Molecular Structural Changes in Alfalfa Detected by ATR-FTIR Spectroscopy in Response to Silencing of TT8 and HB12 Genes

Attenuated total reflection Fourier-transform infrared spectroscopy reveals environment specific phenotypes in clonal Japanese knotweed

BACKGROUND

Japanese knotweed (Reynoutria japonica var. japonica), a problematic invasive species, has a wide geographical distribution. We have previously shown the potential for attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy and chemometrics to segregate regional differentiation between Japanese knotweed plants. However, the contribution of environment to spectral differences remains unclear. Herein, the response of Japanese knotweed to varied environmental habitats has been studied. Eight unique growth environments were created by manipulation of the red: far-red light ratio (R: FR), water availability, nitrogen, and micronutrients. Their impacts on plant growth, photosynthetic parameters, and ATR-FTIR spectral profiles, were explored using chemometric techniques, including principal component analysis (PCA), linear discriminant analysis, support vector machines (SVM) and partial least squares regression. Key wavenumbers responsible for spectral differences were identified with PCA loadings, and molecular biomarkers were assigned. Partial least squared regression (PLSR) of spectral absorbance and root water potential (RWP) data was used to create a predictive model for RWP.

RESULTS

Spectra from plants grown in different environments were differentiated using ATR-FTIR spectroscopy coupled with SVM. Biomarkers highlighted through PCA loadings corresponded to several molecules, most commonly cell wall carbohydrates, suggesting that these wavenumbers could be consistent indicators of plant stress across species. R: FR most affected the ATR-FTIR spectra of intact dried leaf material. PLSR prediction of root water potential achieved an R2 of 0.8, supporting the potential use of ATR-FTIR spectrometers as sensors for prediction of plant physiological parameters.

CONCLUSIONS

Japanese knotweed exhibits environmentally induced phenotypes, indicated by measurable differences in their ATR-FTIR spectra. This high environmental plasticity reflected by key biomolecular changes may contribute to its success as an invasive species. Light quality (R: FR) appears critical in defining the growth and spectral response to environment. Cross-species conservation of biomarkers suggest that they could function as indicators of plant-environment interactions including abiotic stress responses and plant health.

Mannose-Binding Lectins as Potent Antivirals against SARS-CoV-2

The SARS-CoV-2 entry into host cells is mainly mediated by the interactions between the viral spike protein (S) and the ACE-2 cell receptor, which are highly glycosylated. Therefore, carbohydrate binding agents may represent potential candidates to abrogate virus infection. Here, we evaluated the in vitro anti-SARS-CoV-2 activity of two mannose-binding lectins isolated from the Brazilian plants Canavalia brasiliensis and Dioclea violacea (ConBR and DVL). These lectins inhibited SARS-CoV-2 Wuhan-Hu-1 strain and variants Gamma and Omicron infections, with selectivity indexes (SI) of 7, 1.7, and 6.5, respectively for ConBR; and 25, 16.8, and 22.3, for DVL. ConBR and DVL inhibited over 95% of the early stages of the viral infection, with strong virucidal effect, and also protected cells from infection and presented post-entry inhibition. The presence of mannose resulted in the complete lack of anti-SARS-CoV-2 activity by ConBR and DVL, recovering virus titers. ATR-FTIR, molecular docking, and dynamic simulation between SARS-CoV-2 S and either lectins indicated molecular interactions with predicted binding energies of -85.4 and -72.0 Kcal/Mol, respectively. Our findings show that ConBR and DVL lectins possess strong activities against SARS-CoV-2, potentially by interacting with glycans and blocking virus entry into cells, representing potential candidates for the development of novel antiviral drugs.

