Molecular chemistry imaging to reveal structural features of various plant feed tissues

Synchrotron Fourier transform infrared (FTIR) microspectroscopy as a rapid, direct, and non-destructive analytical technique can explore molecular chemical features of the micro-structure of biological samples. However, the application of this synchrotron technology to feed science and feed chemistry is extremely rare. This article reviews that with synchrotron FTIR microspectroscopy, the molecular chemistry of various feed tissues could be imaged. These images revealed spatial intensity and distribution of chemical functional groups in various feeds tissues within cellular dimensions. Such information can be used for plant breeding program for selecting superior variety of plant for targeted feed purposes and for prediction of feed quality and nutritive value. The final purpose of this article shows that Synchrotron FTIR microspectroscopy can be used for biological structure study.     

The comparison of hair from gastric cancer patients and from healthy persons studied by infrared microspectroscopy and imaging using synchrotron radiation

Objective: The objective is to apply synchrotron-based FTIR microspectroscopy and imaging to human hair tissue and investigate the possibility of the method in gastric cancer research and diagnosis. Methods: Human hair from gastric cancer patients’ scalp and normal persons’ scalp were studied by synchrotron-based FTIR microspectroscopy and imaging. Results: The micro-spectra and imaging show the difference between the normal and malignant hair tissues. Obvious peak shift of symmetric phosphate band is observed in micro-spectra of medulla region for the hair tissue of gastric cancer patients. Chemical imaging shows the distributions of lipid and amide II/v_sPO₂^? have changed in the gastric cancer cases. Conclusions: The study indicates that the hair tissue's infrared microspectroscopy and imaging using synchrotron will be a potentially useful method for rapid early gastric cancer diagnosis.     

Use of infrared microspectroscopy to determine leaf biochemical composition of cassava in response to Bacillus subtilis CaSUT007

The objective of this study was to investigate the growth stimulating properties of Bacillus subtilis CaSUT007 applied to cassava plants using fourier transform infrared (FTIR) microspectroscopy to monitor the production of cellular components involved in plant growth and development. Cassava stakes treated with CaSUT007 or sterile distilled water were germinated in soil. After incubation for 2 months, CaSUT007 treated plants had higher growth rate and greater biomass than the control. FTIR analysis revealed that the leaves of cassava plants treated with CaSUT007 display FTIR spectra changes in the epidermis and mesophyll tissue. These changes associated with proteins, lipids, and pectins, which are related to changes in plant cell growth and development. FTIR microspectroscopy can be used as a new tool to examine the biochemical changes within the plant tissue. This technique allows us to reveal structural chemical makeup and features of different tissue types.     

Infrared microspectroscopy: Sampling heterogeneity in plant cell wall composition and architecture

The use of probes such as monoclonal and polyclonal antibodies to specific cell wall components, at both the light and electron microscope levels, has demonstrated the diversity in cell wall composition between species, between tissues, between different regions of the cell surface, and even within a single wall. Traditional methods of cell wall analysis have provided valuable information on wall composition and architecture, but, by having to rely on the use of bulk samples, have averaged out this intrinsic heterogeneity. Fourier Transform Infrared (FTIR) microspectroscopy addresses this problem by providing chemical information from an area as small as 10×10 μm of a single cell wall fragment or area of a tissue section that has been imaged with a microscope accessory.
We have used FTIR microspectroscopy as a powerful and extremely rapid assay for wall components and putative cross-links in muro. The spectra are sensitive to polymer conformation, and the use of polarisers in the microscope accessory allows the orientation of particular functional groups to be determined, with respect to the long axis of elongating cells. The spectra constitute species and tissue-specific 'fingerprints', and the use of classical discriminant analysis may provide the opportunity for correlating spectral features with chemical, architectural or rheological wall properties. Spectral mapping of an area of a specimen allows the morphological features resulting from cell growth and differentiation to be characterised chemically at the single cell level.     

