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1.  Responses of Haloarchaea to Simulated Microgravity 
Astrobiology  2011;11(3):199-205.
Abstract
Various effects of microgravity on prokaryotes have been recognized in recent years, with the focus on studies of pathogenic bacteria. No archaea have been investigated yet with respect to their responses to microgravity. For exposure experiments on spacecrafts or on the International Space Station, halophilic archaea (haloarchaea) are usually embedded in halite, where they accumulate in fluid inclusions. In a liquid environment, these cells will experience microgravity in space, which might influence their viability and survival. Two haloarchaeal strains, Haloferax mediterranei and Halococcus dombrowskii, were grown in simulated microgravity (SMG) with the rotary cell culture system (RCCS, Synthecon). Initially, salt precipitation and detachment of the porous aeration membranes in the RCCS were observed, but they were avoided in the remainder of the experiment by using disposable instead of reusable vessels. Several effects were detected, which were ascribed to growth in SMG: Hfx. mediterranei's resistance to the antibiotics bacitracin, erythromycin, and rifampicin increased markedly; differences in pigmentation and whole cell protein composition (proteome) of both strains were noted; cell aggregation of Hcc. dombrowskii was notably reduced. The results suggest profound effects of SMG on haloarchaeal physiology and cellular processes, some of which were easily observable and measurable. This is the first report of archaeal responses to SMG. The molecular mechanisms of the effects induced by SMG on prokaryotes are largely unknown; haloarchaea could be used as nonpathogenic model systems for their elucidation and in addition could provide information about survival during lithopanspermia (interplanetary transport of microbes inside meteorites). Key Words: Haloferax mediterranei—Halococcus dombrowskii—Simulated microgravity—Rotary cell culture system—Antibiotic resistance—Lithopanspermia. Astrobiology 11, 199–205.
doi:10.1089/ast.2010.0536
PMCID: PMC3079168  PMID: 21417742
2.  Raman spectroscopy in halophile research 
Raman spectroscopy plays a major role in robust detection of biomolecules and mineral signatures in halophile research. An overview of Raman spectroscopic investigations in halophile research of the last decade is given here to show advantages of the approach, progress made as well as limits of the technique. Raman spectroscopy is an excellent tool to monitor and identify microbial pigments and other biomolecules in extant and extinct halophile biomass. Studies of bottom gypsum crusts from salterns, native evaporitic sediments, halite inclusions, and endoliths as well as cultures of halophilic microorganisms permitted to understand the content, distribution, and behavior of important molecular species. The first papers describing Raman spectroscopic detection of microbiological and geochemical key markers using portable instruments are highlighted as well.
doi:10.3389/fmicb.2013.00380
PMCID: PMC3857566  PMID: 24339823
Raman spectroscopy; halophilic; salterns; gypsum crusts; compatible solutes; carotenoids
3.  The Miniaturized Raman System and Detection of Traces of Life in Halite from the Atacama Desert: Some Considerations for the Search for Life Signatures on Mars 
Astrobiology  2012;12(12):1095-1099.
Abstract
Raman spectroscopy is being adopted as a nondestructive instrumentation for the robotic exploration of Mars to search for traces of life in the geological record. Here, miniaturized Raman spectrometers of two different types equipped with 532 and 785 nm lasers for excitation, respectively, were compared for the detection of microbial biomarkers in natural halite from the hyperarid region of the Atacama Desert. Measurements were performed directly on the rock as well as on the homogenized, powdered samples prepared from this material—the effects of this sample preparation and the excitation wavelength employed in the analysis are compared and discussed. From these results, 532 nm excitation was found to be superior for the analysis of powdered specimens due to its high sensitivity toward carotenoids and hence a higher capability for their detection at relatively low concentration in bulk powdered specimens. For the same reason, this wavelength was a better choice for the detection of carotenoids in direct measurements made on the rock samples. The 785 nm excitation wavelength, in contrast, proved to be more sensitive toward the detection of scytonemin. Key Words: Miniaturized portable Raman—Atacama—Mars—Biomarker detection. Astrobiology 12, 1095–1099.
doi:10.1089/ast.2012.0879
PMCID: PMC3522129  PMID: 23151300
4.  Diagnostic potential of near-infrared Raman spectroscopy in the stomach: differentiating dysplasia from normal tissue 
British Journal of Cancer  2008;98(2):457-465.
