Science.gov

Sample records for biological spectroscopy part

  1. Noise Spectroscopy Used in Biology

    NASA Astrophysics Data System (ADS)

    Žacik, Michal

    This thesis contains glossary topic of spectroscopic measurement methods in broad bands of frequency. There is designed experimental measurement method for simple samples and biological samples measurements for noise spectroscopy in frequency range of 0.1 - 6 GHz, using broadband noise generator. There is realized the workplace and the measurement method is verified by measuring on selected samples. Measurements a displayed and analyzed.

  2. An Introduction to Biological NMR Spectroscopy*

    PubMed Central

    Marion, Dominique

    2013-01-01

    NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP). PMID:23831612

  3. Using Raman spectroscopy to characterize biological materials.

    PubMed

    Butler, Holly J; Ashton, Lorna; Bird, Benjamin; Cinque, Gianfelice; Curtis, Kelly; Dorney, Jennifer; Esmonde-White, Karen; Fullwood, Nigel J; Gardner, Benjamin; Martin-Hirsch, Pierre L; Walsh, Michael J; McAinsh, Martin R; Stone, Nicholas; Martin, Francis L

    2016-04-01

    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. PMID:26963630

  4. Submillimeter wave spectroscopy of biological macromolecules

    NASA Astrophysics Data System (ADS)

    Globus, Tatiana

    2005-03-01

    The recently emergence of submillimeter-wave or terahertz (THz) spectroscopy of biological molecules has demonstrated the capability to detect low-frequency internal molecular vibrations involving the weakest hydrogen bonds of the DNA base pairs and/or non-bonded interactions. These multiple bonds, although having only ˜ 5% of the strength of covalent bonds, stabilize the structure of bio-polymers, by holding the two strands of the DNA double helix together, or polypeptides together in different secondary structure conformations. There will be a review of THz-frequency transmission (absorption) results for biological materials obtained from Fourier Transform Infrared (FTIR) spectroscopy during the last few years^1,2. Multiple resonances, due to low frequency vibrational modes within biological macromolecules, have been unambiguously demonstrated in qualitative agreement with theoretical prediction, thereby confirming the fundamental physical nature of observed resonance features. The discovery of resonance character of interaction between THz radiation and biological materials opens many possible applications for THz spectroscopy technique in biological sensing and biomedicine using multiple resonances as distinctive spectral fingerprints. However, many issues still require investigation. Kinetics of interactions with radiation at THz has not been studied and vibrational lifetimes have not been measured directly as a function of frequency. The strength of resonant modes of bio-molecules in aqueous environment and strong dependence of spectra on molecular orientation need explanation. Vibrational modes have not been assigned to specific motions within molecules. THz spectroscopy of bio-polymers makes it only in first steps. 1. T. Globus, D. Woolard, M. Bykhovskaia, B. Gelmont, L. Werbos, A. Samuels. International Journal of High Speed Electronics and Systems (IJHSES), 13, No. 4, 903-936 (2003). 2. T. Globus, T. Khromova, D. Woolard and B. Gelmont. Proceedings of

  5. APD detectors for biological fluorescence spectroscopy

    NASA Astrophysics Data System (ADS)

    Mazères, S.; Borrel, V.; Magenc, C.; Courrech, J. L.; Bazer-Bachi, R.

    2006-11-01

    Fluorescence spectroscopy is a very convenient and widely used method for studying the molecular background of biological processes [L. Salomé, J.L. Cazeil, A. Lopez, J.F. Tocanne, Eur. Biophys. J. 27 (1998) 391-402]. Chromophores are included in the structure under study and a flash of laser light induces fluorescence (Fluorescence Recovery After Photo-bleaching), the decay of which yields information on the polarity, the speed of rotation, and the speed of diffusion as well as on the temporal and spatial evolution of interactions between molecular species. The method can even be used to study living cells [J.F. Tocanne, L. Cézanne, A. Lopez, Prog. Lipid Res. 33 (1994) 203-237, L. Cezanne, A. Lopez, F. Loste, G. Parnaud, O. Saurel, P. Demange, J.F. Tocanne, Biochemistry 38 (1999) 2779-2786]. This is classically performed with a PM-based system. For biological reasons a decrease of the excitation of the cells is highly desirable. Because the fluorescence response then becomes fainter a significant improvement in detector capability would be welcome. We present here results obtained with an Avalanche Photo Diode (APD)-based system. The small sensitive area of detection allows a very significant improvement in signal/noise ratio, improvement in gain, and the opening-up of a new parameter space. With these new detectors we can begin the study of information transmission between cells through morphine receptors. This work involves both electronics engineers and biophysicists, so results and techniques in both fields will be presented here.

  6. Targeted Development of Registries of Biological Parts

    PubMed Central

    Peccoud, Jean; Blauvelt, Megan F.; Cai, Yizhi; Cooper, Kristal L.; Crasta, Oswald; DeLalla, Emily C.; Evans, Clive; Folkerts, Otto; Lyons, Blair M.; Mane, Shrinivasrao P.; Shelton, Rebecca; Sweede, Matthew A.; Waldon, Sally A.

    2008-01-01

    Background The design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea. Methods/Principal Findings By analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified. Conclusions/Significance Organizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users. PMID:18628824

  7. Spectroscopy, colorimetry, and biological chemistry in the nineteenth century.

    PubMed Central

    Rinsler, M G

    1981-01-01

    The development of colorimetry and spectroscopy in the nineteenth century is described. An account is given of the application of their techniques to biological chemistry during that period. PMID:7014652

  8. Raman Spectroscopy of Optically Trapped Single Biological Micro-Particles

    PubMed Central

    Redding, Brandon; Schwab, Mark J.; Pan, Yong-le

    2015-01-01

    The combination of optical trapping with Raman spectroscopy provides a powerful method for the study, characterization, and identification of biological micro-particles. In essence, optical trapping helps to overcome the limitation imposed by the relative inefficiency of the Raman scattering process. This allows Raman spectroscopy to be applied to individual biological particles in air and in liquid, providing the potential for particle identification with high specificity, longitudinal studies of changes in particle composition, and characterization of the heterogeneity of individual particles in a population. In this review, we introduce the techniques used to integrate Raman spectroscopy with optical trapping in order to study individual biological particles in liquid and air. We then provide an overview of some of the most promising applications of this technique, highlighting the unique types of measurements enabled by the combination of Raman spectroscopy with optical trapping. Finally, we present a brief discussion of future research directions in the field. PMID:26247952

  9. Fourier Transform Infrared Spectroscopy Part III. Applications.

    ERIC Educational Resources Information Center

    Perkins, W. D.

