Biomedical Spectroscopy and Imaging - Volume 3, issue 4

Authors: Haris, Parvez I.

Article Type: Other

DOI: 10.3233/BSI-140096

Citation: Biomedical Spectroscopy and Imaging, vol. 3, no. 4, pp. 307-309, 2014

Authors: Macnab, Andrew J.

Article Type: Review Article

Abstract: In the 50 year history of NIRS, biomedical applications in urology are recent. This review summarizes technical advances and novel enquiry that have led to hemodynamic monitoring of the testis, measures of renal function, evaluation of the pelvic floor in women, and interrogation of the bladder. An overview is given of how bladder spectroscopy has evolved and the evidence that non-invasive transcutaneous optical monitoring of the anterior bladder wall now enables variations in the organ's hemodynamics and oxygen supply and demand to be identified in real time. Research indicates that bladder blood flow and oxygenation differ in health and disease, …and because NIRS monitors changes in the microcirculation bladder spectroscopy adds physiologic information not available by other means, including via the current invasive method for evaluation of voiding dysfunction. Confidence that bladder NIRS yields physiologic data comes from the patterns of chromophore change and tissue oxygen saturation observed corresponding to variations in these parameters in NIRS studies of other tissues in response to known physiologic events. Importantly, when interpreted based on this prior research, novel insight is gained about probable causal pathologies underlying bladder dysfunction. Studies to date warrant further research, continued refinement of instrumentation, extension of the scope of monitoring, and exploration of diagnostic software algorithms. Show more

Keywords: Bladder, near infrared spectroscopy (NIRS), spatially resolved spectroscopy (SRS), urinary incontinence, urinary tract, urology

DOI: 10.3233/BSI-140091

Citation: Biomedical Spectroscopy and Imaging, vol. 3, no. 4, pp. 311-344, 2014

Authors: Chikhirzhina, Elena | Chikhirzhina, Galina | Polyanichko, Alexander

Article Type: Research Article

Abstract: Structural organization of chromatin in eukaryotic cells plays an important role in the functioning of the genetic apparatus of the cell. The nucleoprotein complex is formed due to the interactions of DNA with histones and non-histone proteins. Here we describe the main levels of the structural organization of the chromatin. Special attention is paid to the spectroscopic techniques such as infrared absorption spectroscopy, electronic and vibrational circular dichroism and their impact to the investigation of the chromatin structure. The linker proteins: histone H1 and non-histone protein HMGB1 and their role in the formation of the super compact chromatin is discussed.

Keywords: Circular dichroism, atomic force microscopy, chromatin structure, nucleosome, DNA, histones, linker histones of H1 family, HMGB1 protein

DOI: 10.3233/BSI-140093

Citation: Biomedical Spectroscopy and Imaging, vol. 3, no. 4, pp. 345-358, 2014

Authors: Qi, Ji | Bechtel, Kate L. | Shih, Wei-Chuan

Article Type: Research Article

Abstract: Raman spectroscopy and microscopy can provide molecular information for complex materials such as biological tissue and cells. In these applications, light-collection throughput is essential for speedy acquisition of high-quality data. To improve throughput, two-dimensional detectors and high numerical aperture (NA) optical systems have been employed. However, owing to the out-of-plane diffraction in grating-based dispersive spectrograph, the entrance slit image formed at the detector plane is curved along the vertical direction. Direct vertical binning of individual detector rows without correcting the curvature results in degraded spectral resolution and peak misalignment. We evaluate two software approaches to remove the image curvature after …high-throughput data acquisition, with the objective to retain instrument spectral resolution and peak accuracy as if a linear-array detector were used. Curvature correction and detection are achieved in two steps: calibration of the image curvature using a Raman active material and application of the correction to future curved images. This method has been employed for a high-NA, large CCD Raman spectroscopic system deigned for non-invasive glucose sensing, a medium-NA, medium-size CCD line-scan Raman microscope designed for high-throughput tissue and cellular imaging, and an active-illumination Raman microscope. We show that remarkable improvement in data fidelity can be obtained as assessed by peak misalignment, distribution of data variance, and the waveform of principal component spectra. High quality curvature correction is essential for quantitative analysis such as the multivariate calibration, spectral pattern recognition, and peak shift detection based techniques. The software approach is highly flexible for instrument modification. Show more

Keywords: Raman spectroscopy, Raman microscopy, SERS, curvature assessment, curvature correction

DOI: 10.3233/BSI-140092

Citation: Biomedical Spectroscopy and Imaging, vol. 3, no. 4, pp. 359-368, 2014

Authors: Jenkins, Richard O. | Kwok, Rachel W.L. | Goncharov, Nikolay V. | Halliwell, Richard J.S. | Haris, Parvez I.

