Ensemble multivariate analysis to improve identification of articular cartilage disease in noisy Raman spectra

The development of new methods for the early diagnosis of cartilage disease could offer significant improvement in patient care. Raman spectroscopy is an emerging biomedical technology with unique potential to recognize disease tissues, though difficulty in obtaining the samples needed to train a diagnostic and excessive signal noise could slow its development into a clinical tool. In the current report we detail the use of principal component analysis – linear discriminant analysis (PCA‐LDA) on spectra from pairs of materials modeling cartilage disease to create multiple spectral scoring metrics, which could limit the reliance on primary training data for identifying disease in low signal‐to‐noise‐ratio (SNR) Raman spectra. Our proof‐of‐concept experiments show that combinations of these model‐metrics has the potential to improve the classification of low‐SNR Raman spectra from human normal and osteoarthritic (OA) cartilage over a single metric trained with spectra from the same healthy and OA tissues.

Scatter plot showing the PCA‐LDA derived human‐disease‐metric scores versus rat‐model‐metric scores for 7656 low signal‐to‐noise spectra from healthy (blue) and osteoarthritic (red) cartilage. Light vertical and horizontal lines represent the optimized single metric classification boundary. Dark diagonal line represents the classification of boundary resulting from the optimized combination of the two metrics. Abbreviations: er (error rate), PCA‐LDA (principal component analysis – linear discriminant analysis), HOA (human osteoarthritis), HAC (human articular cartilage), RIF (rat injury fibrocartilage), RAC (rat articular cartilage).     

Ultra‐sensitive immunoassay biosensors using hybrid plasmonic‐biosilica nanostructured materials

We experimentally demonstrate an ultra‐sensitive immunoassay biosensor using diatom biosilica with self‐assembled plasmonic nanoparticles. As the nature‐created photonic crystal structures, diatoms have been adopted to enhance surface plasmon resonances of metal nanoparticles on the surfaces of diatom frustules and to increase the sensitivity of surface‐enhanced Raman scattering (SERS). In this study, a sandwich SERS immunoassay is developed based on the hybrid plasmonic‐biosilica nanostructured materials that are functionalized with goat anti‐mouse IgG. Our experimental results show that diatom frustules improve the detection limit of mouse IgG to 10 pg/mL, which is ?100× better than conventional colloidal SERS sensors on flat glass.

Ultra‐sensitive immunoassay biosensor using diatom biosilica with self‐assembled plasmonic nanoparticles.     

Biochemical,biophysical, and genetic changes of porcine trophoblast‐derived stem‐like cells during differentiation as evaluated using Raman microspectroscopy,Atomic force microscopy,and quantitative polymerase chain reaction

Porcine trophoblast‐derived stem‐like cells grown into serum medium start to differentiate and become senescent within 30 days. However, trophoblast‐derived cells, cultured in vitro in a defined and non‐serum medium, have the regenerative properties, such as indefinite passage and foreign DNA receptivity, similar to stem cells. To evaluate the biochemical, biophysical, and genetic changes of the terminal differentiation of trophoblast derived cells, Raman microspectroscopy, atomic force microscopy, and qPCR were applied. It was found that Raman spectral intensities of characteristic peaks, cell morphology, and Young's modulus can be used to distinguish differentiated and undifferentiated trophoblast cells. In addition, 17 cytoskeleton and extracellular matrix‐related genes were significantly impacted by medium type (non‐serum versus serum). Our findings suggest that Raman microspectroscopy and atomic force microscopy—both considered as label‐free, non‐invasive techniques—can be applied to distinguish differentiated trophoblast cells, and cellular biochemical information and biophysical properties can be indicative of cellular differences during cell differentiation. In addition, most of cytoskeleton‐related genes exhibit similar pattern to that of Young's modulus during trophoblast cell differentiation, indicating the potential connection between cytoskeleton‐related genes and cellular stiffness. genesis 53:749–761, 2015. © 2015 Wiley Periodicals, Inc.     

