Raman detection of proteomic analytes

Analytical applications of droplet deposition Raman spectroscopy

The droplet deposition methods in Raman spectroscopy have received considerable attention in the field of analytical sensing focusing on effective pre-concentration of the studied analyte (coffee-ring effect or small spots). This review covers different analytical applications of drop-coating deposition Raman scattering (DCDRS) and droplet deposition surface-enhanced Raman scattering (SERS) spectroscopy. Two main advantages of droplet deposition Raman techniques are considered: the drying-induced segregation of the components from the mixtures (such as body fluids) and the sensitivity of detection of various analytically important molecules. Some recent advanced applications, including clinical cancer diagnosis, are discussed and summarized. Finally, the potential and further perspectives of the droplet deposition Raman methods for analytical studies are introduced.

Photoactivated plasmonic nanohybrid fibers with prolonged trapping of excited charge carriers for SERS analysis of biomolecules

The quest to enhance Raman spectroscopic signals through the rational design of plasmonic substrates has enabled the detection and characterization of pharmaceutically important molecules with low scattering cross-sections, such as amino acids and proteins, and is helping in making forays into the diverse field of biomedical sciences. This work presents a simple strategy for synthesizing silver nanoparticles-incorporated alumina nanofibers (Ag-AlNFs) utilizing controlled microwave synthesis for enhancing the surface-enhanced Raman chemical enhancement factor through photo-induced charge accumulation at the plasmonic-dielectric interface. The plasmonic-dielectric fibers serve as excellent charge carrier trappers, as evident from the ultrafast transient absorption spectroscopy studies. Apart from chemical enhancement, the increase in electronic surface charge also enables the protein disulfide bonds to capture these electrons and form a transient disulfide electron adduct radical, which converts to free thiol radical on dissociation. This allows protein molecules to bind to the nanoparticle's surface with the favorable silver thiol bond leading to greater surface affinity and larger SERS enhancement. The proposed Ag-AlNFs represent a cost-effective material that can be potentially used to probe biological systems in a label-free manner by photoactivating the SERS substrate for obtaining higher enhancement factors.

Single versus Double Coffee-Ring Effect Patterns in Thin-Layer Chromatography Coupled with Surface-Enhanced Raman Spectroscopic Analysis of Anti-Diabetic Drugs Adulterated in Herbal Products

In thin-layer chromatography coupled with surface-enhanced Raman spectroscopy (TLC-SERS), the coffee ring effect (CRE) describes the formation of a ring-shape spot (blank in the middle and darker on the edge) caused by the aggregation of silver nanoparticles (Ag NPs), alone (single CRE) or with the analytes (double CRE). In this work, the SCRE and DCRE were investigated in two anti-diabetic drugs, hydrophobic glibenclamide (GLB) and more hydrophilic metformin (MET). The SCRE occurred in GLB analysis, as opposed to the DCRE that occurred in MET. It was proven that for optimization of the TLC-SERS analytical procedure, it is necessary to distinguish the CRE patterns of analytes. Additionally, MET and GLB were analyzed with the developed TLC-SERS method and confirmed by another validated method using high-performance liquid chromatography. Four herbal products collected on the market were found to be adulterated with GLB or/and MET; among those, one product was adulterated with both MET and GLB, and two products were adulterated with GLB at a higher concentration than the usual GLB prescription dose. The TLC-SERS method provided a useful tool for the simultaneous detection of adulterated anti-diabetic herbal products, and the comparison of the SCRE and DCRE provided more evidence to predict CRE patterns in TLC-SERS.

Detection and Characterization of Nodularin by Using Label-Free Surface-Enhanced Spectroscopic Techniques

Nodularin (NOD) is a potent toxin produced by Nodularia spumigena cyanobacteria. Usually, NOD co-exists with other microcystins in environmental waters, a class of cyanotoxins secreted by certain cyanobacteria species, which makes identification difficult in the case of mixed toxins. Herein we report a complete theoretical DFT-vibrational Raman characterization of NOD along with the experimental drop-coating deposition Raman (DCDR) technique. In addition, we used the vibrational characterization to probe SERS analysis of NOD using colloidal silver nanoparticles (AgNPs), commercial nanopatterned substrates with periodic inverted pyramids (Klarite^TM substrate), hydrophobic Tienta^® SpecTrim^TM slides, and in-house fabricated periodic nanotrenches by nanoimprint lithography (NIL). The 532 nm excitation source provided more well-defined bands even at LOD levels, as well as the best performance in terms of SERS intensity. This was reflected by the results obtained with the Klarite^TM substrate and the silver-based colloidal system, which were the most promising detection approaches, providing the lowest limits of detection. A detection limit of 8.4 × 10^-8 M was achieved for NOD in solution by using AgNPs. Theoretical computation of the complex vibrational modes of NOD was used for the first time to unambiguously assign all the specific vibrational Raman bands.

Insights on Aggregation of Hen Egg-White Lysozyme from Raman Spectroscopy and MD Simulations

Protein misfolding and aggregation play a significant role in several neurodegenerative diseases. In the present work, the spontaneous aggregation of hen egg-white lysozyme (HEWL) in an alkaline pH 12.2 at an ambient temperature was studied to obtain molecular insights. The time-dependent changes in spectral peaks indicated the formation of β sheets and their effects on the backbone and amino acids during the aggregation process. Introducing iodoacetamide revealed the crucial role of intermolecular disulphide bonds amidst monomers in the aggregation process. These findings were corroborated by Molecular Dynamics (MD) simulations and protein-docking studies. MD simulations helped establish and visualize the unfolding of the proteins when exposed to an alkaline pH. Protein docking revealed a preferential dimer formation between the HEWL monomers at pH 12.2 compared with the neutral pH. The combination of Raman spectroscopy and MD simulations is a powerful tool to study protein aggregation mechanisms.

