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Borșa RM, Toma V, Onaciu A, Moldovan CS, Mărginean R, Cenariu D, Știufiuc GF, Dinu CM, Bran S, Opriș HO, Văcăraș S, Onișor-Gligor F, Sentea D, Băciuț MF, Iuga CA, Știufiuc RI. Developing New Diagnostic Tools Based on SERS Analysis of Filtered Salivary Samples for Oral Cancer Detection. Int J Mol Sci 2023; 24:12125. [PMID: 37569501 PMCID: PMC10418512 DOI: 10.3390/ijms241512125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Cancer still represents one of the biggest challenges in current medical practice. Among different types of cancer, oral cancer has a huge impact on patients due to its great visibility, which is more likely to create social stigma and increased anxiety. New early diagnose methods are still needed to improve treatment efficiency and patients' life quality. Raman/SERS (Surface Enhanced Raman Spectroscopy) spectroscopy has a unique and powerful potential for detecting specific molecules that can become priceless biomarkers in different pathologies, such as oral cancer. In this study, a batch of saliva samples obtained from a group of 17 patients with oro-maxillofacial pathologies compared with saliva samples from 18 healthy donors using the aforementioned methods were evaluated. At the same time, opiorphin, potassium thiocyanate and uric acid were evaluated as potential specific biomarkers for oro-maxillofacial pathologies using multivariate analysis. A careful examination of SERS spectra collected on saliva samples showed that the spectra are dominated by the vibrational bands of opiorphin, potassium thiocyanate and uric acid. Given the fact that all these small molecules are found in very small amounts, we filtrated all the samples to get rid of large molecules and to improve our analysis. By using solid plasmonic substrates, we were able to gain information about molecular concentration and geometry of interaction. On the other hand, the multivariate analysis of the salivary spectra contributed to developing a new detection method for oral cancer.
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Affiliation(s)
- Rareș-Mario Borșa
- Dental Medicine Faculty, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4, 400349 Cluj-Napoca, Romania; (R.-M.B.); (C.-M.D.); (S.B.); (H.-O.O.); (S.V.); (F.O.-G.); (M.-F.B.)
- Research Center for Advanced Medicine—MedFuture, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4-6, 400337 Cluj-Napoca, Romania; (V.T.); (A.O.); (C.-S.M.); (R.M.); (D.C.); (C.-A.I.)
| | - Valentin Toma
- Research Center for Advanced Medicine—MedFuture, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4-6, 400337 Cluj-Napoca, Romania; (V.T.); (A.O.); (C.-S.M.); (R.M.); (D.C.); (C.-A.I.)
| | - Anca Onaciu
- Research Center for Advanced Medicine—MedFuture, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4-6, 400337 Cluj-Napoca, Romania; (V.T.); (A.O.); (C.-S.M.); (R.M.); (D.C.); (C.-A.I.)
| | - Cristian-Silviu Moldovan
- Research Center for Advanced Medicine—MedFuture, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4-6, 400337 Cluj-Napoca, Romania; (V.T.); (A.O.); (C.-S.M.); (R.M.); (D.C.); (C.-A.I.)
| | - Radu Mărginean
- Research Center for Advanced Medicine—MedFuture, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4-6, 400337 Cluj-Napoca, Romania; (V.T.); (A.O.); (C.-S.M.); (R.M.); (D.C.); (C.-A.I.)
| | - Diana Cenariu
- Research Center for Advanced Medicine—MedFuture, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4-6, 400337 Cluj-Napoca, Romania; (V.T.); (A.O.); (C.-S.M.); (R.M.); (D.C.); (C.-A.I.)
| | | | - Cristian-Mihail Dinu
- Dental Medicine Faculty, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4, 400349 Cluj-Napoca, Romania; (R.-M.B.); (C.-M.D.); (S.B.); (H.-O.O.); (S.V.); (F.O.-G.); (M.-F.B.)
- Department of Maxillofacial Surgery and Implantology, “Iuliu Hațieganu” University of Medicine and Pharmacy, Iuliu Hossu 37, 400029 Cluj-Napoca, Romania
- County Emergency Hospital Cluj, Clinicilor 3-5, 400006 Cluj-Napoca, Romania;
| | - Simion Bran
- Dental Medicine Faculty, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4, 400349 Cluj-Napoca, Romania; (R.-M.B.); (C.-M.D.); (S.B.); (H.-O.O.); (S.V.); (F.O.-G.); (M.-F.B.)
