Raman, AFM and SNOM high resolution imaging of carotene crystals in a model carrot cell system

Influence of suspended particles and dissolved organic matters on virus enrichment in reclaimed water by two-step tangential flow ultrafiltration: Phenomena and mechanisms

Enteric virus concentration in large-volume water samples is crucial for detection and essential for assessing water safety. Certain dissolution and suspension components can affect the enrichment process. In this study, tangential flow ultrafiltration (TFUF) was used as an enrichment method for recovering enteric virus in water samples. Interestingly, the bacteriophage MS2 recovery in reclaimed water and the reclaimed water without particles were higher than that in ultrapure water. The simulated reclaimed water experiments showed that humic acid (HA) (92.16% ± 4.32%) and tryptophan (Try) (81.50 ± 7.71%) enhanced MS2 recovery, while the presence of kaolin (Kaolin) inhibited MS2 recovery with an efficiency of 63.13% ± 11.17%. Furthermore, Atomic force microscopy (AFM) revealed that the MS2-HA cluster and the MS2-Try cluster had larger roughness values on the membrane surface, making it difficult to be eluted, whereas MS2-Kaolin cluster had compact surfaces making it difficult to be eluted. Additionally, the MS2-HA cluster is bound to the membrane by single hydrogen bond with SO, whereas both the MS2-Try cluster and the MS2-Kaolin cluster are bound to the membrane by two hydrogen bonds, making eluting MS2 challenging. These findings have potential implications for validating standardized methods for virus enrichment in water samples.

Photoinduced force microscopy as a novel method for the study of microbial nanostructures

A detailed comparison of the capabilities of electron microscopy and nano-infrared (IR) microscopy for imaging microbial nanostructures has been carried out for the first time. The surface sensitivity, chemical specificity, and non-destructive nature of spectroscopic mapping is shown to offer significant advantages over transmission electron microscopy (TEM) for the study of biological samples. As well as yielding important topographical information, the distribution of amides, lipids, and carbohydrates across cross-sections of bacterial (Escherichia coli, Staphylococcus aureus) and fungal (Candida albicans) cells was demonstrated using PiFM. The unique information derived from this new mode of spectroscopic mapping of the surface chemistry and biology of microbial cell walls and membranes, may provide new insights into fungal/bacterial cell function as well as having potential use in determining mechanisms of antimicrobial resistance, especially those targeting the cell wall.

Recent advances and applications of laser-based imaging techniques in food crops and products: a critical review

To meet the growing demand for food quality and safety, there is a pressing need for fast and visible techniques to monitor the food crop and product production processing, and to understand the chemical changes that occur during these processes. Herein, the fundamental principles, instruments, and characteristics of three major laser-based imaging techniques (LBITs), namely, laser-induced breakdown spectroscopy, Raman spectroscopy, and laser ablation-inductively coupled plasma-mass spectrometry, are introduced. Additionally, the advances, challenges, and prospects for the application of LBITs in food crops and products are discussed. In recent years, LBITs have played a crucial role in mapping primary metabolites, secondary metabolites, nanoparticles, toxic metals, and mineral elements in food crops, as well as visualizing food adulteration, composition changes, pesticide residue, microbial contamination, and elements in food products. However, LBITs are still facing challenges in achieving accurate and sensitive quantification of compositions due to the complex sample matrix and minimal laser sampling quantity. Thus, further research is required to develop comprehensive data processing strategies and signal enhancement methods. With the continued development of imaging methods and equipment, LBITs have the potential to further explore chemical distribution mechanisms and ensure the safety and quality of food crops and products.

Super-resolution Raman imaging towards visualisation of nanoplastics

Confocal Raman imaging can potentially identify and visualise microplastics and nanoplastics, but the imaging lateral resolution is hampered by the diffraction of the laser, making it difficult to analyse nanoplastics that are smaller than the laser spot and the lateral resolution limit (λ/2NA). Fortunately, once a nanoplastic is scanned to collect the spectrum via a position/pixel array as a spectrum matrix, akin to a hyperspectral matrix, the nanoplastic can be imaged by mapping the spectrum intensity as a pattern that is transcended axially and can be fitted as a 2D Gaussian surface. The Gaussian fitting and image re-construction by deconvolution can precisely predict the nanoplastic's position and approximate size, and potentially enhance the signal intensity. Several algorithms are also employed to decode the spectrum matrix, to improve the Raman images before the subsequent image re-construction. Overall, general confocal microscopy can also break through the diffraction limit of the excitation light by using algorithms, resulting in super-resolution Raman imaging to capture nanoplastics.