Raman spectroscopy is a molecular vibrational spectroscopic technique that is capable of optically probing the biomolecular changes associated with diseased transformation. The purpose of this study was to explore near-infrared (NIR) Raman spectroscopy for identifying dysplasia from normal gastric mucosa tissue. A rapid-acquisition dispersive-type NIR Raman system was utilised for tissue Raman spectroscopic measurements at 785 nm laser excitation. A total of 76 gastric tissue samples obtained from 44 patients who underwent endoscopy investigation or gastrectomy operation were used in this study. The histopathological examinations showed that 55 tissue specimens were normal and 21 were dysplasia. Both the empirical approach and multivariate statistical techniques, including principal components analysis (PCA), and linear discriminant analysis (LDA), together with the leave-one-sample-out cross-validation method, were employed to develop effective diagnostic algorithms for classification of Raman spectra between normal and dysplastic gastric tissues. High-quality Raman spectra in the range of 800–1800 cm−1 can be acquired from gastric tissue within 5 s. There are specific spectral differences in Raman spectra between normal and dysplasia tissue, particularly in the spectral ranges of 1200–1500 cm−1 and 1600–1800 cm−1, which contained signals related to amide III and amide I of proteins, CH3CH2 twisting of proteins/nucleic acids, and the C=C stretching mode of phospholipids, respectively. The empirical diagnostic algorithm based on the ratio of the Raman peak intensity at 875 cm−1 to the peak intensity at 1450 cm−1 gave the diagnostic sensitivity of 85.7% and specificity of 80.0%, whereas the diagnostic algorithms based on PCA-LDA yielded the diagnostic sensitivity of 95.2% and specificity 90.9% for separating dysplasia from normal gastric tissue. Receiver operating characteristic (ROC) curves further confirmed that the most effective diagnostic algorithm can be derived from the PCA-LDA technique. Therefore, NIR Raman spectroscopy in conjunction with multivariate statistical technique has potential for rapid diagnosis of dysplasia in the stomach based on the optical evaluation of spectral features of biomolecules.
doi:10.1038/sj.bjc.6604176
PMCID: PMC2361456  PMID: 18195711
dysplasia; near-infrared Raman spectroscopy; optical diagnosis; stomach; principal components analysis; linear discriminant analysis
5.  Investigating the Effects of Simulated Martian Ultraviolet Radiation on Halococcus dombrowskii and Other Extremely Halophilic Archaebacteria 
Astrobiology  2009;9(1):104-112.
The isolation of viable extremely halophilic archaea from 250-million-year-old rock salt suggests the possibility of their long-term survival under desiccation. Since halite has been found on Mars and in meteorites, haloarchaeal survival of martian surface conditions is being explored. Halococcus dombrowskii H4 DSM 14522T was exposed to UV doses over a wavelength range of 200–400 nm to simulate martian UV flux. Cells embedded in a thin layer of laboratory-grown halite were found to accumulate preferentially within fluid inclusions. Survival was assessed by staining with the LIVE/DEAD kit dyes, determining colony-forming units, and using growth tests. Halite-embedded cells showed no loss of viability after exposure to about 21 kJ/m2, and they resumed growth in liquid medium with lag phases of 12 days or more after exposure up to 148 kJ/m2. The estimated D37 (dose of 37 % survival) for Hcc. dombrowskii was ≥ 400 kJ/m2. However, exposure of cells to UV flux while in liquid culture reduced D37 by 2 orders of magnitude (to about 1 kJ/m2); similar results were obtained with Halobacterium salinarum NRC-1 and Haloarcula japonica. The absorption of incoming light of shorter wavelength by color centers resulting from defects in the halite crystal structure likely contributed to these results. Under natural conditions, haloarchaeal cells become embedded in salt upon evaporation; therefore, dispersal of potential microscopic life within small crystals, perhaps in dust, on the surface of Mars could resist damage by UV radiation.
doi:10.1089/ast.2007.0234
PMCID: PMC3182532  PMID: 19215203
Halococcus dombrowskii; Simulated martian UV radiation; LIVE/DEAD staining; Halite fluid inclusions; UV transmittance and reflectance; Desiccation
6.  Excitation energy-dependent nature of Raman scattering spectrum in GaInNAs/GaAs quantum well structures 
Nanoscale Research Letters  2012;7(1):656.
The excitation energy-dependent nature of Raman scattering spectrum, vibration, electronic or both, has been studied using different excitation sources on as-grown and annealed n- and p-type modulation-doped Ga1 − xInxNyAs1 − y/GaAs quantum well structures. The samples were grown by molecular beam technique with different N concentrations (y = 0%, 0.9%, 1.2%, 1.7%) at the same In concentration of 32%. Micro-Raman measurements have been carried out using 532 and 758 nm lines of diode lasers, and the 1064 nm line of the Nd-YAG laser has been used for Fourier transform-Raman scattering measurements. Raman scattering measurements with different excitation sources have revealed that the excitation energy is the decisive mechanism on the nature of the Raman scattering spectrum. When the excitation energy is close to the electronic band gap energy of any constituent semiconductor materials in the sample, electronic transition dominates the spectrum, leading to a very broad peak. In the condition that the excitation energy is much higher than the band gap energy, only vibrational modes contribute to the Raman scattering spectrum of the samples. Line shapes of the Raman scattering spectrum with the 785 and 1064 nm lines of lasers have been observed to be very broad peaks, whose absolute peak energy values are in good agreement with the ones obtained from photoluminescence measurements. On the other hand, Raman scattering spectrum with the 532 nm line has exhibited only vibrational modes. As a complementary tool of Raman scattering measurements with the excitation source of 532 nm, which shows weak vibrational transitions, attenuated total reflectance infrared spectroscopy has been also carried out. The results exhibited that the nature of the Raman scattering spectrum is strongly excitation energy-dependent, and with suitable excitation energy, electronic and/or vibrational transitions can be investigated.
doi:10.1186/1556-276X-7-656
PMCID: PMC3552774  PMID: 23190628
GaInNAs; Photoluminescence; Raman; FT-Raman; FT-IR; Local modes; 71.55.Eq; 63.22.+m
7.  Femtosecond broadband stimulated Raman spectroscopy: Apparatus and methods 
The Review of scientific instruments  2004;75(11):4971-4980.
