidiae Biovar 3 in Kiwifruit Infected Plantlets. PLANT DISEASE 2021; 105:1748-1757. [PMID: 33206018 DOI: 10.1094/pdis-08-20-1703-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pseudomonas syringae pv. actinidiae is the etiological agent of kiwifruit canker disease, causing severe economic losses in kiwifruit production areas around the world. Rapid diagnosis, understanding of bacterial virulence, and rate of infection in kiwifruit cultivars are important in applying effective measures of disease control. P. syringae pv. actinidiae load in kiwifruit is currently determined by a labor-intense colony counting method with no high-throughput and specific quantification method being validated. In this work, we used three alternative P. syringae pv. actinidiae quantification methods in two infected kiwifruit cultivars: start of growth time, quantitative PCR (qPCR), and droplet digital PCR (ddPCR). Method performance in each case was compared with the colony counting method. Methods were validated using calibration curves obtained with serial dilutions of P. syringae pv. actinidiae biovar 3 (Psa3) inoculum and standard growth curves obtained from kiwifruit samples infected with Psa3 inoculum. All three alternative methods showed high correlation (r > 0.85) with the colony counting method. qPCR and ddPCR were very specific, sensitive (5 × 102 CFU/cm2), highly correlated to each other (r = 0.955), and flexible, allowing for sample storage. The inclusion of a kiwifruit biomass marker increased the methods' accuracy. The qPCR method was efficient and allowed for high-throughput processing, and the ddPCR method showed highly accurate results but was more expensive and time consuming. While not ideal for high-throughput processing, ddPCR was useful in developing accurate standard curves for the qPCR method. The combination of the two methods is high-throughput, specific for Psa3 quantification, and useful for research studies (e.g., disease phenotyping and host-pathogen interactions).
Collapse
Affiliation(s)
| | - Mark Andersen
- New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | | | - Heather Jenkins
- New Zealand Institute for Plant and Food Research Limited, Christchurch 8140, New Zealand
| | - Shannon Hunter
- New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Jonathan Reese-George
- New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Mirco Montefiori
- New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Mark Wohlers
- New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Erik Rikkerink
- New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Matt Templeton
- New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Simona Nardozza
- New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| |
Collapse
|
23
|
Maheshwari Y, Selvaraj V, Godfrey K, Hajeri S, Yokomi R. Multiplex detection of "Candidatus Liberibacter asiaticus" and Spiroplasma citri by qPCR and droplet digital PCR. PLoS One 2021; 16:e0242392. [PMID: 33730040 PMCID: PMC7968697 DOI: 10.1371/journal.pone.0242392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/03/2021] [Indexed: 11/24/2022] Open
Abstract
“Candidatus Liberibacter asiaticus” (CLas) and Spiroplasma citri are phloem-limited bacteria that infect citrus and are transmitted by insect vectors. S. citri causes citrus stubborn disease (CSD) and is vectored by the beet leafhopper in California. CLas is associated with the devastating citrus disease, Huanglongbing (HLB), and is vectored by the Asian citrus psyllid. CLas is a regulatory pathogen spreading in citrus on residential properties in southern California and is an imminent threat to spread to commercial citrus plantings. CSD is endemic in California and has symptoms in citrus that can be easily confused with HLB. Therefore, the objective of this study was to develop a multiplex qPCR and duplex droplet digital PCR (ddPCR) assay for simultaneous detection of CLas and S. citri to be used where both pathogens can co-exist. The multiplex qPCR assay was designed to detect multicopy genes of CLas—RNR (5 copies) and S. citri–SPV1 ORF1 (13 copies), respectively, and citrus cytochrome oxidase (COX) as internal positive control. Absolute quantitation of these pathogens was achieved by duplex ddPCR as a supplement for marginal qPCR results. Duplex ddPCR allowed higher sensitivity than qPCR for detection of CLas and S. citri. ddPCR showed higher tolerance to inhibitors and yielded highly reproducible results. The multiplex qPCR assay has the benefit of testing both pathogens at reduced cost and can serve to augment the official regulatory protocol for CLas detection in California. Moreover, the ddPCR provided unambiguous absolute detection of CLas and S. citri at very low concentrations without any standards for pathogen titer.
