The substrate matters in the Raman spectroscopy analysis of cells

Analysis of lipids by Raman spectroscopy and mass spectrometry provides a detection tool and mechanistic insight into imatinib resistance in CML-BC

Resistance to tyrosine kinase inhibitors (TKIs) is a major challenge in the treatment of chronic myeloid leukemia (CML). Established tests based on the known mechanisms of resistance in the initial chronic phase (CP) confirm resistance, reveal the underlying reason and thereby direct treatment modifications. In the terminal phase of blast crisis (BC), however, additional partially identified mechanisms of resistance exist which necessitates developing modalities to detect resistance regardless of the underlying mechanism and concurrent exploration of the resistance mechanism to assist in identification of appropriate drug targets. In this study both the clinical objectives were achieved by analysing lipids in BC cells, sensitive and resistant to TKIs, using the complementary strengths of distinct analytical technologies. Raman spectroscopy, through the spectral signatures with lipids as a significant differentiating component could segregate resistant from sensitive cells in the Principal Component Analysis (PCA) and Principal Component based Linear Discriminant Analysis (PC-LDA). This provided a tool to rapidly detect resistance in CML-BC despite unclear mechanism of TKI resistance. The depth of coverage achievable by mass spectrometry allowed the generation of quantitative differential profile of individual lipids in resistant cells. The alterations were in diverse classes of lipids which are involved in cell signalling and inhibition studies could link these alterations to modulation of phospholipase A2 (PLA2) levels mediated by p38 mitogen activated protein kinase (p38MAPK), which is causally associated with TKI resistance in CML-BC. Together, lipid analysis using the two platforms, contributed to the detection and mechanistic understanding of imatinib resistance in CML-BC.

SERS of nitro group compounds for sensing of explosives

Detecting small concentrations of nitro-compounds via surface-enhanced Raman spectroscopy (SERS) is reported. In particular, explosive analogues, such as 4-nitrophenol, 1-nitronaphthalene, and 5-nitroisoquinoline, and an explosive material (picric acid) are investigated and prepared by measurements using two different methods. One method involved mixing the analyte with plasmonic silver nanoparticles (Ag NPs) in a solution, followed by subsequent drop-casting of the mixture onto a silicon substrate. In the second method, the analyte solution was drop-casted onto SERS substrates formed by annealing of thin Ag films deposited over self-assembled layers of SiO2 spheres. Both approaches allowed for the SERS detection of analyte concentrations down to 10-4-10-7 M. Furthermore, the possible reasons for the different enhancements of the above analytes as well as their differences in the liquid (drop) and dried states are discussed.

Machine Learning-Assisted SERS Reveals the Biochemical Signature of Enhanced Protein Secretion from Surface-Modified Magnetic Nanoparticles

This study introduces a novel investigation of the interaction between Komagataella phaffii cells and iron oxide-based magnetic nanoparticles (Fe3O4 MNPs) via protein secretion and machine learning (ML)-assisted surface-enhanced Raman scattering (SERS). For the first time, we produced Fe3O4, Fe3O4@PEG, Fe3O4@PEI10kDa, and Fe3O4@PEI25kDa MNPs by a one-pot coprecipitation reaction. The addition of polymers to the reaction conditions significantly affected the shape, surface charge, size, and size distribution of the MNPs. The surface modification of MNPs is effectively accomplished using polyethylenimine (PEI), and the ζ-potential values of the MNPs exceed +25 mV under the NH4OH control. The homogeneity of MNPs synthesized with NH4OH is more pronounced according to transmission electron microscopy (TEM) pictures. All MNPs exhibited excellent immobilization efficiency (>92%) when we used 250 ppm Fe-containing MNP solutions. Smaller MNPs uniformly encapsulated the surface of K. phaffii cells, whereas larger MNPs exhibited irregular accumulation. K. phaffii cells exhibited excellent viability in all MNP solutions at up to 1000 ppm of Fe concentrations. Finally, the highest recombinant azurin protein secretion rate was obtained in Fe3O4@PEI10kDa MNP-immobilized cells (about 1.3 times). The ML-assisted SERS analysis revealed that MNP interactions with K. phaffii cells were mediated by proteins such as mannoproteins and membrane transporter proteins as well as N-acetylglucosamine (i.e., chitin). These findings revealed the effect of the size and surface properties of MNPs on the immobilization of K. phaffii cells and the enormous potential of magnetic immobilization for protein secretion.

Harnessing Raman spectroscopy for cell therapy bioprocessing

Cell therapy manufacturing requires precise monitoring of critical parameters to ensure product quality, consistency and to facilitate the implementation of cost-effective processes. While conventional analytical methods offer limited real-time insights, integration of process analytical technology tools such as Raman spectroscopy in bioprocessing has the potential to drive efficiency and reliability during the manufacture of cell-based therapies while meeting stringent regulatory requirements. The non-destructive nature of Raman spectroscopy, combined with its ability to be integrated on-line with scalable platforms, allows for continuous data acquisition, enabling real-time correlations between process parameters and critical quality attributes. Herein, we review the role of Raman spectroscopy in cell therapy bioprocessing and discuss how simultaneous measurement of distinct parameters and attributes, such as cell density, viability, metabolites and cell identity biomarkers can streamline on-line monitoring and facilitate adaptive process control. This, in turn, enhances productivity and mitigates process-related risks. We focus on recent advances integrating Raman spectroscopy across various manufacturing stages, from optimizing culture media feeds to monitoring bioprocess dynamics, covering downstream applications such as detection of co-isolated contaminating cells, cryopreservation, and quality control of the drug product. Finally, we discuss the potential of Raman spectroscopy to revolutionize current practices and accelerate the development of advanced therapy medicinal products.