The laser, detection system, and methods that enable femtosecond broadband stimulated Raman spectroscopy (FSRS) are presented in detail. FSRS is a unique tool for obtaining high time resolution (<100 fs) vibrational spectra with an instrument response limited frequency resolution of <10 cm–1. A titanium:Sapphire-based laser system produces the three different pulses needed for FSRS: (1) A femtosecond visible actinic pump that initiates the photochemistry, (2) a narrow bandwidth picosecond Raman pump that provides the energy reservoir for amplification of the probe, and (3) a femtosecond continuum probe that is amplified at Raman resonances shifted from the Raman pump. The dependence of the stimulated Raman signal on experimental parameters is explored, demonstrating the expected exponential increase in Raman intensity with concentration, pathlength, and Raman pump power. Raman spectra collected under different electronic resonance conditions using highly fluorescent samples highlight the fluorescence rejection capabilities of FSRS. Data are also presented illustrating our ability: (i) To obtain spectra when there is a large transient absorption change by using a shifted excitation difference technique and (ii) to obtain high time resolution vibrational spectra of transient electronic states.
doi:10.1063/1.1807566
PMCID: PMC1712672  PMID: 17183413
8.  Raman and SEM analysis of a biocolonised hot spring travertine terrace in Svalbard, Norway 
Background
A profile across 8 layers from a fossil travertine terrace from a low temperature geothermal spring located in Svalbard, Norway has been studied using both Raman spectroscopy and SEM (Scanning Electron Microscopy) techniques to identify minerals and organic life signals.
Results
Calcite, anatase, quartz, haematite, magnetite and graphite as well as scytonemin, three different carotenoids, chlorophyll and a chlorophyll-like compound were identified as geo- and biosignatures respectively, using 785 and/or 514 nm Raman laser excitation wavelengths. No morphological biosignatures representing remnant microbial signals were detected by high-resolution imaging, although spectral analyses indicated the presence of organics. In contrast, in all layers, Raman spectra identified a series of different organic pigments indicating little to no degradation or change of the organic signatures and thus indicating the preservation of fossil biomarker compounds throughout the life time of the springs despite the lack of remnant morphological indicators.
Conclusion
With a view towards planetary exploration we discuss the implications of the differences in Raman band intensities observed when spectra were collected with the different laser excitations. We show that these differences, as well as the different detection capability of the 785 and 514 nm laser, could lead to ambiguous compound identification. We show that the identification of bio and geosignatures, as well as fossil organic pigments, using Raman spectroscopy is possible. These results are relevant since both lasers have been considered for miniaturized Raman spectrometers for planetary exploration.
doi:10.1186/1467-4866-8-8
PMCID: PMC2110888  PMID: 17697380
9.  In vivo Molecular Evaluation of Guinea Pig Skin Incisions Healing after Surgical Suture and Laser Tissue Welding Using Raman Spectroscopy 
The healing process in guinea pig skin following surgical incisions was evaluated at the molecular level, in vivo, by the use of Raman spectroscopy. After the incisions were closed either by suturing or by laser tissue welding (LTW), differences in the respective Raman spectra were identified. The study determined that the ratio of the Raman peaks of the amide III (1247 cm−1) band to a peak at 1326 cm−1 (the superposition of elastin and keratin bands) can be used to evaluate the progression of wound healing. Conformational changes in the amide I band (1633 cm−1 to 1682 cm−1) and spectrum changes in the range of 1450 cm−1 to 1520 cm−1 were observed in LTW and sutured skin. The stages of the healing process of the guinea pig skin following LTW and suturing were evaluated by Raman spectroscopy, using histopathology as the gold standard. LTW skin demonstrated better healing than sutured skin, exhibiting minimal hyperkeratosis, minimal collagen deposition, near-normal surface contour, and minimal loss of dermal appendages. A wavelet decomposition-reconstruction baseline correction algorithm was employed to remove the fluorescence wing from the Raman spectra.
doi:10.1016/j.jphotobiol.2009.06.004
PMCID: PMC2737253  PMID: 19581109
Laser tissue welding; Raman spectroscopy; skin wound healing; collagen deposition; wavelet; vibrational modes
10.  Detection and Monitoring of Neurotransmitters - a Spectroscopic Analysis 
Objectives
We demonstrate that confocal Raman mapping spectroscopy provides rapid, detailed and accurate neurotransmitter analysis, enabling millisecond time resolution monitoring of biochemical dynamics. As a prototypical demonstration of the power of the method, we present real-time in vitro serotonin, adenosine, and dopamine detection, and dopamine diffusion in an inhomogeneous organic gel, which was used as a substitute for neurologic tissue.
Materials and Methods
Dopamine, adenosine and serotonin were used to prepare neurotransmitter solutions in DI water. The solutions were applied to the surfaces of glass slides, where they inter-diffused. Raman mapping was achieved by detecting non-overlapping spectral signatures characteristic of the neurotransmitters with an alpha 300 WITec confocal Raman system, using 532 nm Nd:YAG laser excitation. Every local Raman spectrum was recorded in milliseconds and complete Raman mapping in a few seconds.
