Multiplex single-cell quantification of rare RNA transcripts from protoplasts in a model plant system

Single-Cell Analysis with Silver-Coated Pipette by Combined SERS and SICM

The study of individual cell processes that occur both on their surface and inside is highly interesting for the development of new medical drugs, cytology and cell technologies. This work presents an original technique for fabricating the silver-coated pipette and its use for the cell analysis by combination with surface-enhanced Raman spectroscopy (SERS) and scanning ion-conducting microscopy (SICM). Unlike the majority of other designs, the pipette opening in our case remains uncovered, which is important for SICM. SERS-active Ag nanoparticles on the pipette surface are formed by vacuum-thermal evaporation followed by annealing. An array of nanoparticles had a diameter on the order of 36 nm and spacing of 12 nm. A two-particle model based on Laplace equations is used to calculate a theoretical enhancement factor (EF). The surface morphology of the samples is investigated by scanning electron microscopy while SICM is used to reveal the surface topography, to evaluate Young's modulus of living cells and to control an injection of the SERS-active pipettes into them. A Raman microscope-spectrometer was used to collect characteristic SERS spectra of cells and cell components. Local Raman spectra were obtained from the cytoplasm and nucleus of the same HEK-293 cancer cell. The EF of the SERS-active pipette was 7 × 105. As a result, we demonstrate utilizing the silver-coated pipette for both the SICM study and the molecular composition analysis of cytoplasm and the nucleus of living cells by SERS. The probe localization in cells is successfully achieved.

Developing New Diagnostic Tools Based on SERS Analysis of Filtered Salivary Samples for Oral Cancer Detection

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.

SERS Signature of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs: Towards Perspective COVID-19 Point-of-Care Diagnostics

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 R²_cal 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.

Seed Nano-Priming with Calcium Oxide Maintains the Redox State by Boosting the Antioxidant Defense System in Water-Stressed Carom (Trachyspermum ammi L.) Plants to Confer Drought Tolerance

This paper explores the potential of nano seed priming with calcium oxide nanoparticles in maintaining the redox status in carom (Trachyspermum ammi L.) plants by modulating non-enzymatic antioxidants and enzymatic antioxidants. Calcium oxide nanoparticles were prepared in four testing regimes comprising 25, 50, 75, and 100 ppm along with the control treatment of 0 ppm (distilled water). Priming was performed by soaking the carom seeds in the aerated water, and plants were grown under split plots corresponding to drought and water. Seed priming with 75 ppm CaONPs reduced hydrogen peroxide, malondialdehyde contents and electrolyte leakage by 23.3%, 35.9% and 31.6%, respectively, in the water-stressed carom plants. The glutathione s-transferase, superoxide dismutase and peroxidase functions improved under water stress by 42.3%, 24.1% and 44.8%, respectively, in the carom plants raised through 100 ppm primed seeds with CaO_NPs. Priming induced better Ca²⁺ signaling, which affected the enzymes of the ascorbate glutathione cycle, enabling them to maintain redox status in the carom plants exposed to drought stress. The morpho-agronomic traits of carom plants in terms of number of umbels, hundred seeds weights, shoot and root length and biomass improved significantly upon seed priming treatments. Seed priming with CaO_NPs is a viable strategy to combat reactive oxygen species-mediated damages in the carom plants.

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

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.

RNA methylation in plants: An overview

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.

Aptamer-based CRISPR-Cas powered diagnostics of diverse biomarkers and small molecule targets

CRISPR-Cas systems have been widely used in genome editing and transcriptional regulation. Recently, CRISPR-Cas effectors are adopted for biosensor construction due to its adjustable properties, such as simplicity of design, easy operation, collateral cleavage activity, and high biocompatibility. Aptamers' excellent sensitivity, specificity, in vitro synthesis, base-pairing, labeling, modification, and programmability has made them an attractive molecular recognition element for inclusion in CRISPR-Cas systems. Here, we review current advances in aptamer-based CRISPR-Cas sensors. We briefly discuss aptamers and the knowledge of Cas effector proteins, crRNA, reporter probes, analytes, and applications of target-specific aptamers. Next, we provide fabrication strategies, molecular binding, and detection using fluorescence, electrochemical, colorimetric, nanomaterials, Rayleigh, and Raman scattering. The application of CRISPR-Cas systems in aptamer-based sensing of a wide range of biomarkers (disease and pathogens) and toxic contaminants is growing. This review provides an update and offers novel insights into developing CRISPR-Cas-based sensors using ssDNA aptamers with high efficiency and specificity for point-of-care setting diagnostics.