Chromatographic framework for coffee ring effect-driven separation of small molecules in surface enhanced Raman spectroscopy analysis

The applications of coffee ring effect (CRE) in analytical chemistry have been increasingly expanded from particles and macromolecules to small molecules, in particular coupled to surface-enhanced Raman spectroscopy (SERS). Despite the theory behind the formation of CRE itself from a single drop evaporation onto the dry surface is well established, the theoretical aspects of CRE-driven separation, especially the analyte-surface interactions involving small molecules, have not been conceived. Herein, we have developed a theoretical framework to describe the CRE-driven separation process of small molecules, using SERS analysis of dimethylarsinic acid (DMA^V), dimethylmonothioarsinic acid (DMMTA^V), and dimethyldithioarsinic acid (DMDTA^V) on gold nanofilm (AuNF) as an example. By combining the CRE theory for the radial flow and the Extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory for mass transfer between solution and AuNF surface, we adapted the conventional chromatographic theory to derive a modified van Deemter equation for the CRE-driven separation. By using this model, we predicted the travel distances of arsenicals based on the different affinity of analytes to the AuNF and evaluated the possibility of separation of unknown analytes by CRE-based SERS, demonstrating the successful adaptation of classic chromatographic theory to CRE-driven nanochromatography.

Single-Molecule Classification of Aspartic Acid and Leucine by Molecular Recognition through Hydrogen Bonding and Time-Series Analysis

Amino acid detection/identification methods are important for understanding biological systems. In this study, we developed the single-molecule measurement for investigated quantum tunneling enhancement by chemical modification and machine learning based time series analysis for develop accurate amino acid discrimination. We performed single-molecule measurement of L-aspartic Acid (Asp) and L-leucine (Leu) with mercaptoacetic acid (MAA) chemical modified nano-gap. The measured current was investigated by machine learning based time series analysis method for accurate amino acid discrimination. Compared to measurements using bare nano-gap, it is found that MAA modification improves the difference in the conductance-time profiles between Asp and Leu through the hydrogen bonding facilitated tunneling phenomena. It is also found that this method enables determination of relative concentration. even in the mixture of Asp and Leu. It improves selective analysis for amino acids, and therefore would be applicable in medicine, diagnosis, and single-molecule peptide sequencing.

An Experimental Investigation of Evaporation of Ethanol-Water Droplets Laden with Alumina Nanoparticles on a Critically Inclined Heated Substrate

We experimentally investigate the evaporation of water-ethanol binary sessile droplets loaded with alumina nanoparticles on a critically inclined heated surface and compare it to the no-loading condition. In contrast to a droplet of pure fluids, several distinct and interesting phenomena observed in a binary-nanofluid droplet on a critically inclined substrate are reported for the first time. The critical angle at which a droplet begins to slide increases for ethanol-rich binary droplets up to 0.6 wt % nanoparticle loading. The critical angle for binary droplets also increases as the substrate temperature increases and as the ethanol concentration decreases for modest loading conditions. It is observed that the advancing side of a binary droplet is pinned in both the loading and no-loading scenarios, whereas the receding side is pinned in the loading case but shrinks continuously in the no-loading case. The pinning effect caused by nanoparticles results in a larger perimeter and surface area for the nanoparticle-laden droplets, enhancing the evaporation rates and significantly decreasing the lifetime of the nanoparticle-containing droplets compared to the no-loading case. Increasing the ethanol percentage in the binary droplet placed on an inclined substrate produces complex thermosolutal Marangoni convection, which becomes more affluent in the case of nanoparticles loading than the no-loading condition. The radial symmetry of the circular coffee ring structure observed on a horizontal surface is shattered in the inclined case because the droplet elongates and preferentially deposits toward the advancing side of the triple line due to the action of the body force. Despite its fundamental nature, the present study can contribute to understanding many practical applications.

Mitochondrial Dysfunction: A Prelude to Neuropathogenesis of SARS-CoV-2

The SARS-CoV-2 virus is notorious for its neuroinvasive capability, causing multiple neurological conditions. The neuropathology of SARS-CoV-2 is increasingly attributed to mitochondrial dysfunction of brain microglia cells. However, the changes in biochemical content of mitochondria that drive the progression of neuro-COVID remain poorly understood. Here we introduce a Raman microspectrometry approach that enables the molecular profiling of single cellular organelles to characterize the mitochondrial molecular makeup in the infected microglia cells. We found that microglia treated with either spike protein or heat-inactivated SARS-CoV-2 trigger a dramatic reduction in mtDNA content and an increase in phospholipid saturation levels. At the same time, no significant changes were detected in Golgi apparatus and in lipid droplets, the organelles that accommodate biogenesis and storage of lipids. We hypothesize that transformations in mitochondria are caused by increased synthesis of reactive oxygen species in these organelles. Our findings call for the development of mitochondria-targeted therapeutic approaches to limit neuropathology associated with SARS-CoV-2.

Liposome-Polymer Complex for Drug Delivery System and Vaccine Stabilization

Liposomes have been used extensively as micro- and nanocarriers for hydrophobic or hydrophilic molecules. However, conventional liposomes are biodegradable and quickly eliminated, making it difficult to be used for delivery in specific routes, such as the oral and systemic routes. One way to overcome this problem is through complexation with polymers, which is referred to as a liposome complex. The use of polymers can increase the stability of liposome with regard to pH, chemicals, enzymes, and the immune system. In some cases, specific polymers can condition the properties of liposomes to be explicitly used in drug delivery, such as targeted delivery and controlled release. These properties are influenced by the type of polymer, crosslinker, interaction, and bond in the complexation process. Therefore, it is crucial to study and review these parameters for the development of more optimal forms and properties of the liposome complex. This article discusses the use of natural and synthetic polymers, ways of interaction between polymers and liposomes (on the surface, incorporation in lamellar chains, and within liposomes), types of bonds, evaluation standards, and their effects on the stability and pharmacokinetic profile of the liposome complex, drugs, and vaccines. This article concludes that both natural and synthetic polymers can be used in modifying the structure and physicochemical properties of liposomes to specify their use in targeted delivery, controlled release, and stabilizing drugs and vaccines.