- Department of Maxillofacial Surgery and Implantology, “Iuliu Hațieganu” University of Medicine and Pharmacy, Iuliu Hossu 37, 400029 Cluj-Napoca, Romania
- County Emergency Hospital Cluj, Clinicilor 3-5, 400006 Cluj-Napoca, Romania;
| | - Horia-Octavian Opriș
- Dental Medicine Faculty, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4, 400349 Cluj-Napoca, Romania; (R.-M.B.); (C.-M.D.); (S.B.); (H.-O.O.); (S.V.); (F.O.-G.); (M.-F.B.)
- Department of Maxillofacial Surgery and Implantology, “Iuliu Hațieganu” University of Medicine and Pharmacy, Iuliu Hossu 37, 400029 Cluj-Napoca, Romania
- County Emergency Hospital Cluj, Clinicilor 3-5, 400006 Cluj-Napoca, Romania;
| | - Sergiu Văcăraș
- Dental Medicine Faculty, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4, 400349 Cluj-Napoca, Romania; (R.-M.B.); (C.-M.D.); (S.B.); (H.-O.O.); (S.V.); (F.O.-G.); (M.-F.B.)
- Department of Maxillofacial Surgery and Implantology, “Iuliu Hațieganu” University of Medicine and Pharmacy, Iuliu Hossu 37, 400029 Cluj-Napoca, Romania
- County Emergency Hospital Cluj, Clinicilor 3-5, 400006 Cluj-Napoca, Romania;
| | - Florin Onișor-Gligor
- Dental Medicine Faculty, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4, 400349 Cluj-Napoca, Romania; (R.-M.B.); (C.-M.D.); (S.B.); (H.-O.O.); (S.V.); (F.O.-G.); (M.-F.B.)
- Department of Maxillofacial Surgery and Implantology, “Iuliu Hațieganu” University of Medicine and Pharmacy, Iuliu Hossu 37, 400029 Cluj-Napoca, Romania
- County Emergency Hospital Cluj, Clinicilor 3-5, 400006 Cluj-Napoca, Romania;
| | - Dorin Sentea
- County Emergency Hospital Cluj, Clinicilor 3-5, 400006 Cluj-Napoca, Romania;
| | - Mihaela-Felicia Băciuț
- Dental Medicine Faculty, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4, 400349 Cluj-Napoca, Romania; (R.-M.B.); (C.-M.D.); (S.B.); (H.-O.O.); (S.V.); (F.O.-G.); (M.-F.B.)
- Department of Maxillofacial Surgery and Implantology, “Iuliu Hațieganu” University of Medicine and Pharmacy, Iuliu Hossu 37, 400029 Cluj-Napoca, Romania
- County Emergency Hospital Cluj, Clinicilor 3-5, 400006 Cluj-Napoca, Romania;
| | - Cristina-Adela Iuga
- Research Center for Advanced Medicine—MedFuture, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4-6, 400337 Cluj-Napoca, Romania; (V.T.); (A.O.); (C.-S.M.); (R.M.); (D.C.); (C.-A.I.)
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, Pasteur 6, 400349 Cluj-Napoca, Romania
| | - Rareș-Ionuț Știufiuc
- Research Center for Advanced Medicine—MedFuture, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 4-6, 400337 Cluj-Napoca, Romania; (V.T.); (A.O.); (C.-S.M.); (R.M.); (D.C.); (C.-A.I.)