    1987-01-01

    Discusses the use of the FT-IR spectrometer in analyses that were previously avoided. Examines some of the applications of this spectroscopy with aqueous solutions, circular internal reflection, samples with low transmission, diffuse reflectance, infrared emission, and the infrared microscope. (TW)

  10. Positron annihilation spectroscopy of biological tissue in 11C irradiation

    NASA Astrophysics Data System (ADS)

    Sakurai, Hiroshi; Itoh, Fumitake; Hirano, Yoshiyuki; Nitta, Munetaka; Suzuki, Kosuke; Kato, Daisuke; Yoshida, Eiji; Nishikido, Fumihiko; Wakizaka, Hidekatsu; Kanai, Tatsuaki; Yamaya, Taiga

    2014-11-01

    Positron annihilation spectroscopy (PAS) spectra of biological tissue in 11C irradiation are reported and spatial resolution coefficient of positron emission tomography (PET) obtained from the PAS spectrum is discussed for 11C irradiation. A PAS spectrum of the biological tissue with water is the same as that of the water pool phantom in 11C irradiation. However, a PAS spectrum of the biological tissue with less water differs from that of the water pool phantom. The PET spatial resolution coefficient depends on the kind of biological tissue. However, the PET spatial resolution coefficient, 0.00243  ±  0.00014, can be used as a common value of maximum limit.

  11. Terahertz time-domain spectroscopy of biological tissues

    SciTech Connect

    Nazarov, M M; Shkurinov, A P; Kuleshov, E A; Tuchin, V V

    2008-07-31

    Terahertz absorption spectra and dispersion of biologically important substances such as sugar, water, hemoglobin, lipids and tissues are studied. The characteristic absorption lines in the frequency range of a terahertz spectrometer (0.1-3.5 THz) are found. The refraction indices and absorption coefficients of human tooth enamel and dentine are measured. The method of terahertz phase reflection spectroscopy is developed for strongly absorbing substances. Simple and reliable methods of time-resolved terahertz spectroscopy are developed. (biophotonics)

  12. Photoacoustic resonance spectroscopy for biological tissue characterization

    NASA Astrophysics Data System (ADS)

    Gao, Fei; Feng, Xiaohua; Zheng, Yuanjin; Ohl, Claus-Dieter

    2014-06-01

    By "listening to photons," photoacoustics allows the probing of chromosomes in depth beyond the optical diffusion limit. Here we report the photoacoustic resonance effect induced by multiburst modulated laser illumination, which is theoretically modeled as a damped mass-string oscillator and a resistor-inductor-capacitor (RLC) circuit. Through sweeping the frequency of multiburst modulated laser, the photoacoustic resonance effect is observed experimentally on phantoms and porcine tissues. Experimental results demonstrate different spectra for each phantom and tissue sample to show significant potential for spectroscopic analysis, fusing optical absorption and mechanical vibration properties. Unique RLC circuit parameters are extracted to quantitatively characterize phantom and biological tissues.

  13. Photoacoustic resonance spectroscopy for biological tissue characterization.

    PubMed

    Gao, Fei; Feng, Xiaohua; Zheng, Yuanjin; Ohl, Claus-Dieter

    2014-06-01

    By "listening to photons," photoacoustics allows the probing of chromosomes in depth beyond the optical diffusion limit. Here we report the photoacoustic resonance effect induced by multiburst modulated laser illumination, which is theoretically modeled as a damped mass-string oscillator and a resistor-inductor-capacitor (RLC) circuit. Through sweeping the frequency of multiburst modulated laser, the photoacoustic resonance effect is observed experimentally on phantoms and porcine tissues. Experimental results demonstrate different spectra for each phantom and tissue sample to show significant potential for spectroscopic analysis, fusing optical absorption and mechanical vibration properties. Unique RLC circuit parameters are extracted to quantitatively characterize phantom and biological tissues. PMID:24928154

  14. Computational Laser Spectroscopy in a Biological Tissue

    PubMed Central

    Gantri, M.; Trabelsi, H.; Sediki, E.; Ben Salah, R.

    2010-01-01

    We present a numerical spectroscopic study of visible and infrared laser radiation in a biological tissue. We derive a solution of a general two-dimensional time dependent radiative transfer equation in a tissue-like medium. The used model is suitable for many situations especially when the external source is time-dependent or continuous. We use a control volume-discrete ordinate method associated with an implicit three-level second-order time differencing scheme. We consider a very thin rectangular biological-tissue-like medium submitted to a visible or a near infrared light sources. The RTE is solved for a set of different wavelength source. All sources are assumed to be monochromatic and collimated. The energetic fluence rate is computed at a set of detector points on the boundaries. According to the source type, we investigate either the steady-state or transient response of the medium. The used model is validated in the case of a heterogeneous tissue-like medium using referencing experimental results from the literature. Also, the developed model is used to study changes on transmitted light in a rat-liver tissue-like medium. Optical properties depend on the source wavelength and they are taken from the literature. In particular, light-transmission in the medium is studied for continuous wave and for short pulse. PMID:20396377

  15. BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts

    PubMed Central

    Yang, Kun; Stracquadanio, Giovanni; Luo, Jingchuan; Boeke, Jef D.; Bader, Joel S.