Human γS-Crystallin Resists Unfolding Despite Extensive Chemical Modification from Exposure to Ionizing Radiation

Ionizing radiation has dramatic effects on living organisms, causing damage to proteins, DNA, and other cellular components. γ radiation produces reactive oxygen species (ROS) that damage biological macromolecules. Protein modification due to interactions with hydroxyl radical is one of the most common deleterious effects of radiation. The human eye lens is particularly vulnerable to the effects of ionizing radiation, as it is metabolically inactive and its proteins are not recycled after early development. Therefore, radiation damage accumulates and eventually can lead to cataract formation. Here we explore the impact of γ radiation on a long-lived structural protein. We exposed the human eye lens protein γS-crystallin (HγS) to high doses of γ radiation and investigated the chemical and structural effects. HγS accumulated many post-translational modifications (PTMs), appearing to gain significant oxidative damage. Biochemical assays suggested that cysteines were affected, with the concentration of free thiol reduced with increasing γ radiation exposure. SDS-PAGE analysis showed that irradiated samples form protein-protein cross-links, including nondisulfide covalent bonds. Tandem mass spectrometry on proteolytic digests of irradiated samples revealed that lysine, methionine, tryptophan, leucine, and cysteine were oxidized. Despite these chemical modifications, HγS remained folded past 10.8 kGy of γ irradiation as evidenced by circular dichroism and intrinsic tryptophan fluorescence spectroscopy.

Drop coating deposition Raman (DCDR) spectroscopy of contaminants

Raman spectroscopy is a useful technique to identify small organic molecules, including contaminants. The drop coating deposition Raman (DCDR) is more sensitive than conventional Raman spectroscopy from solution. It is based on Raman measurement from a small drop dried on a hydrophobic surface where studied molecules are preconcentrated. In this paper, DCDR spectra of dried drops of selected contaminants (food contaminant melamine, fungicide thiram, herbicides bentazon and picloram) on the hydrophobic substrate were acquired for the first time, whereas Raman spectra from stock solutions were impossible to obtain under the same experimental conditions. The lowest DCDR detected concentrations were determined as 6.4 µM, 0.31 µM, 20 µM and 2 µM in deposited concentrations for melamine, thiram, bentazon and picloram, respectively. Therefore, DCDR spectroscopy can serve to detect these molecules in concentrations relevant in food/groundwater contaminations.

Nanostructured Plasma Polymerized Fluorocarbon Films for Drop Coating Deposition Raman Spectroscopy (DCDRS) of Liposomes

Raman spectroscopy is one of the most used biodetection techniques. However, its usability is hampered in the case of low concentrated substances because of the weak intensity of the Raman signal. To overcome this limitation, the use of drop coating deposition Raman spectroscopy (DCDRS), in which the liquid samples are allowed to dry into well-defined patterns where the non-volatile solutes are highly concentrated, is appropriate. This significantly improves the Raman sensitivity when compared to the conventional Raman signal from solution/suspension. As DCDRS performance strongly depends on the wetting properties of substrates, we demonstrate here that the smooth hydrophobic plasma polymerized fluorocarbon films prepared by magnetron sputtering (contact angle 108°) are well-suited for the DCDRS detection of liposomes. Furthermore, it was proved that even better improvement of the Raman signal might be achieved if the plasma polymer surfaces are roughened. In this case, 100% higher intensities of Raman signal are observed in comparison with smooth fluorocarbon films. As it is shown, this effect, which has no influence on the profile of Raman spectra, is connected with the increased hydrophobicity of nanostructured fluorocarbon films. This results in the formation of dried liposomal deposits with smaller diameters and higher preconcentration of liposomes.

Surface amplification of tetraphenylporphyrin overtone and combination Raman bands in drop coating deposition Raman (DCDR) on electrically conductive surfaces

It is essential to realize a Raman measurement technique without artifact or fluorescence signals for high-quality and reliable data in a valid molecular-level analysis and interpretation. This requirement applies especially to a molecule with strong fluorescence like porphyrin. Here, the surface of a gold substrate performs better as a DCDR substrate for tetraphenylporphyrin than other surfaces, such as tantalum, indium tin oxide glass, or aluminium. Polarized Raman spectra of tetraphenylporphyrin demonstrated the oriented deposition of porphyrin crystallites on the Au substrate using the drop coating technique. The emission anisotropy suggests that the deposited crystallites are arranged outward radially with the porphyrin ring orientation. The orientation is signed by the NHHN axis that is parallel to the radial vector along the X-axis. Moreover, it also demonstrates high chemical stability after preservation and repeated measurements. The Raman signal on a gold substrate is enhanced more than on other substrates beyond mere preconcentration of analytes or the coffee-ring effect only, which might be due to the contribution of the SERRS effect. This effect will be discussed based on the interactions among localized surface plasmons, vibronic transitions, and Raman active vibrational modes.

