This research was funded by Regione Lombardia in the framework of the Project MOBARTECH: una piattaforma mobile tecnologica, interattiva e partecipata per lo studio, la conservazione e la valorizzazione di beni storico-artistici - Call Accordi per la Ricerca e l&#39;Innovazione.
The authors are grateful to the staff at Museo del Novecento for the support during the&#160;in situ&#160;experimental sessions and to the Associazione Pellizza da Volpedo for the access to Studio Museo.

<ol>
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K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+insights+into+Pablo+Picasso's+La+Mis&#233;reuse+accroupie+using+X-ray+fluorescence+imaging+and+reflectance+spectroscopies+combined+with+micro-analyses+of+samples.">New insights into Pablo Picasso's La Mis&#233;reuse accroupie using X-ray fluorescence imaging and reflectance spectroscopies combined with micro-analyses of samples.</a> SN Applied Sciences. 2, 1-6 (2020).</li><li>Garofano, I., Perez-Rodriguez, J. L., Robador, M. D., Duran, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+innovative+combination+of+non-invasive+UV-Visible-FORS,+XRD+and+XRF+techniques+to+study+Roman+wall+paintings+from+Seville,+Spain.">An innovative combination of non-invasive UV-Visible-FORS, XRD and XRF techniques to study Roman wall paintings from Seville, Spain.</a> Journal of Cultural Heritage. 22, 1028-1039 (2016).</li><li>Dupuis, G., Elias, M., Simonot, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pigment+identification+by+fiber-optics+diffuse+reflectance+spectroscopy.">Pigment identification by fiber-optics diffuse reflectance spectroscopy.</a> Applied Spectroscopy. 56, 1329-1336 (2002).</li><li>Bacci, M., Picollo, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Non-destructive+spectroscopic+detection+of+cobalt+(II)+in+paintings+and+glass.">Non-destructive spectroscopic detection of cobalt (II) in paintings and glass.</a> Studies in Conservation. 41, 136-144 (1996).</li><li>Cosentino, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FORS+spectral+database+of+historical+pigments+in+different+binders.">FORS spectral database of historical pigments in different binders.</a> E-Conservation Journal. , 54-65 (2014).</li><li>Leona, M., Winter, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fiber+optics+reflectance+spectroscopy:+a+unique+tool+for+the+investigation+of+Japanese+paintings.">Fiber optics reflectance spectroscopy: a unique tool for the investigation of Japanese paintings.</a> Studies in Conservation. 46, 153-162 (2001).</li><li>Cheilakou, E., Troullinos, M., Koui, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+pigments+on+Byzantine+wall+paintings+from+Crete+(14th+century+AD)+using+non-invasive+Fiber+Optics+Diffuse+Reflectance+Spectroscopy+(FORS).">Identification of pigments on Byzantine wall paintings from Crete (14th century AD) using non-invasive Fiber Optics Diffuse Reflectance Spectroscopy (FORS).</a> Journal of Archaeological Science. 41, 541-555 (2014).</li><li>Kubik, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hyperspectral+imaging:+a+new+technique+for+the+non-invasive+study+of+artworks.">Hyperspectral imaging: a new technique for the non-invasive study of artworks.</a> Physical Techniques in the Study of Art, Archaeology and Cultural. 2, 199-259 (2007).</li><li>Fischer, C., Kakoulli, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multispectral+and+hyperspectral+imaging+technologies+in+conservation:+current+research+and+potential+applications.">Multispectral and hyperspectral imaging technologies in conservation: current research and potential applications.</a> Studies in Conservation. 51, 3-16 (2006).</li><li>Daniel, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hyperspectral+imaging+applied+to+the+analysis+of+Goya+paintings+in+the+Museu+of+Zaragoza+(Spain).">Hyperspectral imaging applied to the analysis of Goya paintings in the Museu of Zaragoza (Spain).</a> Microchemical Journal. 126, 113-120 (2016).</li><li>Baronti, S., Casini, A., Lotti, F., Porcinai, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Principal+component+analysis+of+visible+and+near-infrared+multispectral+images+of+works+of+art.">Principal component analysis of visible and near-infrared multispectral images of works of art.</a> Chemometrics and Intelligent Laboratory Systems. 39, 103-114 (1997).</li><li>Mansfield, J. 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A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+spectral+image+processing+system+(SIPS)-interactive+visualization+and+analysis+of+imaging+spectrometer+data.">The spectral image processing system (SIPS)-interactive visualization and analysis of imaging spectrometer data.</a> AIP Conference Proceedings. , (1993).</li><li>Yang, C., Everitt, J. H., Bradford, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Yield+estimation+from+hyperspectral+imagery+using+spectral+angle+mapper+(SAM).">Yield estimation from hyperspectral imagery using spectral angle mapper (SAM).</a> Transactions of the ASABE. 51, 729-737 (2008).</li><li>Delaney, J. K. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Integrated+X-ray+fluorescence+and+diffuse+visible-to-near-infrared+reflectance+scanner+for+standoff+elemental+and+molecular+spectroscopic+imaging+of+paints+and+works+on+paper.">Integrated X-ray fluorescence and diffuse visible-to-near-infrared reflectance scanner for standoff elemental and molecular spectroscopic imaging of paints and works on paper.</a> Heritage Science. 6, 1-12 (2018).</li><li>Richards, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Remote sensing digital image analysis. 3, (1999).</li><li>Mobaraki, N., Amigo, J. 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The authors have nothing to disclose.