Effect of Anaerobic Calcium Oxide Alkalization on the Carbohydrate Molecular Structures, Chemical Profiles, and Ruminal Degradability of Rape Straw

To improve the utilization efficiency of rape straw, anaerobic calcium oxide (CaO) alkalization was conducted, and advanced molecular spectroscopy was applied, to detect the internal molecular structural changes. Rape straw was treated with different combinations of CaO (3%, 5%, and 7%) and moisture levels (50% and 60%) and stored under anaerobic conditions. We investigated the carbohydrate chemical constituents, the ruminal neutral detergent fiber (aNDF) and acid detergent fiber (ADF) degradation kinetics, and the carbohydrate molecular structural features. CaO-treated groups were higher (p < 0.05) for ash, Ca, non-fiber carbohydrate, soluble fiber, and the ruminal degradability of aNDF and ADF. In contrast, they were lower (p < 0.05) for the contents of aNDF, ADF, and indigestible fiber. With CaO levels rising from 3% to 7%, the content of aNDF and ADF linearly decreased (p < 0.05). CaO treatment and anaerobic storage changed the molecular characteristics, including structural parameters related to total carbohydrates (TC), cellulosic compounds (CEC), and structural carbohydrates (STC). Alterations in cellulosic compounds' spectral regions were highly correlated with the differences in carbohydrate chemical constituents and the ruminal digestibility of rape straw. In summary, CaO treatment and anaerobic storage altered the molecular structural parameters of carbohydrates, leading to an enhancement in the effective degradability (ED) of aNDF and ADF in rape straw. From the perspective of processing cost and effectiveness, 5% CaO + 60% moisture could be suggested as a recommended treatment combination.

Using attenuated-total-reflection Fourier-transformed spectroscopy to reveal molecular structural differences among willow (Salix spp.) foliage cultivars in relation to their potential as fodders

BACKGROUND

Willow trees represent a suitable species for the development of agroforestry systems, integrating bioenergy and animal feed production. However, there is a lack of information regarding the suitability of leaves and stems, considered a bioenergy by-product, as animal feed. The aim of this study was the employment of attenuated total reflectance Fourier transform infrared spectroscopy (550-4000 cm^-1 ) to investigate differences in the nutrient molecular structure profile of leaves and stems of selected willow cultivars to understand their utility for ruminant nutrition.

RESULTS

Univariate analysis of variance of leaves showed lower intensities of cellulosic compounds and higher of protein in comparison with stems, which suggests higher leaf dry matter and protein digestibility. Spectral analyses revealed differences in both plant parts between Salix cv. Terra Nova and Salix cv. Beagle, cv. Resolution, and cv. Olof. The higher α-helix to β-sheet ratio, which is related to a higher protein digestibility, was in correlation with the lower content of condensed tannins. Principal component and agglomerative hierarchical cluster analyses showed significant discrimination among willow cultivars in the cellulosic, structural carbohydrate, and amide regions, whereas differences were less evident for total carbohydrate and lipid-related regions.

CONCLUSION

The application of attenuated total reflectance Fourier transform infrared molecular spectroscopy is an effective tool to rapidly identify spectral features related to the nutritional composition of willow foliage and to discriminate between cultivars and parts of the plant. This information would be useful to optimize the use of willow fodders in agroforestry systems. © 2021 Society of Chemical Industry.

An excellent antibacterial and high self-adhesive hydrogel can promote wound fully healing driven by its shrinkage under NIR

The lacks of antibacterial properties, low adhesion and delayed wound healing of the hydrogel wound dressings limit their applications in wound treatment. To resolve these, a novel hydrogel composed of polydopamine (PDA), Ag and graphene oxide (GO) is fabricated for wound dressing via the chemical crosslinking of N-isopropylacrylamide (NIPAM) and N,N'-methylene bisacrylamide (BIS). The prepared hydrogel containing PDA@Ag5GO1 (Ag5GO1 denotes the mass ratio between Ag and GO is 5:1) exhibits effective antibacterial properties and high inhibition rate against E. coli and S. aureus. It shows high adhesion ability to various substrate materials, implying a simpler method to the wound obtained by self-fixing rather than suturing. More important, it can produce strong contractility under the irradiation of near-infrared light (NIR), exerting a centripetal force that helps accelerate wound healing. Thus, the hydrogel containing a high concentration PDA@Ag5GO1 irradiated by NIR can completely repair the wound defect (1.0 × 1.0 cm²) within 15 days, the wound healing rate can reach 100%, which was far higher than other groups. Taken together, the new hydrogel with excellent antibacterial, high adhesion and strong contractility will subvert the traditional treatment methods on wound defect, extending its new application range in wound dressing.