Human tear fluid analysis for clinical applications: progress and prospects

Introduction: Human blood and saliva are increasingly under investigation for the detection of biomarkers for early diagnosis of non-communicable (e.g.cancers) and communicable diseases like COVID-19. Exploring the potential application of human tears, an easily accessible body fluid, for the diagnosis of various diseases is the need of the hour.Areas covered: This review deals with a comprehensive account of applications of tear analysis using different techniques, their comparison and overall progress achieved till now. The techniques used for tear fluid analysis are HPLC/UPLC/SDS-PAGE, CE, etc., together with ELISA, Mass Spectrometry, etc. But, with advances in instrumentation and data processing methods, it has become easy to couple the various separation methods with highly sensitive optical techniques for the analysis of body fluids.Expert opinion: Tear analysis can provide valuable information about the health condition of the eyes since it contains several molecular constituents, and their relative concentrations may alter under abnormal conditions. Tear analysis has the advantage that it is totally non-invasive. This study recommends tear fluid as a reliable clinical sample to be probed by highly sensitive optical techniques to diagnose different health conditions, with special emphasis on eye diseases.

Vibrational Spectroscopic Investigation of Blood Plasma and Serum by Drop Coating Deposition for Clinical Application

In recent decades, vibrational spectroscopic methods such as Raman and FT-IR spectroscopy are widely applied to investigate plasma and serum samples. These methods are combined with drop coating deposition techniques to pre-concentrate the biomolecules in the dried droplet to improve the detected vibrational signal. However, most often encountered challenge is the inhomogeneous redistribution of biomolecules due to the coffee-ring effect. In this study, the variation in biomolecule distribution within the dried-sample droplet has been investigated using Raman and FT-IR spectroscopy and fluorescence lifetime imaging method. The plasma-sample from healthy donors were investigated to show the spectral differences between the inner and outer-ring region of the dried-sample droplet. Further, the preferred location of deposition of the most abundant protein albumin in the blood during the drying process of the plasma has been illustrated by using deuterated albumin. Subsequently, two patients with different cardiac-related diseases were investigated exemplarily to illustrate the variation in the pattern of plasma and serum biomolecule distribution during the drying process and its impact on patient-stratification. The study shows that a uniform sampling position of the droplet, both at the inner and the outer ring, is necessary for thorough clinical characterization of the patient’s plasma and serum sample using vibrational spectroscopy.

Raman Spectroscopic Stratification of Multiple Myeloma Patients Based on Exosome Profiling

Multiple myeloma (MM) is a hematological malignancy characterized by abnormal plasma cell proliferation within the bone marrow which leads to progressive bone marrow failure, skeletal osteolytic lesions, and renal insufficiency, thus severely affecting the quality of life. MM is always preceded by monoclonal gammopathy of uncertain significance (MGUS), which progresses to asymptomatic-MM (aMM) or symptomatic-MM (sMM) at a rate of 1% per year. Despite impressive progress in the therapy of the disease, MM remains incurable. Based on these premises, the identification of biomarkers of MGUS progression to MM is a crucial issue in disease management. In this regard, exosomes (EXs) and their precious biomolecular cargo could play a pivotal role in MM detection, stratification, and follow-up. Raman spectroscopy, a label- and manipulation-free technique, and its enhanced version, surface-enhanced Raman spectroscopy (SERS), have been used for characterizing MGUS, aMM, and sMM patient-derived EXs. Here, we have demonstrated the capability of Raman spectroscopy for discriminating EXs along the progression from MGUS to aMM and sMM, thus providing useful clinical indications for patient care. The used SERS devices, based on random nanostructures, have shown good potential in terms of sensitivity, but further developments are needed for achieving reproducible and quantitative SERS results.

Raman spectra-based deep learning: A tool to identify microbial contamination

Deep learning has the potential to enhance the output of in‐line, on‐line, and at‐line instrumentation used for process analytical technology in the pharmaceutical industry. Here, we used Raman spectroscopy‐based deep learning strategies to develop a tool for detecting microbial contamination. We built a Raman dataset for microorganisms that are common contaminants in the pharmaceutical industry for Chinese Hamster Ovary (CHO) cells, which are often used in the production of biologics. Using a convolution neural network (CNN), we classified the different samples comprising individual microbes and microbes mixed with CHO cells with an accuracy of 95%–100%. The set of 12 microbes spans across Gram‐positive and Gram‐negative bacteria as well as fungi. We also created an attention map for different microbes and CHO cells to highlight which segments of the Raman spectra contribute the most to help discriminate between different species. This dataset and algorithm provide a route for implementing Raman spectroscopy for detecting microbial contamination in the pharmaceutical industry.

Tap water fingerprinting using a convolutional neural network built from images of the coffee-ring effect

A low-cost tap water fingerprinting technique was evaluated using the coffee-ring effect, a phenomenon by which tap water droplets leave distinguishable "fingerprint" residue patterns after water evaporates. Tap waters from communities across southern Michigan dried on aluminum and photographed with a cell phone camera and 30× loupe produced unique and reproducible images. A convolutional neural network (CNN) model was trained using the images from the Michigan tap waters, and despite the small size of the image dataset, the model assigned images into groups with similar water chemistry with 80% accuracy. Synthetic solutions containing only the majority species measured in Detroit, Lansing, and Michigan State University tap waters did not display the same residue patterns as collected waters; thus, the lower concentration species also influence the tap water "fingerprint". Residue pattern images from salt mixtures with an array of sodium, calcium, magnesium, chloride, bicarbonate, and sulfate concentrations were analyzed by measuring features observed in the photographs as well as using principal component analysis (PCA) on the image files and particles measurements. These analyses together highlighted differences in the residue patterns associated with the water chemistry in the sample. The results of these experiments suggest that the unique and reproducible residue patterns of tap water samples that can be imaged with a cell phone camera and a loupe contain a wealth of information about the overall composition of the tap water, and thus, the phenomenon should be further explored for potential use in low-cost tap water fingerprinting.

Perspectives of DCDR-GERS in the analysis of amino acids

Graphene-enhanced Raman scattering (GERS) has attracted increasing attention from many scientists in recent years as a novel and potentially strong analytical technique since its discovery in 2010.