- Department of Pharmaceutical Physics-Biophysics, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Pasteur 6, 400349 Cluj-Napoca, Romania
- TRANSCEND Research Center, Regional Institute of Oncology, 700483 Iasi, Romania
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Berus SM, Nowicka AB, Wieruszewska J, Niciński K, Kowalska AA, Szymborski TR, Dróżdż I, Borowiec M, Waluk J, Kamińska A. SERS Signature of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs: Towards Perspective COVID-19 Point-of-Care Diagnostics. Int J Mol Sci 2023; 24:ijms24119706. [PMID: 37298658 DOI: 10.3390/ijms24119706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
In this study, the intrinsic surface-enhanced Raman spectroscopy (SERS)-based approach coupled with chemometric analysis was adopted to establish the biochemical fingerprint of SARS-CoV-2 infected human fluids: saliva and nasopharyngeal swabs. The numerical methods, partial least squares discriminant analysis (PLS-DA) and support vector machine classification (SVMC), facilitated the spectroscopic identification of the viral-specific molecules, molecular changes, and distinct physiological signatures of pathetically altered fluids. Next, we developed the reliable classification model for fast identification and differentiation of negative CoV(-) and positive CoV(+) groups. The PLS-DA calibration model was described by a great statistical value-RMSEC and RMSECV below 0.3 and R2cal at the level of ~0.7 for both type of body fluids. The calculated diagnostic parameters for SVMC and PLS-DA at the stage of preparation of calibration model and classification of external samples simulating real diagnostic conditions evinced high accuracy, sensitivity, and specificity for saliva specimens. Here, we outlined the significant role of neopterin as the biomarker in the prediction of COVID-19 infection from nasopharyngeal swab. We also observed the increased content of nucleic acids of DNA/RNA and proteins such as ferritin as well as specific immunoglobulins. The developed SERS for SARS-CoV-2 approach allows: (i) fast, simple and non-invasive collection of analyzed specimens; (ii) fast response with the time of analysis below 15 min, and (iii) sensitive and reliable SERS-based screening of COVID-19 disease.
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Affiliation(s)
- Sylwia M Berus
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Ariadna B Nowicka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Julia Wieruszewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Krzysztof Niciński
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Aneta A Kowalska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz R Szymborski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Izabela Dróżdż
- Department of Clinical Genetics, Medical University of Łódź, Pomorska 251, 92-213 Łódź, Poland
| | - Maciej Borowiec
- Department of Clinical Genetics, Medical University of Łódź, Pomorska 251, 92-213 Łódź, Poland
| | - Jacek Waluk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Faculty of Mathematics and Science, Cardinal Stefan Wyszyński University, Dewajtis 5, 01-815 Warsaw, Poland
| | - Agnieszka Kamińska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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Lee HT, Park HY, Lee KC, Lee JH, Kim JK. Two Arabidopsis Splicing Factors, U2AF65a and U2AF65b, Differentially Control Flowering Time by Modulating the Expression or Alternative Splicing of a Subset of FLC Upstream Regulators. PLANTS (BASEL, SWITZERLAND) 2023; 12:1655. [PMID: 37111878 PMCID: PMC10145705 DOI: 10.3390/plants12081655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 06/19/2023]
Abstract
We investigated the transcriptomic changes in the shoot apices during floral transition in Arabidopsis mutants of two closely related splicing factors: AtU2AF65a (atu2af65a) and AtU2AF65b (atu2af65b). The atu2af65a mutants exhibited delayed flowering, while the atu2af65b mutants showed accelerated flowering. The underlying gene regulatory mechanism of these phenotypes was unclear. We performed RNA-seq analysis using shoot apices instead of whole seedlings and found that the atu2af65a mutants had more differentially expressed genes than the atu2af65b mutants when they were compared to wild type. The only flowering time gene that was significantly up- or down-regulated by more than two-fold in the mutants were FLOWERING LOCUS C (FLC), a major floral repressor. We also examined the expression and alternative splicing (AS) patterns of several FLC upstream regulators, such as COOLAIR, EDM2, FRIGIDA, and PP2A-b'ɤ, and found that those of COOLAIR, EDM2, and PP2A-b'ɤ were altered in the mutants. Furthermore, we demonstrated that AtU2AF65a and AtU2AF65b genes partially influenced FLC expression by analyzing these mutants in the flc-3 mutant background. Our findings indicate that AtU2AF65a and AtU2AF65b splicing factors modulate FLC expression by affecting the expression or AS patterns of a subset of FLC upstream regulators in the shoot apex, leading to different flowering phenotypes.