    2016-01-01

    Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder. Contact: joel.bader@jhu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26568632

  16. Critical appraisal: dental amalgam update--part II: biological effects.

    PubMed

    Wahl, Michael J; Swift, Edward J

    2013-12-01

    Dental amalgam restorations have been controversial for over 150 years. In Part I of this Critical Appraisal, the clinical efficacy of dental amalgam was updated. Here in Part II, the biological effects of dental amalgam are addressed. PMID:24320063

  17. Electrophoretic separator for purifying biologicals, part 1

    NASA Technical Reports Server (NTRS)

    Mccreight, L. R.

    1978-01-01

    A program to develop an engineering model of an electrophoretic separator for purifying biologicals is summarized. An extensive mathematical modeling study and numerous ground based tests were included. Focus was placed on developing an actual electrophoretic separator of the continuous flow type, configured and suitable for flight testing as a space processing applications rocket payload.

  18. Nanosecond and femtosecond laser spectroscopy of molecules of biological interest

    NASA Astrophysics Data System (ADS)

    Villani, P.; Orlando, S.; Santagata, A.; De Bonis, A.; Veronesi, S.; Giardini, A.

    2007-07-01

    This paper mainly concerns on nanosecond and femtosecond laser spectroscopy of aromatic organic compounds as neurotransmitters, and plume diagnostics of the ablated species, in order to characterize the plasma dynamics, i.e. the temporal and spatial evolution of the plume. Optical emission spectroscopy has been applied to characterize the transient species produced in the femtosecond (fs) and nanosecond (ns) regimes. The laser sources employed for optical emission spectroscopy are a frequency-doubled Nd:YAG Handy ( λ = 532 nm, τ = 5 ns) and a frequency-doubled Nd:glass ( λ = 527 nm, τ = 250 fs). These studies aim to detect and give information on the photoexcitation and photodissociation of these biological molecules and to compare the plasma characteristics in the two ablation regimes.

  19. High-Resolution Waveguide THz Spectroscopy of Biological Molecules☆

    PubMed Central

    Laman, N.; Harsha, S. Sree; Grischkowsky, D.; Melinger, Joseph S.

    2008-01-01

    Abstract Low-frequency vibrational modes of biological molecules consist of intramolecular modes, which are dependent on the molecule as a whole, as well as intermolecular modes, which arise from hydrogen-bonding interactions and van der Waals forces. Vibrational modes thus contain important information about conformation dynamics of biological molecules, and can also be used for identification purposes. However, conventional Fourier transform infrared spectroscopy and terahertz time-domain spectroscopy (THz-TDS) often result in broad, overlapping features that are difficult to distinguish. The technique of waveguide THz-TDS has been recently developed, resulting in sharper features. For this technique, an ordered polycrystalline film of the molecule is formed on a metal sample plate. This plate is incorporated into a metal parallel-plate waveguide and probed via waveguide THz-TDS. The planar order of the film reduces the inhomogeneous broadening, and cooling of the samples to 77K reduces the homogenous broadening. This combination results in the line-narrowing of THz vibrational modes, in some cases to an unprecedented degree. Here, this technique has been demonstrated with seven small biological molecules, thymine, deoxycytidine, adenosine, D-glucose, tryptophan, glycine, and L-alanine. The successful demonstration of this technique shows the possibilities and promise for future studies of internal vibrational modes of large biological molecules. PMID:17933879

  20. The biological microprocessor, or how to build a computer with biological parts

    PubMed Central

    Moe-Behrens, Gerd HG

    2013-01-01

    Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system. PMID:24688733

  1. The biological microprocessor, or how to build a computer with biological parts.

    PubMed

    Moe-Behrens, Gerd Hg

    2013-01-01

    Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts. Here we describe these building blocks and how they can be assembled to a general purpose computer system, a biological microprocessor. Such a system consists of biological parts building an input / output device, an arithmetic logic unit, a control unit, memory, and wires (busses) to interconnect these components. A biocomputer can be used to monitor and control a biological system. PMID:24688733

  2. Plant and Animal Gravitational Biology. Part 1

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Session TA2 includes short reports covering: (1) The Interaction of Microgravity and Ethylene on Soybean Growth and Metabolism; (2) Structure and G-Sensitivity of Root Statocytes under Different Mass Acceleration; (3) Extracellular Production of Taxanes on Cell Surfaces in Simulated Microgravity and Hypergravity; (4) Current Problems of Space Cell Phytobiology; (5) Biological Consequences of Microgravity-Induced Alterations in Water Metabolism of Plant Cells; (6) Localization of Calcium Ions in Chlorella Cells Under Clinorotation; (7) Changes of Fatty Acids Content of Plant Cell Plasma Membranes under Altered Gravity; (8) Simulation of Gravity by Non-Symmetrical Vibrations and Ultrasound; and (9) Response to Simulated weightlessness of In Vitro Cultures of Differentiated Epithelial Follicular Cells from Thyroid.

  3. Electromagnetic fields-Part 1; Biological effects

    SciTech Connect

    Nair, I.; Morgan, M.G. )

    1990-08-01

    It is known that low-frequency electric and magnetic fields can produce a variety of effects in biological systems. Pulsed magnetic fields, for instance, are used to mend broken bones, and other beneficial medical applications are being developed. But in more chronic and less controlled environments, can exposure to such fields also pose health risks No one knows. Today that possibility, however, requires serious consideration. Though present knowledge is fragmentary, and a coherent theory to explain the observations seems far off, the continuous presence of power-frequency fields in the modern environment makes potential health effects a matter of serious scientific and public health policy concern. That concern has focused on cancer - especially leukemia and brain tumors - and developmental abnormalities, and, to a lesser extent on endocrine and nervous system disorders, including chronic depression. The authors focus on 60-hertz fields, where the mechanism of interaction probably involves the cell membrane, is nonlinear, and may act by causing some cooperative phenomena among the components of the cell membrane.