Coherent Raman spectroscopic imaging to characterize microglia activation pathway

Microglia are immune cells, which densely populate the central nervous system (CNS), and play essential role in suppression of neurodegenerative diseases, clearance of debris after CNS trauma, as well as serve as the last line of immune defense in response to any potential threat by being activated to eliminate diverse pathogens ranging from bacteria to cancer. The activated microglia cells are commonly used as a diagnostic biomarker of diverse brain conditions, however detection and classification of microglia activated phenotypes is a cumbersome and imprecise procedure. Here, we report on development of optical assay for detection and quantitative analysis of activated microglia. In this study, we investigated overall changes in the metabolism of microglia cells during their activation by monitoring the signal from cellular proteins and lipids using label-free coherent anti-Stokes Raman scattering imaging. Our data demonstrate that the activation of microglia in the presence of bacterial liposaccharide is accompanied by intense upregulation of synthesis of proteins and lipids. We further propose that elevated intracellular content of these types of macromolecules can serve as early supplementary marker for identification of active microglia cells in the brain samples by Raman imaging techniques.

SEM-Raman image cytometry of cells

Correlative and integrated scanning electron microscopy (SEM) and Raman micro-spectroscopy is presented that enables the characterization and identification of different cancer and non-cancer cells through SEM-Raman image cytometry. The hybrid microscopy system enables the acquisition of high resolution SEM images of uncoated cells and the spatial correlation with chemical information as obtained from Raman micro-spectroscopic imaging. A sample preparation protocol and a workflow are presented that are compatible with the demands of hybrid SEM-Raman microscopy. Stainless steel cell substrates were used that are both conductive and give a low optical response in Raman scattering. Correlative and integrated SEM-Raman micro-spectroscopy is illustrated with cells from blood and cells from a SKBR-3 breast cancer cell line.

Pattern Formation in Drying Sessile and Pendant Droplet: Interactions of Gravity Settling, Interface Shrinkage, and Capillary Flow

We reported the interactions of the gravitational sedimentation, interface shrinkage, and outward capillary flow in drying droplets. This coupling effect is the inference we draw from deposition patterns of both sessile and pendant droplets, which contain particles of different sizes, evaporating on a patterned substrate. The deposition difference between sessile and pendant droplets containing microparticles indicated that gravitational sedimentation has a significant influence on the deposition morphology. The phase diagram shows that the particle deposition process can be divided into two stages: in the first stage, the competition between the interface shrinkage and the gravitational sedimentation determines whether the particles can be captured by the liquid-air interface; in the second stage, the capillary flow takes the particles inside the droplet toward the edge. The deposition morphology is the result of competition and cooperation interactions of the free setting, interface shrinkage, and outward capillary flow.

BCAbox Algorithm Expands Capabilities of Raman Microscope for Single Organelles Assessment

Raman microspectroscopy is a rapidly developing technique, which has an unparalleled potential for in situ proteomics, lipidomics, and metabolomics, due to its remarkable capability to analyze the molecular composition of live cells and single cellular organelles. However, the scope of Raman spectroscopy for bio-applications is limited by a lack of software tools for express-analysis of biomolecular composition based on Raman spectra. In this study, we have developed the first software toolbox for immediate analysis of intracellular Raman spectra using a powerful biomolecular component analysis (BCA) algorithm. Our software could be easily integrated with commercial Raman spectroscopy instrumentation, and serve for precise analysis of molecular content in major cellular organelles, including nucleoli, endoplasmic reticulum, Golgi apparatus, and mitochondria of either live or fixed cells. The proposed software may be applied in broad directions of cell science, and serve for further advancement and standardization of Raman spectroscopy.

Texture analysis of protein deposits produced by droplet evaporation

The deposit patterns derived from droplet evaporation allow current development of medical tests and new strategies for diagnostic in patients. For such purpose, the development and implementation of algorithms capable of characterizing and differentiating deposits are crucial elements. We report the study of deposit patterns formed by the droplet evaporation of binary mixtures of proteins containing NaCl. Optical microscopy reveals aggregates such as tip arrow-shaped, dendritic and semi-rosette patterns, needle-like and scalloped lines structures, as well as star-like and prism-shaped salt crystals. We use the first-order statistics (FOS) and gray level co-occurrence matrix (GLCM) to characterize the complex texture of deposit patterns. Three significant findings arise from this analysis: first, the FOS and GLCM parameters structurally characterize protein deposits. Secondly, they conform to simple exponential laws that change as a function of the NaCl concentration. Finally, the parameters are capable of revealing the different structural changes that occur during the droplet evaporation.

Structural Insight of Amyloidogenic Intermediates of Human Insulin

Engaging Raman spectroscopy as a primary tool, we investigated the early events of insulin fibrilization and determined the structural content present in oligomer and protofibrils that are formed as intermediates in the fibril formation pathway. Insulin oligomer, as obtained upon incubation of zinc-free insulin at 60 °C, was mostly spherical in shape, with a diameter of 3-5 nm. Longer incubation produced "necklace"-like beaded protofibrillar assembly species. These intermediates eventually transformed into 5-8 nm thick fibers with smooth surface texture. A broad amide I band in the Raman spectrum of insulin monomer appeared at 1659 cm^-1, with a shoulder band at 1676 cm^-1. This signature suggested the presence of major helical and extended secondary structure of the protein backbone. In the oligomeric state, the protein maintained its helical imprint (∼50%) and no substantial increment of the compact cross-β-sheet structure was observed. A nonamide helix signature band at 940 cm^-1 was present in the oligomeric state, and it was weakened in the fibrillar structure. The 1-anilino-8-naphthalene-sulfonate binding study strongly suggested that a collapse in the tertiary structure, not the major secondary structural realignment, was the dominant factor in the formation of oligomers. In the fibrillar state, the contents of helical and disordered secondary structures decreased significantly and the β-sheet amount increased to ∼62%. The narrow amide I Raman band at 1674 cm^-1 in the fibrillar state connoted the formation of vibrationally restricted highly organized β-sheet structure with quaternary realignment into steric-zipped species.