An integrated spectroscopic and wet chemical approach to investigate grass litter decomposition chemistry

The chemical transformations that occur during litter decomposition are key processes for soil organic matter formation and terrestrial biogeochemistry; yet we still lack complete understanding of these chemical processes. Thus, we monitored the chemical composition of Andropogon gerardii (big bluestem grass) litter residue over a 36 month decomposition experiment in a prairie ecosystem using: traditional wet chemical fractionation based upon digestibility, solid state ¹³C nuclear magnetic resonance (NMR) spectroscopy and Fourier transform infrared (FTIR) spectroscopy. The goals of this study were to (1) determine the chemical changes occurring during A. gerardii litter decomposition, and (2) compare the information obtained from each method to assess agreement. Overall, we observed a 97 % mass loss of the original litter, through a two-stage decomposition process. In the first stage, within 12 months, non-structural, cellulose and hemicellulose fractions not encrusted in lignin were preferentially and rapidly lost, while the acid unhydrolyzable residue (AUR) and microbial components increased. During the second stage, 12–36 months, all wet chemical fraction masses decreased equivalently and slowly with time, and the AUR and the lignin-encrusted cellulose fractions decomposition rates were comparable to each other. Method comparisons revealed that wet chemical fractionation did not accurately follow the initial litter structures, particularly lignin, likely because of chemical transformations and accumulation of microbial biomass. FTIR and NMR were able to determine bulk structural characteristics, and aid in elucidating chemical transformations but lacked the ability to measure absolute quantities of structural groups. As a result, we warn from the sole use of wet chemical methods, and strongly encourage coupling them with spectroscopic methods. Our results overall support the traditional chemical model of selective preservation of lignin, but shows that this is limited to the early stages of decomposition, while lignin is not selectively preserved at subsequent stages. Our study also provides important evidence regarding the impact of chemically different litter structures on decomposition rates and pathways.     

Changes in pectin structure and localization during the growth of unadapted and NaCl-adapted tobacco cells

Tobacco cells adapted to grow in high concentrations of NaCl exhibit a drastically altered growth physiology that results in cells whose fully expanded volume is only one-fifth to one-eighth those of unadapted cells. Comparison between NaCl-adapted and unadapted tobacco cells provides an opportunity to evaluate current concepts of the structural and mechanical determinants of cell wall expansion. Both biochemical studies of pectic polymers and the ultrastructural localization of pectic epitopes at three specific phases of cell culture, maximal cell division, maximal elongation, and stationary phase are reported here. One-half of the galactosyluronic acid units in wall polymers of NaCl-adapted cells are esterified throughout the culture period, while wall polymers of unadapted cells show a rise in esterified polygalacturonic acid from 50 to 80% during elongation and then a decrease to 70% at stationary phase. Methyl esters account for only a proportion of the total esterified polygalacturonic acid at any stage in both unadapted and NaCl-adapted cell walls. Using monoclonal antibodies, we show differences in the localization of relatively methyl-esterified and unesterified pectic epitopes at different stages of growth and corroborate the chemical determinations. Fourier transform infrared (FTIR) microspectroscopy of representative walls of both NaCl-adapted and unadapted cells confirms, at the single cell wall level, that results obtained from chemical analysis of bulk samples are applicable to the entire cell population. FTIR microspectroscopy also reveals an increase in wall protein in the walls of adapted cells. Images obtained by the fast-freeze, deep-etch, rotary-shadowed replica technique show clearly different cell wall architectures in NaCl-adapted compared with unadapted cells; walls of elongating unadapted cells contain long, thin fibres that show a net orientation with respect to the long axis of the cell, whereas walls of adapted cells have thicker, flatter bundles of fibres with no clear net orientation. Polarized FTIR microspectroscopy indicates that, in unadapted tobacco cells during elongation, pectin molecules may be oriented within the wall in a similar manner to cellulose. Possible ways in which pectin structure and conformation may affect the behaviour of the cellulose-xyloglucan network are discussed.     