Recent advances in the application of atomic force microscopy to structural biology

The application of atomic force microscopy (AFM) for (functional) imaging and manipulating biomolecules at all levels of organization has enabled great progress in the structural biology field over the last decades, contributing to the discovery of novel structural entities of biological significance across many disciplines ranging from biochemistry, biomedicine and biophysics to molecular and cell biology, up to food systems and beyond. AFM has the capability to generate high-resolution topographic images spanning from the submolecular to the (sub)cellular range and can probe biochemical and biophysical sample properties in close to native conditions with excellent temporal resolution. Instrumental developments in the past decade enable dynamical structural and conformational studies of single biomolecules and new techniques for structural and chemical modification of the AFM probe have converted the cantilever into a versatile tool to study different biological phenomena, such as the mechanical stability of biomolecular complexes or the force induced dynamic changes of mechanically stressed proteins at the nanoscopic level. To improve the functionality of AFM and approach dynamic processes of complex biological systems ex vivo, AFM is combined with complementary microscopy, nanoscopy and spectroscopy tools. These multimethodological approaches provide unprecedented possibilities of probing physical, chemical and biological properties of complex cellular systems with high spatio-temporal resolution, leading to novel applications that correlate structural results with functional biochemical, biophysical, immunological, or genetic data on the system under study.

Structural and physicochemical properties of composites between starch nanoparticles and β-carotene prepared via nanoprecipitation

To apply starch nanoparticles (SNP) as host materials for β-carotene encapsulation, aqueous SNP dispersions (10, 25, 50, and 100 mg/10 mL) and β-carotene in acetone (10, 50, 100, 150, and 200 μg/mL) were mixed. The acetone in the mixture was evaporated to prepare SNP and β-carotene composites, which were homogeneously dispersed in aqueous media with over 90 % solubility. When SNP content was higher than 50 mg, over 80 % of β-carotene was encapsulated in the composite matrix. X-ray diffraction, nuclear magnetic resonance spectroscopy, and transmission electron microscopic analyses confirmed the micellar-shaped composite particles with diameters <120 nm and an amorphous structure. High SNP content in the composites enhanced β-carotene stability under extremely hot and acidic conditions as well as against ultraviolet rays and oxidation reactions. The encapsulated β-carotene was not readily released in simulated gastric fluid, but was gradually released in simulated intestinal fluid via SNP digestion in the composites.

Repression of Carotenoid Accumulation by Nitrogen and NH4+ Supply in Carrot Callus Cells In Vitro

The effect of mineral nutrition on the accumulation of the main health beneficial compounds in carrots, the carotenoid pigments, remains ambiguous; here, a model-based approach was applied to reveal which compounds are responsible for the variation in carotenoid content in carrot cells in vitro. For this purpose, carotenoid-rich callus was cultured on either BI (modified Gamborg B5) or R (modified Murashige and Skoog MS) mineral media or on modified media obtained by exchanging compounds between BI and R. Callus growing on the BI medium had abundant carotene crystals in the cells and a dark orange color in contrast to pale orange callus with sparse crystals on the R medium. The carotenoid content, determined by HPLC and spectrophotometrically after two months of culture, was 5.3 higher on the BI medium. The replacement of media components revealed that only the N concentration and the NO3:NH4 ratio affected carotenoid accumulation. Either the increase of N amount above 27 mM or decrease of NO3:NH4 ratio below 12 resulted in the repression of carotenoid accumulation. An adverse effect of the increased NH4+ level on callus growth was additionally found. Somatic embryos were formed regardless of the level of N supplied. Changes to other media components, i.e., macroelements other than N, microelements, vitamins, growth regulators, and sucrose had no effect on callus growth and carotenoid accumulation. The results obtained from this model system expand the range of factors, such as N availability, composition of N salts, and ratio of nitrate to ammonium N form, that may affect the regulation of carotenoid metabolism.