A review on suppression and utilization of the coffee-ring effect

Evaporation of sessile droplets containing non-volatile solutes dispersed in a volatile solvent leaves behind ring-like solid stains. As the volatile species evaporates, pinning of the contact line gives rise to capillary flows that transport non-volatile solutes to the contact line. This phenomenon, called the coffee-ring effect, compromises the overall performance of industrially relevant manufacturing processes involving evaporation such as printing, biochemical analysis, manufacturing of nano-structured materials through colloidal and macromolecular patterning. Various approaches have been developed to suppress this phenomenon, which is otherwise difficult to avoid. The coffee-ring effect has also been leveraged to prepare new materials through convection induced assembly. This review underlines not only the strategies developed to suppress the coffee-ring effect but also sheds light on approaches to arrive at novel processes and materials. Working principles and applicability of these strategies are discussed together with a critical comparison.

Triggering molecular assembly at the mesoscale for advanced Raman detection of proteins in liquid

An advanced optofluidic system for protein detection based on Raman signal amplification via dewetting and molecular gathering within temporary mesoscale assemblies is presented. The evaporation of a microliter volume of protein solution deposited in a circular microwell precisely follows an outward-receding geometry. Herein the combination of liquid withdrawal with intermolecular interactions induces the formation of self-assembled molecular domains at the solid-liquid interface. Through proper control of the evaporation rate, amplitude of the assemblies and time for spectral collection at the liquid edge are extensively raised, resulting in a local enhancement and refinement of the Raman response, respectively. Further signal amplification is obtained by taking advantage of the intense local electromagnetic fields generated upon adding a plasmonic coating to the microwell. Major advantages of this optofluidic method lie in the obtainment of high-quality, high-sensitivity Raman spectra with detection limit down to sub-micromolar values. Peculiarly, the assembled proteins in the liquid edge region maintain their native-like state without displaying spectral changes usually occurring when dried drop deposits are considered.

Modulation of Spatiotemporal Particle Patterning in Evaporating Droplets: Applications to Diagnostics and Materials Science

Spatiotemporal particle patterning in evaporating droplets lacks a common design framework. Here, we demonstrate autonomous control of particle distribution in evaporating droplets through the imposition of a salt-induced self-generated electric field as a generalized patterning strategy. Through modeling, a new dimensionless number, termed "capillary-phoresis" (CP) number, arises, which determines the relative contributions of electrokinetic and convective transport to pattern formation, enabling one to accurately predict the mode of particle assembly by controlling the spontaneous electric field and surface potentials. Modulation of the CP number allows the particles to be focused in a specific region in space or distributed evenly. Moreover, starting with a mixture of two different particle types, their relative placement in the ensuing pattern can be controlled, allowing coassemblies of multiple, distinct particle populations. By this approach, hypermethylated DNA, prevalent in cancerous cells, can be qualitatively distinguished from normal DNA of comparable molecular weights. In other examples, we show uniform dispersion of several particle types (polymeric colloids, multiwalled carbon nanotubes, and molecular dyes) on different substrates (metallic Cu, metal oxide, and flexible polymer), as dictated by the CP number. Depending on the particle, the highly uniform distribution leads to surfaces with a lower sheet resistance, as well as superior dye-printed displays.

Patterns produced by dried droplets of protein binary mixtures suspended in water

Patterns formed by the evaporation of a drop containing biological molecules have provided meaningful information about certain pathologies. In this context, several works propose the study of protein solutions as a model to understand the formation of deposits of biological fluids. Generally, dry droplets of proteins in a saline solution create complex aggregates. Here, we present an experimental study on the formation of patterns produced by the evaporation of droplet suspensions containing a protein binary mixture. We explore the structural aspect of such deposits by using optical and atomic force microscopy. We found that salt is unnecessary for the formation of complex structures such as crystal clusters, dendritic and undulated branches, and interlocked chains. Such structural features allow us to differentiate among protein binary mixtures. Finally, we discuss the potential use of this finding to reveal the presence of a protein suspensions, the folded and unfolded state of a protein, as well as their structural changes.

Drop coating deposition Raman spectroscopy of proteinogenic amino acids compared with their solution and crystalline state

The Raman spectra of 20 proteinogenic amino acids were recorded in the solution, glass phase (as drop coating deposition Raman (DCDR) samples) and crystalline forms in the wide spectral range of 200-3200cm^-1. The most apparent spectral differences between the Raman spectra of the crystalline forms, glass phases and aqueous solutions of amino acids were briefly discussed and described in the frame of published works. The possible density dependencies of spectral bands were noted. In some cases, a strong influence of the sample density, as well as of the organization of the water envelope, was observed. The most apparent changes were observed for Ser and Thr. Nevertheless, for the majority of amino acids, the DCDR sample form is an intermediate between the solution and crystalline forms. In contrast, aromatic amino acids have only a small sensitivity to the form of the sample. Our reference set of Raman spectra is useful for revealing discrepancies between the SERS and solid/solution spectra of amino acids. We also found that some previously published Raman spectra of polycrystalline samples resemble glassy state rather than crystalline spectra. Therefore, this reference set of spectra will find application in every branch of Raman spectroscopy where the spectra of biomolecules are collected from coatings.