Results
Without damage, dyeing, or preferential sample preparation, confocal Raman mapping provided positive detection of each neurotransmitter, allowing association of the high-resolution spectra with specific micro-scale image regions. Such information is particularly important for complex, heterogeneous samples, where changes in composition can influence neurotransmission processes. We also report an estimated dopamine diffusion coefficient two orders of magnitude smaller than that calculated by the flow-injection method.
Conclusions
Accurate nondestructive characterization for real-time detection of neurotransmitters in inhomogeneous environments without the requirement of sample labeling is a key issue in neuroscience. Our work demonstrates the capabilities of Raman spectroscopy in biological applications, possibly providing a new tool for elucidating the mechanism and kinetics of deep brain stimulation.
doi:10.1111/j.1525-1403.2012.00502.x
PMCID: PMC3537900  PMID: 22989218
Basic science; Raman spectroscopy; neurotransmitters; brain
11.  Nanoscale optical and electrical characterization of horizontally aligned single-walled carbon nanotubes 
Nanoscale Research Letters  2012;7(1):682.
During the recent years, a significant amount of research has been performed on single-walled carbon nanotubes (SWCNTs) as a channel material in thin-film transistors (Pham et al. IEEE Trans Nanotechnol 11:44–50, 2012). This has prompted the application of advanced characterization techniques based on combined atomic force microscopy (AFM) and Raman spectroscopy studies (Mureau et al. Electrophoresis 29:2266–2271, 2008). In this context, we use confocal Raman microscopy and current sensing atomic force microscopy (CS-AFM) to study phonons and the electronic transport in semiconducting SWCNTs, which were aligned between palladium electrodes using dielectrophoresis (Kuzyk Electrophoresis 32:2307–2313, 2011). Raman imaging was performed in the region around the electrodes on the suspended CNTs using several laser excitation wavelengths. Analysis of the G+/G− splitting in the Raman spectra (Sgobba and Guldi Chem Soc Rev 38:165–184, 2009) shows CNT diameters of 2.5 ± 0.3 nm. Neither surface modification nor increase in defect density or stress at the CNT-electrode contact could be detected, but rather a shift in G+ and G− peak positions in regions with high CNT density between the electrodes. Simultaneous topographical and electrical characterization of the CNT transistor by CS-AFM confirms the presence of CNT bundles having a stable electrical contact with the transistor electrodes. For a similar load force, reproducible current–voltage (I/V) curves for the same CNT regions verify the stability of the electrical contact between the nanotube and the electrodes as well as the nanotube and the AFM tip over different experimental sessions using different AFM tips. Strong variations observed in the I/V response at different regions of the CNT transistor are discussed.
doi:10.1186/1556-276X-7-682
PMCID: PMC3552840  PMID: 23259903
Single-walled carbon nanotubes; CNT transistor; Raman imaging; Current sensing AFM; Atomic force microscopy
12.  Evaluation of the LIVE/DEAD BacLight Kit for Detection of Extremophilic Archaea and Visualization of Microorganisms in Environmental Hypersaline Samples 
Applied and Environmental Microbiology  2004;70(11):6884-6886.
Extremophilic archaea were stained with the LIVE/DEAD BacLight kit under conditions of high ionic strength and over a pH range of 2.0 to 9.3. The reliability of the kit was tested with haloarchaea following permeabilization of the cells. Microorganisms in hypersaline environmental samples were detectable with the kit, which suggests its potential application to future extraterrestrial halites.
doi:10.1128/AEM.70.11.6884-6886.2004
PMCID: PMC525124  PMID: 15528557
13.  Near-Infrared Micro-Raman Spectroscopy for in Vitro Detection of Cervical Cancer 
Applied spectroscopy  2010;64(3):255-261.
Near-infrared Raman spectroscopy is a powerful analytical tool for detecting critical differences in biological samples with minimum interference in the Raman spectra from the native fluorescence of the samples. The technique is often suggested as a potential screening tool for cancer. In this article we report in vitro Raman spectra of squamous cells in normal and cancerous cervical human tissue from seven patients, which have good signal-to-noise ratio and which were found to be reproducible. These preliminary results show that several Raman features in these spectra could be used to distinguish cancerous cervical squamous cells from normal cervical squamous cells. In general, the Raman spectra of cervical cancer cells show intensity differences compared to those of normal squamous cell spectra. For example, several well-defined Raman peaks of collagen in the 775 to 975 cm −1 region are observed in the case of normal squamous cells, but these are below the detection limit of normal Raman spectroscopy in the spectra of invasive cervical cancer cells. In the high frequency 2800 to 3100 cm −1 region, it is found that the peak area under the CH stretching band is lower by a factor of approximately six in the spectra of cervical cancer cells as compared with that of the normal cells. The Raman chemical maps of regions of cancer and normal cells in the cervical epithelium made from the spectral features in the 775 to 975 cm −1 and 2800 to 3100 cm −1 regions are also found to show good correlation with each other.
doi:10.1366/000370210790918364
PMCID: PMC2880181  PMID: 20223058
Micro-Raman spectroscopy; Cervix tissues; Cervical cancer; Squamous cell epithelium; Raman maps
14.  Raman Tweezers Spectroscopy of Live, Single Red and White Blood Cells 
PLoS ONE  2010;5(4):e10427.
