Query: Using  spectroscopy to characterize biological materials

Candidate papers:

abstract: Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and polymer science fields. The application of Raman spectroscopy and microscopy within biology is rapidly increasing because it can provide chemical and compositional information, but it does not typically suffer from interference from water molecules. Analysis does not conventionally require extensive sample preparation; biochemical and structural information can usually be obtained without labeling. In this protocol, we aim to standardize and bring together multiple experimental approaches from key leaders in the field for obtaining Raman spectra using a microspectrometer. As examples of the range of biological samples that can be analyzed, we provide instructions for acquiring Raman spectra, maps and images for fresh plant tissue, formalin fixed and fresh frozen mammalian tissue, fixed cells and biofluids. We explore a robust approach for sample preparation, instrumentation, acquisition parameters and data processing. By using this approach, we expect that a typical Raman experiment can be performed by a nonspecialist user to generate high quality data for biological materials analysis.
author_names: Holly J Butler

Lorna Ashton

Benjamin Bird

Gianfelice Cinque

Kelly Curtis

Jennifer Dorney

Karen Esmonde-White

Nigel J Fullwood

Benjamin Gardner

Pierre P L Martin-Hirsch

Michael J Walsh

Martin Robert McAinsh

Nicholas Stone

Francis L Martin
title: Using Raman spectroscopy to characterize biological materials
venue: Nature Protocols
year: 2016

abstract: Raman spectroscopy is a non destructive, label free, highly specific approach which provides the chemical information of materials. Thus, it is suitable to be used as an effective analytical tool to characterize biological samples. Here we introduce a novel method which uses artificial intelligence to analyze biological Raman spectra and identify the microbes at a single cell level. The combination of a framework of convolutional neural network (ConvNet) and Raman spectroscopy allows the extraction of the Raman spectral features of a single microbial cell and then categorizes cells according to their spectral features. As the proof of concept, we measured Raman spectra of 14 microbial species at a single cell level and constructed an optimal ConvNet model using the Raman data. The average accuracy of classification by ConvNet is 95.64+ 5.46% Meanwhile, we introduced an occlusion based Raman spectra feature extraction (ORSFE) to visualize the weights of Raman features for distinguishing different species.
author_names: W Lu

Xiuqiang Chen

Li-li Wang

Hanfei Li

Yu Vincent Fu
title: The combination of an artificial intelligence approach and laser tweezers Raman spectroscopy for microbial identification.
venue: Analytical chemistry
year: 2020

abstract: A condom can be described as a protective sheath used as a contraceptive or to protect against sexually transmitted diseases. However, individuals also use condoms during the commission of sexual assaults to prevent identification through deposited biological material. Raman spectroscopy offers a novel approach to identifying the presence of condom lubricant components. Furthermore, Raman chemical imaging expands on conventional Raman spectroscopy to characterize multiple condom lubricant components simultaneously in a manner that effectively demonstrates heterogeneous sample mixtures both spectrally and spatially. Known reference materials, liquid and solid lubricant components of common condom brands were successfully characterized using Raman dispersive spectroscopy and Raman chemical imaging without extensive sample preparation inherent to other analytical methods. The characterization of these materials demonstrates the potential of this technique to become a routine screening method for condom lubricants. This preliminary investigation provides a basis for future studies to determine the feasibility of Raman spectroscopy and Raman chemical imaging for condom lubricant trace detection in case type samples.
author_names: Julianne Wolfe

David L Exline
title: Characterization of condom lubricant components using Raman spectroscopy and Raman chemical imaging.
venue: Journal of forensic sciences
year: 2003

abstract: A wet chemical approach to synthesize Au graphene (Au G) Ag G and Ag@Au G hybrid nanocomposites in the water vitamin C system using graphene oxide and noble metal nanoparticles (NPs) is reported in this paper. AFM, TEM, UV vis absorption, Raman spectroscopy and XRD are employed to characterize the morphology, optical properties and analyze crystal characteristics. Ag@Au G nanocomposites have stronger surface enhanced Raman scattering (SERS) activity than that of pure Au G and Ag G. So the Ag@Au G nanocomposites can be used not only for SERS, but also to exhibit good compatibility in biological detection. It is expected that these hybrid materials can be used as new functional building blocks to assemble novel three dimensional (3D) complex multicomponent nanostructures, which are believed to be useful for nanodevices.
author_names: Liang Zhou