Rapid Identification of Drug Mechanisms with Deep Learning-Based Multichannel Surface-Enhanced Raman Spectroscopy

Rapid identification of drug mechanisms is vital to the development and effective use of chemotherapeutics. Herein, we develop a multichannel surface-enhanced Raman scattering (SERS) sensor array and apply deep learning approaches to realize the rapid identification of the mechanisms of various chemotherapeutic drugs. By implementing a series of self-assembled monolayers (SAMs) with varied molecular characteristics to promote heterogeneous physicochemical interactions at the interfaces, the sensor can generate diversified SERS signatures for directly high-dimensionality fingerprinting drug-induced molecular changes in cells. We further train the convolutional neural network model on the multidimensional SAM-modulated SERS data set and achieve a discriminatory accuracy toward 99%. We expect that such a platform will contribute to expanding the toolbox for drug screening and characterization and facilitate the drug development process.

Unveiling the efficacy of a bulk Raman spectra-based model in predicting single cell Raman spectra of microorganisms

In a previous publication, we trained predictive models based on Raman bulk spectra of microorganisms placed on a silicon dioxide protected silver mirror slide to make predictions for new Raman spectra, unknown to the models, of microorganisms placed on a different substrate, namely stainless steel. Now we have combined large sections of this data and trained a convolutional neural network (CNN) to make predictions for single cell Raman spectra. We show that a database based on microbial bulk material is conditionally suited to make predictions for the same species in terms of single cells. Data of 13 different microorganisms (bacteria and yeasts) were used. Two of the 13 species could be identified 90% correctly and five other species 71%-88%. The six remaining species were correctly predicted by only 0%-49%. Especially stronger fluorescence in bulk material compared to single cells but also photodegradation of carotenoids are some effects that can complicate predictions for single cells based on bulk data. The results could be helpful in assessing universal Raman tools or databases.

Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms

Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.

Visualization-enhanced under-oil open microfluidic system for in situ characterization of multi-phase chemical reactions

Under-oil open microfluidic system, utilizing liquid-liquid boundaries for confinements, offers inherent advantages including clogging-free flow channels, flexible access to samples, and adjustable gas permeation, making it well-suited for studying multi-phase chemical reactions that are challenging for closed microfluidics. However, reports on the novel system have primarily focused on device fabrication and functionality demonstrations within biology, leaving their application in broader chemical analysis underexplored. Here, we present a visualization-enhanced under-oil open microfluidic system for in situ characterization of multi-phase chemical reactions with Raman spectroscopy. The enhanced system utilizes a semi-transparent silicon (Si) nanolayer over the substrate to enhance visualization in both inverted and upright microscope setups while reducing Raman noise from the substrate. We validated the system's chemical stability and capability to monitor gas evolution and gas-liquid reactions in situ. The enhanced under-oil open microfluidic system, integrating Raman spectroscopy, offers a robust open-microfluidic platform for label-free molecular sensing and real-time chemical/biochemical process monitoring in multi-phase systems.

Self-Organized SERS Substrates with Efficient Analyte Enrichment in the Hot Spots

One of the requirements of an efficient surface-enhanced Raman spectroscopy (SERS) substrate is a developed surface morphology with a high density of "hot spots", nm-scale spacings between plasmonic nanoparticles. Of particular interest are plasmonic architectures that could enable self-localization (enrichment) of the analyte in the hot spots. We report a straightforward method of fabrication of efficient SERS substrates that comply with these requirements. The basis of the substrate is a large-area film of tightly packed SiO2 spheres formed by their quick self-assembling upon drop casting from the solution. Thermally evaporated thin Ag layer is converted by quick thermal annealing into nanoparticles (NPs) self-assembled in the trenches between the silica spheres, i.e., in the places where the analyte molecules get localized upon deposition from solution and drying. Therefore, the obtained substrate morphology enables an efficient enrichment of the analyte in the hot spots formed by the densely arranged plasmonic NPs. The high efficiency of the developed SERS substrates is demonstrated by the detection of Rhodamine 6G down to 10-13 mol/L with an enhancement factor of ∼108, as well as the detection of low concentrations of various nonresonant analytes, both small dye molecules and large biomolecules. The developed approach to SERS substrates is very straightforward for implementation and can be further extended to using gold or other plasmonic NPs.

SERS-substrates based on ZnO nanoflowers prepared by green synthesis

ZnO nanoparticles (NPs) with a flower-like morphology, synthesized by an affordable colloidal route using an aqueous fungi extract of Ganoderma lucidum as a reducing agent and stabilizer, are investigated as SERS-substrate. Each "flower" has large effective surface that is preserved at packing particles into a dense film and thus exhibits an advantageous property for SERS and similar sensing applications. The mycoextract used in our low-cost and green synthesis as surface stabilizer allows subsequent deposition of metal NPs or layers. One type of SERS substrates studied here was ZnO NPs decorated in situ in the solution by Ag NPs, another type was prepared by thermally evaporating Ag layer on the ZnO NP film on a substrate. A huge difference in the enhancement of the same analyte in the solution and in the dried form is found and discussed. Detection down to 10-7 M of standard dye analytes such as rhodamine 6G and methylene blue was achieved without additional optimization of the SERS substrates. The observed SERS-activity demonstrate the potential of both the free-standing flower-like ZnO NPs and thereof made dense films also for other applications where large surface area accessible for the external agent is crucial, such as catalysis or sensing.

Substrate Signal Inhibition in Raman Analysis of Microplastic Particles

In Raman analysis, the substrate material serves very often for signal enhancement, especially when metallic surfaces are involved; however, in other cases, the substrate has an opposite effect as it is the source of a parasitic signal preventing the observation of the sample material of interest. This is particularly true with the advent of microfluidic devices involving either silicon or polymer surfaces. On the other hand, in a vast majority of Raman experiments, the analysis is made on a horizontal support holding the sample of interest. In our paper, we report that a simple tilting of the supporting substrate, in this case, silicon, can drastically decrease and eventually inhibit the Raman signal of the substrate material, leading to an easier observation of the target analyte of the sample, in this case, microplastic particles. This effect is very pronounced especially when looking for tiny particles. Explanation of this trend is provided thanks to a supporting experiment and further numerical simulations that suggest that the lensing effect of the particles plays an important role. These findings may be useful for Raman analysis of other microscale particles having curved shapes, including biological cells.