Surface Enhanced Raman Spectroscopy Detection of Biomolecules Using EBL Fabricated Nanostructured Substrates

Fabrication and characterization of conjugate nano-biological systems interfacing metallic nanostructures on solid supports with immobilized biomolecules is reported. The entire sequence of relevant experimental steps is described, involving the fabrication of nanostructured substrates using electron beam lithography, immobilization of biomolecules on the substrates, and their characterization utilizing surface-enhanced Raman spectroscopy (SERS). Three different designs of nano-biological systems are employed, including protein A, glucose binding protein, and a dopamine binding DNA aptamer. In the latter two cases, the binding of respective ligands, D-glucose and dopamine, is also included. The three kinds of biomolecules are immobilized on nanostructured substrates by different methods, and the results of SERS imaging are reported. The capabilities of SERS to detect vibrational modes from surface-immobilized proteins, as well as to capture the protein-ligand and aptamer-ligand binding are demonstrated. The results also illustrate the influence of the surface nanostructure geometry, biomolecules immobilization strategy, Raman activity of the molecules and presence or absence of the ligand binding on the SERS spectra acquired.     

Dispersive Raman spectroscopy allows the identification and quantification of melanin types

Melanins are the most prevalent pigments in animals and are involved in visual communication by producing colored traits that often evolve as intraspecific signals of quality. Identifying and quantifying melanins are therefore essential to understand the function and evolution of melanin‐based signals. However, the analysis of melanins is difficult due to their insolubility and the lack of simple methods that allow the identification of their chemical forms. We recently proposed the use of Raman spectroscopy as a simple, noninvasive technique that can be used to identify and quantify melanins in feathers and hairs. Contrarily, other authors later stated that melanins are characterized by a lack of defined Raman signals. Here, we use confocal Raman microscopy to confirm previous analyses showing that the two main chemical forms of melanins (eumelanin and pheomelanin) exhibit distinct Raman signal and compare different excitation wavelengths to analyze synthetic pheomelanin and natural melanins in feathers of different species of birds. Our analyses indicate that only laser excitation wavelengths below 1064 nm are useful for the analysis of melanins by Raman spectroscopy, and only 780‐nm laser in the case of melanins in feathers. These findings show that the capacity of Raman spectroscopy to distinguish different chemical forms of melanins depends on laser power and integration time. As a consequence, Raman spectroscopy should be applied after preliminar analyses using a range of these parameters, especially in fragile biological tissues such as feathers.     

Resonance Raman and FTIR spectroscopic characterization of the closed and open states of channelrhodopsin-1

Channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) is a light-activated cation channel, which is a promising optogenetic tool. We show by resonance Raman spectroscopy and retinal extraction followed by high pressure liquid chromatography (HPLC) that the isomeric ratio of all-trans to 13-cis of solubilized channelrhodopsin-1 is with 70:30 identical to channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2). Critical frequency shifts in the retinal vibrations are identified in the Raman spectrum upon transition to the open (conductive P₂³⁸⁰) state. Fourier transform infrared spectroscopy (FTIR) spectra indicate different structures of the open states in the two channelrhodopsins as reflected by the amide I bands and the protonation pattern of acidic amino acids.     

The role of protein dynamics and thermal fluctuations in regulating cytochrome c/cytochrome c oxidase electron transfer

In this overview we present recent combined electrochemical, spectroelectrochemical, spectroscopic and computational studies from our group on the electron transfer reactions of cytochrome c and of the primary electron acceptor of cytochrome c oxidase, the Cu_A site, in biomimetic complexes. Based on these results, we discuss how protein dynamics and thermal fluctuations may impact on protein ET reactions, comment on the possible physiological relevance of these results, and finally propose a regulatory mechanism that may operate in the Cyt/CcO electron transfer reaction in vivo. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.     