Hyperspectral reflectance imaging datasets are large reservoirs of information; therefore, the development of robust and, possibly, automated protocols to analyze the data is a key turn to exploit their potential15,17. The proposed algorithm answers this need in the field of cultural heritage with particular attention to the characterization of the pigments of paintings. Based on SAM20,21, the algorithm s...

Reflectance Spectroscopy (RS) and Fiber Optics Reflectance Spectroscopy (FORS) are based on the detection of the light reflected by surfaces once illuminated by a light source, typically a tungsten-halogen lamp. The output of the acquisition system is constituted by spectra where the reflectance is monitored as a function of the wavelength in a range that depends on the characteristics of the employed experimental setup1,2,3. Introduced during the last four decades4,5, RS and FORS are typically used in combination with X-ray fluorescence and other spectroscopies to describe the materials and the techniques used by artists to realize their masterpieces6,7,8,9. The study of the reflectance spectra is usually performed by comparing the data from the sample with a group of reference spectra selected by the user in personal or public databases. Once the reference spectra that comply with the realization period of the sample and with the&#160;modus operandi&#160;of the artist have been identified, the user recognizes the main features of the reflectance spectra (i.e., transition, absorption, and reflection bands1,2,10,11) and then, with the help of other techniques6,7,8 they distinguish&#160;the pigments that have been used in the paintings. Finally they discusses the slight differences that there exist between the references and the experimental spectra7,9.
In most cases, the experimental datasets are composed of a few spectra, collected from areas chosen by art experts and assumed to be significant for the characterization of the painting6, 12,13. Despite the skills and the experience of the user, a few spectra cannot fully exhaust the characteristics of the whole painted surface. Moreover, the result of the analysis will always be strongly dependent on the expertise of the performer. In this scenario, Hyperspectral Reflectance Imaging (HRI3,14,15) could be a useful resource. Instead of a few isolated spectra, the experimental setups return the reflectance properties of extended portions or even of the whole artefact under investigation16. The two main advantages with respect to the acquisition of the isolated spectra are evident. On one hand, the availability of the spatial distribution of the reflectance properties allows the identification of areas that hide interesting features, even though they may not seem peculiar17. On the other hand, the hypercubes guarantee a number of spectra high enough to enable the statistical analysis of the data. These facts support the comprehension of the distribution of pigments within the painted surface18,19.
With HRI, the comparison of the experimental data with the references could be hard to handle15. A typical detector returns hypercubes of at least 256 x 256 spectra. This would require the user to evaluate more than 65,000 reflectance spectra against each reference, a task almost impossible to be carried out manually in a reasonable time. Therefore, the request for robust and, possibly, automated protocols to manage and analyze HRI datasets is more than justified15,17. The proposed method answers this need by handling the whole analytic procedure with the minimum involvement and the maximum flexibility.
An algorithm comprising a set of home-made codes (Table of Materials) reads, manages, and organizes the files returned by the experimental setup. It allows the fine selection of the portions of the Fields of View (FOVs, one field of view is the area of the painting monitored by a single hypercube) to be studied and performs the analysis of the data based on the Spectral Angle Mapper (SAM) method20,21 and on the manipulation of the original spectra. SAM returns false color gray-scale images called similarity maps. The values of the pixels of these maps correspond to the spectral angles that are the angles between the spectra stored