  4. Sub-terahertz resonance spectroscopy of biological macromolecules and cells

    NASA Astrophysics Data System (ADS)

    Globus, Tatiana; Moyer, Aaron; Gelmont, Boris; Khromova, Tatyana; Sizov, Igor; Ferrance, Jerome

    2013-05-01

    Recently we introduced a Sub-THz spectroscopic system for characterizing vibrational resonance features from biological materials. This new, continuous-wave, frequency-domain spectroscopic sensor operates at room temperature between 315 and 480 GHz with spectral resolution of at least 1 GHz and utilizes the source and detector components from Virginia Diode, Inc. In this work we present experimental results and interpretation of spectroscopic signatures from bacterial cells and their biological macromolecule structural components. Transmission and absorption spectra of the bacterial protein thioredoxin, DNA and lyophilized cells of Escherichia coli (E. coli), as well as spores of Bacillus subtillis and B. atrophaeus have been characterized. Experimental results for biomolecules are compared with absorption spectra calculated using molecular dynamics simulation, and confirm the underlying physics for resonance spectroscopy based on interactions between THz radiation and vibrational modes or groups of modes of atomic motions. Such interactions result in multiple intense and narrow specific resonances in transmission/absorption spectra from nano-gram samples with spectral line widths as small as 3 GHz. The results of this study indicate diverse relaxation dynamic mechanisms relevant to sub-THz vibrational spectroscopy, including long-lasting processes. We demonstrate that high sensitivity in resolved specific absorption fingerprints provides conditions for reliable detection, identification and discrimination capability, to the level of strains of the same bacteria, and for monitoring interactions between biomaterials and reagents in near real-time. Additionally, it creates the basis for the development of new types of advanced biological sensors through integrating the developed system with a microfluidic platform for biomaterial samples.

  5. X-Ray Absorption Spectroscopy Imaging of Biological Tissues

    NASA Astrophysics Data System (ADS)

    Pickering, Ingrid J.; George, Graham N.

    2007-02-01

    X-ray absorption spectroscopy (XAS) is proving invaluable in determining the average chemical form of metals or metalloids in intact biological tissues. As most tissues have spatial structure, there is great additional interest in visualizing the spatial location of the metal(loid) as well as its chemical forms. XAS imaging gives the opportunity of producing maps of specific chemical types of elements in vivo in dilute biological systems. X-ray fluorescence microprobe techniques are routinely used to study samples with spatial heterogeneity. Microprobe produces elemental maps, with chemical sensitivity obtained by recording micro-XAS spectra at selected point locations on the map. Unfortunately, using these procedures spatial detail may be lost as the number of point spectra recorded generally is limited. A powerful extension of microprobe is XAS imaging or chemically specific imaging. Here, the incident energy is tuned to features in the near-edge which are characteristic of the expected chemical forms of the element. With a few simple assumptions, these XAS images can then be converted to quantitative images of specific chemical form, yielding considerable clarity in the distributions.

  6. Interest in biology. Part I: A multidimensional construct

    NASA Astrophysics Data System (ADS)

    Gardner, Paul L.; Tamir, Pinchas

    Interest in a school subject (e.g., biology) is conceptualized in terms of three components: topics, activities, and motives, each of which has several dimensions. In this study, seven instruments were developed and administered to grade-10 biology students in Israel. Factor analysis provided support for the conceptualization which underlies the development of the instruments. Topic dimensions included biochemical processes, nonhuman organisms, human biology, personal hygiene, and practical applications; the activity dimensions were experiential learning, reception learning, writing/summarizing and group discussion; motives included environmental issues, moral issues, examination success, personal independence, problem solving, and four career dimensions (research, high-status professions, lower-status careers, woodsy-birdsy careers). In an analysis described in Part II of this paper, the students were classified into four groups on the basis of their grade-11 subject enrollment intentions: H (high-level biology), L (low-level biology), P (physical science), and N (no science). Zero-order and multiple correlations were found between interest and other variables and membership/nonmembership of the four groups. Students in Group H were characterized by higher achievement in year-10 biology, higher levels of enjoyment of biology, career orientations towards research or high-status biology-based professions, greater interest in various biology topics, especially reproduction/cell division/genetics, and a greater tendency to regard the Bagrut (grade-12) examination as interesting. Students in Group N displayed lower levels of interest in various topics (especially the microscope, plants, and reproduction), were less motivated to solve problems, had poorer grades in biology (and chemistry), were less likely to perceive biology as useful, were less likely to regard the Bagrut examination as fair, and were less likely to be interested in social modes of learning. There

  7. Using Fourier transform IR spectroscopy to analyze biological materials

    PubMed Central

    Baker, Matthew J; Trevisan, Júlio; Bassan, Paul; Bhargava, Rohit; Butler, Holly J; Dorling, Konrad M; Fielden, Peter R; Fogarty, Simon W; Fullwood, Nigel J; Heys, Kelly A; Hughes, Caryn; Lasch, Peter; Martin-Hirsch, Pierre L; Obinaju, Blessing; Sockalingum, Ganesh D; Sulé-Suso, Josep; Strong, Rebecca J; Walsh, Michael J; Wood, Bayden R; Gardner, Peter; Martin, Francis L

    2015-01-01

    IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing. PMID:24992094

  8. Spectroscopy of Multilayered Biological Tissues for Diabetes Care

    NASA Astrophysics Data System (ADS)