Integrated Transcriptome and Targeted Metabolite Analysis Reveal miRNA-mRNA Networks in Low-Light-Induced Lotus Flower Bud Abortion

Most Nelumbo nucifera (lotus) flower buds were aborted during the growing season, notably in low-light environments. How lotus produces so many aborted flower buds is largely unknown. An integrated transcriptome and targeted metabolite analysis was performed to reveal the genetic regulatory networks underlying lotus flower bud abortion. A total of 233 miRNAs and 25,351 genes were identified in lotus flower buds, including 68 novel miRNAs and 1108 novel genes. Further enrichment analysis indicated that sugar signaling plays a potential central role in regulating lotus flower bud abortion. Targeted metabolite analysis showed that trehalose levels declined the most in the aborting flower buds. A potential regulatory network centered on miR156 governs lotus flower bud abortion, involving multiple miRNA-mRNA pairs related to cell integrity, cell proliferation and expansion, and DNA repair. Genetic analysis showed that miRNA156-5p-overexpressing lotus showed aggravated flower bud abortion phenotypes. Trehalose-6-P synthase 1 (TPS1), which is required for trehalose synthase, had a negative regulatory effect on miR156 expression. TPS1-overexpression lotus showed significantly decreased flower bud abortion rates both in normal-light and low-light environments. Our study establishes a possible genetic basis for how lotus produces so many aborted flower buds, facilitating genetic improvement of lotus’ shade tolerance.

Identification and structural analysis of novel malathion-specific DNA aptameric sensors designed for food testing

Malathion is an organophosphate chemical (OPC) and a toxic contaminant that adversely impacts food quality, human health, biodiversity, and the environment. Due to its small size and unavailability of sensitive sensors, detection of malathion remains a challenging task. Often chromatographic methods employed to analyze OPCs suffer from several shortcomings, including cost, immobility, laboriousness, and unsuitability for point-of-care settings. Hence, developing a specific and sensitive diagnostic sensor for quick and inexpensive food testing is essential. We discovered four unique malathion-specific ssDNA aptamers; designed two independent sensing strategies using fluorescence labeling and Thioflavin T (ThT) displacement. Selected aptamers formed the G4-quadruplex-like (G4Q) structure, which helped develop a label-free detection approach with a 2.01 ppb limit of detection. Additionally, 3D structures of aptamers were generated and validated using a series of computational modeling programs. Furthermore, we explored structural features using CD spectroscopy and molecular docking, probing ligands' binding mode, and revealed vital intermolecular interactions with aptamers. Subsequently, the novel sensors were optimized to detect malathion from food samples. The novel sensors could be further developed to meet the demands of sensing and quantifying toxic contaminants from real food samples in field conditions.

Raman Spectroscopy Enables Confirmatory Diagnostics of Fusarium Wilt in Asymptomatic Banana

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.

Assessment of genetic diversity and volatile content of commercially grown banana (Musa spp.) cultivars