in the hypercubes&#160;and the so-called End Members (EMs, a group of reference spectra that should describe the features of the surface monitored by the hypercubes)22. In the case of RS applied to paintings, the EMs are the reflectance spectra of pigments that should match the palette of the Master. They are chosen based on the available information about the artist, the realization period of the painting, and the expertise of the user. Therefore, the output of the SAM is a set of maps that describes the spatial distributions of these pigments over the painting surface and that supports the user to infer the materials used by the artist and their organization in the artefact. The algorithm offers the possibility of employing all kind of references independently from their origin. The references can be specific spectra selected within the hypercubes, come from databases, be acquired by a different instrument on a different surface (such as samples of pigments or the palette of the artist, for instance), or be obtained employing any kind of reflectance spectroscopy, FORS included.
SAM has been preferred among the available classification methods because it has been demonstrated to be effective for characterizing pigments (refer to the book by Richard23&#160;to have an overview of the main available classification methods).&#160;Instead, the idea of developing a home-made protocol rather than adopting one of the many tools freely available on the net24,25 relies on a practical consideration. Despite the effectiveness and scientific foundation of the existing GUIs and software, a single tool hardly satisfies all the needs of the user. There could be an Input/Output (I/O) issue because a tool does not manage the file containing the raw data. There could be an issue regarding the analysis of the data because another tool does not provide the desired approach. There could be a limitation in the handling of the data because the simultaneous analysis of multiple datasets is not supported. In any case, a perfect tool does not exist. Each method must be adjusted to the data or vice versa. Therefore, the development of a home-made protocol has been preferred.
The presented approach offers neither a complete set of analytical methods (see, for comparison, the tool proposed by Mobaraki and Amigo24) nor an easy-to-manage user-interface (see, for comparison, the software employed by Zhu and co-workers25), but, in exchange, it focuses on a still underrated aspect of hyperspectral data analysis: the opportunity to manipulate the detected spectra. The power of the approach is illustrated by applying it to the painting Quarto Stato by Giuseppe Pellizza da Volpedo (Figure 1), an iconic oil on canvas held in the Museo del Novecento in Milan, Italy. Note that, since the approach requires running home-made codes, the developer arbitrarily chose the names of the codes and both the input and output variables used in the description of the protocol. The names of the variables can be changed by the user but they must be provided as follow: the input and out variables must be written respectively within brackets and eventually separated by comma and within square brackets and eventually separated by a white space.&#160;On the contrary the names of the codes cannot be altered.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>ImageJ/Fiji</td>
			<td>Specim (Oulo, Finlad)</td>
			<td>N/A</td>
			<td>Portable reflectance hyperspectral camera used to acquire the hypercubes</td>
		</tr>
		<tr>
			<td>MATLAB 2019b</td>
			<td>StellarNet Inc (Tampa, Florida, USA)</td>
			<td>N/A</td>
			<td>Portable reflectance spectrometer used to acquire independent reflectance spectra</td>
		</tr>
		<tr>
			<td>Specim IQ Hyperspectral Camera</td>
			<td>National Institutes of Health (Bethesda, Maryland, USA)</td>
			<td>N/A</td>
			<td>&#160;Open source Java image processing program</td>
		</tr>
		<tr>
			<td>StellarNet BLUE-wave Miniature Spectrometer</td>
			<td>&#160;MathWorks (Natick, Massachusset, USA)</td>
			<td>N/A</td>
			<td>Program Language and numerical computing environment</td>
		</tr>
	</tbody>
</table>

applying hyperspectral reflectance imaging to investigate the palettes and the techniques of painters