Tissue specific changes in elements and organic compounds of alfalfa (Medicago sativa L.) cultivars differing in salt tolerance under salt stress

Soil salinity is a global concern and often the primary factor contributing to land degradation, limiting crop growth and production. Alfalfa (Medicago sativa L.) is a low input high value forage legume with a wide adaptation. Examining the tissue-specific responses to salt stress will be important to understanding physiological changes of alfalfa. The responses of two alfalfa cultivars (salt tolerant 'Halo', salt intolerant 'Vernal') were studied for 12 weeks in five gradients of salt stress in a sand based hydroponic system in the greenhouse. The accumulation and localization of elements and organic compounds in different tissues of alfalfa under salt stress were evaluated using synchrotron beamlines. The pattern of chlorine accumulation for 'Halo' was: root > stem ~ leaf at 8 dSm^-1, and root ~ leaf > stem at 12 dSm^-1, potentially preventing toxic ion accumulation in leaf tissues. In contrast, for 'Vernal', it was leaf > stem ~ root at 8 dSm^-1 and leaf > root ~ stem at 12 dSm^-1. The distribution of chlorine in 'Halo' was relatively uniform in the leaf surface and vascular bundles of the stem. Amide concentration in the leaf and stem tissues was greater for 'Halo' than 'Vernal' at all salt gradients. This study determined that low ion accumulation in the shoot was a common strategy in salt tolerant alfalfa up to 8 dSm^-1 of salt stress, which was then replaced by shoot tissue tolerance at 12 dSm^-1.

Rapid tannin profiling of tree fodders using untargeted mid-infrared spectroscopy and partial least squares regression

BACKGROUND

The presence of condensed tannins (CT) in tree fodders entails a series of productive, health and ecological benefits for ruminant nutrition. Current wet analytical methods employed for full CT characterisation are time and resource-consuming, thus limiting its applicability for silvopastoral systems. The development of quick, safe and robust analytical techniques to monitor CT's full profile is crucial to suitably understand CT variability and biological activity, which would help to develop efficient evidence-based decision-making to maximise CT-derived benefits. The present study investigates the suitability of Fourier-transformed mid-infrared spectroscopy (MIR: 4000-550 cm^-1) combined with multivariate analysis to determine CT concentration and structure (mean degree of polymerization-mDP, procyanidins:prodelphidins ratio-PC:PD and cis:trans ratio) in oak, field maple and goat willow foliage, using HCl:Butanol:Acetone:Iron (HBAI) and thiolysis-HPLC as reference methods.

RESULTS

The MIR spectra obtained were explored firstly using Principal Component Analysis, whereas multivariate calibration models were developed based on partial least-squares regression. MIR showed an excellent prediction capacity for the determination of PC:PD [coefficient of determination for prediction (R²P) = 0.96; ratio of prediction to deviation (RPD) = 5.26, range error ratio (RER) = 14.1] and cis:trans ratio (R²P = 0.95; RPD = 4.24; RER = 13.3); modest for CT quantification (HBAI: R²P = 0.92; RPD = 3.71; RER = 13.1; Thiolysis: R²P = 0.88; RPD = 2.80; RER = 11.5); and weak for mDP (R²P = 0.66; RPD = 1.86; RER = 7.16).

CONCLUSIONS

MIR combined with chemometrics allowed to characterize the full CT profile of tree foliage rapidly, which would help to assess better plant ecology variability and to improve the nutritional management of ruminant livestock.

Synchrotron-radiation sourced SR-IMS molecular spectroscopy to explore impact of silencing TT8 and HB12 genes in alfalfa leaves on the molecular structure and chemical mapping