An optical trap has been combined with a Raman spectrometer to make high-resolution measurements of Raman spectra of optically-immobilized, single, live red (RBC) and white blood cells (WBC) under physiological conditions. Tightly-focused, near infrared wavelength light (1064 nm) is utilized for trapping of single cells and 785 nm light is used for Raman excitation at low levels of incident power (few mW). Raman spectra of RBC recorded using this high-sensitivity, dual-wavelength apparatus has enabled identification of several additional lines; the hitherto-unreported lines originate purely from hemoglobin molecules. Raman spectra of single granulocytes and lymphocytes are interpreted on the basis of standard protein and nucleic acid vibrational spectroscopy data. The richness of the measured spectrum illustrates that Raman studies of live cells in suspension are more informative than conventional micro-Raman studies where the cells are chemically bound to a glass cover slip.
doi:10.1371/journal.pone.0010427
PMCID: PMC2861675  PMID: 20454686
15.  High Fidelity Nano-Hole Enhanced Raman Spectroscopy 
Surface Enhanced Raman Spectroscopy (SERS) is a sensitive technique that can even detect single molecules. However, in many SERS applications, the strongly inhomogeneous distribution of intense local fields makes it very difficult for a quantitive assessment of the fidelity, or reproducibility of the signal, which limits the application of SERS. Herein we report the development of exceptionally high fidelity Hole-Enhanced Raman Spectroscopy (HERS) from ordered, two-dimensional hexagonal nanohole arrays. We take the fidelity f to be a measure of the percent deviation of the Raman peaks from measurement to measurement. Overall, area averaged fidelities for 12 gold array samples ranged from f ~ 2% – 15% for HERS using aqueous R6G molecules. Furthermore, intensity modulations of the enhanced Raman spectra were measured for the first time as a function of polarization angle. The best of these measurements, which focus on static laser spots on the sample, could be consistent with even higher fidelities than the area-averaged results. Nanohole arrays in silver provided supporting polarization measurements and a more complete enhanced Raman fingerprint for phenylalanine molecules. We also carried out finite-difference time-domain calculations to assist in the interpretation of the experiments, identifying the polarization dependence as possibly arising from hole-hole interactions. Our results represent a step towards making quantitative and reproducible enhanced Raman measurements possible and also open new avenues for a large scale source of highly uniform hot spots.
doi:10.1021/jp900764a
PMCID: PMC2786073  PMID: 20161411
16.  Drop Coating Deposition Raman Spectroscopy of Fluorescein Isothiocyanate Labeled Protein 
Applied spectroscopy  2010;64(10):1078-1085.
Using bovine serum albumin (BSA) as the model protein normal Raman spectra of Fluorescein isothiocyanate (FITC) -conjugated protein was systematically studied for the first time using both solution and the drop coating deposition Raman (DCDR) sampling techniques. The FITC-BSA Raman spectra are dominated by the FITC Raman features that are strongly pH dependent. Current DCDR detection sensitivity obtained with a 10:1 FITC-BSA conjugate is 45 fmol in terms of total protein consumption and ~15 attomol at laser probed volume. Unlike the FITC-BSA solution Raman spectra where the FITC Raman features are photostable, concurrent FITC fluorescence and Raman photobleaching is observed in the DCDR spectra of FITC-BSA. While the FITC Raman photobleaching follows a single exponential decay function with a time constant independent of the FITC labeling ratio, the fluorescence background photobleaching is much more complicated and it depends strongly on the FITC labeling ratio and sample conditions. Mechanistically, the FITC Raman photobleaching is believed to be due to photochemical reaction of the FITC molecules in the electronically excited state. The FITC fluorescence photobleaching involves both concentration quenching and photochemical quenching, and the latter may involve a photochemical intermediate that is fluorescence inactive but Raman active.
doi:10.1366/000370210792973497
PMCID: PMC3218434  PMID: 20925976
Fluorescein isothiocyanate (FITC); Bovine serum albumin (BSA); DCDR; Photobleaching
17.  Micro-Raman Spectroscopy and Univariate Analysis for Monitoring Disease Follow-Up 
Sensors (Basel, Switzerland)  2011;11(9):8309-8322.
Micro-Raman spectroscopy is a very promising tool for medical applications, thanks to its sensitivity to subtle changes in the chemical and structural characteristics of biological specimens. To fully exploit these promises, building a method of data analysis properly suited for the case under study is crucial. Here, a linear or univariate approach using a R2 determination coefficient is proposed for discriminating Raman spectra even with small differences. The validity of the proposed approach has been tested using Raman spectra of high purity glucose solutions collected in the 600 to 1,600 cm−1 region and also from solutions with two known solutes at different concentrations. After this validation step, the proposed analysis has been applied to Raman spectra from oral human tissues affected by Pemphigus Vulgaris (PV), a rare life-threatening autoimmune disease, for monitoring disease follow-up. Raman spectra have been obtained in the wavenumber regions from 1,050 to 1,700 cm−1 and 2,700 to 3,200 cm−1 from tissues of patients at different stages of pathology (active PV, under therapy and PV in remission stage) as confirmed by histopathological and immunofluorescence analysis. Differences in the spectra depending on tissue illness stage have been detected at 1,150–1,250 cm−1 (amide III) and 1,420–1,450 cm−1 (CH3 deformation) regions and around 1,650 cm−1 (amide I) and 2,930 cm−1 (CH3 symmetric stretch). The analysis of tissue Raman spectra by the proposed univariate method has allowed us to effectively differentiate tissues at different stages of pathology.