Collapse
Affiliation(s)
- Yogita Maheshwari
- San Joaquin Valley Agricultural Sciences Center, Agricultural Research Service, United States Department of Agriculture, Parlier, California, United States of America
| | - Vijayanandraj Selvaraj
- San Joaquin Valley Agricultural Sciences Center, Agricultural Research Service, United States Department of Agriculture, Parlier, California, United States of America
- * E-mail: (RY); (VS)
| | - Kristine Godfrey
- Contained Research Facility, University of California, Davis, Davis, California, United States of America
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, California, United States of America
| | - Raymond Yokomi
- San Joaquin Valley Agricultural Sciences Center, Agricultural Research Service, United States Department of Agriculture, Parlier, California, United States of America
- * E-mail: (RY); (VS)
| |
Collapse
|
24
|
Rungkamoltip P, Temisak S, Piboonprai K, Japrung D, Thangsunan P, Chanpanitkitchot S, Chaowawanit W, Chandeying N, Tangjitgamol S, Iempridee T. Rapid and ultrasensitive detection of circulating human papillomavirus E7 cell-free DNA as a cervical cancer biomarker. Exp Biol Med (Maywood) 2020; 246:654-666. [PMID: 33307803 DOI: 10.1177/1535370220978899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has attracted attention as a non-invasive biomarker for diagnosing and monitoring various cancers. Given that human papillomavirus (HPV) DNA integration and overexpression of E6/E7 oncogenes are pivotal events for carcinogenesis, we sought to determine if HPV E7 cfDNA could serve as a specific biomarker for cervical cancer detection. We applied droplet digital PCR (ddPCR) to quantify HPV16/18 E7 cfDNA from the serum of patients with cervical cancer, cervical intraepithelial neoplasia, and controls. HPV16/18 E7 cfDNA was highly specific for cervical cancer, displaying 30.77% sensitivity, 100% specificity, and an area under the curve of 0.65. Furthermore, we developed a sensitive isothermal detection of HPV16/18 E7 and the PIK3CA WT reference gene based on recombinase polymerase amplification combined with a lateral flow strip (RPA-LF). The assay took less than 30 min and the detection limit was 5-10 copies. RPA-LF exhibited 100% sensitivity and 88.24% specificity towards HPV16/18 E7 cfDNA in clinical samples. The agreement between RPA-LF and ddPCR was 83.33% (κ = 0.67) for HPV16 E7 and 100% (κ = 1.0) for HPV18 E7, indicating a good correlation between both tests. Therefore, we conclude that HPV E7 cfDNA represents a potential tumor marker with excellent specificity and moderate sensitivity for minimally invasive cervical cancer monitoring. Moreover, the RPA-LF assay provides an affordable, rapid, and ultrasensitive tool for detecting HPV cfDNA in resource-limited settings.
Collapse
Affiliation(s)
- Phetploy Rungkamoltip
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Sasithon Temisak
- Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani 12120, Thailand
| | - Kitiya Piboonprai
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand.,Laboratory of Host Defense, The World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pattanapong Thangsunan
- Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani 12120, Thailand
| | - Saranya Chanpanitkitchot
- Department of Obstetrics and Gynecology, Rajavithi Hospital, College of Medicine, Rangsit University, Bangkok 10400, Thailand
| | - Woraphot Chaowawanit
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand
| | - Nutthaporn Chandeying
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand
| | - Siriwan Tangjitgamol
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand.,Obstetrics and Gynecology Section, MedPark Hospital, Bangkok 10110, Thailand
| | - Tawin Iempridee
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| |
Collapse
|
25
|
Digital PCR: What Relevance to Plant Studies? BIOLOGY 2020; 9:biology9120433. [PMID: 33266157 PMCID: PMC7760125 DOI: 10.3390/biology9120433] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 01/01/2023]
Abstract
Simple Summary Digital PCR is a third-generation technology based on the subdivision of the analytical sample into numerous partitions that are amplified individually. This review presents the major applications of digital PCR (dPCR) technology developed so far in the field of plant science. In greater detail, dPCR assays have been developed to trace genetically modified plant components, pathogenic and non-pathogenic microorganisms, and plant species. Other applications have concerned the study of the aspects of structural and functional genetics. Abstract Digital PCR (dPCR) is a breakthrough technology that able to provide sensitive and absolute nucleic acid quantification. It is a third-generation technology in the field of nucleic acid amplification. A unique feature of the technique is that of dividing the sample into numerous separate compartments, in each of which an independent amplification reaction takes place. Several instrumental platforms have been developed for this purpose, and different statistical approaches are available for reading the digital output data. The dPCR assays developed so far in the plant science sector were identified in the literature, and the major applications, advantages, disadvantages, and applicative perspectives of the technique are presented and discussed in this review.