Rapid label-free identification of Klebsiella pneumoniae antibiotic resistant strains by the drop-coating deposition surface-enhanced Raman scattering method

Although many methodologies have been developed to identify unknown bacteria, bacterial identification in clinical microbiology remains a complex and time-consuming procedure. To address this problem, we developed a label-free method for rapidly identifying clinically relevant multilocus sequencing typing-verified quinolone-resistant Klebsiella pneumoniae strains. We also applied the method to identify three strains from colony samples, ATCC70063 (control), ST11 and ST15; these are the prevalent quinolone-resistant K. pneumoniae strains in East Asia. The colonies were identified using a drop-coating deposition surface-enhanced Raman scattering (DCD-SERS) procedure coupled with a multivariate statistical method. Our workflow exhibited an enhancement factor of 11.3×10⁶ to Raman intensities, high reproducibility (relative standard deviation of 7.4%), and a sensitive limit of detection (100 pM rhodamine 6G), with a correlation coefficient of 0.98. All quinolone-resistant K. pneumoniae strains showed similar spectral Raman shifts (high correlations) regardless of bacterial type, as well as different Raman vibrational modes compared to Escherichia coli strains. Our proposed DCD-SERS procedure coupled with the multivariate statistics-based identification method achieved excellent performance in discriminating similar microbes from one another and also in subtyping of K. pneumoniae strains. Therefore, our label-free DCD-SERS procedure coupled with the computational decision supporting method is a potentially useful method for the rapid identification of clinically relevant K. pneumoniae strains.

Sessile droplets for chemical and biological assays

Sessile droplets are non-movable droplets spanning volumes in the nL-to-μL range. The sessile-droplet-based platform provides a paradigm shift from the conventional, flow-based lab-on-a-chip philosophy, yet offering similar benefits: low reagent/sample consumption, high throughput, automation, and most importantly flexibility and versatility. Moreover, the platform relies less heavily on sophisticated fabrication techniques, often sufficient with a hydrophobic substrate, and no pump is required for operation. In addition, exploiting the physical phenomena that naturally arise when a droplet evaporates, such as the coffee-ring effect or Marangoni flow, can lead to fascinating applications. In this review, we introduce the physics of droplets, and then focus on the different types of chemical and biological assays that have been implemented in sessile droplets, including analyte concentration, particle separation and sorting, cell-based assays, and nucleic acid amplification. Finally, we provide our perspectives on this unique micro-scale platform.

Drop coating deposition of a liposome suspension on surfaces with different wettabilities: “coffee ring” formation and suspension preconcentration

A study of “coffee ring” formation and preconcentration of a liposome suspension dropped on six surfaces with different physico-chemical characteristics.

Graphene-Enhanced Raman Scattering from the Adenine Molecules

An enhanced Raman scattering from a thin layer of adenine molecules deposited on graphene substrate was detected. The value of enhancement depends on the photon energy of the exciting light. The benzene ring in the structure of adenine molecule suggests π-stacking of adenine molecule on top of graphene. So, it is proposed that the enhancement in the adenine Raman signal is explained by the resonance electron transfer from the Fermi level of graphene to the lowest unoccupied molecular orbital (LUMO) level of adenine.

Origins of concentration gradients for diffusiophoresis

Fluid transport that is driven by gradients of pressure, gravity, or electro-magnetic potential is well-known and studied in many fields. A subtler type of transport, called diffusiophoresis, occurs in a gradient of chemical concentration, either electrolyte or non-electrolyte. Diffusiophoresis works by driving a slip velocity at the fluid-solid interface. Although the mechanism is well-known, the diffusiophoresis mechanism is often considered to be an esoteric laboratory phenomenon. However, in this article we show that concentration gradients can develop in a surprisingly wide variety of physical phenomena - imposed gradients, asymmetric reactions, dissolution, crystallization, evaporation, mixing, sedimentation, and others - so that diffusiophoresis is in fact a very common transport mechanism, in both natural and artificial systems. We anticipate that in georeservoir extractions, physiological systems, drying operations, laboratory and industrial separations, crystallization operations, membrane processes, and many other situations, diffusiophoresis is already occurring - often without being recognized - and that opportunities exist for designing this transport to great advantage.

Raman spectroscopy as a novel tool for monitoring biochemical changes and inter-donor variability in stored red blood cell units

Raman spectroscopy has been used to retrieve biochemical information from the supernatant of stored red blood cells (RBCs), demonstrating that some units of donated RBCs accumulate lactate much more readily than others.

H ferritin silencing induces protein misfolding in K562 cells: A Raman analysis

The redox state of the cell is involved in the regulation of many physiological functions as well as in the pathogenesis of several diseases, and is strictly dependent on the amount of iron in its catalytically active state. Alterations of iron homeostasis determine increased steady-state concentrations of Reactive Oxygen Species (ROS) that cause lipid peroxidation, DNA damage and altered protein folding. Ferritin keeps the intracellular iron in a non-toxic and readily available form and consequently plays a central role in iron and redox homeostasis. The protein is composed by 24 subunits of the H- and L-type, coded by two different genes, with structural and functional differences. The aim of this study was to shed light on the role of the single H ferritin subunit (FHC) in keeping the native correct protein three-dimensional structure. To this, we performed Raman spectroscopy on protein extracts from K562 cells subjected to FHC silencing. The results show a significant increase in the percentage of disordered structures content at a level comparable to that induced by H2O2 treatment in control cells. ROS inhibitor and iron chelator were able to revert protein misfolding. This integrated approach, involving Raman spectroscopy and targeted-gene silencing, indicates that an imbalance of the heavy-to-light chain ratio in the ferritin composition is able to induce severe but still reversible modifications in protein folding and uncovers new potential pathogenetic mechanisms associated to intracellular iron perturbation.