Advanced synchrotron-based vibrational molecular spectroscopy (SR-IMS) has been developed to image molecular chemistry in biological tissues within cellular and subcellular dimension. However, it is seldomly used in gene-transformation and gene-silencing study. The objectives of this study were to apply synchrotron-based vibrational molecular spectroscopy (SR-IMS) to determine the molecular structural changes and chemical mapping of alfalfa leaves induced by silencing of TT8 and HB12 genes in alfalfa in comparison with wild type of alfalfa. Five alfalfa leaves from each alfalfa genotype were selected for FTIR spectra collection and chemical mapping with synchrotron-based FTIR microspectroscopy (SR-IMS). Peak heights and areas of empirical regions were analyzed, and peak areas of previous regions were mapped for each sample using OMNIC 7.3. Results showed that transformed alfalfa had higher peak height and area of carbonyl CO (CCO), compared with wild type (WT). Chemical groups maps for carbohydrate, amide and lipid-related regions were successfully obtained. HB12-silenced (HB12i) had higher carbohydrate intensity both in the mesophyll and epidermises, whereas TT8-silenced (TT8i) and WT only had higher carbohydrate spectral peak intensity in epidermises. In addition, HB12i had higher CCO intensity and lower lignin intensity compared with TT8i and WT. All alfalfa genotypes had higher intensity of amide and asymmetric and symmetric CH2 and CH3 (ASCC) area in mesophylls. In conclusion, silencing of HB12 and TT8 genes in alfalfa both increased CCO profiles of alfalfa leaves, while silencing of HB12 had more impacts on chemical localization in alfalfa leaves.

Application of advanced molecular spectroscopy and modern evaluation techniques in canola molecular structure and nutrition property research

This review aims to provide research update and progress on applications of advanced molecular spectroscopy to current research on canola related bio-processing technology, molecular structure, and nutrient utilization and availability. The studies focused on how inherent molecular structure changes affect nutritional quality of canola and its co-products from bio-processing. The molecular spectroscopic techniques (SR-IMS, DRIFT, ATR-FTIR) used for molecular structure and nutrition association were reviewed, including the synchrotron radiation with infrared microspectroscopy, the synchrotron radiation with soft x-ray microspectroscopy, the diffuse reflectance infrared Fourier transform spectroscopy, the grading near infrared reflectance spectroscopy, and the Fourier transform infrared vibrational spectroscopy. Nutritional evaluation with other techniques in association with molecular structure was also reviewed. This study provides updated research progress on application of molecular spectroscopy in combination with various nutrition evaluation techniques to current research in the canola-related bio-oil/bio-energy processing and nutrition sciences.

DFT Studies of Distinct Anilines with p-Hydroxycinnamic Acids for Antioxidant Profile

BACKGROUND

Life style and jobs in current situations have generated increased free radicals such as hydroxyl (OH•) and superoxide (O2•) radicals, thereby increasing stress in humans. Interest in search of antioxidants that trap these free radicals has increased to relieve stress. β-carotene (provitamin A), ascorbic acid (vitamin C), tocopherol or vitamin E, Trolox; butyl hydroxy toluene and phenolic compounds are the well-known antioxidants. Several methods evaluate the antioxidant property existing in natural substances (medicinal plants and agri-food products) and synthetic compounds (2-methyl-3- (pyrrolidin-2-ylideneamino) quinazolin-4 (3H) -one and 3,3'- (1,4- phenylenebis (methanylylidene)) bis (azanylylidene) (2-methyl-quinazolin-4 (3H) -one).

OBJECTIVE

The objective of this study is to focus on complexes with p-hydroxycinnamic acids to trap free radicals in a greener way.

METHODS

Spectroscopic shifts and structural studies were employed to attribute electronic properties responsible for antioxidant profile. Spectroscopic shifts in wavenumbers were attributed with Fourier Transform Infrared Spectra (FTIR) and Fourier Transform Raman spectra (FT Raman Spectra). Structural studies were performed with Gaussian package, electron density method the B3LYP method, basis set 6-31(d) for attributing electronic properties responsible for antioxidant profile.

RESULTS

Interpretation of FTIR spectra revealed spectroscopic shifts in wavenumbers in all the complexes responsible for bonding. Further, studies confirmed the formation of complex with reduced intensities in Raman spectra. Computational studies revealed enhancement in molecular and electronic properties responsible for antioxidant power.

CONCLUSION

Studies revealed that complex with p-nitroaniline contribute to greater acceptor and donor power responsible for antioxidant power. These higher powers suggest the best antiradicals to trap free radicals.