Collapse
|
26
|
Maldonado-González MM, Del Pilar Martínez-Diz M, Andrés-Sodupe M, Bujanda R, Díaz-Losada E, Gramaje D. Quantification of Cadophora luteo-olivacea From Grapevine Nursery Stock and Vineyard Soil Using Droplet Digital PCR. PLANT DISEASE 2020; 104:2269-2274. [PMID: 32568630 DOI: 10.1094/pdis-09-19-2035-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cadophora luteo-olivacea is the most prevalent Cadophora species associated with Petri disease and esca of grapevine. Accurate, early, and specific detection and quantification of C. luteo-olivacea are essential to alert growers and nurseries to the presence of the pathogens in soil and to prevent the spread of this pathogen through grapevine planting material. The aim of this study was to develop molecular tools to detect and quantify C. luteo-olivacea inoculum from environmental samples. Species specific primers based on the β-tubulin gene and a TaqMan probe for droplet digital PCR (ddPCR) and quantitative PCR (qPCR) were first developed to detect and quantify purified DNA of the target fungus. Specificity tests showed that the primers were able to amplify the C. luteo-olivacea DNA (20 isolates) while none of the 29 nontarget fungal species (58 isolates) tested were amplified. The ddPCR was shown to be more sensitive compared with qPCR in the detection and quantification of C. luteo-olivacea at very low concentrations and was further selected to accurately detect and quantify the fungus from environmental samples. Twenty-five of the 94 grafting plants (26.6%) analyzed by ddPCR tested positive to C. luteo-olivacea DNA (>3 copies/µl). C. luteo-olivacea was barely detected from vineyard soils. The procedure employed in this study revealed the presence of the pathogen in symptomless vines, which makes implementation of this technique suitable for certification schemes of C. luteo-olivacea-free grapevine planting material.
Collapse
Affiliation(s)
- María Mercedes Maldonado-González
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| | - María Del Pilar Martínez-Diz
- Estación de Viticultura y Enología de Galicia (AGACAL-EVEGA), Ponte San Clodio s/n 32428-Leiro-Ourense, Spain
- Universidade da Coruña, Facultade de Ciencias, Zapateira, 15071, A Coruña, Spain
| | - Marcos Andrés-Sodupe
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| | - Rebeca Bujanda
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| | - Emilia Díaz-Losada
- Estación de Viticultura y Enología de Galicia (AGACAL-EVEGA), Ponte San Clodio s/n 32428-Leiro-Ourense, Spain
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| |
Collapse
|
27
|
Lancíková V, Hricová A. Digital Absolute Gene Expression Analysis of Essential Starch-Related Genes in a Radiation Developed Amaranthus cruentus L. Variety in Comparison with Real-Time PCR. PLANTS 2020; 9:plants9080966. [PMID: 32751665 PMCID: PMC7464018 DOI: 10.3390/plants9080966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022]
Abstract
We investigated the expression pattern of four major starch genes at different seed developmental stages in the radiation-bred amaranth variety “Pribina” (Amaranthus cruentus L.) and corresponding control genotype “Ficha” (Amaranthus cruentus L.). Two platforms were used and compared for the gene expression analysis of GBSSI, SSSI, SBE, and DBE amaranth genes, including a standard quantitative real-time PCR (qPCR) technique and relatively novel droplet digital PCR (ddPCR) assay. In our conditions, both methods showed great accuracy and revealed higher expression of the investigated genes in the mutant variety than in the control genotype. Here we report for the first time, a ddPCR gene expression assay for the cultivated grain amaranth, as the most important group of the species in the genus Amaranthus.
