Mid-infrared spectroscopy is a fast screening method for selecting Arabidopsis genotypes with altered leaf cuticular wax

Applying synchrotron radiation-based attenuated total reflection-fourier transform infrared to chemically characterise organic functional groups in terrestrial soils of King George Island, Antarctica

Anthropogenic activities, especially associated with fossil fuel combustion, are raising concerns worldwide, but remote areas with extreme climate conditions, such as Antarctica, are isolated from the adverse influence of human civilisation. Antarctica is considered as the most untouched place on Earth. Such pristine areas, which have extremely low chemical pollutant concentrations owing to restricted anthropogenic impacts, exemplify plausible model environments to test the reliability and sensitivity of advanced analytical techniques employed to chemically characterise and evaluate the spatial distribution of chemical pollutants. Here, synchrotron radiation-based attenuated total reflection-Fourier transform infrared (SR-ATR-FTIR) spectroscopy was employed to evaluate the variations in the organic functional groups (OFGs) of terrestrial soils of King George Island, Antarctica. Second-derivative SR-ATR-FTIR spectroscopy coupled with several multivariate statistical techniques highlighted the influence of anthropogenic activities on the alterations of OFGs in terrestrial soils collected near airports. Moreover, the daily activities of penguins could also have caused fluctuations in some OFGs of the samples the close to the Tombolo area and Ardley Island. The findings proved the effectiveness of SR-ATR-FTIR in evaluating the potential sources of variations in the chemical constituents, especially OFGs, in Antarctic terrestrial soils.

Use of ATR-FTIR spectroscopy for analysis of water deficit tolerance in Physalis peruviana L

Treatments that allow plants to better tolerate water deficit become essential, such as the application of chemical priming. In addition, it is essential to use analyses capable of measuring these effects at the biomolecular level, complementing the other physiological evaluations. In view of the above, this study aimed to evaluate the use of attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy for analyses of water deficit tolerance in Physalis peruviana plants. For this, samples of leaves, stems and roots of plants subjected to different pretreatments with proline (10 mM and 20 mM), sodium nitroprusside (SNP 25 μM and 50 μM) and H₂O as control, aiming at increasing tolerance to water deficit, were evaluated. The chemical agents used attenuated water deficit in P. peruviana plants, influencing phenotypic characterization and spectral analyses. Analysis of FTIR spectra indicates that different functional groups present in leaves, stems and roots were influenced by water deficit and priming treatments. Changes in lipid levels contributed to reducing water losses by increasing the thickness of cuticular wax. Accumulation of proteins and carbohydrates promoted osmoregulation and maintenance of the water status of plants. Thus, water deficit causes changes in the functional groups present in the organs of P. peruviana, and the ATR-FTIR technique is able to detect these biomolecular changes, helping in the selection of priming treatments to increase tolerance to water deficit.

Role of Foliar Biointerface Properties and Nanomaterial Chemistry in Controlling Cu Transfer into Wild-Type and Mutant Arabidopsis thaliana Leaf Tissue

Seven Arabidopsis thaliana mutants with differences in cuticle thickness and stomatal density were foliar exposed to 50 mg L^-1 Cu₃(PO₄)₂ nanosheets (NS), CuO NS, CuO nanoparticles, and CuSO₄. Three separate fractions of Cu (surface-attached, cuticle, interior leaf) were isolated from the leaf at 0.25, 2, 4, and 8 h. Cu transfer from the surface through the cuticle and into the leaf varied with mutant and particle type. The Cu content on the surface decreased significantly over 8 h but increased in the cuticle. Cu derived from the ionic form had the greatest cuticle concentration, suggesting greater difficulty in moving across this barrier and into the leaf. Leaf Cu in the increased-stomatal mutants was 8.5-44.9% greater than the decreased stomatal mutants, and abscisic acid to close the stomata decreased Cu in the leaf. This demonstrates the importance of nanomaterial entry through the stomata and enables the optimization of materials for nanoenabled agriculture.

New approaches with ATR-FTIR, SEM, and contact angle measurements in the adaptation to extreme conditions of some endemic Gypsophila L. taxa growing in gypsum habitats