Aging of Dry Desiccation-Tolerant Pollen Does Not Affect Protein Secondary Structure

Protein secondary structure and membrane phase behavior in aging Typha latifolia pollen were studied by means of Fourier transform infrared microspectroscopy (FTIR). Membranes isolated from fresh pollen occurred mainly in the liquid crystalline phase at room temperature, whereas the membrane fluidity of aged pollen was drastically decreased. This decrease did not result in large-scale irreversible protein aggregation, as was concluded from in situ FTIR assessment of the amide-1 bands. Curve-fitting on the infrared absorbance spectra enabled estimation of the proportion of different classes of protein secondary structure. Membrane proteins had a relatively large amount of [alpha]-helical structure (48%; band at 1658 cm-1), and turn-like structures (at 1637 and 1680 cm-1) were also detected. The secondary protein structure of isolated cytoplasmic proteins resembled that of proteins in whole pollen and was conserved upon drying in the absence of sucrose. The isolated cytoplasmic proteins had a large amount of [alpha]-helical structure (43%), and also [beta]-sheet (at 1637 and 1692 cm-1) and turn structures were detected. Heat-denaturing experiments with intact hydrated pollen showed low (1627 cm-1) and high (1692 cm-1) wave number bands indicating irreversible protein aggregates. The results presented in this paper show that FTIR is an extremely suitable technique to study protein secondary structure in intact plant cells of different hydration levels and developmental stages.     

An information-theory model of cellular survival, mutation and transformation and the relevance of this model to chemical carcinogenesis

A model of cellular survival, mutation and transformation is presented in accordance with information theory. A cellular system is considered to be stable with respect to its environment when the vital information the cell expresses at least equals the information requirements of the environment. Environmental agents, such as mutagens, perturb the cell's expression of information such that an imbalance occurs between the cell's information requirement and the cell's ability to express vital information. This imbalance, which is interpreted as the intrinsic entropy of the cell, serves as a measure of biological cell death. If the cell compensates for the altered ability to express information by adapting to a less restricted set of information requirements, then one may view the cell as having undergone a "transformation" to a less restricted phenotype. This paper will elucidate the mathematical inter-relationships of cellular survival, mutation and transformation and will relate these mathematical concepts to chemical carcinogenesis.     

Grayscale representation of infrared microscopy images by extended multiplicative signal correction for registration with histological images

Fourier‐transform infrared (FTIR) microspectroscopy is rounding the corner to become a label‐free routine method for cancer diagnosis. In order to build infrared‐spectral based classifiers, infrared images need to be registered with Hematoxylin and Eosin (H&E) stained histological images. While FTIR images have a deep spectral domain with thousands of channels carrying chemical and scatter information, the H&E images have only three color channels for each pixel and carry mainly morphological information. Therefore, image representations of infrared images are needed that match the morphological information in H&E images. In this paper, we propose a novel approach for representation of FTIR images based on extended multiplicative signal correction highlighting morphological features that showed to correlate well with morphological information in H&E images. Based on the obtained representations, we developed a strategy for global‐to‐local image registration for FTIR images and H&E stained histological images of parallel tissue sections.     

Fixation protocols for subcellular imaging by synchrotron-based Fourier transform infrared microspectroscopy

Synchrotron-based Fourier transform infrared (SR-FTIR) microspectroscopy is a powerful bioanalytical technique for the simultaneous analysis of lipids, proteins, carbohydrates, and a variety of phosphorylated molecules within intact cells. SR-FTIR microspectroscopy can be used in the imaging mode to generate biospectroscopic maps of the distribution and intensity profiles of subcellular biomolecular domains at diffraction-limited spatial resolution. However, the acquisition of highly spatially resolved IR images of cells is not only a function of instrumental parameters (source brightness, sampling aperture size) but also the cell preparation method employed. Additionally, for the IR data to be biochemically relevant the cells must be preserved in a life-like state without introducing artefacts. In the present study we demonstrate, for the first time, the differences in biomolecular localizations observed in SR-FTIR images of cells fixed by formalin, formalin-critical point drying (CPD), and glutaraldehyde-osmium tetroxide-CPD, using the PC-3 prostate cancer cell line. We compare these SR-FTIR images of fixed cells to unfixed cells. The influence of chemical fixatives on the IR spectrum is discussed in addition to the biological significance of the observed localizations. Our experiments reveal that formalin fixation at low concentration preserves lipid, phosphate, and protein components without significantly influencing the IR spectrum of the cell.     