DFT study of Raman spectra of polyenes and ß-carotene: Dependence on length of polyene chain and isomer type

We carried out calculations of non-resonance Raman spectra of ß-carotene and polyenes CH₂(CHCH)_n-2CHCH₂ using the density functional theory (DFT). We revealed that the peak positions and intensities of the CC and CC stretching bands depend on length of the polyene chain and type of the isomer. Our experimental non-resonance Raman spectra of ß-carotene powder match well the DFT-simulated Raman spectrum of ß-carotene in the all-trans form. The peak positions and relative intensities of the CC and CC stretching bands of ß-carotene turned out to be similar in the resonance and non-resonance Raman spectra. An increase in the number of conjugated double bonds (n = 3-30) in a polyene structure results in a monotonous shift of the positions of the most intense CC and CC bands towards lower wavenumbers with an increase in the band intensities. An increase in the isomer number results in the monotonous decrease of the CC stretching band intensity for polyenes with 9, 10, 11, 15 and 24 double bonds. An increase in the isomer number inhomogeneously influences the form, position and intensity of the CC stretching band.

Inhibition of Carotenoid Biosynthesis by CRISPR/Cas9 Triggers Cell Wall Remodelling in Carrot

Recent data indicate that modifications to carotenoid biosynthesis pathway in plants alter the expression of genes affecting chemical composition of the cell wall. Phytoene synthase (PSY) is a rate limiting factor of carotenoid biosynthesis and it may exhibit species-specific and organ-specific roles determined by the presence of psy paralogous genes, the importance of which often remains unrevealed. Thus, the aim of this work was to elaborate the roles of two psy paralogs in a model system and to reveal biochemical changes in the cell wall of psy knockout mutants. For this purpose, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated (Cas9) proteins (CRISPR/Cas9) vectors were introduced to carotenoid-rich carrot (Daucus carota) callus cells in order to induce mutations in the psy1 and psy2 genes. Gene sequencing, expression analysis, and carotenoid content analysis revealed that the psy2 gene is critical for carotenoid biosynthesis in this model and its knockout blocks carotenogenesis. The psy2 knockout also decreased the expression of the psy1 paralog. Immunohistochemical staining of the psy2 mutant cells showed altered composition of arabinogalactan proteins, pectins, and extensins in the mutant cell walls. In particular, low-methylesterified pectins were abundantly present in the cell walls of carotenoid-rich callus in contrast to the carotenoid-free psy2 mutant. Transmission electron microscopy revealed altered plastid transition to amyloplasts instead of chromoplasts. The results demonstrate for the first time that the inhibited biosynthesis of carotenoids triggers the cell wall remodelling.

How did correlative atomic force microscopy and super-resolution microscopy evolve in the quest for unravelling enigmas in biology?

With the invention of the Atomic Force Microscope (AFM) in 1986 and the subsequent developments in liquid imaging and cellular imaging it became possible to study the topography of cellular specimens under nearly physiological conditions with nanometric resolution. The application of AFM to biological research was further expanded with the technological advances in imaging modes where topographical data can be combined with nanomechanical measurements, offering the possibility to retrieve the biophysical properties of tissues, cells, fibrous components and biomolecules. Meanwhile, the quest for breaking the Abbe diffraction limit restricting microscopic resolution led to the development of super-resolution fluorescence microscopy techniques that brought the resolution of the light microscope comparable to the resolution obtained by AFM. The instrumental combination of AFM and optical microscopy techniques has evolved over the last decades from integration of AFM with bright-field and phase-contrast imaging techniques at first to correlative AFM and wide-field fluorescence systems and then further to the combination of AFM and fluorescence based super-resolution microscopy modalities. Motivated by the many developments made over the last decade, we provide here a review on AFM combined with super-resolution fluorescence microscopy techniques and how they can be applied for expanding our understanding of biological processes.

Developmental Toxicity of Few-Layered Black Phosphorus toward Zebrafish

Black phosphorus (BP) has extensive applications in various fields. The release of BP into aquatic ecosystems and the potential toxic effects on aquatic organisms are becoming major concerns. Here, we investigated the developmental toxicity of few-layered BP toward the zebrafish. We found that BP could adsorb on the surface of the chorion and could subsequently penetrate within the embryo. After exposure of embryos to 10 mg/L BP, developmental malformations appeared at 96 hpf, especially heart deformities such as pericardial edema and bradycardia, accompanied by severe circulatory system failure. Using transgenic zebrafish larvae, we further characterized cardiovascular defects with cardiac enlargement and impaired cardiac vessels as indicators of damage to the cardiovascular system upon BP exposure. We performed transcriptomic analysis on zebrafish embryos treated with a lower concentration of 2 mg/L. The results showed disruption in genes associated with muscle development, oxygen involved processes, focal adhesion, and VEGF and MAPK signaling pathways. These alterations also indicated that BP carries a risk of developmental perturbation at lower concentrations. This study provides new insights into the effects of BP on aquatic organisms.