Enhanced characterization of breast cancer phenotypes using Raman micro-spectroscopy on stainless steel substrate

Biochemical insights into varying breast cancer (BC) phenotypes can provide a fundamental understanding of BC pathogenesis, while identifying novel therapeutic targets. Raman spectroscopy (RS) can gauge these biochemical differences with high specificity. For routine RS, cells are traditionally seeded onto calcium fluoride (CaF₂) substrates that are costly and fragile, limiting its widespread adoption. Stainless steel has been interrogated previously as a less expensive alternative to CaF₂ substrates, while reporting increased Raman signal intensity than the latter. We sought to further investigate and compare the Raman signal quality measured from stainless steel versus CaF₂ substrates by characterizing different BC phenotypes with altered human epidermal growth factor receptor 2 (HER2) expression. Raman spectra were obtained on stainless steel and CaF₂ substrates for HER2 negative cells - MDA-MB-231, MDA-MB-468 and HER2 overexpressing cells - AU565, SKBr3. Upon analyzing signal-to-noise ratios (SNR), stainless steel provided a stronger Raman signal, improving SNR by 119% at 1450 cm^-1 and 122% at 2925 cm^-1 on average compared to the CaF₂ substrate. Utilizing only 22% of laser power on sample relative to the CaF₂ substrate, stainless steel still yielded improved spectral characterization over CaF₂, achieving 96.0% versus 89.8% accuracy in BC phenotype discrimination and equivalent 100.0% accuracy in HER2 status classification. Spectral analysis further highlighted increased lipogenesis and altered metabolism in HER2 overexpressing cells, which was subsequently visualized with coherent anti-Stokes Raman scattering microscopy. Our findings demonstrate that stainless steel substrates deliver improved Raman signal and enhanced spectral characterization, underscoring its potential as a cost-effective alternative to CaF₂ for non-invasively monitoring cellular biochemical dynamics in translational cancer research.

Comparative Study of Sample Carriers for the Identification of Volatile Compounds in Biological Fluids Using Raman Spectroscopy

Vibrational spectroscopic techniques and especially Raman spectroscopy are gaining ground in substituting the officially established chromatographic methods in the identification of ethanol and other volatile substances in body fluids, such as blood, urine, saliva, semen, and vaginal fluids. Although a couple of different carriers and substrates have been employed for the biochemical analysis of these samples, most of them are suffering from important weaknesses as far as the analysis of volatile compounds is concerned. For this reason, in this study three carriers are proposed, and the respective sample preparation methods are described for the determination of ethanol in human urine samples. More specifically, a droplet of the sample on a highly reflective carrier of gold layer, a commercially available cuvette with a mirror to enhance backscattered radiation sealed with a lid, and a home designed microscope slide with a cavity coated with gold layer and covered with transparent cling film have been evaluated. Among the three proposed carriers, the last one achieved a quick, simple, and inexpensive identification of ethanol, which was used as a case study for the volatile compound, in the biological samples. The limit of detection (LoD) was found to be 1.00 μL/mL, while at the same time evaporation of ethanol was prevented.

Raman Microscopic Identification of Microorganisms on Metal Surfaces via Support Vector Machines

An easy, inexpensive, and rapid method to identify microorganisms is in great demand in various areas such as medical diagnostics or in the food industry. In our study, we show the development of several predictive models based on Raman spectroscopy combined with support vector machines (SVM) for 21 species of microorganisms. The microorganisms, grown under standardized conditions, were placed on a silver mirror slide to record the data for model development. Additional data was obtained from microorganisms on a polished stainless-steel slide in order to validate the models in general and to assess possible negative influences of the material change on the predictions. The theoretical prediction accuracies for the most accurate models, based on a five-fold cross-validation, are 98.4%. For practical validation, new spectra (from stainless-steel surfaces) have been used, which were not included in the calibration data set. The overall prediction accuracy in practice was about 80% and the inaccurate predictions were only due to a few species. The development of a database provides the basis for further investigations such as the application and extension to single-cell analytics and for the characterization of biofilms.

Microplastics and nanoplastics science: collecting and characterizing airborne microplastics in fine particulate matter

Microplastic (MP) pollution in the environment is increasing, leading to growing concerns about human exposures and the subsequent impact on health. Although marine MP research has received significant attention in recent years, only a few studies have attempted characterization of MP in air and examined the MP uptake and influence via inhalation on human health. Moreover, the methods used for MP characterization in the marine environment require further optimization to be applicable to MP in the air. This paper details method for collecting and characterizing MP < 2.5 μm in air samples for the purposes of toxicological assessment. The first phase of the study evaluated (a) the suitability of various filter types to collect respirable airborne MP <2.5 μm, and; (b) the ability of Raman and enhanced darkfield-hyperspectral spectroscopy methods to identify MP reference standards collected from spiked filters and in cells after exposure to reference MP. In the second phase, these methods were employed to characterize MP <2.5 μm in personal, indoor and outdoor filter air samples and in cells following exposure to filter extracted material. The results showed the presence of a variety of MP in the respirable size fraction (0.1-1 µm aerodynamic diameter). Silver membrane filters were found not suitable for collecting and analyzing MP <2.5 μm. While it was easy to detect reference MP in cells post-exposure, the identity of only two types of air-borne MP was confirmed in cells. The study highlighted possible sources of artifacts and inconsistencies in analyzing airborne MP.