Second- and third-harmonic generation microscopies for the structural imaging of intact tissues

One principal advantage of multiphoton excitation microscopy is that it preserves its three-dimensional micrometer resolution when imaging inside light-scattering samples. For that reason two-photon-excited fluorescence microscopy has become an invaluable tool for cellular imaging in intact tissue, with applications in many fields of physiology. This success has driven increasing interest in other forms of nonlinear microscopy that can provide additional information on cells and tissues, such as second- (SHG) and third- (THG) harmonic generation microscopies. In recent years, significant progress has been made in understanding the contrast mechanisms of these recent methodologies, and high-resolution imaging based on intrinsic sources of signal has been demonstrated in cells and tissues. Harmonic generation exhibits structural rather than chemical specificity and can be obtained from a variety of non-fluorescent samples. SHG is observed specifically in dense, non-centrosymmetric arrangements of polarizable molecules, such as collagen fibrils, myofilaments, and polarized microtubule bundles. SHG imaging is therefore emerging as a novel approach for studying processes such as the physiopathological remodelling of the collagen matrix and myofibrillogenesis in intact tissue. THG does not require a non-centrosymmetric system ; however no signal can be obtained from a homogeneous medium. THG imaging therefore provides maps of sub-micrometer heterogeneities (interfaces, inclusions) in unstained samples, and can be used as a general purpose structural imaging tool. Recent studies showed that this technique can be used to image embryo development in small organisms and to characterize the accumulation of large lipid bodies in specialized cells. SHG and THG microscopy both rely on femtosecond laser technology and are easily combined with two-photon microscopy.     

Correlation of histology and linear and nonlinear microscopy of the living human cornea

The morphology and the function of cellular and non‐cellular structures in the living human cornea can be determined with modern correlative linear and nonlinear optical microscopic techniques and histology. Correlative microscopy is based on the use of different optical techniques to study the same specimen, ideally at the same location within the specimen, in order to increase the functional and/or morphological understanding of the specimen. A case study to assess the effect of overnight lid‐closure on in vivo human corneal morphology is presented to illustrate correlative linear microscopy and optical low‐coherence reflectometry. Nonlinear multiphoton excitation microscopy provides functional information on cellular metabolism based on the intrinsic fluorescence from the reduced pyridine nucleotides and the oxidized flavoproteins. Second‐harmonic generation microscopy, a scattering process that does not deposit net energy into the tissue, provides structural information on corneal collagen organization. Molecular third‐harmonic generation microscopy generates a signal in all materials and it an emerging technique. Coherent anti‐Stokes Raman scattering microscopy provides chemical imaging for biology and medicine. The comparison and limitations of these microscopic modalities, linear and nonlinear microscopy applied to the cornea, and a review of some key findings is analyzed. A correlative integration and correlation of linear and nonlinear microscopies to study corneal function and structure is proposed to validate the clinical interpretation of microscopic images of the cornea. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

FTIR-microspectroscopy of prion-infected nervous tissue

The family of transmissible spongiform encephalopathies (TSE), also termed prion diseases, is a group of fatal, neurodegenerative diseases characterized by the accumulation of a misfolded protein, the disease-associated prion protein PrP^Sc. This glycoprotein differs in secondary structure from its normal, cellular isoform PrP^C, which is physiologically expressed mostly by neurons. Scrapie is a prion disease first described in the 18th century in sheep and goats, and has been established as a model in rodents to study the pathogenesis and pathology of prion diseases. Assuming a multitude of molecular parameters change in the tissue in the course of the disease, FTIR microspectroscopy has been proposed as a valuable new method to study and identify prion-affected tissues due to its ability to detect a variety of changes in molecular structure and composition simultaneously. This paper reviews and discusses results from previous FTIR microspectroscopic studies on nervous tissue of scrapie-infected hamsters in the context of histological and molecular alterations known from conventional pathogenesis studies. In particular, data from studies reporting on disease-specific changes of protein structure characteristics, and also results of a recent study on hamster dorsal root ganglia (DRG) are discussed. These data include an illustration on how the application of a brilliant IR synchrotron light source enables the in situ investigation of localized changes in protein structure and composition in nervous cells or tissue due to PrP^Sc deposition, and a demonstration on how the IR spectral information can be correlated with results of complementary studies using immunohistochemistry and x-ray fluorescence techniques. Using IR microspectroscopy, some neurons exhibited a high accumulation of disease-associated prion protein evidenced by an increased amount of β-sheet at narrow regions in or around the infected nervous cells. However, not all neurons from terminally diseased hamsters showed PrP^Sc deposition. Generally, the average spectral differences between all control and diseased DRG spectra are small but consistent as demonstrated by independent experiments. Along with studies on the purified misfolded prion protein, these data suggest that synchrotron FTIR microspectroscopy is capable of detecting the misfolded prion protein in situ without the necessity of immunostaining or purification procedures.     