Effects of silencing TT8 and HB12 on in vitro nutrients degradation and VFA production in relation to molecular structures of alfalfa (Medicago sativa)

BACKGROUND

Transparent Testa8 (TT8) and Homeobox12 (HB12) are two transcriptional factors in plant phenylpropanoid pathways and were reported to be positively related to lignin content. Alfalfa with silenced TT8 (TT8i) and HB12 (HB12i) was therefore generated using the RNA interference (RNAi) technique. Although lignin was found to be high in HB12i, such gene-silencing of alfalfa resulted in nutrient profiles that might be suitable for grazing. To extend the nutritional evaluation of transformed alfalfa, ground samples of 11 HB12i, 5 TT8i and 4 wild type (WT) were incubated in rumen fluid : buffer solution for 0, 2, 4, 8, 12, 24 and 48 h at 39 °C. Dry matter (DM) and neutral detergent fiber (NDF) degradations at each time point, and production of volatile fatty acids (VFA) at 4, 12, 24 and 48 h were analyzed, as well as degradation and production kinetics. The correlations and regressions between nutritive profiles and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectral parameters were determined.

RESULTS

Both transformed genotypes had lower DM degradation and HB12i had lower VFA production compared with WT. Structural carbohydrate (STC) parameters were found to be negatively correlated with DM degradation and VFA production. The kinetics of DM degradation and VFA production were predicted from spectral parameters with good estimation power.

CONCLUSION

Silencing of HB12 and TT8 affected fermentation characteristics of alfalfa and some fermentation characteristics were predictable from spectral parameters using ATR-FTIR spectroscopy. © 2019 Society of Chemical Industry.

Silencing TT8 and HB12 Decreased Protein Degradation and Digestion, Microbial Synthesis, and Metabolic Protein in Relation to Molecular Structures of Alfalfa (Medicago sativa)

This study aimed to explore the effects of silencing HB12 and TT8 genes on protein utilization characteristics of alfalfa. Ground samples of 11 HB12-silenced (HB12i), 5 TT8-silenced (TT8i) and 4 wild type (WT) were incubated in a Daisy II incubator with N¹⁵ labeled ammonium sulfate for 0, 4, 8, 12, and 24 h. CP degradation and degradational kinetics, microbial nitrogen fractions, and protein metabolic profiles were determined. Moreover, relationships between protein profiles and FTIR spectral parameters were estimated. Results showed that transgenic alfalfa had lower CP degradation, microbial protein, and total available protein compared with WT, especially for HB12i. In addition, CP degradation and protein metabolic profiles were closely correlated with FTIR spectral parameters and thereby could be predicted from spectral parameters. In conclusion, silencing of HB12 and TT8 genes in alfalfa decreased protein degradational and metabolic profiles, which were predictable with FTIR spectral parameters.

Application of FT/IR-ATR vibrational spectroscopy to reveal protein molecular structure of feedstock and co-products from Canadian and Chinese canola processing in relation to microorganism bio-degradation and enzyme bio-digestion

The principal objective of this study was to apply FT/IR-ATR vibrational spectroscopy to inspect the relationship between rumen dry matter (DM) and protein degradation, rumen undegraded protein (RUP) intestinal digestion and processing induced protein molecular structure changes in feedstock (canola oil seeds) and co-products (canola meal) from bio-oil processing from different crushing plants in Canada and China. The rumen DM and protein degradation, rumen undegraded protein intestinal digestion and protein molecular structure affected by bio-oil processing were examined using in situ, three step in vitro digestion and Fourier transform infrared (FT/IR) molecular spectroscopy techniques, respectively. The results showed that the protein molecular structure; α-helix height and α-helix to β-sheet height ratio had a close association with rumen DM and protein degradation and rumen undegraded protein intestinal digestibility. Multiple regression analyses showed that protein β-sheet height and α-helix to β-sheet height ratio spectral intensity can be used to predict rumen DM and protein degradation, while intestinal digestibility of rumen undegraded protein can be predicted by α-helix height and β-sheet height. In conclusion, the co-product canola meal from bio-oil processing is a good source of intestinally digestible protein. Rumen DM and protein degradation and intestinal digestibility of rumen undegraded protein are related to the protein molecular structures of the co-products affected by changes during bio-oil processing.