Collapse
|
28
|
Yokomi R, Rattner R, Osman F, Maheshwari Y, Selvaraj V, Pagliaccia D, Chen J, Vidalakis G. Whole genome sequence of five strains of Spiroplasma citri isolated from different host plants and its leafhopper vector. BMC Res Notes 2020; 13:320. [PMID: 32620150 PMCID: PMC7333264 DOI: 10.1186/s13104-020-05160-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/27/2020] [Indexed: 11/12/2022] Open
Abstract
Objectives Spiroplasma citri is a bacterium with a wide host range and is the causal agent of citrus stubborn and brittle root diseases of citrus and horseradish, respectively. S. citri is transmitted in a circulative, persistent manner by the beet leafhopper, Neoaliturus (Circulifer) tenellus (Baker), in North America. Five strains of S. citri were cultured from citrus, horseradish, and N. tenellus from different habitats and times. DNA from cultures were sequenced and genome assembled to expand the database to improve detection assays and better understand its genetics and evolution. Data description The whole genome sequence of five strains of S. citri are described herein. The S. citri chromosome was circularized for all five strains and ranged from 1,576,550 to 1,742,208 bp with a G + C content of 25.4–25.6%. Characterization of extrachromosomal DNAs resulted in identification of one or two plasmids, with a G + C content of 23.3 to 27.6%, from plant hosts; and eight or nine plasmids, with a G + C content of 21.65 to 29.19%, from N. tenellus. Total genome size ranged from 1,611,714 to 1,832,173 bp from plants and 1,968,976 to 2,155,613 bp from the leafhopper. All sequence data has been deposited in DDBJ/ENA/GenBank under the accession numbers CP046368-CP046373 and CP047426-CP047446.
Collapse
Affiliation(s)
- Raymond Yokomi
- United States Department of Agriculture -Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA.
| | - Rachel Rattner
- United States Department of Agriculture -Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Yogita Maheshwari
- United States Department of Agriculture -Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Vijayanandraj Selvaraj
- United States Department of Agriculture -Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Deborah Pagliaccia
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Jianchi Chen
- United States Department of Agriculture -Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| |
Collapse
|
29
|
Zhang P, Li S, Chen M. Characterization and Function of Circular RNAs in Plants. Front Mol Biosci 2020; 7:91. [PMID: 32509801 PMCID: PMC7248317 DOI: 10.3389/fmolb.2020.00091] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/22/2020] [Indexed: 12/14/2022] Open
Abstract
CircRNAs are covalently closed-loop single-stranded RNA molecules ubiquitously expressing in eukaryotes. As an important member of the endogenous ncRNA family, circRNAs are associated with diverse biological processes and can regulate transcription, modulate alternative splicing, and interact with miRNAs or proteins. Compared to abundant advances in animals, studies of circRNAs in plants are rapidly emerging. The databases and analysis tools for plant circRNAs are constantly being developed. Large numbers of circRNAs have been identified and characterized in plants and proved to play regulatory roles in plant growth, development, and stress responses. Here, we review the biogenesis, characteristics, bioinformatics resources, and biological functions of plant circRNAs, and summarize the distinct circularization features and differentially expression patterns comparison with animal-related results.