doi:10.3390/s110908309
PMCID: PMC3231482  PMID: 22164077
oral tissues; Raman microspectroscopy; univariate data analysis; follow-up monitoring
18.  Orientation Determination of Protein Helical Secondary Structure Using Linear and Nonlinear Vibrational Spectroscopy 
The journal of physical chemistry. B  2009;113(36):12169-12180.
In this paper, we systematically presented the orientation determination of protein helical secondary structures using vibrational spectroscopic methods, particularly the nonlinear Sum Frequency Generation (SFG) vibrational spectroscopy, along with linear vibrational spectroscopic techniques such as infrared spectroscopy and Raman scattering. SFG amide I signals can be collected using different polarization combinations of the input laser beams and output signal beam to measure the second order nonlinear optical susceptibility components of the helical amide I modes, which are related to their molecular hyperpolarizability elements through the orientation distribution of these helices. The molecular hyperpolarizability elements of amide I modes of a helix can be calculated based on the infrared transition dipole moment and Raman polarizability tensor of the helix; these quantities are determined by using the bond additivity model to sum over the individual infrared dipole transition moments and Raman polarizability tensors, respectively, of the peptide units (or the amino acid residues). The computed overall infrared transition dipole moment and Raman polarizability tensor of a helix can be validated by experimental data using polarized infrared and polarized Raman spectroscopy on samples with well-aligned helical structures.
From the deduced SFG hyperpolarizability elements and measured SFG second order nonlinear susceptibility components, orientation information regarding helical structures can be determined. Even though such orientation information can also be measured using polarized infrared or polarized Raman amide I signals, SFG has a much lower detection limit, which can be used to study the orientation of a helix when its surface coverage is much lower than a monolayer. In addition, the combination of different vibrational spectroscopic techniques, e.g., SFG and Attenuated Total Reflectance – Fourier Transform Infrared spectroscopy, provides more measured parameters for orientation determination, aiding in the deduction of more complicated orientation distributions. In this paper, we discussed two types of helices: the α-helix and 3–10 helix. However, the orientation determination method presented here is general, and thus can be applied to study other helices as well.
The calculations of SFG amide I hyperpolarizability components for α-helical and 3–10 helical structures with different chain lengths have also been performed. It was found that when the helices reach a certain length, the number of peptide units in the helix should not alter the data analysis substantially. It was shown in the calculation, however, that when the helix chain is short, the SFG hyperpolarizability component ratios can vary substantially when the chain length is changed. Because 3–10 helical structures can be quite short in proteins, the orientation determination for a short 3–10 helix needs to take into account the number of peptide units in the helix.
doi:10.1021/jp904153z
PMCID: PMC2799944  PMID: 19650636
19.  A Microbial Oasis in the Hypersaline Atacama Subsurface Discovered by a Life Detector Chip: Implications for the Search for Life on Mars 
Astrobiology  2011;11(10):969-996.
Abstract
The Atacama Desert has long been considered a good Mars analogue for testing instrumentation for planetary exploration, but very few data (if any) have been reported about the geomicrobiology of its salt-rich subsurface. We performed a Mars analogue drilling campaign next to the Salar Grande (Atacama, Chile) in July 2009, and several cores and powder samples from up to 5 m deep were analyzed in situ with LDChip300 (a Life Detector Chip containing 300 antibodies). Here, we show the discovery of a hypersaline subsurface microbial habitat associated with halite-, nitrate-, and perchlorate-containing salts at 2 m deep. LDChip300 detected bacteria, archaea, and other biological material (DNA, exopolysaccharides, some peptides) from the analysis of less than 0.5 g of ground core sample. The results were supported by oligonucleotide microarray hybridization in the field and finally confirmed by molecular phylogenetic analysis and direct visualization of microbial cells bound to halite crystals in the laboratory. Geochemical analyses revealed a habitat with abundant hygroscopic salts like halite (up to 260 g kg−1) and perchlorate (41.13 μg g−1 maximum), which allow deliquescence events at low relative humidity. Thin liquid water films would permit microbes to proliferate by using detected organic acids like acetate (19.14 μg g−1) or formate (76.06 μg g−1) as electron donors, and sulfate (15875 μg g−1), nitrate (13490 μg g−1), or perchlorate as acceptors. Our results correlate with the discovery of similar hygroscopic salts and possible deliquescence processes on Mars, and open new search strategies for subsurface martian biota. The performance demonstrated by our LDChip300 validates this technology for planetary exploration, particularly for the search for life on Mars. Key Words: Atacama Desert—Life detection—Biosensor—Biopolymers—In situ measurement. Astrobiology 11, 969–996.
doi:10.1089/ast.2011.0654
PMCID: PMC3242637  PMID: 22149750
20.  Amide I vibrational mode suppression in surface (SERS) and tip (TERS) enhanced Raman spectra of protein specimens 
The Analyst  2013;138(6):1665-1673.