A review of surface-enhanced Raman spectroscopy in pathological processes

With the continuous growth of the human population and new challenges in the quality of life, it is more important than ever to diagnose diseases and pathologies with high accuracy, sensitivity and in different scenarios from medical implants to the operation room. Although conventional methods of diagnosis revolutionized healthcare, alternative analytical methods are making their way out of academic labs into clinics. In this regard, surface-enhanced Raman spectroscopy (SERS) developed immensely with its capability to achieve single-molecule sensitivity and high-specificity in the last two decades, and now it is well on its way to join the arsenal of physicians. This review discusses how SERS is becoming an essential tool for the clinical investigation of pathologies including inflammation, infections, necrosis/apoptosis, hypoxia, and tumors. We critically discuss the strategies reported so far in nanoparticle assembly, functionalization, non-metallic substrates, colloidal solutions and how these techniques improve SERS characteristics during pathology diagnoses like sensitivity, selectivity, and detection limit. Moreover, it is crucial to introduce the most recent developments and future perspectives of SERS as a biomedical analytical method. We finally discuss the challenges that remain as bottlenecks for a routine SERS implementation in the medical room from in vitro to in vivo applications. The review showcases the adaptability and versatility of SERS to resolve pathological processes by covering various experimental and analytical methods and the specific spectral features and analysis results achieved by these methods.

Antibacterial and Antifungal Properties of Silver Nanoparticles-Effect of a Surface-Stabilizing Agent

The biocidal properties of silver nanoparticles (AgNPs) prepared with the use of biologically active compounds seem to be especially significant for biological and medical application. Therefore, the aim of this research was to determine and compare the antibacterial and fungicidal properties of fifteen types of AgNPs. The main hypothesis was that the biological activity of AgNPs characterized by comparable size distributions, shapes, and ion release profiles is dependent on the properties of stabilizing agent molecules adsorbed on their surfaces. Escherichia coli and Staphylococcus aureus were selected as models of two types of bacterial cells. Candida albicans was selected for the research as a representative type of eukaryotic microorganism. The conducted studies reveal that larger AgNPs can be more biocidal than smaller ones. It was found that positively charged arginine-stabilized AgNPs (ARGSBAgNPs) were the most biocidal among all studied nanoparticles. The strongest fungicidal properties were detected for negatively charged EGCGAgNPs obtained using (-)-epigallocatechin gallate (EGCG). It was concluded that, by applying a specific stabilizing agent, one can tune the selectivity of AgNP toxicity towards desired pathogens. It was established that E. coli was more sensitive to AgNP exposure than S. aureus regardless of AgNP size and surface properties.

Raman Spectroscopy-Based 3D Analysis of Odontogenic Differentiation of Human Dental Pulp Stem Cell Spheroids

Numerous efforts have been made to establish three-dimensional (3D) cell cultures that mimic the structure, cell composition, and functions of actual tissues and organs in vitro; however, owing to its intrinsic complexity, precise characterization of 3D differentiation remains challenging and often results in high variations in the resulting differentiated spheroids. This study reports a 3D Raman mapping-based analytical method that helps us to identify the crucial factors responsible for inducing variability in differentiated stem cell spheroids. Human dental pulp stem cell spheroids were generated at various cell densities using the hanging drop (HD) and molded parafilm-based (MP) methods and were then further subjected to odontogenic differentiation. Thereafter, the 3D cellular differentiation in these spheroids was analyzed based on three different Raman peaks, namely, 960, 1156/1528, and 2935 cm^-1, which correspond to hydroxyapatite (HA, odontogenic differentiation marker), β-carotene (precursor of HA), and proteins/cellular components (cell reference). By correlating such cell differentiation-related peaks and water/medium peaks (3400 cm^-1), we discovered that the diffusion of the medium containing various nutrients and differentiation factors was crucial in determining the variations in 3D differentiation of stem cell spheroids. Odontogenic differentiation was majorly induced at the outer shell of HD spheroids (up to ∼20 μm), whereas odontogenic differentiation was markedly induced in MP spheroids (up to 40-50 μm). Considering the challenges associated with high variations in spheroid and organoid differentiation, we conclude that the proposed Raman-based 3D analysis plays a pivotal role in stem cell-based regenerative therapy and drug screening.

Optimization of High-Density Fe-Au Nano-Arrays for Surface-Enhanced Raman Spectroscopy of Biological Samples

The method of realizing nanostructures using porous alumina templates has attracted interest due to the precise geometry and cheap cost of nanofabrication. In this work, nanoporous alumina membranes were utilized to realize a forest of nanowires, providing a bottom-up nanofabrication method suitable for surface-enhanced Raman spectroscopy (SERS). Gold and iron were electroplated through the straight channels of the membrane. The resulting nanowires are, indeed, made of an active element for plasmonic resonance and SERS as the hexagonal distribution of the nanowires and the extreme high density of the nanowires allows to excite the plasmon and detect the Raman signal. The method to reduce the distance between pores and, consequently, the distance of the nanowires after electrodeposition is optimized here. Indeed, it has been predicted that the light intensity enhancement factor is up to 10¹² when the gap is small than 10 nm. Measurements of Raman signal of thiol groups drying on the gold nanowires show that the performance of the device is improved. As the thiol group can be linked to proteins, the device has the potential of a biosensor for the detection of a few biomolecules. To assess the performance of the device and demonstrate its ability to analyze biological solutions, we used it as SERS substrates to examine solutions of IgG in low abundance ranges. The results of the test indicate that the sensor can convincingly detect biomolecules in physiologically relevant ranges.

The current state of the art of plasmonic nanofibrous mats as SERS substrates: design, fabrication and sensor applications

Surface-enhanced Raman scattering (SERS) is a widely used analytical tool that allows molecular fingerprint-based ultra-sensitive detection through an enhanced electromagnetic field generated by plasmonic metal nanoparticles (MNPs) by virtue of their localized surface plasmon resonance (LSPR). Although significant progress has been made in the design and fabrication of a variety of SERS substrates, MNP-decorated electrospun nanofibrous (NF) mats have attracted much attention due to their unique nanoscale structural and functional properties. This review focuses on the current state of the art in the fabrication of plasmonic NF mats with the main focus on the pre-mix, in situ, and ex situ approaches. The characteristic functional advantages and limitations of these strategies are also highlighted, which might be helpful for the research community when adopting a suitable approach. The potential of these plasmonic NF mats as a SERS-active optical sensor substrate, and their performance parameters such as the limit of detection, analytical range, and enhancement factor, and real-world applications are also discussed. The summary and futuristic discussion in this review might be of significant value in developing plasmonic NF mat-based SERS-active point-of-care diagnostic chips for a wide range of applications.