Article Type: Research Article

Abstract: BACKGROUND: Limited success has been reported for matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) differentiation of staphylococci, including methicillin resistant Staphylococcus aureus (MRSA) strains. Chemical pretreatment of cells prior to MALDI-TOF-MS analysis has not been systematically investigated for enhanced discrimination of S. aureus strains. OBJECTIVES: To evaluate various chemical pretreatment of cells for MALDI-TOF-MS discrimination of clinical staphylococcal isolates, with a focus on differentiation of MRSA from methicillin sensitive S. aureus (MSSA) strains and from other staphylococcal species. METHOD: MALDI-TOF-MS of a well-characterised S. aureus strain(s) was optimised with respect to matrix chemical(s), matrix solvent and target …plating method. Various chemical pretreatments (solvents, reductants, detergents) and pretreatment application methods were then evaluated for enhancement of spectral richness. The three most promising pretreatments were applied to MALDI-TOF-MS discrimination of three set of clinical isolates comprising non-S. aureus staphylococci (77 isolates), MSSA (36) and MRSA (43), with analysis by total or set specific resolved peaks. RESULTS: The optimized MALDI-TOF-MS protocol involved α-cyano-4-hydroxycinnamic acid (CHCA) as matrix chemical (in 1:2 acetonitrile:H2 O and 2% trifluoroacetic acid), with application as an overlay onto smeared cells (on-probe). On-probe application of chemical pretreatment was most effective at enhancing MALDI-TOF-MS spectral richness. Use of reductants and detergents as pretreatments were ineffective. The three most effective solvents/acid pretreatments – ethanol:formate, ethanol:acetate and formate:isopropanol – each generated reproducible and distinct spectra over the 2,000–10,000 m/z range. For the combined sets of clinical isolates (114), all three of these pretreatments increased the total number of resolved peaks in comparison with no pretreatment controls. The ethanol:formate pretreatment gave 100% clustering of non-S. aureus staphylococci, based on total resolved peaks. The formate:isopropanol pretreatment generated the largest increase in number of MRSA set specific peaks (from 18 to 32; 78% increase) and clustered the majority (77%) of the MRSA strains together, although compete discrimination of the MSSA and MRSA was not achieved. CONCLUSION: MALDI-TOF-MS discrimination of clinical isolates of staphylococci is enhanced through chemical pretreatment of cells. Three chemical pretreatments, not previously applied to staphylococci, are highlighted for enhancing spectral richness and offering new opportunities for improved discrimination of staphylococci, including MRSA and MSSA strains. Show more

Keywords: MALDI-TOF-MS, Staphylococcus, S. aureus, MRSA, MSSA

DOI: 10.3233/BSI-140094

Citation: Biomedical Spectroscopy and Imaging, vol. 3, no. 4, pp. 369-380, 2014

Authors: Awad, Fathi | Ramprasath, Chandrasekaran | Mathivanan, Narayanasamy | Aruna, Prakasa Rao | Ganesan, Singaravelu

Article Type: Research Article

Abstract: This study focuses on identification and classification of Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella typhi and Klebsiella pneumoniae based on steady-state and fluorescence lifetime spectroscopy. Bacterial samples were cultured under controlled conditions and diluted in saline to 4×106 cell/ml for analysis. Two excitations at 250 nm (aromatic amino acids and nucleic acids, AAA+NA) and 280 nm (tryptophan) were used for steady-state while fluorescence lifetime decays were acquired at 280 nm excitation. A small range of difference was obtained for tryptophan lifetime from the four bacteria for the fast lifetime component (1.61–1.73 ns) and the slow lifetime component (5.25–5.44 ns). The …application of principal component analysis (PCA) to steady-state fluorescence spectra resulted in the successful classification of the four bacteria and highest percentage of good classification was obtained for tryptophan (λexc =280 nm). Our results demonstrated that steady-state fluorescence spectroscopy coupled to PCA is a powerful tool for identification and classification of bacterial pathogens at genus level. Show more

Keywords: Fluorescence spectroscopy, bacterial pathogens, identification, principal component analysis

DOI: 10.3233/BSI-140095

Citation: Biomedical Spectroscopy and Imaging, vol. 3, no. 4, pp. 381-391, 2014

Article Type: Other

Citation: Biomedical Spectroscopy and Imaging, vol. 3, no. 4, pp. 393-397, 2014

Article Type: Other

Citation: Biomedical Spectroscopy and Imaging, vol. 3, no. 4, pp. 399-400, 2014