    Yudovsky, Dmitry

    Neurological and vascular complications of diabetes mellitus are known to cause foot ulceration in diabetic patients. Present clinical screening techniques enable the diabetes care provider to triage treatment by identifying diabetic patients at risk of foot ulceration. However, these techniques cannot effectively identify specific areas of the foot at risk of ulceration. This study aims to develop non-invasive optical techniques for accurate assessment of tissue health and viability with spatial resolution on the order of 1 mm². The thesis can be divided into three parts: (1) the use of hyperspectral tissue oximetry to detect microcirculatory changes prior to ulcer formation, (2) development of a two-layer tissue spectroscopy algorithm and its application to detection of callus formation or epidermal degradation prior to ulceration, and (3) multi-layered tissue fluorescence modeling for identification of bacterial growth in existing diabetic foot wounds. The first part of the dissertation describes a clinical study in which hyperspectral tissue oximetry was performed on multiple diabetic subjects at risk of ulceration. Tissue oxyhemoglobin and deoxyhemoglobin concentrations were estimated using the Modified Beer-Lambert law. Then, an ulcer prediction algorithm was developed based on retrospective analysis of oxyhemoglobin and deoxyhemoglobin concentrations in sites that were known to ulcerate. The ulcer prediction algorithm exhibited a large sensitivity but low specificity of 95 and 80%, respectively. The second part of the dissertation revisited the hyperspectral data presented in part one with a new and novel two-layer tissue spectroscopy algorithm. This algorithm was able to detect not only oxyhemoglobin and deoxyhemoglobin concentrations, but also the thickness of the epidermis, and the tissue's scattering coefficient. Specifically, change in epidermal thickness provided insight into the formation of diabetic foot ulcers over time. Indeed, callus formation or

  9. Automated selection of synthetic biology parts for genetic regulatory networks.

    PubMed

    Yaman, Fusun; Bhatia, Swapnil; Adler, Aaron; Densmore, Douglas; Beal, Jacob

    2012-08-17

    Raising the level of abstraction for synthetic biology design requires solving several challenging problems, including mapping abstract designs to DNA sequences. In this paper we present the first formalism and algorithms to address this problem. The key steps of this transformation are feature matching, signal matching, and part matching. Feature matching ensures that the mapping satisfies the regulatory relationships in the abstract design. Signal matching ensures that the expression levels of functional units are compatible. Finally, part matching finds a DNA part sequence that can implement the design. Our software tool MatchMaker implements these three steps. PMID:23651287

  10. Steady-state spectroscopy of new biological probes

    NASA Astrophysics Data System (ADS)

    Abou-Zied, Osama K.

    2007-02-01

    The steady state absorption and fluorescence spectroscopy of 2-(2'-hydroxyphenyl)benzoxazole (HBO) and (2,2'-bipyridine)-3,3'-diol (BP(OH) II) were studied here free in solution and in human serum albumin (HSA) in order to test their applicability as new biological probes. HBO and BP(OH) II are known to undergo intramolecular proton transfers in the excited state. Their absorption and fluorescence spectra are sensitive to environmental change from hydrophilic to hydrophobic, thus allowing the opportunity to use them as environment-sensitive probes. The effect of water on the steady state spectra of the two molecules also shows unique features which may position them as water sensors in biological systems. For HBO in buffer, fluorescence is only due to the syn-keto tautomer, whereas in HSA the fluorescence is due to four species in equilibrium in the excited state (the syn-keto tautomer, the anti-enol tautomer, the solvated syn-enol tautomer, and the anion species of HBO). Analysis of the fluorescence spectra of HBO in HSA indicates that HBO is exposed to less water in the HBO:HSA complex. For the BP(OH) II molecule, unique absorption due to water was observed in the spectral region of 400-450 nm. This absorption decreases in the presence of HSA due to less accessibility to water as a result of binding to HSA. Fluorescence of BP(OH) II is due solely to the di-keto tautomer after double proton transfer in the excited state. The fluorescence peak of BP(OH) II shows a red-shift upon HSA recognition which is attributed to the hydrophobic environment inside the binding site of HSA. We discuss also the effect of probe-inclusion inside well-defined hydrophobic cavities of cyclodextrins.

  11. Mining Environmental Plasmids for Synthetic Biology Parts and Devices.

    PubMed

    Martínez-García, Esteban; Benedetti, Ilaria; Hueso, Angeles; De Lorenzo, Víctor

    2015-02-01

    The scientific and technical ambition of contemporary synthetic biology is the engineering of biological objects with a degree of predictability comparable to those made through electric and industrial manufacturing. To this end, biological parts with given specifications are sequence-edited, standardized, and combined into devices, which are assembled into complete systems. This goal, however, faces the customary context dependency of biological ingredients and their amenability to mutation. Biological orthogonality (i.e., the ability to run a function in a fashion minimally influenced by the host) is thus a desirable trait in any deeply engineered construct. Promiscuous conjugative plasmids found in environmental bacteria have evolved precisely to autonomously deploy their encoded activities in a variety of hosts, and thus they become excellent sources of basic building blocks for genetic and metabolic circuits. In this article we review a number of such reusable functions that originated in environmental plasmids and keep their properties and functional parameters in a variety of hosts. The properties encoded in the corresponding sequences include inter alia origins of replication, DNA transfer machineries, toxin-antitoxin systems, antibiotic selection markers, site-specific recombinases, effector-dependent transcriptional regulators (with their cognate promoters), and metabolic genes and operons. Several of these sequences have been standardized as BioBricks and/or as components of the SEVA (Standard European Vector Architecture) collection. Such formatting facilitates their physical composability, which is aimed at designing and deploying complex genetic constructs with new-to-nature properties. PMID:26104565

  12. Fluorescence correlation spectroscopy: Statistical analysis and biological applications

    NASA Astrophysics Data System (ADS)

    Saffarian, Saveez

    2002-01-01

    The experimental design and realization of an apparatus which can be used both for single molecule fluorescence detection and also fluorescence correlation and cross correlation spectroscopy is presented. A thorough statistical analysis of the fluorescence correlation functions including the analysis of bias and errors based on analytical derivations has been carried out. Using the methods developed here, the mechanism of binding and cleavage site recognition of matrix metalloproteinases (MMP) for their substrates has been studied. We demonstrate that two of the MMP family members, Collagenase (MMP-1) and Gelatinase A (MMP-2) exhibit diffusion along their substrates, the importance of this diffusion process and its biological implications are discussed. We show through truncation mutants that the hemopexin domain of the MMP-2 plays and important role in the substrate diffusion of this enzyme. Single molecule diffusion of the collagenase MMP-1 has been observed on collagen fibrils and shown to be biased. The discovered biased diffusion would make the MMP-1 molecule an active motor, thus making it the first active motor that is not coupled to ATP hydrolysis. The possible sources of energy for this enzyme and their implications are discussed. We propose that a possible source of energy for the enzyme can be in the rearrangement of the structure of collagen fibrils. In a separate application, using the methods developed here, we have observed an intermediate in the intestinal fatty acid binding protein folding process through the changes in its hydrodynamic radius also the fluctuations in the structure of the IFABP in solution were measured using FCS.