Features of the crystallization of multicomponent solutions: a dipeptide, its salt and potassium carbonate

Various stages of crystallization of the dipeptide potassium salt on graphite and gold. Possible molecular structures of the dipeptide (a) and its potassium salt (b).

Development of an inexpensive Raman-compatible substrate for the construction of a microarray screening platform

Biomaterial microarrays are being developed to facilitate identifying the extrinsic cues that elicit stem cell fate decisions to self-renew, differentiate and remain quiescent. Raman microspectroscopy, often combined with multivariate analysis techniques such as partial least square-discriminant analysis (PLS-DA), could enable the non-invasive identification of stem cell fate decisions made in response to extrinsic cues presented at specific locations on these microarrays. Because existing biomaterial microarrays are not compatible with Raman microspectroscopy, here, we develop an inexpensive substrate that is compatible with both single-cell Raman spectroscopy and the chemistries that are often used for biomaterial microarray fabrication. Standard deposition techniques were used to fabricate a custom Raman-compatible substrate that supports microarray construction. We validated that spectra from living cells on functionalized polyacrylamide (PA) gels attached to the custom Raman-compatible substrate are comparable to spectra acquired from a more expensive commercially available substrate. We also showed that the spectra acquired from individual living cells on functionalized PA gels attached to our custom substrates were of sufficient quality to enable accurate identification of cell phenotypes using PLS-DA models of the cell spectra. We demonstrated this by using cells from laboratory lines (CHO and transfected CHO cells) as well as adult stem cells that were freshly isolated from mice (long-term and short-term hematopoietic stem cells). The custom Raman-compatible substrate reported herein may be used as an inexpensive substrate for constructing biomaterial microarrays that enable the use of Raman microspectroscopy to non-invasively identify the fate decisions of stem cells in response to extrinsic cues.

Shell-isolated nanoparticle-enhanced Raman spectroscopy for characterization of living yeast cells

Studying the biochemistry of yeast cells has enabled scientists to understand many essential cellular processes in human cells. Further development of biotechnological and medical progress requires revealing surface chemistry in living cells by using a non-destructive and molecular structure sensitive technique. In this study shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) was applied for probing the molecular structure of Metschnikowia pulcherrima yeast cells. Important function of studied cells is the ability to eliminate iron from growth media by precipitating the insoluble pigment pulcherrimin. Comparative SERS and SHINERS analysis of the yeast cells in combination with bare Au and shell-isolated Au@SiO₂ nanoparticles were performed. It was observed that additional bands, such as adenine ring-related vibrational modes appear due to interaction with bare Au nanoparticles; the registered spectra do not coincide with the spectra where Au@SiO₂ nanoparticles were used. SHINERS spectra of M. pulcherrima were significantly enhanced comparing to the Raman spectra. Based on first-principles calculations and 830-nm excited Raman analysis of pulcherrimin, the SHINERS signatures of iron pigment in yeast cells were revealed. Being protected from direct interaction of metal with adsorbate, Au@SiO₂ nanoparticles yield reproducible and reliable vibrational signatures of yeast cell wall constituents.

Spectroscopic studies on the temperature-dependent molecular arrangements in hybrid chitosan/1,3-β-D-glucan polymeric matrices

Chitosan/1,3-β-D-glucan matrices have been recently used in various biomedical applications. Within this study, the structural changes in hybrid polysaccharide chitosan/1,3-β-D-glucan matrices cross-linked at 70 °C and 80 °C were detected with Attenuated Total Reflection Fourier Transform Infrared spectroscopy (ATR FT-IR) and Raman spectroscopy enabled thorough insights into molecular structure of studied biomaterials, whereas X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) provided their surface characteristics with confirmation of their effective and non-destructive properties. There are temperature-dependent differences in the chemical interactions between 1,3-β-D-glucan units and N-glucosamine in chitosan, resulting in surface polarity changes. The second order derivatives and deconvolution revealed the alterations in the secondary structure of studied matrices, along with different sized grain-like structures revealed by AFM. Since surface physicochemical properties of biomaterials have great impact on cell behavior, abovementioned techniques may allow to optimize and modify the preparation of polymeric matrices with desired features.

Surface enhanced Raman scattering artificial nose for high dimensionality fingerprinting

Label-free surface-enhanced Raman spectroscopy (SERS) can interrogate systems by directly fingerprinting their components' unique physicochemical properties. In complex biological systems however, this can yield highly overlapping spectra that hinder sample identification. Here, we present an artificial-nose inspired SERS fingerprinting approach where spectral data is obtained as a function of sensor surface chemical functionality. Supported by molecular dynamics modeling, we show that mildly selective self-assembled monolayers can influence the strength and configuration in which analytes interact with plasmonic surfaces, diversifying the resulting SERS fingerprints. Since each sensor generates a modulated signature, the implicit value of increasing the dimensionality of datasets is shown using cell lysates for all possible combinations of up to 9 fingerprints. Reliable improvements in mean discriminatory accuracy towards 100% are achieved with each additional surface functionality. This arrayed label-free platform illustrates the wide-ranging potential of high-dimensionality artificial-nose based sensing systems for more reliable assessment of complex biological matrices.