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Affiliation(s)
- Hee Tae Lee
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hyo-Young Park
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Keh Chien Lee
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jeong Hwan Lee
- Division of Life Sciences, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju 54896, Jeollabuk-do, Republic of Korea
| | - Jeong-Kook Kim
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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Shinde H, Dudhate A, Kadam US, Hong JC. RNA methylation in plants: An overview. FRONTIERS IN PLANT SCIENCE 2023; 14:1132959. [PMID: 36938064 PMCID: PMC10014531 DOI: 10.3389/fpls.2023.1132959] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
RNA methylation is an important post-transcriptional modification that influences gene regulation. Over 200 different types of RNA modifications have been identified in plants. In animals, the mystery of RNA methylation has been revealed, and its biological role and applications have become increasingly clear. However, RNA methylation in plants is still poorly understood. Recently, plant science research on RNA methylation has advanced rapidly, and it has become clear that RNA methylation plays a critical role in plant development. This review summarizes current knowledge on RNA methylation in plant development. Plant writers, erasers, and readers are highlighted, as well as the occurrence, methods, and software development in RNA methylation is summarized. The most common and abundant RNA methylation in plants is N6-methyladenosine (m6A). In Arabidopsis, mutations in writers, erasers, and RNA methylation readers have affected the plant's phenotype. It has also been demonstrated that methylated TRANSLATIONALLY CONTROLLED TUMOR PROTEIN 1-messenger RNA moves from shoot to root while unmethylated TCTP1-mRNA does not. Methylated RNA immunoprecipitation, in conjunction with next-generation sequencing, has been a watershed moment in plant RNA methylation research. This method has been used successfully in rice, Arabidopsis, Brassica, and maize to study transcriptome-wide RNA methylation. Various software or tools have been used to detect methylated RNAs at the whole transcriptome level; the majority are model-based analysis tools (for example, MACS2). Finally, the limitations and future prospects of methylation of RNA research have been documented.
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Affiliation(s)
- Harshraj Shinde
- Department of Animal and Food Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
| | - Ambika Dudhate
- Sequencing and Genome Discovery Center, Stowers Institute for Medical Research, Kansas City, MO, United States
| | - Ulhas S. Kadam
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju-daero, Jinju, Gyeongnam, Republic of Korea
| | - Jong Chan Hong
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science and Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju-daero, Jinju, Gyeongnam, Republic of Korea
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
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Liu Z, Sun J, Quan J, Li L, Zhao G, Lu J. Effect of selenium nanoparticles on alternative splicing in heat-stressed rainbow trout primary hepatocytes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101042. [PMID: 36455514 DOI: 10.1016/j.cbd.2022.101042] [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: 08/28/2022] [Revised: 11/04/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022]
Abstract
Alternative splicing (AS) is a ubiquitous post-transcriptional regulatory mechanism in eukaryotes that generates multiple mRNA isoforms from a single gene, increasing diversity of mRNAs and proteins that are essential for eukaryotic developmental processes and responses to environmental stress. Results showed that a total of 37,463 AS events were identified in rainbow trout hepatocytes. In addition, a total of 364 differential alternative splicing (DAS) events were identified in hepatocytes under selenium nanoparticles (SeNPs) and 3632 DAS events were identified under a combination of SeNPs and heat stress (24 °C). Gene Ontology (GO) enrichment showed that some subcategories "immune effector processes", "response to stimuli" and "antioxidant activity" were associated with immunity, abiotic stimuli and antioxidants. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment showed that differentially expressed genes (DEGs) were significantly enriched in spliceosomes by adding SeNPs in heat-stressed hepatocytes. Splicing factor family (SRSF3, SRSF7, SRSF9, U2AF1 and U2AF2) and pre-RNA splicing factors (ACIN1 and PPRF18) were significantly upregulated and promoted AS. Furthermore, addition of SeNPs activated the phosphatidylinositol signaling system and upregulated the related genes PI4KA, DGKH, ITPK1 and Ocrl, and thus attenuated the inflammatory response to heat stress and enhanced resistance to heat stress by activating the adherent plaque kinase-PI3K-Akt signaling pathway and calcium channels. Those findings suggested that AS could be an essential regulatory mechanism in adaptation of rainbow trout to heat-stressed environments.