Reflectance Spectroscopy (RS) and Fiber Optics Reflectance Spectroscopy (FORS) are well-established techniques for the investigation of works of art with particular attention to paintings. Most modern museums put at the disposal of their research groups portable equipment that, together with the intrinsic non-invasiveness of RS and FORS, makes possible the in situ collection of reflectance spectra from the surface of artefacts. The comparison, performed by experts in pigments and painting materials, of the experimental data with databases of reference spectra drives the characterization of the palettes and of the techniques used by the artists. However, this approach requires specific skills and it is time consuming especially if the number of the spectra to be investigated becomes large as is the case of Hyperspectral Reflectance Imaging (HRI) datasets. The HRI experimental setups are multi-dimensional cameras that associate the spectral information, given by the reflectance spectra, with the spatial localization of the spectra over the painted surface. The resulting datasets are 3D-cubes (called hypercubes or data-cubes) where the first two dimensions locate the spectrum over the painting and the third is the spectrum itself (i.e., the reflectance of that point of the painted surface versus the wavelength in the operative range of the detector). The capability of the detector to simultaneously collect a great number of spectra (typically much more than 10,000 for each hypercube) makes the HRI datasets large reservoirs of information and justifies the need for the development of robust and, possibly, automated protocols to analyze the data. After the description of the procedure designed for the data acquisition, we present an analysis method that systematically exploits the potential of the hypercubes. Based on Spectral Angle Mapper (SAM) and on the manipulation of the collected spectra, the algorithm handles and analyzes thousands of spectra while at the same time it supports&#160;the user to unveil the features of the samples under investigation. The power of the approach is illustrated by applying it to Quarto Stato, the iconic masterpiece by Giuseppe Pellizza da Volpedo, held in the Museo del Novecento in Milan (Italy).

The proposed protocol offers a set of interesting features for the management and the analysis of HRI data. The I/O (step 3.1) of the raw data is always the first problem that must be solved before applying any analysis method and it can become a critical issue when dealing with large amounts of data. In the present case, the only task regarding the raw data is to store the experimental results into a dedicated folder and select it by browsing the hard disk when running the reading code (step 3.1.1). Thereafter, the crop...

Watch this Scientific Journal Video about Applying Hyperspectral Reflectance Imaging to Investigate the Palettes and the Techniques of Painters at JoVE.com

Applying Hyperspectral Reflectance Imaging to Investigate the Palettes and the Techniques of Painters

Hyperspectral Reflectance Imaging hypercubes include remarkable information into a large amount of data. Therefore, the request for automated protocols to manage and study the datasets is widely justified. The combination of Spectral Angle Mapper, data manipulation, and a user-adjustable analysis method constitutes a key-turn for exploring the experimental results.

Reflectance Spectroscopy (RS) and Fiber Optics Reflectance Spectroscopy (FORS) are well-established techniques for the investigation of works of art with ...

applying-hyperspectral-reflectance-imaging-to-investigate-palettes

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Chemistry

2.3K Views.  Università degli Studi di Milano-Bicocca. Hyperspectral Reflectance Imaging hypercubes include remarkable information into a large amount of data. Therefore, the request for automated protocols to manage and study the datasets is widely justified. The combination of Spectral Angle Mapper, data manipulation, and a user-adjustable analysis method constitutes a key-turn for exploring the experimental results.

Video: Applying Hyperspectral Reflectance Imaging to Investigate the Palettes and the Techniques of Painters