Aberrant Protein Phosphorylation in Cancer by Using Raman Biomarkers

(1) Background: Novel methods are required for analysing post-translational modifications of protein phosphorylation by visualizing biochemical landscapes of proteins in human normal and cancerous tissues and cells. (2) Methods: A label-free Raman method is presented for detecting spectral changes that arise in proteins due to phosphorylation in the tissue of human breasts, small intestines, and brain tumours, as well as in the normal human astrocytes and primary glioblastoma U-87 MG cell lines. Raman spectroscopy and Raman imaging are effective tools for monitoring and analysing the vibrations of functional groups involved in aberrant phosphorylation in cancer without any phosphorecognition of tag molecules. (3) Results: Our results based on 35 fresh human cancer and normal tissues prove that the aberrant tyrosine phosphorylation monitored by the unique spectral signatures of Raman vibrations is a universal characteristic in the metabolic regulation in different types of cancers. Overexpressed tyrosine phosphorylation in the human breast, small intestine and brain tissues and in the human primary glioblastoma U-87 MG cell line was monitored by using Raman biomarkers. (4) We showed that the bands at 1586 cm-1 and 829 cm-1, corresponding to phosphorylated tyrosine, play a pivotal role as a Raman biomarker of the phosphorylation status in aggressive cancers. We found that the best Raman biomarker of phosphorylation is the 1586/829 ratio showing the statistical significance at p Values of ≤ 0.05. (5) Conclusions: Raman spectroscopy and imaging have the potential to be used as screening functional assays to detect phosphorylated target proteins and will help researchers to understand the role of phosphorylation in cellular processes and cancer progression. The abnormal and excessive high level of tyrosine phosphorylation in cancer samples compared with normal samples was found in the cancerous human tissue of breasts, small intestines and brain tumours, as well as in the mitochondria and lipid droplets of the glioblastoma U-87 MG cell line. Detailed insights are presented into the intracellular oncogenic metabolic pathways mediated by phosphorylated tyrosine.

Gold nanoisland substrates for SERS characterization of cultured cells

We demonstrate a simple approach for fabricating cell-compatible SERS substrates, using repeated gold deposition and thermal annealing. The substrates exhibit SERS enhancement up to six orders of magnitude and high uniformity. We have carried out Raman imaging of fixed mesenchymal stromal cells cultured directly on the substrates. Results of viability assays confirm that the substrates are highly biocompatible and Raman imaging confirms that cell attachment to the substrates is sufficient to realize significant SERS enhancement of cellular components. Using the SERS substrates as an in vitro sensing platform allowed us to identify multiple characteristic molecular fingerprints of the cells, providing a promising avenue towards non-invasive chemical characterization of biological samples.

Investigation on the Cancer Invasion and Metastasis of Skin Squamous Cell Carcinoma by Raman Spectroscopy

Raman spectroscopy facilitates accurate and minimally invasive investigation on biomedical samples to reveal their molecular-level biological information. In this work, the cancer field effects of squamous cell carcinoma (SCC) tissues were illustrated by Raman microspectroscopy. Referenced with hematoxylin and eosin (H&E) stained microscopic images, the biochemical variations during SCC progress were meticulously described by the Raman spectral features in different pathological areas of two lesion types, including the biochemical changes in collagen, lipids, DNA, and other components of SCC diffusion and metastasis. The experimental results demonstrated that the intensities of the Raman peaks representing collagen (853, 936, and 1248 cm⁻¹) were decreased, whereas the intensities of peaks corresponding to DNA (720, 1327 cm⁻¹) and lipids (1305 cm⁻¹) were increased significantly in cancerous lesions, which testified that SCC originates from the epidermis and invades the dermis gradually. The achieved results not only described the molecular mechanism of skin carcinogenesis, but also provided vital reference data for in vivo skin cancer diagnosis using Raman spectroscopy.

Tracing Size and Surface Chemistry-Dependent Endosomal Uptake of Gold Nanoparticles Using Surface-Enhanced Raman Scattering

Surface-enhanced Raman scattering (SERS)-based single-cell analysis is an emerging approach to obtain molecular level information from molecular dynamics in a living cell. In this study, endosomal biochemical dynamics was investigated based on size and surface chemistry-dependent uptake of gold nanoparticles (AuNPs) on single cells over time using SERS. MDA-MB-231 breast cancer cells were exposed to 13 and 50 nm AuNPs and their polyadenine oligonucleotide-modified forms by controlling the order and combination of AuNPs. The average spectra obtained from 20 single cells were analyzed to study the nature of the biochemical species or processes taking place on the AuNP surfaces. The spectral changes, especially from proteins and lipids of endosomal vesicles, were observed depending on the size, surface chemistry, and combination as well as the duration of the AuNP treatment. The results demonstrate that SERS spectra are sensitive to trace biochemical changes not only the size, surface chemistry, and aggregation status of AuNPs but also the endosomal maturation steps over time, which can be simple and fast way for understanding the AuNP behavior in single cell and useful for the assisting and controlling of AuNP-based gene or drug delivery applications.

Zinc oxide nanorod based immunosensing platform for the determination of human leukemic cells

Zinc oxide (ZnO) based nanostructures owing unique physical properties - high photoluminescence, biocompatibility and other characteristics, therefore, they attract attention as building blocks suitable for biosensor development. In this research as a target we have used human leukemic cell line IM9 (IM9). IM9 was derived from the patient with a multiple myeloma and expressed cluster of differentiation proteins СD19 on the surface of 85-95% here investigated cancer cells. As a control sample healthy human's peripheral blood mononuclear cells (PBMC) were used and the expression of CD19 protein was found only in 5-9% of these cells. Two types of antibodies labeled by fluorescein isothiocyanate (FITC) were used for the labeling of human leukemic cells: FITC-conjugated mouse antibodies against Human CD19 protein (anti-CD19-FITC*) and FITC-conjugated mouse antibodies against Human IgG1 protein (anti-IgG1-FITC*). In order to demonstrate the applicability of zinc oxide nanorods (ZnO-NRs) based platforms three types of ZnO-NRs-based structures were investigated: (i) ZnO-NRs modified by anti-CD19-FITC*; (ii) ZnO-NRs modified by IM9 cells, which were pre-incubated with anti-CD19-FITC*; (iii) ZnO-NRs modified by PBMC cells, which were pre-incubated with anti-CD19-FITC*. It was demonstrated that IM9 cells after specific interaction with anti-CD19-FITC* bind to ZnO-NRs (ZnO-NRs/IM9 +anti-CD19-FITC*) and photoluminescence based signal significantly increase in comparison with that observed in control samples, which contained PBMC cells incubated with anti-CD19-FITC* (ZnO-NRs/PBMC+anti-CD19-FITC*). The photoluminescence results are in good correlation with the data obtained by flow cytometry. This study illustrate that ZnO-NRs exhibit a photoluminescence signal suitable for the determination of anti-CD19-FITC* labeled IM9 cell line at concentrations - from 10 till 500 cells adsorbed per 1 mm² of ZnO-NRs platform.