Huai-min Gu

Canchen Wang

Juling Zhang

Meng Lv

Ruoyu He
title: Study on the synthesis and surface enhanced Raman spectroscopy of graphene based nanocomposites decorated with noble metal nanoparticles
year: 2013

abstract: An approach binary spectronephelometry (BSN) to perform real time simultaneous noninvasive in situ physical and chemical analysis of bacterial cultures in fluid media is described. We choose to characterize cultures of Escherichia coli (NC) Pseudomonas aeruginosa (PA) and Shewanella oneidensis (SO) in the specific case of complex media whose Raman spectrum cannot be unambiguously assigned. Nevertheless, organism number density and a measure of the chemical makeup of the fluid medium can be monitored noninvasively, simultaneously, and continuously, despite changing turbidity and medium chemistry. The method involves irradiating a culture in fluid medium in an appropriate vessel (in this case a standard 1 cm cuvette) using a near infrared laser and collecting all the backscattered light from the cuvette, i.e. the Rayleigh Mie line and the inelastically emitted light which includes unresolved Raman scattered light and fluorescence. Complex "legacy" media contain materials of biological origin whose chemical composition cannot be fully delineated. We independently calibrate this approach to a commonly used reference, optical density at 600 nm (OD600) for characterizing the number density of organisms. We suggest that the total inelastically emitted light could be a measure of the chemical state of a biologically based medium, e.g. lysogeny broth (LB) This approach may be useful in a broad range of basic and applied studies and enterprises that utilize bacterial cultures in any medium or container that permits optical probing in the single scattering limit.
author_names: Steve Ortiz

Ricky McDonough

Paul Dent

Jerry Goodisman

Joseph Chaiken
title: Coupled Turbidity and Spectroscopy Problems: A Simple Algorithm for Volumetric Analysis of Optically Thin or Dilute, In Vitro Bacterial Cultures in Various Media
venue: Applied spectroscopy
year: 2019

abstract: Abstract A System has been developed to simulate biofouling of metal surfaces under a range of physical, chemical, and biological conditions. Items of equipment to eliminate and concentrate organic constituents from seawater and to analyze for proteins, glycoproteins, and carbohydrates have been acquired. Teflon fouling chambers have been developed to characterize surface properties of metals in seawater, i.e. adsorption of organic materials, using optical and electrochemical spectroscopic probes. Preliminary studies using these chambers and surface enhanced Raman spectroscopy demonstrated ability to detect thin layers of pyridine, tryptophan, and phenylalanine adsorbed to silver electrodes. A system to perform waveguide Internal Reflectance Raman Spectroscopy (WIRRS) on thin films adsorbed to a substratum was developed and tested. During preliminary studies, an excellent Raman spectrum was obtained from a 1 micrometer layer of polystyrene. For Electrochemical Impedance Spectroscopy (EIS) electronic hardware was acquired and software was developed to determine the impedance attributes of fouled metal coupons. Preliminary EIS studies using the enzyme, Ribulose Biphosphate Carboxylase, demonstrated the ability to detect adsorption of this protein to a silver electrode.
author_names: Gordon T Taylor
title: Examination of Chemical Adsorption and Marine Biofouling on Metal Surfaces Using Raman Scattering Techniques and Electrochemical Impedance Spectroscopy
year: 1991

abstract: In the latest literature search, the technology based on graphite oxide (GO) nanomaterials exhibits a great potential in many aspects of wastewater treatment involving adsorption, photocatalysis, disinfection and membrane process. In this study experimental data involving the carbon element in different forms such as active carbon (AC) graphite and graphene oxide (GO) applied as the active reagents in wastewater treatment are summarized and discussed. The first step was to characterize the aforementioned carbon materials and nanoparticles using various complementary techniques. These include optical microscopy, scanning electron microscopy (SEM) energy dispersive spectroscopy (EDS) Raman spectrophotometry and zeta potential measurements. The second issue was to design the relatively simple experiment enabling us to observe the physicochemical and biological effects of carbon nanoparticles in the presence of sewage water and/or active sludge. Obtained experimental data have been inspected using univariate and multivariate (principal component analysis, PCA) approaches confirming the complex interaction of GO nanoparticles with microorganisms that are present in activated sludge. This experiment enabled the collection of an initial data set to design different large scale investigations focusing on active nanoparticles affecting wastewater purification. PCA calculations clearly revealed that GO strongly affects the wastewater technological processes investigated. It is hoped that the described results will allow the design of smart environmental protection systems in the future.
author_names: Krzysztof Piaskowski