Origami Inspired Self-assembly of Patterned and Reconfigurable Particles

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two dimensional (2D) structures. These technologies are mature, offer high precision and many of them can be implemented in a high-throughput manner. We leverage the advantages of planar lithography and combine them with self-folding methods1-20 wherein physical forces derived from surface tension or residual stress, are used to curve or fold planar structures into three dimensional (3D) structures. In doing so, we make it possible to mass produce precisely patterned static and reconfigurable particles that are challenging to synthesize.
In this paper, we detail visualized experimental protocols to create patterned particles, notably, (a) permanently bonded, hollow, polyhedra that self-assemble and self-seal due to the minimization of surface energy of liquefied hinges21-23 and (b) grippers that self-fold due to residual stress powered hinges24,25. The specific protocol described can be used to create particles with overall sizes ranging from the micrometer to the centimeter length scales. Further, arbitrary patterns can be defined on the surfaces of the particles of importance in colloidal science, electronics, optics and medicine. More generally, the concept of self-assembling mechanically rigid particles with self-sealing hinges is applicable, with some process modifications, to the creation of particles at even smaller, 100 nm length scales22, 26 and with a range of materials including metals21, semiconductors9 and polymers27. With respect to residual stress powered actuation of reconfigurable grasping devices, our specific protocol utilizes chromium hinges of relevance to devices with sizes ranging from 100 &mu;m to 2.5 mm. However, more generally, the concept of such tether-free residual stress powered actuation can be used with alternate high-stress materials such as heteroepitaxially deposited semiconductor films5,7 to possibly create even smaller nanoscale grasping devices.

We describe experimental details of the synthesis of patterned and reconfigurable particles from two dimensional (2D) precursors. This methodology can be used to create particles in a variety of shapes including polyhedra and grasping devices at length scales ranging from the micro to centimeter scale.

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two ...

Isolation and Chemical Characterization of Lipid A from Gram-negative Bacteria

Lipopolysaccharide (LPS) is the major cell surface molecule of gram-negative bacteria, deposited on the outer leaflet of the outer membrane bilayer. LPS can be subdivided into three domains: the distal O-polysaccharide, a core oligosaccharide, and the lipid A domain consisting of a lipid A molecular species and 3-deoxy-D-manno-oct-2-ulosonic acid residues (Kdo). The lipid A domain is the only component essential for bacterial cell survival. Following its synthesis, lipid A is chemically modified in response to environmental stresses such as pH or temperature, to promote resistance to antibiotic compounds, and to evade recognition by mediators of the host innate immune response. The following protocol details the small- and large-scale isolation of lipid A from gram-negative bacteria. Isolated material is then chemically characterized by thin layer chromatography (TLC) or mass-spectrometry (MS). In addition to matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS, we also describe tandem MS protocols for analyzing lipid A molecular species using electrospray ionization (ESI) coupled to collision induced dissociation (CID) and newly employed ultraviolet photodissociation (UVPD) methods. Our MS protocols allow for unequivocal determination of chemical structure, paramount to characterization of lipid A molecules that contain unique or novel chemical modifications. We also describe the radioisotopic labeling, and subsequent isolation, of lipid A from bacterial cells for analysis by TLC. Relative to MS-based protocols, TLC provides a more economical and rapid characterization method, but cannot be used to unambiguously assign lipid A chemical structures without the use of standards of known chemical structure. Over the last two decades isolation and characterization of lipid A has led to numerous exciting discoveries that have improved our understanding of the physiology of gram-negative bacteria, mechanisms of antibiotic resistance, the human innate immune response, and have provided many new targets in the development of antibacterial compounds.

Isolation and characterization of the lipid A domain of lipopolysaccharide (LPS) from gram-negative bacteria provides insight into cell surface based mechanisms of antibiotic resistance, bacterial survival and fitness, and how chemically diverse lipid A molecular species differentially modulate host innate immune responses.

Lipopolysaccharide (LPS) is the major cell surface molecule of gram-negative bacteria, deposited on the outer leaflet of the outer membrane bilayer. LPS ...

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy.
NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. Due to difficulty in crystallization to provide single crystals suitable for X-ray crystallography, the NMR technique is extremely valuable, especially as it provides information on the solution state rather than the solid state. Herein we describe all steps that are required for full three-dimensional structure determinations by NMR. The protocol includes sample preparation in an NMR tube, 1D and 2D data collection and processing, peak assignment and integration, molecular mechanics calculations, and structure analysis. Importantly, the analysis was first conducted without any preset metal-ligand bonds, to assure a reliable structure determination in an unbiased manner.

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

The NMR-solution structure of a metallochaperone model peptide with Cu (I) was determined, and a detailed protocol from sample preparation and 1D and 2D data collection to a three-dimensional structure is described.

Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox ...

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control self-assembly and mimicking this process in vitro will bring about major advances in the areas of materials science and nanotechnology. Among the available biological building blocks, peptides have several advantages as they present substantial diversity, their synthesis in large scale is straightforward, and they can easily be modified with biological and chemical entities1,2. Several classes of designed peptides such as cyclic peptides, amphiphile peptides and peptide-conjugates self-assemble into ordered structures in solution. Homoaromatic dipeptides, are a class of short self-assembled peptides that contain all the molecular information needed to form ordered structures such as nanotubes, spheres and fibrils3-8. A large variety of these peptides is commercially available.
This paper presents a procedure that leads to the formation of ordered structures by the self-assembly of homoaromatic peptides. The protocol requires only commercial reagents and basic laboratory equipment. In addition, the paper describes some of the methods available for the characterization of peptide-based assemblies. These methods include electron and atomic force microscopy and Fourier-Transform Infrared Spectroscopy (FT-IR). Moreover, the manuscript demonstrates the blending of peptides (coassembly) and the formation of a &#34;beads on a string&#34;-like structure by this process.9 The protocols presented here can be adapted to other classes of peptides or biological building blocks and can potentially lead to the discovery of new peptide-based structures and to better control of their assembly.

This paper describes the formation of highly ordered peptide-based structures by the spontaneous process of self-assembly. The method utilizes commercially available peptides and common lab equipment. This technique can be applied to a large variety of peptides and may lead to the discovery of new peptide-based assemblies.

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control ...

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid phase by using combinatorial chemistry. One of the most well studied classes of peptidomimetics is peptoids. Peptoids are easy to synthesize and have been shown to be proteolysis-resistant and cell-permeable. Over the past decade, many useful protein ligands have been identified through screening of peptoid libraries. However, most of the ligands identified from peptoid libraries do not display high affinity, with rare exceptions. This may be due, in part, to the lack of chiral centers and conformational constraints in peptoid molecules. Recently, we described a new synthetic route to access peptide tertiary amides (PTAs). PTAs are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. With side chains on both &#945;-carbon and main chain nitrogen atoms, the conformation of these molecules are greatly constrained by sterical hindrance and allylic 1,3 strain. (Figure 1) Our study suggests that these PTA molecules are highly structured in solution and can be used to identify protein ligands. We believe that these molecules can be a future source of high-affinity protein ligands. Here we describe the synthetic method combining the power of both split-and-pool and sub-monomer strategies to synthesize a sample one-bead one-compound (OBOC) library of PTAs.

Peptide tertiary amides (PTAs) are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. Here we describe a synthetic method which combines&#160;both split-and-pool and sub-monomer strategies to synthesize a one-bead one-compound library of PTAs.

Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid ...

Amide Coupling Reaction for the Synthesis of Bispyridine-based Ligands and Their Complexation to Platinum as Dinuclear Anticancer Agents

Amide coupling reactions can be used to synthesize bispyridine-based ligands for use as bridging linkers in multinuclear platinum anticancer drugs. Isonicotinic acid, or its derivatives, are coupled to variable length diaminoalkane chains under an inert atmosphere in anhydrous DMF or DMSO with the use of a weak base, triethylamine, and a coupling agent, 1-propylphosphonic anhydride. The products precipitate from solution upon formation or can be precipitated by the addition of water. If desired, the ligands can be further purified by recrystallization from hot water. Dinuclear platinum complex synthesis using the bispyridine ligands is done in hot water using transplatin. The most informative of the chemical characterization techniques to determine the structure and gross purity of both the bispyridine ligands and the final platinum complexes is 1H NMR with particular analysis of the aromatic region of the spectra (7-9 ppm). The platinum complexes have potential application as anticancer agents and the synthesis method can be modified to produce trinuclear and other multinuclear complexes with different hydrogen bonding functionality in the bridging ligand.

This protocol describes the use of amide coupling reactions of isonicotinic acid and diaminoalkanes to form bridging ligands suitable for use in the synthesis of multinuclear platinum complexes, which combine aspects of the anticancer drugs BBR3464 and picoplatin.