  13. Fourier Transform Infrared Spectroscopy: Part II. Advantages of FT-IR.

    ERIC Educational Resources Information Center

    Perkins, W. D.

    1987-01-01

    This is Part II in a series on Fourier transform infrared spectroscopy (FT-IR). Described are various advantages of FT-IR spectroscopy including energy advantages, wavenumber accuracy, constant resolution, polarization effects, and stepping at grating changes. (RH)

  14. The Didactics of Biology. A Selected Bibliography for 1979. Part I [and] Part II.

    ERIC Educational Resources Information Center

    Altmann, Antonin, Ed.; Lipertova, Pavla, Ed.

    Selected articles on various aspects of biology teaching published in 1979 have been annotated in this two-part bibliography. Entries from 18 journals representing 11 different countries are presented according to a topic area classification scheme listed in the table of contents. Countries represented include: Australia; Bulgaria; Czechoslovakia;…

  15. The Didactics of Biology. Selected Bibliography for 1980. Part I [and] Part II.

    ERIC Educational Resources Information Center

    Altmann, Antonin, Ed.; Lipertova, Pavla, Ed.

    Selected articles on various aspects of biology teaching published in 1979 have been annotated in this two-part bibliography. Entries from 19 journals representing 11 different countres are presented according to a topic area classification scheme listed in the table of contents. Countries represented include: Australia; Bulgaria; Czechoslovakia;…

  16. Didactics of Biology. Selective Bibliography, 1981. Part I [and] Part II. Information Bulletin.

    ERIC Educational Resources Information Center

    Altmann, Antonin, Ed.; Lipertova, Pavla, Ed.

    Selected articles on various aspects of biology teaching published in 1980 have been annotated in this two-part bibliography. Entries from 19 journals representing 11 different countries are presented according to a topic area classification scheme listed in the table of contents. Countries represented include: Australia; Bulgaria; Czechoslovakia;…

  17. Evolving together: the biology of symbiosis, part 1

    PubMed Central

    2000-01-01

    Symbioses, prolonged associations between organisms often widely separated phylogenetically, are more common in biology than we once thought and have been neglected as a phenomenon worthy of study on its own merits. Extending along a dynamic continuum from antagonistic to cooperative and often involving elements of both antagonism and mutualism, symbioses involve pathogens, commensals, and mutualists interacting in myriad ways over the evolutionary history of the involved “partners.” In this first of 2 parts, some remarkable examples of symbiosis will be explored, from the coral-algal symbiosis and nitrogen fixation to the great diversity of dietary specializations enabled by the gastrointestinal microbiota of animals. PMID:16389385

  18. Analytical Chemistry of Surfaces: Part II. Electron Spectroscopy.

    ERIC Educational Resources Information Center

    Hercules, David M.; Hercules, Shirley H.

    1984-01-01

    Discusses two surface techniques: X-ray photoelectron spectroscopy (ESCA) and Auger electron spectroscopy (AES). Focuses on fundamental aspects of each technique, important features of instrumentation, and some examples of how ESCA and AES have been applied to analytical surface problems. (JN)

  19. The year's new drugs & biologics 2014 - Part II: trends & challenges.

    PubMed

    Graul, A I; Serebrov, M; Cruces, E; Tracy, M; Dulsat, C

    2015-02-01

    2014 was a year of continued high activity in the pharma and biotech industry, as evidenced in part I of this annual two-part review article published last month in this journal (1). As of December 23, 2014, a total of 55 new chemical and biological entities had reached their first markets worldwide, together with another 29 important new line extensions. Another 19 products were approved for the first time during the year but not yet launched by December 23. Furthermore, during the now-traditional year-end sprint, several regulatory agencies issued last-minute approvals for other compounds that missed the deadline for inclusion in that article, bringing the total of new approvals for the year to a somewhat higher number. In addition to the successful development, registration and launch of new drugs and biologics, there are various other trends and tendencies that serve as indicators of the overall health and status of the industry. These include the pursuit of novel programs designed by regulators to stimulate the development of drugs for diseases that are currently under-treated; the regular and pragmatic culling by companies of their R&D pipelines; and the decision to unify pipelines, portfolios and sales forces through mergers and acquisitions. PMID:25756068

  20. Application of UV-Raman spectroscopy to the detection of chemical and biological threats

    NASA Astrophysics Data System (ADS)

    Sedlacek, Arthur J., III; Christesen, Steven D.; Chyba, Tom; Ponsardin, Pat

    2004-03-01

    Brookhaven National Laboratory (BNL), Edgewood Chemical and Biological Center (ECBC) and ITT Industries Advanced Engineering and Sciences Division (AES) have been collaborating on the transitioning and subsequent development of a short-range, non-contact Raman lidar system specifically designed to detect and identify chemical agents on the battlefield. [The instrument, referred to as LISA (Laser Interrogation of Surface Agents), will the subject of an accompanying paper.] As part of this collaboration, BNL has the responsibility for developing a spectral database (library) of surrogates and precursors for use with LISA"s pattern recognition algorithms. In this paper, the authors discuss the phenomenon of UV Raman and resonance-enhanced Raman spectroscopy, the development of an instrument-independent Raman spectral library, and highlight the exploitable characteristics present in the acquired spectral signatures that suggest potential utility in our country"s efforts on Homeland Security.

  1. Raman and multichannel Raman spectroscopy of biological systems

    NASA Astrophysics Data System (ADS)

    Bertoluzza, Alessandro; Caramazza, R.; Fagnano, C.