Low concentration structural dynamics of lanreotide and somatostatin‐14

Lanreotide, a synthetic cyclic octapeptide, analogue of the peptide hormone somatostatin‐14 (SST‐14), is routinely used as a long‐acting medication in the management of neuroendocrine tumors. Despite its therapeutic importance, low concentration structural data is still lacking for lanreotide. In fact, the major part of the previous structural investigations were focused on the remarkable aggregation properties of this peptide, appearing at high concentrations (>5 mM). Here, we have applied three optical spectroscopic techniques, i.e. fluorescence, circular dichroism and Raman scattering, for analyzing the structural dynamics at the concentrations below 5 mM, where lanreotide exists either in a monomer state or at the first stages of aggregation. The obtained data from lanreotide were discussed through their comparison with those collected from SST‐14, leading us to the following conclusions: (i) The central D‐Trp residue, forming with its adjacent Lys the main receptor interacting part of lanreotide, keeps a constant high rotational freedom whatever the environment (water, water/methanol, methanol). (ii) A solvent‐dependent tight β‐turn, belonging to the type‐II' family, is revealed in lanreotide. (iii) Raman data analyzed by band decomposition in the amide (I and III) regions allowed estimation of different secondary structural elements within the millimolar range. Interestingly, the applied protocol shows a perfect agreement between the structural features provided by the amide I and amide III Raman markers. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 1019–1028, 2014.     

G‐fibres in storage roots of Trifolium pratense (Fabaceae): tensile stress generators for contraction

Root contraction has been described for many species within the plant kingdom for over a century, and many suggestions have been made for mechanisms behind these contractions. To move the foliage buds deeper into the soil, the proximal part of the storage root of Trifolium pratense contracts by up to 30%. Anatomical studies have shown undeformed fibres next to strongly deformed tissues. Raman imaging revealed that these fibres are chemically and structurally very similar to poplar (Populus) tension wood fibres, which are known to generate high tensile stresses and bend leaning stems or branches upright. Analogously, an almost pure cellulosic layer is laid down in the lumen of certain root fibres, on a thin lignified secondary cell wall layer. To reveal its stress generation capacities, the thick cellulosic layer, reminiscent of a gelatinous layer (G‐layer) in tension wood, was selectively removed by enzymatic treatment. A substantial change in the dimensions of the isolated wood fibre bundles was observed. This high stress relaxation indicates the presence of high tensile stress for root contraction. These findings indicate a mechanism of root contraction in T. pratense (red clover) actuated via tension wood fibres, which follows the same principle known for poplar tension wood.     

Validation model for Raman based skin carotenoid detection

Raman spectroscopy holds promise as a rapid objective non-invasive optical method for the detection of carotenoid compounds in human tissue in vivo. Carotenoids are of interest due to their functions as antioxidants and/or optical absorbers of phototoxic light at deep blue and near UV wavelengths. In the macular region of the human retina, carotenoids may prevent or delay the onset of age-related tissue degeneration. In human skin, they may help prevent premature skin aging, and are possibly involved in the prevention of certain skin cancers. Furthermore, since carotenoids exist in high concentrations in a wide variety of fruits and vegetables, and are routinely taken up by the human body through the diet, skin carotenoid levels may serve as an objective biomarker for fruit and vegetable intake. Before the Raman method can be accepted as a widespread optical alternative for carotenoid measurements, direct validation studies are needed to compare it with the gold standard of high performance liquid chromatography. This is because the tissue Raman response is in general accompanied by a host of other optical processes which have to be taken into account. In skin, the most prominent is strongly diffusive, non-Raman scattering, leading to relatively shallow light penetration of the blue/green excitation light required for resonant Raman detection of carotenoids. Also, sizable light attenuation exists due to the combined absorption from collagen, porphyrin, hemoglobin, and melanin chromophores, and additional fluorescence is generated by collagen and porphyrins. In this study, we investigate for the first time the direct correlation of in vivo skin tissue carotenoid Raman measurements with subsequent chromatography derived carotenoid concentrations. As tissue site we use heel skin, in which the stratum corneum layer thickness exceeds the light penetration depth, which is free of optically confounding chromophores, which can be easily optically accessed for in vivo RRS measurement, and which can be easily removed for subsequent biochemical measurements. Excellent correlation (coefficient R = 0.95) is obtained for this tissue site which could serve as a model site for scaled up future validation studies of large populations. The obtained results provide proof that resonance Raman spectroscopy is a valid non-invasive objective methodology for the quantitative assessment of carotenoid antioxidants in human skin in vivo.