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Affiliation(s)
- Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, No. 1, Yingmen Village, Anning District, Lanzhou City, Gansu Province 730070, PR China.
| | - Jun Sun
- College of Animal Science and Technology, Gansu Agricultural University, No. 1, Yingmen Village, Anning District, Lanzhou City, Gansu Province 730070, PR China
| | - Jinqiang Quan
- College of Animal Science and Technology, Gansu Agricultural University, No. 1, Yingmen Village, Anning District, Lanzhou City, Gansu Province 730070, PR China
| | - Lanlan Li
- College of Animal Science and Technology, Gansu Agricultural University, No. 1, Yingmen Village, Anning District, Lanzhou City, Gansu Province 730070, PR China
| | - Guiyan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, No. 1, Yingmen Village, Anning District, Lanzhou City, Gansu Province 730070, PR China
| | - Junhao Lu
- College of Animal Science and Technology, Gansu Agricultural University, No. 1, Yingmen Village, Anning District, Lanzhou City, Gansu Province 730070, PR China
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Parlamas S, Goetze PK, Humpal D, Kurouski D, Jo YK. Raman Spectroscopy Enables Confirmatory Diagnostics of Fusarium Wilt in Asymptomatic Banana. FRONTIERS IN PLANT SCIENCE 2022; 13:922254. [PMID: 35837469 PMCID: PMC9275401 DOI: 10.3389/fpls.2022.922254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Fusarium oxysporum f. sp. cubense (FOC) causes Fusarium wilt, one of the most concerning diseases in banana (Musa spp.), compromising global banana production. There are limited curative management options after FOC infections, and early Fusarium wilt symptoms are similar with other abiotic stress factors such as drought. Therefore, finding a reliable and timely form of early detection and proper diagnostics is critical for disease management for FOC. In this study, Portable Raman spectroscopy (handheld Raman spectrometer equipped with 830 nm laser source) was applied for developing a confirmatory diagnostic tool for early infection of FOC on asymptomatic banana. Banana plantlets were inoculated with FOC; uninoculated plants exposed to a drier condition were also prepared compared to well-watered uninoculated control plants. Subsequent Raman readings from the plant leaves, without damaging or destroying them, were performed weekly. The conditions of biotic and abiotic stresses on banana were modeled to examine and identify specific Raman spectra suitable for diagnosing FOC infection. Our results showed that Raman spectroscopy could be used to make highly accurate diagnostics of FOC at the asymptomatic stage. Based on specific Raman spectra at vibrational bands 1,155, 1,184, and 1,525 cm-1, Raman spectroscopy demonstrated nearly 100% accuracy of FOC diagnosis at 40 days after inoculation, differentiating FOC-infected plants from uninoculated plants that were well-watered or exposed to water deficit condition. This study first reported that Raman spectroscopy can be used as a rapid and non-destructive tool for banana Fusarium wilt diagnostics.
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Affiliation(s)
- Stephen Parlamas
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Paul K. Goetze
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
| | - Dillon Humpal
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- Institute for Advancing Health Through Agriculture, Texas A&M University, College Station, TX, United States
| | - Young-Ki Jo
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
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Farber C, Kurouski D. Raman Spectroscopy and Machine Learning for Agricultural Applications: Chemometric Assessment of Spectroscopic Signatures of Plants as the Essential Step Toward Digital Farming. FRONTIERS IN PLANT SCIENCE 2022; 13:887511. [PMID: 35557733 PMCID: PMC9087799 DOI: 10.3389/fpls.2022.887511] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/05/2022] [Indexed: 05/07/2023]
Abstract
A growing body of evidence suggests that Raman spectroscopy (RS) can be used for diagnostics of plant biotic and abiotic stresses. RS can be also utilized for identification of plant species and their varieties, as well as assessment of the nutritional content and commercial values of seeds. The power of RS in such cases to a large extent depends on chemometric analyses of spectra. In this work, we critically discuss three major approaches that can be used for advanced analyses of spectroscopic data: summary statistics, statistical testing and chemometric classification. On the example of Raman spectra collected from roses, we demonstrate the outcomes and the potential of all three types of spectral analyses. We anticipate that our findings will help to design the most optimal spectral processing and preprocessing that is required to achieved the desired results. We also expect that reported collection of results will be useful to all researchers who work on spectroscopic analyses of plant specimens.