Collapse
Affiliation(s)
- Peijing Zhang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sida Li
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China.,James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
30
|
Barisic D, Erb M, Follo M, Al-Mudaris D, Rolauffs B, Hart ML. Lack of a skeletal muscle phenotype in adult human bone marrow stromal cells following xenogeneic-free expansion. Stem Cell Res Ther 2020; 11:79. [PMID: 32087752 PMCID: PMC7036219 DOI: 10.1186/s13287-020-1587-0] [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: 11/11/2019] [Revised: 01/22/2020] [Accepted: 02/05/2020] [Indexed: 02/07/2023] Open
Abstract
Background Many studies have elegantly shown that murine and rat bone marrow-derived mesenchymal stromal cells (bmMSCs) contribute to muscle regeneration and improve muscle function. Yet, the ability of transplanted human bmMSCs to manifest myogenic potential shows conflicting results. While human adipose- and umbilical cord-derived MSCs can be differentiated into a skeletal muscle phenotype using horse serum (HS), bmMSCs have only been shown to differentiate towards the skeletal muscle lineage using a complex mixture of cytokines followed by transfection with notch intracellular domain. Methods Since xenogeneic-free growth supplements are increasingly being used in the expansion of bmMSCs in clinical trials, we investigated the effects of human plasma and platelet lysate (P/PL) on the expression of neuromuscular markers and whether P/PL-expanded human bmMSCs could be differentiated towards a skeletal myogenic phenotype. Neuromuscular markers were measured using the highly sensitive droplet digital polymerase chain reaction for measuring the expression of Myf5, MyoD, MyoG, ACTA1, Desmin, GAP-43, and Coronin 1b transcripts, by performing immunofluorescence for the expression of Desmin, GAP-43, and MEF2, and flow cytometry for the expression of CD56/neural cell adhesion molecule (NCAM). Results Despite that bmMSCs expressed the myogenic regulatory factor (MRF) MEF2 after expansion in P/PL, bmMSCs cultured under such conditions did not express other essential MRFs including Myf5, MyoD, MyoG, or ACTA1 needed for myogenesis. Moreover, HS did not induce myogenesis of bmMSCs and hence did not induce the expression of any of these myogenic markers. P/PL, however, did lead to a significant increase in neurogenic GAP-43, as well as Desmin expression, and resulted in a high baseline expression of the neurogenic gene Coronin 1b which was sustained under further P/PL or HS culture conditions. Fetal bovine serum resulted in equally high levels of GAP-43 and Coronin 1b. Moreover, the proportion of CD56/NCAM-positive bmMSCs cultured in P/PL was 5.9 ± 2.1. Conclusions These data suggest that P/PL may prime a small portion of bmMSCs towards an early neural precursor cell type. Collectively, this shows that P/PL partially primes the cells towards a neurogenic phenotype, but does not prime adult human bmMSCs towards the skeletal muscle lineage.
Collapse
Affiliation(s)
- Dominik Barisic
- G.E.R.N. Center for Tissue Replacement, Regeneration and Neogenesis, Department of Orthopaedics and Trauma Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marita Erb
- G.E.R.N. Center for Tissue Replacement, Regeneration and Neogenesis, Department of Orthopaedics and Trauma Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marie Follo
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dahlia Al-Mudaris
- G.E.R.N. Center for Tissue Replacement, Regeneration and Neogenesis, Department of Orthopaedics and Trauma Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bernd Rolauffs
- G.E.R.N. Center for Tissue Replacement, Regeneration and Neogenesis, Department of Orthopaedics and Trauma Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Melanie L Hart
- G.E.R.N. Center for Tissue Replacement, Regeneration and Neogenesis, Department of Orthopaedics and Trauma Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
31
|
Jarocki P, Komoń-Janczara E, Podleśny M, Kholiavskyi O, Pytka M, Kordowska-Wiater M. Genomic and Proteomic Characterization of Bacteriophage BH1 Spontaneously Released from Probiotic Lactobacillus rhamnosus Pen. Viruses 2019; 11:E1163. [PMID: 31888239 PMCID: PMC6950654 DOI: 10.3390/v11121163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Lactobacillus rhamnosus Pen is a human endogenous strain used for the production of probiotic formula, which is effective in the prevention of antibiotic-associated diarrhoea. Our study showed that this probiotic strain releases bacteriophage BH1 without the addition of any inducing agent. Our research revealed that phage BH1 has a circular genome with a length of 40721 nt and a GC content of 44.8%. The genome of phage BH1 possesses 57 open reading frames which could be divided into functional modules associated with DNA packaging, morphogenesis, lysis, integration, genetic switch, and replication. In spite of similarity in morphology and genomic organization, comparative analysis revealed substantial genetic diversity and mosaic genomic architecture among phages described for the Lactobacillus casei group. Additionally, qPCR and ddPCR analysis confirmed earlier microscopic observations indicating that L. rhamnosus Pen liberates bacteriophage particles during growth. This occurs spontaneously, and is not a result of external inducing factors. For samples collected after 4 and 24 h of L. rhamnosus Pen culture, the number of attB and attP copies increased 2.5 and 12 times, respectively. This phenomenon, by introducing resistance to other phages or enhancing the biofilm-forming capabilities, may increase the survivability of microorganisms in their natural ecological niche. Conversely, spontaneous phage induction may be an important virulence factor for bacteria, posing a potential threat for the human host.