Amide coupling reactions can be used to synthesize bispyridine-based ligands for use as bridging linkers in multinuclear platinum anticancer drugs. ...

Synthesis of Protein Bioconjugates via Cysteine-maleimide Chemistry

The chemical linking or bioconjugation of proteins to fluorescent dyes, drugs, polymers and other proteins has a broad range of applications, such as the development of antibody drug conjugates (ADCs) and nanomedicine, fluorescent microscopy and systems chemistry. For many of these applications, specificity of the bioconjugation method used is of prime concern. The Michael addition of maleimides with cysteine(s) on the target proteins is highly selective and proceeds rapidly under mild conditions, making it one of the most popular methods for protein bioconjugation.
We demonstrate here the modification of the only surface-accessible cysteine residue on yeast cytochrome c with a ruthenium(II) bisterpyridine maleimide. The protein bioconjugation is verified by gel electrophoresis and purified by aqueous-based fast protein liquid chromatography in 27% yield of isolated protein material. Structural characterization with MALDI-TOF MS and UV-Vis is then used to verify that the bioconjugation is successful. The protocol shown here is easily applicable to other cysteine - maleimide coupling of proteins to other proteins, dyes, drugs or polymers.

Synthesis of Protein Bioconjugates via Cysteine-maleimide Chemistry

This protocol details the important steps required for the bioconjugation of a cysteine containing protein to a maleimide, including reagent purification, reaction conditions, bioconjugate purification and bioconjugate characterization.

The chemical linking or bioconjugation of proteins to fluorescent dyes, drugs, polymers and other proteins has a broad range of applications, such as the ...

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

Carboxylic acids are organic acids containing one or more terminal carboxyl (COOH) functional groups. Short chain carboxylic acids (SCCAs; carboxylic acids containing three to six carbons), such as malate and citrate, are critical to the proper functioning of many biological systems, where they function in cellular respiration and can serve as indicators of cell health. In foods, organic acid content can have significant impact on taste, with increased SCCA levels resulting in a sour or &#34;acid&#34; taste. Because of this, methods for the rapid analysis of organic acid levels are of particular interest to the food and beverage industries. Unfortunately, however, most methods used for SCCA quantification are dependent on time-consuming protocols requiring the derivatization of samples with hazardous reagents, followed by costly chromatographic and/or mass spectrometric analyses. This method details an alternate method for the detection and quantification of organic acids from plant material and food samples using free zonal capillary electrophoresis (CZE), sometimes simply referred to as capillary electrophoresis (CE). CZE provides a cost-effective method for measuring SCCAs with a low limit of detection (0.005 mg/ml). This article details the extraction and quantification of SCCAs from plant samples. While the method provided focuses on measurement of SCCAs from coffee beans, the method provided can be applied to multiple plant-based food materials.

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

This article presents a method for the detection and quantification of organic acids from plant material using free zonal capillary electrophoresis. An example of the potential application of this method, determining the effects of a secondary fermentation on organic acid levels in coffee seeds, is provided.

Carboxylic acids are organic acids containing one or more terminal carboxyl (COOH) functional groups. Short chain carboxylic acids (SCCAs; carboxylic ...

Regioselective O-Glycosylation of Nucleosides via the Temporary 2',3'-Diol Protection by a Boronic Ester for the Synthesis of Disaccharide Nucleosides

Disaccharide nucleosides, which consist of disaccharide and nucleobase moieties, have been known as a valuable group of natural products having multifarious bioactivities. Although chemical O-glycosylation is a commonly beneficial strategy to synthesize disaccharide nucleosides, the preparation of substrates such as glycosyl donors and acceptors requires&#160;tedious protecting&#160;group manipulations and a purification at each synthetic step. Meanwhile, several research groups have reported that boronic and borinic esters serve as a protecting or activating group of carbohydrate derivatives to achieve the regio- and/or stereoselective acylation, alkylation, silylation, and glycosylation. In this article, we demonstrate the procedure for the regioselective O-glycosylation of unprotected ribonucleosides utilizing boronic acid. The esterification of 2&#39;,3&#39;-diol of ribonucleosides with boronic acid makes the temporary protection of diol, and, following O-glycosylation with a glycosyl donor in the presence of p-toluenesulfenyl chloride and silver triflate, permits the regioselective reaction of the 5&#39;-hydroxyl group to afford the disaccharide nucleosides. This method could be applied to various nucleosides, such as guanosine, adenosine, cytidine, uridine, 5-metyluridine, and 5-fluorouridine. This article and the accompanying video represent&#160;useful (visual) information for the O-glycosylation of unprotected nucleosides and their analogs for the synthesis of not only disaccharide nucleosides, but also a variety of biologically relevant derivatives.