Gypsophila L. taxa growing on gypsum soils have to withstand limiting and restrictive conditions for plant life. This study aims to identify functional mechanisms determine the main functional groups in the vegetative and reproductive organs of some endemic Gypsophila taxa growing in gypsum soils, as well as to understand the relationship between the hidrophobicities and their micromorphological structures of the leaves of these plants grown in arid conditions. In this context, a series of Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR), water contact angle (CA) measurements, and scanning electron microscopy (SEM) analyses were performed that may help to understand the survival mechanisms of Gypsophila eriocalyx Boiss., Gypsophila germanicopolitana Hub.-Mor. and Gypsophila simonii Hub.-Mor. growing in gypsum habitats. Our results showed the presence of O-H and C-O stretching bands belong to gypsum and calcium oxalate in the roots, stems, leaves and flowers of Gypsophila taxa is thought to be a way of tolerating the excess Ca and sulphate in the extreme habitat where these species grow. Leaves of Gypsophila taxa showed CAs above 90°, which indicates that G. eriocalyx, G. germanicopolitana, and G. simonii were hydrophobic. This study offers new approaches to understanding the adaptation of Gypsophila taxa to the extreme conditions typical of gypsum soils. The characterization of gypsum plants such as Gypsophila taxa, whose mechanisms for competition and survival on gypsum are still not fully understood, is very important in terms of shedding light on the adaptation of endemic plants to gypsum habitats.

Grade classification of human glioma using a convolutional neural network based on mid-infrared spectroscopy mapping

This study proposes a convolutional neural network (CNN)-based computer-aided diagnosis (CAD) system for the grade classification of human glioma by using mid-infrared (MIR) spectroscopic mappings. Through data augmentation of pixels recombination, the mappings in the training set increased almost 161 times relative to the original mappings. The pixels of the recombined mappings in the training set came from all of the one-dimensional (1D) vibrational spectroscopy of 62 (almost 80% of all 77 patients) patients at specific bands. Compared with the performance of the CNN-CAD system based on the 1D vibrational spectroscopy, we found that the mean diagnostic accuracy of the recombined MIR spectroscopic mappings at peaks of 2917 cm^-1 , 1539 cm^-1 and 1234 cm^-1 on the test set performed higher and the model also had more stable patterns. This research demonstrates that two-dimensional MIR mapping at a single frequency can be used by the CNN-CAD system for diagnosis and the research also gives a prompt that the mapping collection process can be replaced by a single-frequency IR imaging system, which is cheaper and more portable than a Fourier transform infrared microscopy and thus may be widely utilized in hospitals to provide meaningful assistance for pathologists in clinics.

Know your enemy: Application of ATR-FTIR spectroscopy to invasive species control

Extreme weather and globalisation leave our climate vulnerable to invasion by alien species, which have negative impacts on the economy, biodiversity, and ecosystem services. Rapid and accurate identification is key to the control of invasive alien species. However, visually similar species hinder conservation efforts, for example hybrids within the Japanese Knotweed complex.We applied the novel method of ATR-FTIR spectroscopy combined with chemometrics (mathematics applied to chemical data) to historic herbarium samples, taking 1580 spectra in total. Samples included five species from within the interbreeding Japanese Knotweed complex (including three varieties of Japanese Knotweed), six hybrids and five species from the wider Polygonaceae family. Spectral data from herbarium specimens were analysed with several chemometric techniques: support vector machines (SVM) for differentiation between plant types, supported by ploidy levels; principal component analysis loadings and spectral biomarkers to explore differences between the highly invasive Reynoutria japonica var. japonica and its non-invasive counterpart Reynoutria japonica var. compacta; hierarchical cluster analysis (HCA) to investigate the relationship between plants within the Polygonaceae family, of the Fallopia, Reynoutria, Rumex and Fagopyrum genera.ATR-FTIR spectroscopy coupled with SVM successfully differentiated between plant type, leaf surface and geographical location, even in herbarium samples of varying age. Differences between Reynoutria japonica var. japonica and Reynoutria japonica var. compacta included the presence of two polysaccharides, glucomannan and xyloglucan, at higher concentrations in Reynoutria japonica var. japonica than Reynoutria japonica var. compacta. HCA analysis indicated that potential genetic linkages are sometimes masked by environmental factors; an effect that can either be reduced or encouraged by altering the input parameters. Entering the absorbance values for key wavenumbers, previously highlighted by principal component analysis loadings, favours linkages in the resultant HCA dendrogram corresponding to expected genetic relationships, whilst environmental associations are encouraged using the spectral fingerprint region.The ability to distinguish between closely related interbreeding species and hybrids, based on their spectral signature, raises the possibility of using this approach for determining the origin of Japanese knotweed infestations in legal cases where the clonal nature of plants currently makes this difficult and for the targeted control of species and hybrids. These techniques also provide a new method for supporting biogeographical studies.