Banana is an important fruit crop in the tropics and subtropics; however, limited information on biomarkers and signature volatiles is available for selecting commercial cultivars. Clonal fidelity is a major contributor to banana yield and aroma; however, there are no useful biomarkers available to validate clonal fidelity. In this study, we performed the molecular profiling of 20 banana cultivars consisting of diploid (AA or AB) and triploid (AAA or AAB or ABB) genomic groups. We screened 200 molecular markers, of which 34 markers (11 RAPD, 11 ISSR, and 12 SSR) yielded unequivocally scorable biomarker profiles. About 75, 69, and 24 allelic loci per marker were detected for RAPD, ISSR, and SSR markers, respectively. The statistical analysis of molecular variance (AMOVA) exhibited a high genetic difference of 77% with a significant FST value of 0.23 (p < 0.001). Interestingly, the UBC-858 and SSR CNMPF-13 markers were unique to Grand Nain and Ardhapuri cultivars, respectively, which could be used for clonal fidelity analysis. Furthermore, the analysis of banana fruit volatilome using headspace solid-phase microextraction-gas chromatography-tandem mass spectrometry (HS-SPME-GCMS) revealed a total of fifty-four volatile compounds in nine banana cultivars with 56% of the total volatile compounds belonging to the ester group as the significant contributor of aroma. The study assumes significance with informative biomarkers and signature volatiles which could be helpful in breeding and for the authentic identification of commercial banana cultivars.

Development of novel fluorescence-based and label-free noncanonical G4-quadruplex-like DNA biosensor for facile, specific, and ultrasensitive detection of fipronil

Fipronil is a broad-spectrum insecticide widely used in agriculture and residential areas; its indiscriminate use leads to environmental pollution and poses health hazards. Early detection of fipronil is critical to prevent the deleterious effects. However, current insecticide analysis methods such as HPLC, LC/MS, and GC/MS are incompetent; they are costly, immobile, time-consuming, laborious, and need skilled technicians. Hence, a sensitive, specific, and cheap biosensor are essential to containing the contamination. Here, we designed two novel biosensors-the first design relied on fluorescent labeling/quenching, while the second sensor focused on label-free detection using Thioflavin T displacement. Altogether, we identified four candidate aptamers, predicted secondary structures, and performed 3D molecular modeling to predict the binding pocket of fipronil in FiPA6B aptamer. Furthermore, the aptameric sensors showed high sensitivity to fipronil of sub-ppb level LOD, attributed to stringent experimental design. The biosensors displayed high specificity against other phenylpyrazole insecticides and demonstrated robust sensitivity for fipronil in real samples like cabbage and cucumber. Notably, to the best of our knowledge, this is the first demonstration of noncanonical G4-quadruplex-like aptamer binding to fipronil, verified using CD spectroscopy. Such aptasensors possess considerable potential for real-time measurements of hazardous insecticides as point-of-care technology.

Raman Spectroscopy and Machine Learning for Agricultural Applications: Chemometric Assessment of Spectroscopic Signatures of Plants as the Essential Step Toward Digital Farming

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.

Nanoscale Drug Delivery Systems: From Medicine to Agriculture

The main challenges in drug delivery systems are to protect, transport and release biologically active compounds at the right time in a safe and reproducible manner, usually at a specific target site. In the past, drug nano-carriers have contributed to the development of precision medicine and to a lesser extent have focused on its inroads in agriculture. The concept of engineered nano-carriers may be a promising route to address confounding challenges in agriculture that could perhaps lead to an increase in crop production while reducing the environmental impact associated with crop protection and food production. The main objective of this review is to contrast the advantages and disadvantages of different types of nanoparticles and nano-carriers currently used in the biomedical field along with their fabrication methods to discuss the potential use of these technologies at a larger scale in agriculture. Here we explain what is the problem that nano-delivery systems intent to solve as a technological platform and describe the benefits this technology has brought to medicine. Also here we highlight the potential drawbacks that this technology may face during its translation to agricultural applications, based on the lessons learned so far from its use for biomedical purposes. We discuss not only the characteristics of an ideal nano-delivery system, but also the potential constraints regarding the fabrication including technical, environmental, and legal aspects. A key motivation is to evaluate the potential use of these systems in agriculture, especially in the area of plant breeding, growth promotion, disease control, and post-harvest quality control. Further, we highlight the importance of a rational design of nano-carriers and identify current research gaps to enable scale-up relevant to applications in the treatment of plant diseases, controlled release of fertilizers, and plant breeding.

Concerns regarding 'off-target' activity of genome editing endonucleases

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.