Collapse
Affiliation(s)
- Piotr Jarocki
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland
| | - Elwira Komoń-Janczara
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland
| | - Marcin Podleśny
- Process and Development Department, Al. Tysiąclecia Państwa Polskiego 13, Grupa Azoty Zakłady Azotowe “Puławy” S.A, 24-110 Puławy, Poland
| | - Oleksandr Kholiavskyi
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland
| | - Monika Pytka
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland
| | - Monika Kordowska-Wiater
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland
| |
Collapse
|
32
|
Dupas E, Legendre B, Olivier V, Poliakoff F, Manceau C, Cunty A. Comparison of real-time PCR and droplet digital PCR for the detection of Xylella fastidiosa in plants. J Microbiol Methods 2019; 162:86-95. [DOI: 10.1016/j.mimet.2019.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 12/14/2022]
|
33
|
Yao Y, Ding Q, Ou L. Biosynthesis of (deoxy)guanosine-5'-triphosphate by GMP kinase and acetate kinase fixed on the surface of E. coli. Enzyme Microb Technol 2018; 122:82-89. [PMID: 30638512 DOI: 10.1016/j.enzmictec.2018.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/23/2018] [Accepted: 12/19/2018] [Indexed: 11/19/2022]
Abstract
(Deoxy)guanosine-5'-triphosphate (5'-(d)GTP), the precursor for synthesizing DNA or RNA in vivo, is an important raw material for various modern biotechnologies based on PCR. In this study, we investigated the application of whole-cell catalysts constructed by bacterial cell surface display in biosynthetic reactions of 5'-(d)GTP from (deoxy)guanosine-5'-monophosphate (5'-(d)GMP). By N-terminal or N- and C-terminal fusion of the ice nucleation protein, we successfully displayed the GMP kinase of Lactobacillus bulgaricus and the acetate kinase of E. coli on the surface of E. coli cells. A large amount of soluble target protein was obtained upon induction with 0.2 mM IPTG at 25 °C for 30 h. The conversion of dGMP was up to 91% when catalysed by the surface-displayed enzymes at 37 °C for 4 h. Up to 95% of the GMP was converted after 3 h of reaction. The stability of the whole-cell catalyst at 37 °C was very good. The enzyme activity was maintained above 50% after 9 rounds of recovery. Our research showed that only one-twentieth of the initial substrate concentration of added ATP was sufficient to meet the reaction requirements.
Collapse
Affiliation(s)
- Yefeng Yao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Qingbao Ding
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA.
| | - Ling Ou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| |
Collapse
|
34
|
Selvaraj V, Maheshwari Y, Hajeri S, Chen J, McCollum TG, Yokomi R. Development of a duplex droplet digital PCR assay for absolute quantitative detection of "Candidatus Liberibacter asiaticus". PLoS One 2018; 13:e0197184. [PMID: 29772016 PMCID: PMC5957411 DOI: 10.1371/journal.pone.0197184] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/27/2018] [Indexed: 11/23/2022] Open
Abstract
Huanglongbing (HLB, citrus greening) is a devastating citrus disease affecting citrus production worldwide. It is associated with the bacterium “Candidatus Liberibacter asiaticus” (CLas) and is vectored by the Asian citrus psyllid (ACP). Currently, diagnosis of CLas in regulatory samples is based on real-time quantitative polymerase chain reaction (qPCR) using 16S rRNA gene specific primers/probe. The detection of CLas using qPCR is challenging due to low pathogen titer and uneven distribution in infected plants and exacerbated by sampling issues and presence of inhibitors. This study evaluated a duplex droplet digital polymerase chain reaction (ddPCR) using multi-copy gene targets, 16S and RNR, to simultaneously detect CLas DNA targets in the same sample for unambiguous detection of the HLB pathogen in DNA extracts from citrus leaves and ACP. Standard curve analyses on tenfold dilution series with plasmid, citrus leaf and ACP DNA showed that both ddPCR and qPCR exhibited good linearity and efficiency in the duplex assay. CLas-infected low titer samples were used to validate the duplex ddPCR and qPCR performance and demonstrated that detection rate is higher when both 16S and RNR primers were used in duplex assay. However, the receiver operating characteristic analysis indicated that area under the curve for RNR primer was significantly broader, compared to 16S primers for CLas detection at low target titer. The absolute quantification of CLas at variable titers was reproducible and repeatable for both primer sets and the ddPCR showed higher resilience to PCR inhibitors with citrus leaf and ACP extracts. Hence, the resultant duplex ddPCR assay resulted in a significantly improved detection platform for diagnosis of CLas in samples with low pathogen titer.