High-resolution confocal imaging and three-dimensional rendering

Intrinsic opacity and inhomeogeniety of most biological tissues have prevented the efficient light penetration and signal detection for high-resolution confocal imaging of thick tissues. Here, we summarize recent technical advances in high-resolution confocal imaging for visualization of cellular structures and gene expression within intact whole-mount thick tissues. First, we introduce features of the FocusClear technology that render biological tissue transparent and thus improve the light penetration and signal detection. Next, a universal fluorescence staining method that labels all nuclei and membranes is described. We then demonstrate the postrecording image processing techniques for 3D visualization. From these images, regions of interest in the whole-mount brain can be segmented and volume rendered. Together, these technical advances in confocal microscopy allow visualization of structures within whole-mount tissues up to 1mm thick at a resolution similar to that of the observation of single cells in culture. Practical uses and limitations of these techniques are discussed.     

FTIR microspectroscopy study of composition fluctuations in extruded amylopectin-gelatin blends

The spatial variation in the composition of nonexpanded biopolymer blends prepared by extrusion of mixtures of gelatin with either native or pregelatinized waxy maize starch was studied using a 30-microm aperture FTIR microspectroscopy technique. The ratio of the areas of the "saccharide" bands (953-1180 cm(-1)) and the amide I and II bands (1483-1750 cm(-1)) was used to monitor the relative distributions of the two components of the blend. Two calibration methods were used to obtain amylopectin concentration values from the ratios of the IR bands. The results suggested a high degree of heterogeneity in these blends, despite the thorough mixing expected by twin-screw extrusion processing. The concentration fluctuations were greater for the blends produced by extruding gelatin and native waxy maize starch mixtures. This was in agreement with the reduced degree of conversion of the starch granules when extruded in the presence of gelatin. The FTIR 2-dimensional maps obtained suggested that in the blends produced from either native or pregelatinized starch at all concentrations studied (25/75, 50/50, and 75/25 amylopectin/gelatin) the gelatin constituted the continuous phase. The effect of the spatial resolution on the FTIR microspectroscopy results was considered and the proposed interpretation was verified by the use of polarized light microscopy and FTIR microspectroscopy acquired at higher spatial resolution (10 microm).     

Non-collagenous ECM proteins in blood vessel morphogenesis and cancer

Background

The extracellular matrix (ECM) is constituted by diverse composite structures, which determine the specific to each organ, histological architecture and provides cells with biological information, mechanical support and a scaffold for adhesion and migration. The pleiotropic effects of the ECM stem from the dynamic changes in its molecular composition and the ability to remodel in order to effectively regulate biological outcomes. Besides collagens, fibronectin and laminin are two major fiber-forming constituents of various ECM structures.

Scope of review

This review will focus on the properties and the biological functions of non-collagenous extracellular matrix especially on laminin and fibronectin that are currently emerging as important regulators of blood vessel formation and function in health and disease.

Major conclusions

The ECM is a fundamental component of the microenvironment of blood vessels, with activities extending beyond providing a vascular scaffold; extremely versatile it directly or indirectly modulates all essential cellular functions crucial for angiogenesis, including cell adhesion, migration, proliferation, differentiation and lumen formation. Specifically, fibronectin and laminins play decisive roles in blood vessel morphogenesis both during embryonic development and in pathological conditions, such as cancer.