Drop-Coating Deposition Raman (DCDR) Spectroscopy as a Tool for Membrane Interaction Studies: Liposome-Porphyrin Complex

Drop-coating deposition Raman (DCDR) spectroscopy is based on the measurement of a sample that has been preconcentrated by being dried on a special hydrophobic plate. In addition to its higher sensitivity, the advantage of DCDR over the conventional Raman spectroscopy is the small sample volume needed, the lack of interference from solvents, and the capability of segregating any impurities present and separating components in more complex samples. In this study, DCDR spectroscopy was employed to investigate the complex of the cationic copper(II) 5,10,15,20-tetrakis(1-methyl-4-pyridyl) porphyrin (CuTMPyP) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) liposomes. Drop-coating deposition Raman spectra were treated using factor analysis (FA), which led to the following conclusions: (i) the distribution of CuTMPyP in the complex is not homogenous, (ii) the DCDR technique segregates complexed and noncomplexed parts of the sample, (iii) the spectral changes caused by the drying process and by the interaction of CuTMPyP with the DPPC liposomes can be distinguished, and (iv) the porphyrin molecules interacting with DPPC affect both the order-disorder properties of the lipid chains and the lipid head.

Colloidal Drop Deposition on Porous Substrates: Competition among Particle Motion, Evaporation, and Infiltration

Recent interest in printable electronics and in particular paper- and textile-based electronics has fueled research in inkjet printing of colloidal drops on porous substrates. On nonporous substrates, the interplay of particle motion and solvent evaporation determines the final deposition morphology of the evaporating colloidal drop. For porous substrates, solvent infiltration into the pores adds a layer of complexity to the deposition patterns that have not been fully elucidated in the literature. In this study, the deposition of picoliter-sized aqueous colloidal droplets containing nanometer- and micrometer-sized particles onto nanoporous anodic aluminum oxide substrates is examined for different drop and particle sizes and relative humidities as well as pore diameters, porosities, and wettabilities of the porous substrates. For the cases considered, solvent infiltration is found to be much faster than both evaporation and particle motion near the contact line, and thus when the substrate fully imbibes the solvent, the well-known "coffee-ring" deposition is suppressed. However, when the solvent is only partially imbibed, a residual droplet volume exists upon completion of the infiltration. For such cases, two time scales are of importance: the time for particle motion to the contact line as a result of both diffusion and advection, t(P), and the evaporation time of the residual drop volume, t(EI). Their ratio, t(P)/t(EI), determines whether the coffee-ring deposition will be formed (t(P)/t(EI) < 1) or suppressed (t(P)/t(EI) > 1).

Drop coating deposition Raman spectroscopy of blood plasma for the detection of colorectal cancer

We have recently applied the technique of drop coating deposition Raman (DCDR) spectroscopy for colorectal cancer (CRC) detection using blood plasma. The aim of this study was to develop a more convenient and stable method based on blood plasma for noninvasive CRC detection. Significant differences are observed in DCDR spectra between healthy (n = 105) and cancer (n = 75) plasma from 15 CRC patients and 21 volunteers, particularly in the spectra that are related to proteins, nucleic acids, and β-carotene. The multivariate analysis principal components analysis and the linear discriminate analysis, together with leave-one-out, cross validation were used on DCDR spectra and yielded a sensitivity of 100% (75/75) and specificity of 98.1% (103/105) for detection of CRC. This study demonstrates that DCDR spectroscopy of blood plasma associated with multivariate statistical algorithms has the potential for the noninvasive detection of CRC.

Identification and relative quantification of tyrosine nitration in a model peptide using two-dimensional infrared spectroscopy

Nitration of tyrosine in proteins and peptides is a post-translational modification that occurs under conditions of oxidative stress. It is implicated in a variety of medical conditions, including neurodegenerative and cardiovascular diseases. However, monitoring tyrosine nitration and understanding its role in modifying biological function remains a major challenge. In this work, we investigate the use of electron-vibration-vibration (EVV) two-dimensional infrared (2DIR) spectroscopy for the study of tyrosine nitration in model peptides. We demonstrate the ability of EVV 2DIR spectroscopy to differentiate between the neutral and deprotonated states of 3-nitrotyrosine, and we characterize their spectral signatures using information obtained from quantum chemistry calculations and simulated EVV 2DIR spectra. To test the sensitivity of the technique, we use mixed-peptide samples containing various levels of tyrosine nitration, and we use mass spectrometry to independently verify the level of nitration. We conclude that EVV 2DIR spectroscopy is able to provide detailed spectroscopic information on peptide side-chain modifications and to detect nitration levels down to 1%. We further propose that lower nitration levels could be detected by introducing a resonant Raman probe step to increase the detection sensitivity of EVV 2DIR spectroscopy.

Comparative study of the self-assembly of gold and silver nanoparticles onto thiophene oil

Nanoparticle self-assembly is fundamentally important for bottom-up functional device fabrication. Currently, most nanoparticle self-assembly has been achieved with gold nanoparticles (AuNPs) functionalized with surfactants, polymeric materials, or cross-linkers. Reported herein is a facile synthesis of gold and silver nanoparticle (AgNP) films assembled onto thiophene oil by simply vortex mixing neat thiophene with colloidal AuNPs or AgNPs for ∼1 min. The AuNP film can be made using every type of colloidal AuNPs we have explored, including sodium borohydride-reduced AuNPs with a diameter of ∼5 nm, tannic acid-reduced AuNPs of ∼10 nm diameter, and citrate-reduced AuNPs with particle sizes of ∼13 and ∼30 nm diameter. The AuNP film has excellent stability and it is extremely flexible. It can be stretched, shrunken, and deformed accordingly by changing the volume or shape of the enclosed thiophene oil. However, the AgNP film is unstable, and it can be rapidly discolored and disintegrated into small flakes that float on the thiophene surface. The AuNP and AgNP films prepared in the glass vials can be readily transferred to glass slides and metal substrates for surface-enhanced Raman spectral acquisition.