Light Microscopy and Raman Imaging of Carotenoids in Plant Cells In Situ and in Released Carotene Crystals

Light microscopy with a bright field mode offers an easy and fast examination of plant specimen for carotenoid presence in its cells. Using basic techniques such as hand sectioned or squashed preparations, carotenoid-rich chromoplasts can be identified without applying any staining procedure and their localization within the cell, their shape and number can be assessed. More detailed information can be obtained by using Raman spectroscopy which is suitable for the analysis of carotenoids due to their unique Raman spectra and allows semiquantification of their contents. Raman imaging (mapping) can be additionally used to show the distribution of carotenoids within the sample. Raman spectra can be taken from extracted carotenoids but can be also obtained directly from plant tissues or cells as Raman measurements are nondestructive for the sample. Here we describe preparations of intact tissue samples, monolayer cell samples, isolated protoplasts as well as carotene crystals released from chromoplasts that are suitable for subsequent observations using light microscopy and for analysis using Raman spectroscopy.

The Diversity of Linear Conjugated Polyenes and Colours in Nature: Raman Spectroscopy as a Diagnostic Tool

This review is centered on the linear conjugated polyenes, which encompasses chromatic biomolecules, such as carotenoids, polyunsaturated aldehydes and polyolefinic fatty acids. The linear extension of the conjugated double bonds in these molecules is the main feature that determines the spectroscopic properties as light-absorbing. These classes of compounds are responsible for the yellow, orange, red and purple colors which are observed in their parent flora and fauna in nature. Raman spectroscopy has been used as analytical tool for the characterization of these molecules, mainly due to the strong light scattering produced by the delocalized pi electrons in the carbon chain. In addition, conjugated polyenes are one of the main target molecular species for astrobiology, and we also present a brief discussion of the use of Raman spectroscopy as one of the main analytical tools for the detection of polyenes extra-terrestrially.

Microplastics contamination in the soil from Urban Landfill site, Dhaka, Bangladesh

Microplastics (MP) pollution has become a matter of global concern because of its several deleterious effects on environmental health, especially on the terrestrial environment. The evidence of MP contamination in terrestrial environment is less explored compared to aquatic bodies. However, in Bangladesh despite having high possibility of MP contamination, there is lacking of available research-based evidence. Urban areas soil is subjected to act as a major environmental reservoir for MPs. Thus, this study was carried out to investigate the presence of MP contamination in constructed landfill sites near Dhaka city, Bangladesh. Ten unmixed soil samples were collected from the Aminbazar Sanitary landfill sites, from that thirty replicated samples were investigated via Fourier Transform Infrared Spectroscopy (FT-IR) analysis and Stereomicroscope. The range of physicochemical parameters were found in the soil samples as follows: moisture content; 15.84%-56.54%; soil pH; 5.76-6.02, electric conductivity; 0.1 μs/cm - 2.43 μs/cm, alkalinity; 6.7 ± 1.528-14.33 ± 0.577, TOC; 0.18% ± 0.02-1.09 ± 0.03. Among the ten samples, 3 samples were identified to have the presence of MP in the form of Low density polyethylene (LDPE), High density polyethylene (HDPE), and Cellulose acetate (CA) respectively. The detection limit ranged from 1 - 2000 μm. Hence, the results show that the procurement and discharge of MPs in the landfills is an overlong process. The results of this study provide an initial evidence and affirm that landfill can be a potential source of MPs. This study indicates that MPs are comparatively overlong outcome of human induced activities which can significantly cause changes in terrestrial ecosystems.

Identification and visualisation of microplastics/ nanoplastics by Raman imaging (ii): Smaller than the diffraction limit of laser?

We recently reported (Sobhani et al., 2020) that when a confocal Raman microscope imaged a nanoplastic with the diameter of 100 nm, the imaging lateral size was 300-400 nm, due to the diffraction limit of the laser spot. In this study, we examine the lateral intensity distribution of the Raman signal emitted by nanoplastics (diameters ranging ∼30-600 nm) within the excitation laser spot. We find that the Raman emission intensity, similar to the excitation power density distributed within a laser spot, also follows a lateral Gaussian distribution. To image and visualise individual nanoplastics, we (i) decrease the mapping pixel size, in a hope to generate an image with high-resolution and simultaneously to pick up items from the "blind point". We can then either (ii) offset the colour to intentionally image only the high-intensity portion of the Raman signal (emitted from the centre of the laser spot), to localise the exact position of the nanoplastic; or (iii) categorise the imaged nanoplastics to different groups via their Raman intensity, to simultaneously and separately visualise large nanoplastics/strong Raman signals, medium nanoplastics and small nanoplastics, in an effort to avoid the shielding and overlooking of weak signals. We (iv) also cross-check multi-images simultaneously mapped at two or three characteristic peaks via either a logic-OR or a logic-AND algorithm. Thus the imaging uncertainty can be significantly reduced from a statistical point of view.