FTIR and Raman Spectroscopy-Based Biochemical Profiling Reflects Genomic Diversity of Clinical Candida Isolates That May Be Useful for Diagnosis and Targeted Therapy of Candidiasis

Despite the fact that Candida albicans is documented to be the main cause of human candidiasis, non-C. albicans Candida (NCAC) species, such as Candida glabrata and Candida tropicalis, are also suggested to be implicated in the etiopathogenesis of opportunistic fungal infections. As biology, epidemiology, pathogenicity, and antifungal resistance of NCAC species may be affected as a result of genomic diversity and plasticity, rapid and unambiguous identification of Candida species in clinical samples is essential for proper diagnosis and therapy. In the present study, 25 clinical isolates of C. albicans, C. glabrata, and C. tropicalis species were characterized in terms of their karyotype patterns, DNA content, and biochemical features. Fourier transform infrared (FTIR) spectra- and Raman spectra-based molecular fingerprints corresponded to the diversity of chromosomal traits and DNA levels that provided correct species identification. Moreover, Raman spectroscopy was documented to be useful for the evaluation of ergosterol content that may be associated with azole resistance. Taken together, we found that vibrational spectroscopy-based biochemical profiling reflects the variability of chromosome patterns and DNA content of clinical Candida species isolates and may facilitate the diagnosis and targeted therapy of candidiasis.

Blood-based near-infrared spectroscopy for the rapid low-cost detection of Alzheimer's disease

Alzheimer's disease (AD) is currently under-diagnosed and is predicted to affect a great number of people in the future, due to the unrestrained aging of the population. An accurate diagnosis of AD at an early stage, prior to (severe) symptomatology, is of crucial importance as it would allow the subscription of effective palliative care and/or enrolment into specific clinical trials. Today, new analytical methods and research initiatives are being developed for the on-time diagnosis of this devastating disorder. During the last decade, spectroscopic techniques have shown great promise in the robust diagnosis of various pathologies, including neurodegenerative diseases and dementia. In the current study, blood plasma samples were analysed with near-infrared (NIR) spectroscopy as a minimally-invasive method to distinguish patients with AD (n = 111) from non-demented volunteers (n = 173). After applying multivariate classification models (principal component analysis with quadratic discriminant analysis - PCA-QDA), AD individuals were correctly identified with 92.8% accuracy, 87.5% sensitivity and 96.1% specificity. Our results show the potential of NIR spectroscopy as a simple and cost-effective diagnostic tool for AD. Robust and early diagnosis may be a first step towards tackling this disease by allowing timely intervention.

Interference-Enhanced Raman Spectroscopy as a Promising Tool for the Detection of Biomolecules on Raman-Compatible Surfaces

Raman spectroscopy in combination with appropriate sample preparation strategies, for example, enrichment of bacteria on metal surfaces, has been proven to be a promising approach for rapidly diagnosing infectious diseases. Unfortunately, the fabrication of the required chip substrates is usually very challenging due to the lack of feasible instruments that can be used for quality control in the surface modification process. The intrinsically weak Raman signal of the biomolecules, employed for the enrichment of the micro-organisms on the chip surface, does not allow for monitoring of the successful immobilization by means of a Raman spectroscopic approach. Within this contribution, we demonstrate how a simple modification of a plain aluminum surface enables enhancement (or a decrease, if desired) of the Raman signal of molecules deposited on that surface. The manipulation of the Raman signal strength is achieved via exploiting interference effects that occur, if the highly reflective aluminum surface is modified with thin layers of transparent dielectrics like aluminum oxide. The thicknesses of these layers were determined by theoretical considerations and calculations. For the first time, it is shown that the interference effects can be used for the detection of biomolecules as well by investigating the siderophore ferrioxamine B. The observed degree of enhancement was approximately 1 order of magnitude. Moreover, the employed aluminum/aluminum oxide layers have been thoroughly characterized using atomic force and scanning electron microscopy as well as X-ray reflectometry and UV-Vis measurements.

Tuberculosis determination using SERS and chemometric methods

Nanostructures have been multiplying the advantages of Raman spectroscopy and further amplify the advantages of Raman spectroscopy is a continuous effort focused on the appropriate design of nanostructures. Herein, we designed different shapes of plasmonic nanostructures such as Vertical, Zig Zag, Slant nanorods and Spherical nanoparticles employing the DC magnetron sputtering system as SERS-active substrates for ultrasensitive detection of target molecules. The fabricated plasmonic nanostructures sensitivity and uniformity were exploited by reference dye analyte. These nanostructures were utilized in the label free detection of infectious disease, Tuberculosis (TB). For the first time, TB detection from serum samples using SERS has been demonstrated. Various multivariate statistical methods such as principal component analysis, support vector machine, decision tree and random forest were developed and tested their ability to discriminate the healthy and active TB samples. The results demonstrate the performance of the SERS spectra, chemometric methods and potential of the method in clinical diagnosis.

In vitroantibacterial activity of oxide and non-oxide bioceramics for arthroplastic devices: II. Fourier transform infrared spectroscopy

The metabolic response of Gram-positiveStaphylococcus epidermidisbacteria to bioceramic substrates was probed by Fourier transform infrared spectroscopy.