Regioselective O-Glycosylation of Nucleosides via the Temporary 2',3'-Diol Protection by a Boronic Ester for the Synthesis of Disaccharide Nucleosides

Here, we present protocols for the synthesis of disaccharide nucleosides by the regioselective O-glycosylation of ribonucleosides via a temporary protection of their 2&#39;,3&#39;-diol moieties utilizing a cyclic boronic ester. This method applies to several unprotected nucleosides such as adenosine, guanosine, cytidine, uridine, 5-methyluridine, and 5-fluorouridine to give corresponding disaccharide nucleosides.

Disaccharide nucleosides, which consist of disaccharide and nucleobase moieties, have been known as a valuable group of natural products having ...

Calcium Carbonate Formation in the Presence of Biopolymeric Additives

Biomineralization is the formation of minerals in the presence of organic molecules, often related with functional and/or structural roles in living organisms. It is a complex process and therefore a simple, in vitro, system is required to understand the effect of isolated molecules on the biomineralization process. In many cases, biomineralization is directed by biopolymers in the extracellular matrix. In order to evaluate the effect of isolated biopolymers on the morphology and structure of calcite in vitro, we have used the vapor diffusion method for the precipitation of calcium carbonate, scanning electron microscopy and micro Raman for the characterization, and ultraviolet-visible (UV/Vis) absorbance for measuring the quantity of a biopolymer in the crystals. In this method, we expose the isolated biopolymers, dissolved in a calcium chloride solution, to gaseous ammonia and carbon dioxide that originate from the decomposition of solid ammonium carbonate. Under the conditions where the solubility product of calcium carbonate is reached, calcium carbonate precipitates and crystals are formed. Calcium carbonate has different polymorphs that differ in their thermodynamic stability: amorphous calcium carbonate, vaterite, aragonite, and calcite. In the absence of biopolymers, under clean conditions, calcium carbonate is mostly present in the calcite form, which is the most thermodynamically stable polymorph of calcium carbonate. This method examines the effect of the biopolymeric additives on the morphology and structure of calcium carbonate crystals. Here, we demonstrate the protocol through the study of an extracellular bacterial protein, TapA, on the formation of calcium carbonate crystals. Specifically, we focus on the experimental set up, and characterization methods, such as optical and electron microscopy as well as Raman spectroscopy.

We describe a protocol for the precipitation and characterization of calcium carbonate crystals that form in the presence of biopolymers.

Biomineralization is the formation of minerals in the presence of organic molecules, often related with functional and/or structural roles in living ...

Applying Hyperspectral Reflectance Imaging to Investigate the Palettes and the Techniques of Painters

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Chapters in this video

Origami Inspired Self-assembly of Patterned and Reconfigurable Particles

Isolation and Chemical Characterization of Lipid A from Gram-negative Bacteria

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D ¹H NMR

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Amide Coupling Reaction for the Synthesis of Bispyridine-based Ligands and Their Complexation to Platinum as Dinuclear Anticancer Agents

Synthesis of Protein Bioconjugates via Cysteine-maleimide Chemistry

Using Capillary Electrophoresis to Quantify Organic Acids from Plant Tissue: A Test Case Examining Coffea arabica Seeds

Regioselective O-Glycosylation of Nucleosides via the Temporary 2',3'-Diol Protection by a Boronic Ester for the Synthesis of Disaccharide Nucleosides

Calcium Carbonate Formation in the Presence of Biopolymeric Additives