Collapse
Affiliation(s)
- Vijayanandraj Selvaraj
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America
- * E-mail: (RKY); (VS)
| | - Yogita Maheshwari
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, CA, United States of America
| | - Jianchi Chen
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America
| | - Thomas Greg McCollum
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States of America
| | - Raymond Yokomi
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States of America
- * E-mail: (RKY); (VS)
| |
Collapse
|
35
|
Philibert R, Dogan M, Noel A, Miller S, Krukow B, Papworth E, Cowley J, Long JD, Beach SRH, Black DW. Dose Response and Prediction Characteristics of a Methylation Sensitive Digital PCR Assay for Cigarette Consumption in Adults. Front Genet 2018; 9:137. [PMID: 29740475 PMCID: PMC5928210 DOI: 10.3389/fgene.2018.00137] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/03/2018] [Indexed: 01/16/2023] Open
Abstract
The tobacco use disorders are the largest preventable cause of morbidity and mortality in the world. A substantial barrier to the development of better intervention and screening measures is the lack of clinically employable biomarkers to detect the existence and extent of tobacco consumption. In prior work, we and others have shown that array based assessment of DNA methylation status at cg05575921 is a sensitive and quantitative method for assessing cigarette consumption. Unfortunately, in general, arrays are not practical clinical tools. Herein, we detail the prediction performance metrics and dose dependency of a clinically implementable droplet digital PCR (ddPCR) assay for cigarette consumption in adults. First, we demonstrate that measurements of cg05575921 as determined by Illumina array and ddPCR are highly correlated (R2 = 0.98, n = 92). Second, using clinical data and biomaterial from 177 subjects ranging from 18 to 78 years of age, we show that the Receiver Operating Characteristic (ROC) area under the curve (AUC) for classifying smoking status using methylation status at cg05575921 is 0.99. Finally, we conduct modeling analyses of cigarette consumption over discrete time periods to show that methylation status is best correlated with mean cigarette consumption over the past year (R2 = 0.5) and that demethylation at cg05575921 is dose dependent with a demethylation (delta beta) of 1% being equivalent to 1.2 cigarettes per day. But we do not find a relationship between Fagerstrom score and DNA methylation. We conclude that ddPCR assessment of cg05575921 methylation is an accurate method for assessing the presence and extent of cigarette consumption in adult subjects. We suggest that skillful clinical implementation of this approach alone or in combination with other assessment methods could lead to substantial reduction of cigarette consumption related morbidity and mortality.
Collapse
Affiliation(s)
- Robert Philibert
- Behavioral Diagnostics LLC, Coralville, IA, United States
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
| | - Meesha Dogan
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
- Cardio Diagnostics, Coralville, IA, United States
| | - Amanda Noel
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Shelly Miller
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Brianna Krukow
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Emma Papworth
- Behavioral Diagnostics LLC, Coralville, IA, United States
| | - Joseph Cowley
- Center for Alcohol and Drug Services, Davenport, IA, United States
| | | | - Steven R. H. Beach
- Center for Family Studies at the University of Georgia, Athens, GA, United States
| | - Donald W. Black
- Department of Psychiatry, University of Iowa, Iowa City, IA, United States
| |
Collapse
|