Pawel Zarzycki
title: Carbon Based Nanomaterials as Promising Material for Wastewater Treatment Processes
venue: International journal of environmental research and public health
year: 2020

abstract: Breast cancer is the most malignant type of cancer in women and is a global health problem, with mortality by metastasis being the main factor among others. Currently, detection and diagnosis of breast cancer is achieved through a variety of procedures, such as clinical examination, medical imaging, biopsy, and histopathological analysis. In contrast, spectroscopic analysis has a variety of advantages such as being noninvasive, not destroying biological materials, and not requiring additional histological analysis. In this study, various approaches using Raman spectroscopy, atomic force microscopy (AFM) and optical microscopy were used together to differentiate between and characterize normal breast cell lines (MCF 10A) and breast cancer cell lines (MDA MB 231, MDA MB 453) Raman spectra of normal breast cell and breast cancer cell lines confirmed visual differences in the concentrations of various compounds. These spectra were also analyzed using principle component analysis (PCA) and the PCA results showed reliable separation of the three cell lines and the cancer cell lines (MDA MB 231, MDA MB 453) With these results, optically synchronizing the AFM morphology, the Raman spectroscopy, and the visible RGB optical transmission intensity provided contrasts for not only conformational differences but also intracellular variation between the normal and cancer cell lines. We observed the inherent characteristic that there is no local difference in cancer cells regardless of morphology in a wide range of optical properties such as absorption, scattering and inelastic scattering.
author_names: Seung Ho Lee

Ok-Kyun Kim

Sanghwa Lee

Jun Ki Kim
title: Local dependency of morphological and optical properties between breast cancer cell lines.
venue: Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy
year: 2018

abstract: Raman spectroscopy has become an essential tool for chemists, physicists, biologists and materials scientists. In this article, we present the challenges in unravelling the molecule specific Raman spectral signatures of different biomolecules like proteins, nucleic acids, lipids and carbohydrates based on the review of our work and the current trends in these areas. We also show how Raman spectroscopy can be used to probe the secondary and tertiary structural changes occurring during thermal denaturation of protein and lysozyme as well as more complex biological systems like bacteria. Complex biological systems like tissues, cells, blood serum etc. are also made up of such biomolecules. Using mice liver and blood serum, it is shown that different tissues yield their unique signature Raman spectra, owing to a difference in the relative composition of the biomolecules. Additionally, recent progress in Raman spectroscopy for diagnosing a multitude of diseases ranging from cancer to infection is also presented. The second part of this article focuses on applications of Raman spectroscopy to materials. As a first example, Raman spectroscopy of a melt cast explosives formulation was carried out to monitor the changes in the peaks which indicates the potential of this technique for remote process monitoring. The second example presents various modern methods of Raman spectroscopy such as spatially offset Raman spectroscopy (SORS) reflection, transmission and universal multiple angle Raman spectroscopy (UMARS) to study layered materials. Studies on chemicals/layered materials hidden in non metallic containers using the above variants are presented. Using suitable examples, it is shown how a specific excitation or collection geometry can yield different information about the location of materials. Additionally, it is shown that UMARS imaging can also be used as an effective tool to obtain layer specific information of materials located at depths beyond a few centimeters.
author_names: Nikki Kuhar

S Sil

Taru Verma

Siva Umapathy
title: Challenges in application of Raman spectroscopy to biology and materials
year: 2018

abstract: Abstract The ability of Raman spectroscopy to characterize amorphous materials makes this technique ideal to study alkali silica reaction (ASR) gels. The structure of several synthetic ASR gels was thoroughly characterized using Raman Spectroscopy. The results were validated with additional techniques such as Fourier transmission infrared spectroscopy, X ray powder diffraction and thermogravimetric analysis. The Raman spectra were found to have two broad bands in the 800 to 1200 cm 1 range and the 400 to 700 cm 1 range indicating the amorphous nature of the gel. Important information regarding the silicate polymerization was deduced from both of these spectral regions. An increase in alkali content of the gels caused a depolymerization in the silicate framework which manifested in the Raman spectra as a gradual shift of predominant peaks in both regions. The trends in silicate depolymerization were in agreement with results from a NMR spectroscopy study on similar synthetic ASR gels.
author_names: Chandni Balachandran

Jose Luis Fernandez Munoz

Terry S Arnold
title: Characterization of alkali silica reaction gels using Raman spectroscopy
year: 2017