High-Yield Synthesis of Monomeric LMWP(CPP)-siRNA Covalent Conjugate for Effective Cytosolic Delivery of siRNA

Because of the unparalleled efficiency and universal utility in treating a variety of disease types, siRNA agents have evolved as the future drug-of-choice. Yet, the inability of the polyanionic siRNA macromolecules to cross the cell membrane remains as the bottleneck of possible clinical applications. With the cell penetrating peptides (CPP) being discovered lately, the most effective tactic to achieve the highest intracellular siRNA delivery deems to be by covalently conjugating the drug to a CPP; for instance, the arginine-rich Tat or low molecular weight protamine (LMWP) peptides. However, construction of such a chemical conjugate has been referred by scientists in this field as the “Holy Grail” challenge due to self-assembly of the cationic CPP and anionic siRNA into insoluble aggregates that are deprived of the biological functions of both compounds. Based on the dynamic motion of PEG, we present herein a concise coupling strategy that is capable of permitting a high-yield synthesis of the cell-permeable, cytosol-dissociable LMWP-siRNA covalent conjugates. Cell culture assessment demonstrates that this chemical conjugate yields by far the most effective intracellular siRNA delivery and its corresponded gene-silencing activities. This work may offer a breakthrough advance towards realizing the clinical potential of all siRNA therapeutics and, presumably, most anionic macromolecular drugs such as anti-sense oligonucleotides, gene compounds, DNA vectors and proteins where conjugation with the CPP encounters with problems of aggregation and precipitation. To this end, the impact of this coupling technique is significant, far-reaching and wide-spread.

Mirrored stainless steel substrate provides improved signal for Raman spectroscopy of tissue and cells

Raman spectroscopy (RS) is a powerful technique that permits the non-destructive chemical analysis of cells and tissues without the need for expensive and complex sample preparation. To date, samples have been routinely mounted onto calcium fluoride (CaF₂) as this material possesses the desired mechanical and optical properties for analysis, but CaF₂ is both expensive and brittle and this prevents the technique from being routinely adopted. Furthermore, Raman scattering is a weak phenomenon and CaF₂ provides no means of increasing signal. For RS to be widely adopted, particularly in the clinical field, it is crucial that spectroscopists identify an alternative, low-cost substrate capable of providing high spectral signal to noise ratios with good spatial resolution. Results show that these desired properties are attainable when using mirrored stainless steel as a Raman substrate. When compared with CaF₂, data show that stainless steel has a low background signal and provides an average signal increase of 1.43 times during tissue analysis and 1.64 times when analyzing cells. This result is attributed to a double-pass of the laser beam through the sample where the photons from the source laser and the forward scattered Raman signal are backreflected and retroreflected from the mirrored steel surface and focused towards collection optics. The spatial resolution on stainless steel is at least comparable to that on CaF₂ and it is not compromised by the reflection of the laser. Steel is a fraction of the cost of CaF₂ and the reflection and focusing of photons improve signal to noise ratios permitting more rapid mapping. The low cost of steel coupled with its Raman signal increasing properties and robust durability indicates that steel is an ideal substrate for biological and clinical RS as it possesses key advantages over routinely used CaF₂. © 2016 The Authors. Journal of Raman Spectroscopy Published by John Wiley & Sons Ltd.

Electrochemistry and surface-enhanced Raman spectroscopy of CTAB modulated interactions of magnetic nanoparticles with biomolecules

In this study, cyclic voltammetry was used to unearth the electrochemical behavior of MNPs/CTAB and their interaction with biomolecules whereas SERS provided an insight into the mode of interaction in these molecular associations.

Raman microscopy of bladder cancer cells expressing green fluorescent protein

Gene engineering is a commonly used tool in cellular biology to determine changes in function or expression of downstream targets. However, the impact of genetic modulation on biochemical effects is less frequently evaluated. The aim of this study is to use Raman microscopy to assess the biochemical effects of gene silencing on T24 and UMUC-13 bladder cancer cell lines. Cellular biochemical information related to nucleic acid and lipogenic components was obtained from deconvolved Raman spectra. We show that the green fluorescence protein (GFP), the chromophore that served as a fluorescent reporter for gene silencing, could also be detected by Raman microscopy. Only the gene-silenced UMUC-13 cell lines exhibited low-to-moderate GFP fluorescence as determined by fluorescence imaging and Raman spectroscopic studies. Moreover, we show that gene silencing and cell phenotype had a greater effect on nucleic acid and lipogenic components with minimal interference from GFP expression. Gene silencing was also found to perturb cellular protein secondary structure in which the amount of disorderd protein increased at the expense of more ordered protein. Overall, our study identified the spectral signature for cellular GFP expression and elucidated the effects of gene silencing on cancer cell biochemistry and protein secondary structure.

Identification of Individual Exosome-Like Vesicles by Surface Enhanced Raman Spectroscopy

Exosome-like vesicles (ELVs) are a novel class of biomarkers that are receiving a lot of attention for the detection of cancer at an early stage. In this study the feasibility of using a surface enhanced Raman spectroscopy (SERS) based method to distinguish between ELVs derived from different cellular origins is evaluated. A gold nanoparticle based shell is deposited on the surface of ELVs derived from cancerous and healthy cells, which enhances the Raman signal while maintaining a colloidal suspension of individual vesicles. This nanocoating allows the recording of SERS spectra from single vesicles. By using partial least squares discriminant analysis on the obtained spectra, vesicles from different origin can be distinguished, even when present in the same mixture. This proof-of-concept study paves the way for noninvasive (cancer) diagnostic tools based on exosomal SERS fingerprinting in combination with multivariate statistical analysis.

Metal nanoparticles reveal the organization of single-walled carbon nanotubes in bundles

Single-walled carbon nanotubes (SWCNTs) were decorated with Ag and Au nanoparticles. The smaller SWCNTs in bundles are preferentially affected by the presence of metal nanoparticles. We postulate that smaller diameter SWCNTs surround larger ones.