Grade diagnosis of human glioma using Fourier transform infrared microscopy and artificial neural network

The World Health Organization (WHO) grade diagnosis of cancer is essential for surgical outcomes and patient treatment. Traditional pathological grading diagnosis depends on dyes or other histological approaches, and the result interpretation highly relies on the pathologists, making the process time-consuming (>60 min, including the steps of dewaxing to water and H&E staining), resource-wasting, and labor-intensive. In the present study, we report an alternative workflow that combines the Fourier transform infrared (FTIR) microscopy and artificial neural network (ANN) to diagnose the grade of human glioma in a way that is faster (~20 min, including the processes of sample dewaxing, spectra acquisition and analysis), accurate (the prediction accuracy, specificity and sensitivity can reach above 99%), and without reagent. Moreover, this method is much superior to the common classification method of principal component analysis-linear discriminate analysis (PCA-LDA) (the prediction accuracy, specificity and sensitivity are only 87%, 89% and 86%, respectively). The ANN mainly learned the characteristic region of 800-1800 cm^-1 to classify the major histopathologic classes of human glioma. These results demonstrate that the grade diagnosis of human glioma by FTIR microscopy plus ANN can be streamlined, and could serve as a complementary pathway that is independent of the traditional pathology laboratory.

"Wax On, Wax Off": In Vivo Imaging of Plant Physiology and Disease with Fourier Transform Infrared Reflectance Microspectroscopy

Analysis of the epicuticular wax layer on the surface of plant leaves can provide a unique window into plant physiology and responses to environmental stimuli. Well-established analytical methodologies can quantify epicuticular wax composition, yet few methods are capable of imaging wax distribution in situ or in vivo. Here, the first report of Fourier transform infrared (FTIR) reflectance spectroscopic imaging as a non-destructive, in situ, method to investigate variation in epicuticular wax distribution at 25 µm spatial resolution is presented. The authors demonstrate in vivo imaging of alterations in epicuticular waxes during leaf development and in situ imaging during plant disease or exposure to environmental stressors. It is envisaged that this new analytical capability will enable in vivo studies of plants to provide insights into how the physiology of plants and crops respond to environmental stresses such as disease, soil contamination, drought, soil acidity, and climate change.

Transcriptome and physiological analyses provide insights into the leaf epicuticular wax accumulation mechanism in yellowhorn

Plantations and production of yellowhorn, one of the most important woody oil and urban greening trees widely cultivated in northern China, have gradually become limited by drought stress. The epicuticular wax layer plays a key role in the protection of yellowhorn trees from drought and other stresses. However, there is no research on the mechanism of wax loading in yellowhorn trees. In this study, we investigated the anatomical and physiological characteristics of leaves from different germplasm resources and different parts of the same tree and compared their cuticle properties. In addition, the different expression patterns of genes involved in wax accumulation were analyzed, and a coexpression network was built based on transcriptome sequencing data. Morphological and physiological comparisons found that the sun leaves from the outer part of the crown had thicker epicuticular wax, which altered the permeability and improved the drought resistance of leaves, than did shade leaves. Based on transcriptome data, a total of 3008 and 1324 differentially expressed genes (DEGs) were identified between the sun leaves and shade leaves in glossy- and non-glossy-type germplasm resources, respectively. We identified 138 DEGs involved in wax biosynthesis and transport, including structural genes (such as LACS8, ECH1, and ns-LTP) and transcription factors (such as MYB, WRKY, and bHLH transcription factor family proteins). The coexpression network showed a strong correlation between these DEGs. The differences in gene expression patterns between G- and NG-type germplasm resources under different light conditions were very clear. These results not only provide a theoretical basis for screening and developing drought-resistant yellowhorn germplasm resources but also provide a data platform to reveal the wax accumulation process of yellowhorn leaves.

Arabidopsis thaliana Cuticle Composition Contributes to Differential Defense Response to Botrytis cinerea

The chemical composition of a plant cuticle can change in response to various abiotic or biotic stresses and plays essential functions in disease resistance responses. Arabidopsis thaliana mutants altered in cutin content are resistant to Botrytis cinerea, presumably because of increased cuticular water and solute permeability, allowing for faster induction of defense responses. Within this context, our knowledge of wax mutants is limited against this pathogen. We tested the contribution of cuticular components to immunity to B. cinerea using mutants altered in either cutin or wax alone, or in both cutin and wax contents. We found that even all the tested mutants showed increased permeability and reactive oxygen species (ROS) accumulation in comparison with wild-type plants and that only cutin mutants showed resistance. To elucidate the early molecular mechanisms underlying cuticle-related immunity, we performed a transcriptomic analysis. A set of upregulated genes involved in cell wall integrity and accumulation of ROS were shared by the cutin mutants bdg, lacs2-3, and eca2, but not by the wax mutants cer1-4 and cer3-6. Interestingly, these genes have recently been shown to be required in B. cinerea resistance. In contrast, we found the induction of genes involved in abiotic stress shared by the two wax mutants. Our study reveals new insight that the faster recognition of a pathogen by changes in cuticular permeability is not enough to induce resistance to B. cinerea, as has previously been hypothesized. In addition, our data suggest that mutants with resistant phenotype can activate other defense pathways, different from those canonical immune ones.