    1991-05-01

    Raman and multichannel Raman spectroscopy are molecular techniques able to monitor the bulk and surface structure of a biomaterial, in a non destructive and non invasive way, giving therefore useful information on physical and chemical aspects of biocompatibility. The same techniques can also be adequately used for the characterization of the biomaterial-host tissue interface, hence providing structural information on the biochemical aspect of biocompatibility. Moreover, multichannel Raman spectroscopy can also determine "in vivo" and "in situ" the bulk and surface structure of a biomaterial and the molecular interactions between biomaterials and tissues. Useful information at a molecular level on the biomaterial-tissue system can so be deduced. In particular, the application of traditional Paman spectroscopy to bioactive glasses (glasses derived from Hench's bioglass and meta and oligophosphates of calcium by themselves and with the addition of sodium and aluminium) useful in orthopedics and the application to hydrophobic (PMMA) and hydrophilic (PHEMA and PVP) organic polymers useful in ophthalmology are shown. Instead the applications of multichannel Paman spectroscopy are elucidated in the case of intraocular lenses (lOLs) based on PMMA and contact lenses (CLs) based on hydrophi I ic polymers.

  2. Oral Mucosal Lesions: Oral Cavity Biology-Part I.

    PubMed

    Sehgal, Virendra N; Syed, Nazim Hussain; Aggarwal, Ashok; Sehgal, Shruti

    2015-01-01

    It is important to evaluate the background of oral cavity biology to define morphologic abrasions in oral mucosa following a host of local and/ or systemic disorders. The oral cavity is not only the beginning of the digestive system, but it also plays a significant role in communication; the voice (although the voice is produced in the throat), tongue, lips, and jaw are its essential components to produce the range of sounds. The vestibule and the oral cavity are its major parts, and are usually moist. The lips and the teeth are in approximation, marking its start up. The anatomy of the oral cavity in brief has been reviewed in right prospective for disease related changed morphology, thus facilitating interpretation. PMID:26861428

  3. Frameworks for programming biological function through RNA parts and devices

    PubMed Central

    Win, Maung Nyan; Liang, Joe C.; Smolke, Christina D.

    2009-01-01

    One of the long-term goals of synthetic biology is to reliably engineer biological systems that perform human-defined functions. Currently, researchers face several scientific and technical challenges in designing and building biological systems, one of which is associated with our limited ability to access, transmit, and control molecular information through the design of functional biomolecules exhibiting novel properties. The fields of RNA biology and nucleic acid engineering, along with the tremendous interdisciplinary growth of synthetic biology, are fueling advances in the emerging field of RNA programming in living systems. Researchers are designing functional RNA molecules that exhibit increasingly complex functions and integrating these molecules into cellular circuits to program higher-level biological functions. The continued integration and growth of RNA design and synthetic biology presents exciting potential to transform how we interact with and program biology. PMID:19318211

  4. Plasma spectroscopy of uranium and tungsten, part 1

    NASA Technical Reports Server (NTRS)

    Wilkerson, T. D.

    1973-01-01

    Results of research on uranium and tungsten spectra are summarized. Measurements of visible line spectra and opacities were carried out on shock tube plasmas which, prior to shock compression, were mixtures of rare gases and UF6 or WF6. Opacities were compared to theoretical predictions. Feasibility of light source methods other than the shock tube was explored for future applications in the spectroscopy of heavy metals and ions.

  5. Infrared Spectroscopy of Noh Suspended in Solid Parahydrogen: Part Two

    NASA Astrophysics Data System (ADS)

    Balabanoff, Morgan E.; Mutunga, Fredrick M.; Anderson, David T.

    2015-06-01

    The only report in the literature on the infrared spectroscopy of the parent oxynitrene NOH was performed using Ar matrix isolation spectroscopy at 10 K. In this previous study, they performed detailed isotopic studies to make definitive vibrational assignments. NOH is predicted by high-level calculations to be in a triplet ground electronic state, but the Ar matrix isolation spectra cannot be used to verify this triplet assignment. In our 2013 preliminary report, we showed that 193 nm in situ photolysis of NO trapped in solid parahydrogen can also be used to prepare the NOH molecule. Over the ensuing two years we have been studying the infrared spectroscopy of this species in more detail. The spectra reveal that NOH can undergo hindered rotation in solid parahydrogen such that we can observe both a-type and b-type rovibrational transitions for the O-H stretch vibrational mode, but only a-type for the mode assigned to the bend. In addition, both observed a-type infrared absorption features (bend and OH stretch) display fine structure; an intense central peak with weaker peaks spaced symmetrically to both lower and higher wavenumbers. The spacing between the peaks is nearly identical for both vibrational modes. We now believe this fine structure is due to spin-rotation interactions and we will present a detailed analysis of this fine structure. Currently, we are performing additional experiments aimed at making 15NOH to test these preliminary assignments. The most recent data and up-to-date analysis will be presented in this talk. G. Maier, H. P. Reisenauer, M. De Marco, Angew. Chem. Int. Ed. 38, 108-110 (1999). U. Bozkaya, J. M. Turney, Y. Yamaguchi, and H. F. Schaefer III, J. Chem. Phys. 136, 164303 (2012). David T. Anderson and Mahmut Ruzi, 68th Ohio State University International Symposium on Molecular Spectroscopy, talk TE01 (2013).

  6. [Analysis of different parts of scorpio by Fourier transform infrared spectroscopy].

    PubMed

    Zhang, Sheng-Jun; Xu, Chang-Hua; Chen, Jian-Bo; Zhou, Qun; Sun, Su-Qin

    2011-10-01

    Fourier transform infrared (FTIR) spectroscopy and second derivative IR spectroscopy were applied to analyze and evaluate different parts of Scorpio. The second derivative IR spectra show clear differences while the origin spectra are quite similar. It was found that proteins are the dominant components in each part and the tail has distinct proteins compared to the others; fats are mainly stored in the trunk; sulfates are ubiquitous in all parts. Interestingly, the back part of the trunk of degenerative Scorpio contains some purine. It was demonstrated that FTIR spectroscopy integrated with second derivative IR spectroscopy not only can offer a fast, comprehensive and objective methodology for analyzing and evaluating the micro-differences among the various parts of same medicinal materials, but also can provide a rational guidance for medicinal and pharmacological studies. PMID:22250541

  7. Parts plus pipes: synthetic biology approaches to metabolic engineering

    PubMed Central

    Boyle, Patrick M.; Silver, Pamela A.