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Affiliation(s)
- Charles Farber
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
- Department of Molecular and Environmental Plant Science, Texas A&M University, College Station, TX, United States
- *Correspondence: Dmitry Kurouski,
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Trinh KH, Kadam US, Song J, Cho Y, Kang CH, Lee KO, Lim CO, Chung WS, Hong JC. Novel DNA Aptameric Sensors to Detect the Toxic Insecticide Fenitrothion. Int J Mol Sci 2021; 22:ijms221910846. [PMID: 34639187 PMCID: PMC8509669 DOI: 10.3390/ijms221910846] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 11/22/2022] Open
Abstract
Fenitrothion is an insecticide belonging to the organophosphate family of pesticides that is widely used around the world in agriculture and living environments. Today, it is one of the most hazardous chemicals that causes severe environmental pollution. However, detection of fenitrothion residues in the environment is considered a significant challenge due to the small molecule nature of the insecticide and lack of molecular recognition elements that can detect it with high specificity. We performed in vitro selection experiments using the SELEX process to isolate the DNA aptamers that can bind to fenitrothion. We found that newly discovered DNA aptamers have a strong ability to distinguish fenitrothion from other organophosphate insecticides (non-specific targets). Furthermore, we identified a fenitrothion-specific aptamer; FenA2, that can interact with Thioflavin T (ThT) to produce a label-free detection mode with a Kd of 33.57 nM (9.30 ppb) and LOD of 14 nM (3.88 ppb). Additionally, the FenA2 aptamer exhibited very low cross-reactivity with non-specific targets. This is the first report showing an aptamer sensor with a G4-quadruplex-like structure to detect fenitrothion. Moreover, these aptamers have the potential to be further developed into analytical tools for real-time detection of fenitrothion from a wide range of samples.
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Affiliation(s)
- Kien Hong Trinh
- Division of Life Science and Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (K.H.T.); (U.S.K.); (J.S.); (Y.C.); (C.H.K.); (K.O.L.); (C.O.L.); (W.S.C.)
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi City 12400, Vietnam
| | - Ulhas Sopanrao Kadam
- Division of Life Science and Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (K.H.T.); (U.S.K.); (J.S.); (Y.C.); (C.H.K.); (K.O.L.); (C.O.L.); (W.S.C.)
| | - Jinnan Song
- Division of Life Science and Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (K.H.T.); (U.S.K.); (J.S.); (Y.C.); (C.H.K.); (K.O.L.); (C.O.L.); (W.S.C.)
| | - Yuhan Cho
- Division of Life Science and Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (K.H.T.); (U.S.K.); (J.S.); (Y.C.); (C.H.K.); (K.O.L.); (C.O.L.); (W.S.C.)
| | - Chang Ho Kang
- Division of Life Science and Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (K.H.T.); (U.S.K.); (J.S.); (Y.C.); (C.H.K.); (K.O.L.); (C.O.L.); (W.S.C.)
| | - Kyun Oh Lee
- Division of Life Science and Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (K.H.T.); (U.S.K.); (J.S.); (Y.C.); (C.H.K.); (K.O.L.); (C.O.L.); (W.S.C.)
| | - Chae Oh Lim
- Division of Life Science and Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (K.H.T.); (U.S.K.); (J.S.); (Y.C.); (C.H.K.); (K.O.L.); (C.O.L.); (W.S.C.)
| | - Woo Sik Chung
- Division of Life Science and Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (K.H.T.); (U.S.K.); (J.S.); (Y.C.); (C.H.K.); (K.O.L.); (C.O.L.); (W.S.C.)
| | - Jong Chan Hong
- Division of Life Science and Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (K.H.T.); (U.S.K.); (J.S.); (Y.C.); (C.H.K.); (K.O.L.); (C.O.L.); (W.S.C.)
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
- Correspondence:
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9
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Kadam US, Shelake RM, Chavhan RL, Suprasanna P. Concerns regarding 'off-target' activity of genome editing endonucleases. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:22-30. [PMID: 29653762 DOI: 10.1016/j.plaphy.2018.03.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 03/21/2018] [Accepted: 03/23/2018] [Indexed: 05/15/2023]
Abstract
Genome editing (GE) tools ensure targeted mutagenesis and sequence-specific modification in plants using a wide resource of customized endonucleases; namely, zinc-finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs), and the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated protein) system. Among these, in recent times CRISPR/Cas9 has been widely used in functional genomics and plant genetic modification. A significant concern in the application of GE tools is the occurrence of 'off-target' activity and induced mutations, which may impede functional analysis and gene activity studies. Moreover, the 'off-target' activity results in either not reported or unknown, difficult to detect, produce non-quantifiable cellular signaling and physiological effects. In the past few years, several experimental methods have been developed to identify undesired mutations and to curtail 'off-target' cleavage. Improvement in target specificity and minimizing 'off-target' activity will offer better applications of GE technology in plant biology and crop improvement.