Surface- and tip-enhanced Raman spectroscopy (SERS and TERS) are modern spectroscopic techniques, which are becoming widely used and show a great potential for the structural characterisation of biological systems. Strong enhancement of the Raman signal through localised surface plasmon resonance enables chemical detection at the single-molecule scale. Enhanced Raman spectra collected from biological specimens, such as peptides, proteins or microorganisms, were often observed to lack the amide I band, which is commonly used as a marker for the interpretation of secondary protein structure. The cause of this phenomenon was unclear for many decades. In this work, we investigated this phenomenon for native insulin and insulin fibrils using both TERS and SERS and compared these spectra to the spectra of well-defined homo peptides. The results indicate that the appearance of the amide I Raman band does not correlate with the protein aggregation state, but is instead determined by the size of the amino acid side chain. For short model peptides, the absence of the amide I band in TERS and SERS spectra correlates with the presence of a bulky side chain. Homo-glycine and -alanine, which are peptides with small side chain groups (H and CH3, respectively), exhibited an intense amide I band in almost 100% of the acquired spectra. Peptides with bulky side chains, such as tyrosine and tryptophan, exhibited the amide I band in 70% and 31% of the acquired spectra, respectively.
doi:10.1039/c2an36478f
PMCID: PMC3586543  PMID: 23330149
21.  Enthalpic and entropic stages in α-helical peptide unfolding, from laser T-jump/UV Raman spectroscopy 
Journal of the American Chemical Society  2007;129(42):12801-12808.
The α-helix is a ubiquitous structural element in proteins, and a number of studies have addressed the mechanism of helix formation and melting in simple peptides. However, fundamental issues remain to be resolved, particularly the temperature (T) dependence of the rate. In this work we report application of a novel kHz repetition rate solid-state tunable NIR (pump) and deep UV Raman (probe) laser system to study the dynamics of helix unfolding in Ac-GSPEA3KA4KA4-CO-D-Arg-CONH2, a peptide designed for helix stabilization in aqueous solution. Its T-dependent UV resonance Raman (UVRR) spectra, excited at 197 nm for optimal enhancement of amide vibrations, were decomposed into variable contributions from helix and coil spectra. The helix fractions derived from the UVRR spectra and from far UV CD spectra were coincident at low T, but deviated increasingly at high T, the UVRR curve giving higher helix content. This difference is consistent with the greater sensitivity of UVRR spectra to local conformation than CD. After a laser-induced T-jump the UVRR-determined helix fractions defined mono-exponential decays, with time-constants of ~120 ns, independent of the final T (Tf =18 to 61°C), provided the initial T (Ti) was held constant (60C). However, there was also a prompt loss of helicity, whose amplitude increased with increasing Tf, thereby defining an initial enthalpic phase, distinct from the subsequent entropic phase. These phases are attributed to disruption of H-bonds followed by reorientation of peptide links, as the chain is extended. When Ti was raised in parallel with Tf (10° C T-jumps), the prompt phase merged into an accelerating slow phase, an effect attributable to the shifting distribution of initial helix lengths. Even greater acceleration with rising Ti has been reported in T-jump experiments monitored by IR and fluorescence spectroscopies. This difference is attributable to the longer range character of these probes, whose responses are therefore more strongly weighted toward the H-bond-breaking enthalpic process.
doi:10.1021/ja073366l
PMCID: PMC2887291  PMID: 17910449
22.  Low-Frequency Dynamics of Caldariomyces fumago Chloroperoxidase Probed by Femtosecond Coherence Spectroscopy† 
Biochemistry  2008;47(18):5156-5167.
Ultrafast laser spectroscopy techniques are used to measure the low-frequency vibrational coherence spectra and nitric oxide rebinding kinetics of Caldariomyces fumago chloroperoxidase (CPO). Comparisons of the CPO coherence spectra with those of other heme species are made to gauge the protein-specific nature of the low-frequency spectra. The coherence spectrum of native CPO is dominated by a mode that appears near 32-33 cm-1 at all excitation wavelengths, with a phase that is consistent with a ground-state Raman-excited vibrational wavepacket. On the basis of a normal coordinate structural decomposition (NSD) analysis, we assign this feature to the thiolate-bound heme doming mode. Spectral resolution of the probe pulse (“detuned” detection) reveals a mode at 349 cm-1, which has been previously assigned using Raman spectroscopy to the Fe-S stretching mode of native CPO. The ferrous species displays a larger degree of spectral inhomogeneity than the ferric species, as reflected by multiple shoulders in the optical absorption spectra. The inhomogeneities are revealed by changes in the coherence spectra at different excitation wavelengths. The appearance of a mode close to 220 cm-1 in the coherence spectrum of reduced CPO excited at 440 nm suggests that a subpopulation of five coordinated histidine-ligated hemes is present in the ferrous state at a physiologically relevant pH. A significant increase in the amplitude of the coherence signal is observed for the resonance with the 440 nm subpopulation. Kinetics measurements reveal that nitric oxide binding to ferric and ferrous CPO can be described as a single-exponential process, with rebinding time constants of 29.4 ± 1 and 9.3 ± 1 ps, respectively. This is very similar to results previously reported for nitric oxide binding to horseradish peroxidase.