Principles and Applications of Vibrational Spectroscopic Imaging in Plant Science: A Review

Detailed knowledge about plant chemical constituents and their distributions from organ level to sub-cellular level is of critical interest to basic and applied sciences. Spectral imaging techniques offer unparalleled advantages in that regard. The core advantage of these technologies is that they acquire spatially distributed semi-quantitative information of high specificity towards chemical constituents of plants. This forms invaluable asset in the studies on plant biochemical and structural features. In certain applications, non-invasive analysis is possible. The information harvested through spectral imaging can be used for exploration of plant biochemistry, physiology, metabolism, classification, and phenotyping among others, with significant gains for basic and applied research. This article aims to present a general perspective about vibrational spectral imaging/micro-spectroscopy in the context of plant research. Within the scope of this review are infrared (IR), near-infrared (NIR) and Raman imaging techniques. To better expose the potential and limitations of these techniques, fluorescence imaging is briefly overviewed as a method relatively less flexible but particularly powerful for the investigation of photosynthesis. Included is a brief introduction to the physical, instrumental, and data-analytical background essential for the applications of imaging techniques. The applications are discussed on the basis of recent literature.

Chiral Amplification in Nature: Studying Cell-Extracted Chiral Carotenoid Microcrystals via the Resonance Raman Optical Activity of Model Systems

Carotenoid microcrystals, extracted from cells of carrot roots and consisting of 95 % of achiral β-carotene, exhibit a very intense chiroptical (ECD and ROA) signal. The preferential chirality of crystalline aggregates that consist mostly of achiral building blocks is a newly observed phenomenon in nature, and may be related to asymmetric information transfer from the chiral seeds (small amount of α-carotene or lutein) present in carrot cells. To confirm this hypothesis, we synthesized several model aggregates from various achiral and chiral carotenoids. Because of the sergeant-and-soldier behavior, a small number of chiral sergeants (α-carotene or astaxanthin) force the achiral soldier molecules (β- or 11,11'-[D₂ ]-β-carotene) to jointly form supramolecular assemblies of induced chirality. The chiral amplification observed in these model systems confirmed that chiral microcrystals appearing in nature might consist predominantly of achiral building blocks and their supramolecular chirality might result from the co-crystallization of chiral and achiral analogues.

Unique chromoplast organisation and carotenoid gene expression in carotenoid-rich carrot callus

MAIN CONCLUSION

The new model orange callus line, similar to carrot root, was rich in carotenoids due to altered expression of some carotenogenesis-associated genes and possessed unique diversity of chromoplast ultrastructure. Callus induced from carrot root segments cultured in vitro is usually pale yellow (p-y) and poor in carotenoids. A unique, non-engineered callus line of dark orange (d-o) colour was developed in this work. The content of carotenoid pigments in d-o callus was at the same level as in an orange carrot storage root and nine-fold higher than in p-y callus. Carotenoids accumulated mainly in abundant crystalline chromoplasts that are also common in carrot root but not in p-y callus. Using transmission electron microscopy, other types of chromoplasts were also found in d-o callus, including membranous chromoplasts rarely identified in plants and not observed in carrot root until now. At the transcriptional level, most carotenogenesis-associated genes were upregulated in d-o callus in comparison to p-y callus, but their expression was downregulated or unchanged when compared to root tissue. Two pathway steps were critical and could explain the massive carotenoid accumulation in this tissue. The geranylgeranyl diphosphate synthase gene involved in the biosynthesis of carotenoid precursors was highly expressed, while the β-carotene hydroxylase gene involved in β-carotene conversion to downstream xanthophylls was highly repressed. Additionally, paralogues of these genes and phytoene synthase were differentially expressed, indicating their tissue-specific roles in carotenoid biosynthesis and metabolism. The established system may serve as a novel model for elucidating plastid biogenesis that coincides with carotenogenesis.