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Affiliation(s)
- Ulhas Sopanrao Kadam
- VD College of Agricultural Biotechnology, Latur, Maharashtra, India; Max-Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Rahul Mahadev Shelake
- Plant Molecular Biology & Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Rahul L Chavhan
- VD College of Agricultural Biotechnology, Latur, Maharashtra, India
| | - Penna Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
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10
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Kadam US, Chavhan RL, Schulz B, Irudayaraj J. Single molecule Raman spectroscopic assay to detect transgene from GM plants. Anal Biochem 2017; 532:60-63. [DOI: 10.1016/j.ab.2017.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/03/2017] [Accepted: 06/05/2017] [Indexed: 01/01/2023]
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11
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Kadam US, Schulz B, Irudayaraj JMK. Multiplex single-cell quantification of rare RNA transcripts from protoplasts in a model plant system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1187-1195. [PMID: 28301688 DOI: 10.1111/tpj.13537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/28/2017] [Accepted: 03/06/2017] [Indexed: 05/23/2023]
Abstract
Here we demonstrate multiplex and simultaneous detection of four different rare RNA species from plant, Arabidopsis thaliana, using surface-enhanced Raman spectroscopy (SERS) and gold nanoprobes at single-cell resolution. We show the applicability of nanoparticle-based Raman spectroscopic sensor to study intracellular RNA copies. First, we demonstrate that gold-nanoparticles decorated with Raman probes and carrying specific nucleic acid probe sequences can be uptaken by the protoplasts. We confirm the internalization of gold nanoprobes by transmission electron microscopy, inductively-coupled plasma-mass spectrometry and fluorescence imaging. Second, we show the utility of a SERS platform to monitor individual alternatively spliced (AS) variants and miRNA copies within single cells. Finally, the distinctive spectral features of Raman-active dyes were exploited for multiplex analysis of AtPTB2, AtDCL2, miR156a and miR172a. Furthermore, single-cell studies were validated by in vitro quantification and evaluation of nanotoxicity of gold probes. Raman tag functionalized gold nanosensors yielded an approach for the tracking of rare RNAs within the protoplasts. The SERS-based approach for quantification of RNAs has the capability to be a highly sensitive, accurate and discerning method for single-cell studies including AS variants quantification and rare miRNA detection in specific plant species.
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Affiliation(s)
- Ulhas S Kadam
- VD College of Agricultural Biotechnology (VNMKV), Latur, Maharashtra, 413512, India
- Agricultural and Biological Engineering, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center at Discovery Park, West Lafayette, IN, 47907, USA
- Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Burkhard Schulz
- Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Joseph M K Irudayaraj
- Agricultural and Biological Engineering, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center at Discovery Park, West Lafayette, IN, 47907, USA
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12
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Cui Y, Liu J, Irudayaraj J. Beyond quantification: in situ analysis of transcriptome and pre-mRNA alternative splicing at the nanoscale. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27813271 DOI: 10.1002/wnan.1443] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/02/2016] [Accepted: 10/02/2016] [Indexed: 11/08/2022]
Abstract
In situ analysis offers a venue for dissecting the complex transcriptome in its natural context to tap into cellular processes that could explain the phenotypic physiology and pathology yet to be understood. Over the past decades, enormous progress has been made to improve the resolution, sensitivity, and specificity of single-cell technologies. The continued efforts in RNA research not only facilitates mechanistic studies of molecular biology but also provides state-of-the-art strategies for diagnostic purposes. The implementation of novel bio-imaging platforms has yielded valuable information for inspecting gene expression, mapping regulatory networks, and classifying cell types. In this article, we discuss the merits and technical challenges in single-molecule in situ RNA profiling. Advanced in situ hybridization methodologies developed for a variety of detection modalities are reviewed. Considering the fact that in mammalian cells the number of protein products immensely exceeds that of the actual coding genes due to pre-mRNA alternative splicing, tools capable of elucidating this process in intact cells are highlighted. To conclude, we point out future directions for in situ transcriptome analysis and expect a plethora of opportunities and discoveries in this field. WIREs Nanomed Nanobiotechnol 2017, 9:e1443. doi: 10.1002/wnan.1443 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Yi Cui
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA.,Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jing Liu
- Department of Nanoscience and Nanoengineering, South Dakota School of Mines & Technology, Rapid City, SD, USA
| | - Joseph Irudayaraj
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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