doi:10.1021/bi7025485
PMCID: PMC2766418  PMID: 18407660
23.  Non-contact, Label-free Monitoring of Cells and Extracellular Matrix using Raman Spectroscopy 
Non-destructive, non-contact and label-free technologies to monitor cell and tissue cultures are needed in the field of biomedical research.1-5 However, currently available routine methods require processing steps and alter sample integrity. Raman spectroscopy is a fast method that enables the measurement of biological samples without the need for further processing steps. This laser-based technology detects the inelastic scattering of monochromatic light.6 As every chemical vibration is assigned to a specific Raman band (wavenumber in cm-1), each biological sample features a typical spectral pattern due to their inherent biochemical composition.7-9 Within Raman spectra, the peak intensities correlate with the amount of the present molecular bonds.1 Similarities and differences of the spectral data sets can be detected by employing a multivariate analysis (e.g. principal component analysis (PCA)).10
Here, we perform Raman spectroscopy of living cells and native tissues. Cells are either seeded on glass bottom dishes or kept in suspension under normal cell culture conditions (37 °C, 5% CO2) before measurement. Native tissues are dissected and stored in phosphate buffered saline (PBS) at 4 °C prior measurements. Depending on our experimental set up, we then either focused on the cell nucleus or extracellular matrix (ECM) proteins such as elastin and collagen. For all studies, a minimum of 30 cells or 30 random points of interest within the ECM are measured. Data processing steps included background subtraction and normalization.
doi:10.3791/3977
PMCID: PMC3468188  PMID: 22688496
Bioengineering;  Issue 63;  Raman spectroscopy;  label-free analysis;  living cells;  extracellular matrix;  tissue engineering
24.  Temperature-dependent Raman investigation of rolled up InGaAs/GaAs microtubes 
Nanoscale Research Letters  2012;7(1):594.
Large arrays of multifunctional rolled-up semiconductors can be mass-produced with precisely controlled size and composition, making them of great technological interest for micro- and nano-scale device fabrication. The microtube behavior at different temperatures is a key factor towards further engineering their functionality, as well as for characterizing strain, defects, and temperature-dependent properties of the structures. For this purpose, we probe optical phonons of GaAs/InGaAs rolled-up microtubes using Raman spectroscopy on defect-rich (faulty) and defect-free microtubes. The microtubes are fabricated by selectively etching an AlAs sacrificial layer in order to release the strained InGaAs/GaAs bilayer, all grown by molecular beam epitaxy. Pristine microtubes show homogeneity of the GaAs and InGaAs peak positions and intensities along the tube, which indicates a defect-free rolling up process, while for a cone-like microtube, a downward shift of the GaAs LO phonon peak along the cone is observed. Formation of other type of defects, including partially unfolded microtubes, can also be related to a high Raman intensity of the TO phonon in GaAs. We argue that the appearance of the TO phonon mode is a consequence of further relaxation of the selection rules due to the defects on the tubes, which makes this phonon useful for failure detection/prediction in such rolled up systems. In order to systematically characterize the temperature stability of the rolled up microtubes, Raman spectra were acquired as a function of sample temperature up to 300°C. The reversibility of the changes in the Raman spectra of the tubes within this temperature range is demonstrated.
doi:10.1186/1556-276X-7-594
PMCID: PMC3511215  PMID: 23101911
Rolled up tubes; Microtubes; Raman spectroscopy defects; Raman imaging; Strain imaging; Gallium arsenide; Dependent Raman spectroscopy; Gallium arsenide TO phonon
25.  Label-free Live Cell Imaging of Nucleic Acids using Stimulated Raman Scattering (SRS) Microscopy 
Imaging of nucleic acids is important for studying cellular processes such as cell division and apoptosis. A noninvasive label-free technique is attractive. Raman spectroscopy provides rich chemical information based on specific vibrational peaks. However, the signal from spontaneous Raman scattering is weak and long integration times are required, which drastically limits the imaging speed when used for microscopy. Coherent Raman scattering techniques, comprising coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) microscopy, overcome this problem by enhancing the signal level by up to five orders of magnitude. CARS microscopy suffers from a nonresonant background signal, which distorts Raman spectra and limits sensitivity. This makes CARS imaging of weak transitions in spectrally congested regions challenging. This is especially the case in the fingerprint region, where nucleic acids show characteristic peaks. The recently developed SRS microscopy is free from these limitations; excitation spectra are identical to those of spontaneous Raman and sensitivity is close to shot-noise limited. Here we demonstrate the use of SRS imaging in the fingerprint region to map the distribution of nucleic acids in addition to proteins and lipids in single salivary gland cells of Drosophila larvae, and in single mammalian cells. This allows the imaging of DNA condensation associated with cell division and opens up possibilities of imaging such processes in vivo.
doi:10.1002/cphc.201100890
PMCID: PMC3516876  PMID: 22368112
CARS; SRS; Microscopy; live cells; DNA

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