General significance

Emerging evidence demonstrates the importance of ECM function during embryonic development, organ formation and tissue homeostasis. A wealth of data also illustrates the crucial role of the ECM in several human pathophysiological processes, including fibrosis, skeletal diseases, vascular pathologies and cancer. Notably, several ECM components have been identified as potential therapeutic targets for various diseases, including cancer. This article is part of a Special Issue entitled Matrix-mediated cell behaviour and properties.     

The prefabricated scapula flap consists of syngeneic bone, connective tissue, and a self-assembled epithelial coating.

The reconstruction of maxillary defects is a challenge in plastic surgery. The so-called prefabricated scapula flap consists of syngeneic bone covered with syngeneic dermis and is used to reconstruct maxillary defects. After placing these flaps into the oral cavity, they are reepithelialized within a short time period, raising the question of the cellular origin of the "neomucosa." We therefore obtained sequential biopsy samples of the prefabricated flap and of the flap after being placed into the oral cavity and analyzed the keratin expression profile of epithelial cells. We expected that after placing the prefabricated flap into the oral cavity, keratinocytes from adnexal structures of the dermal component of the graft would migrate onto the surface and reepithelialize the flap. Unexpectedly, reepithelialization occurred earlier. The flap had acquired a mucosa-like epithelium at the interface between the Gore-Tex coating and the dermis while still being positioned within the scapular region. The keratin expression profile of this epithelium was very similar to that of mucosal epithelium. Thus, the prefabricated scapula flap not only consisted of bone covered with connective tissue, but was also covered with epithelial cells derived from adnexal structures of the dermal graft. This seems to be the reason for the rapid restoration of an intact mucosa and the excellent outcome achieved with this surgical technique.     

New aspects of the alpha-helix to beta-sheet transition in stretched hard alpha-keratin fibers

The putative transformation of alpha-helices into beta-sheets has been studied for more than 50 years in the case of hard alpha-keratin. In a previous study of stretched keratin fibers, we specified the conditions for beta-sheet appearance within horsehair: the formation of beta-sheets requires at least 30% relative humidity. However, this phenomenon was observed in the whole tissue. Then there was no clear chemical identification of the beta-sheets (keratin or matrix proteins) and the exact location of the beta-sheets across the fiber could not be specified. In this study, using wide-angle x-ray scattering and high spatial resolution infrared microspectroscopy, we could determine and characterize the structural elements across hair sections stretched in water, which provides new information about the aforementioned transition. Our results show that the process can be split into three steps: 1), unraveling of the alpha-helical coiled-coil domains, which starts at roughly 5% macroscopic strain; 2), further transformation of the unraveled coiled-coils into beta-sheet structures, which occurs above roughly 20% macroscopic strain; and 3), spatial expanding of the beta-structured zones from the sample center to its periphery.     

Coupled analysis of in vitro and histology tissue samples to quantify structure-function relationship

The structure/function relationship is fundamental to our understanding of biological systems at all levels, and drives most, if not all, techniques for detecting, diagnosing, and treating disease. However, at the tissue level of biological complexity we encounter a gap in the structure/function relationship: having accumulated an extraordinary amount of detailed information about biological tissues at the cellular and subcellular level, we cannot assemble it in a way that explains the correspondingly complex biological functions these structures perform. To help close this information gap we define here several quantitative temperospatial features that link tissue structure to its corresponding biological function. Both histological images of human tissue samples and fluorescence images of three-dimensional cultures of human cells are used to compare the accuracy of in vitro culture models with their corresponding human tissues. To the best of our knowledge, there is no prior work on a quantitative comparison of histology and in vitro samples. Features are calculated from graph theoretical representations of tissue structures and the data are analyzed in the form of matrices and higher-order tensors using matrix and tensor factorization methods, with a goal of differentiating between cancerous and healthy states of brain, breast, and bone tissues. We also show that our techniques can differentiate between the structural organization of native tissues and their corresponding in vitro engineered cell culture models.