    2011-01-01

    Synthetic biologists combine modular biological “parts” to create higher-order devices. Metabolic engineers construct biological “pipes” by optimizing the microbial conversion of basic substrates to desired compounds. Many scientists work at the intersection of these two philosophies, employing synthetic devices to enhance metabolic engineering efforts. These integrated approaches promise to do more than simply improve product yields; they can expand the array of products that are tractable to produce biologically. In this review, we explore the application of synthetic biology techniques to next-generation metabolic engineering challenges, as well as the emerging engineering principles for biological design. PMID:22037345

  8. The application of HPLC and microprobe NMR spectroscopy in the identification of metabolites in complex biological matrices.

    PubMed

    Miao, Zhaoxia; Jin, Mengxia; Liu, Xia; Guo, Wei; Jin, Xiangju; Liu, Hongyue; Wang, Yinghong

    2015-05-01

    Nuclear magnetic resonance (NMR)-based metabolomics can be used directly to identify a variety of metabolites in biological fluids and tissues. Metabolite analysis is an important part of life science and metabolomics research. However, the identification of some metabolites using NMR spectroscopy remains a big challenge owing to low abundance or signal overlap. It is important to develop a method to measure these compounds accurately. Two-dimensional NMR spectroscopy, metabolite prediction software packages, and spike-in experiments with authentic standards are often used to solve these problems, but they are costly and time-consuming. In this study, methods were developed to identify metabolites in complex biological mixtures using both high-performance liquid chromatography (HPLC) and off-line microprobe NMR spectroscopy. With use of these methods, 83 and 73 metabolites were identified in Sprague Dawley rat urine and feces, respectively. Among them, 40 and 45 metabolites, respectively, could not be identified with traditional NMR methods. Our research revealed that the combination of HPLC and NMR techniques could significantly improve the accuracy of trace and overlapped metabolite identification, while offering an effective and convenient approach to identify potential biomarkers in complex biological systems. PMID:25814271

  9. Detection of Taurine in Biological Tissues by 33S NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Musio, Roberta; Sciacovelli, Oronzo

    2001-12-01

    The potential of 33S NMR spectroscopy for biochemical investigations on taurine (2-aminoethanesulfonic acid) is explored. It is demonstrated that 33S NMR spectroscopy allows the selective and unequivocal identification of taurine in biological samples. 33S NMR spectra of homogenated and intact tissues are reported for the first time, together with the spectrum of a living mollusc. Emphasis is placed on the importance of choosing appropriate signal processing methods to improve the quality of the 33S NMR spectra of biological tissues.

  10. NIR Raman spectroscopy in medicine and biology: results and aspects

    NASA Astrophysics Data System (ADS)

    Schrader, B.; Dippel, B.; Erb, I.; Keller, S.; Löchte, T.; Schulz, H.; Tatsch, E.; Wessel, S.

    1999-05-01

    Analyses of biomaterial by 'classical' Raman spectroscopy with excitation in the visible range has not been possible since the fluorescence of many essential constituents of all animal and plant cells and tissues overlays the Raman spectra completely. Fluorescence, however, is virtually avoided, when Raman spectra are excited with the Nd : YAG laser line at 1064 nm. Within seven dissertations we explored different fields of potential applications to medical diagnostics. Identification and qualification of tissues and cells is possible. Tumors show small but significant differences to normal tissues; in order to develop a reliable tool for tumor diagnostics more research is necessary, especially a collection of reference spectra in a data bank is needed. Raman spectra of biomineralization structures in teeth and bones show pathological tissues as well as the development of new mineralized structures. NIR Raman spectra of flowers, leaves, and fruit show, without special preparation, their constituents: alkaloids, the essential oils, natural dyes, flavors, spices and drugs. They allow application to taxonomy, optimizing plant breeding and control of food.

  11. Fluorescence correlation spectroscopy in biology, chemistry, and medicine.

    PubMed

    Perevoshchikova, I V; Kotova, E A; Antonenko, Y N

    2011-05-01

    This review describes the method of fluorescence correlation spectroscopy (FCS) and its applications. FCS is used for investigating processes associated with changes in the mobility of molecules and complexes and allows researchers to study aggregation of particles, binding of fluorescent molecules with supramolecular complexes, lipid vesicles, etc. The size of objects under study varies from a few angstroms for dye molecules to hundreds of nanometers for nanoparticles. The described applications of FCS comprise various fields from simple chemical systems of solution/micelle to sophisticated regulations on the level of living cells. Both the methodical bases and the theoretical principles of FCS are simple and available. The present review is concentrated preferentially on FCS applications for studies on artificial and natural membranes. At present, in contrast to the related approach of dynamic light scattering, FCS is poorly known in Russia, although it is widely employed in laboratories of other countries. The goal of this review is to promote the development of FCS in Russia so that this technique could occupy the position it deserves in modern Russian science. PMID:21639831

  12. Laser-induced breakdown spectroscopy detection and classification of biological aerosols.

    PubMed

    Hybl, John D; Lithgow, Gregg A; Buckley, Steven G

    2003-10-01

    Laser-induced breakdown spectroscopy (LIBS) is examined as a potential method for detecting airborne biological agents. A spectrally broadband LIBS system was used for laboratory measurements on some common biological agent simulants. These measurements were compared to those of common, naturally occurring biological aerosol components (pollen and fungal spores) to determine the potential of LIBS for discriminating biological agents from natural background aerosols. A principal components analysis illustrates that linear combinations of the detected atomic lines, which are present in different ratios in each of the samples tested, can be used to discriminate biological agent simulants from other biological matter. A more sensitive, narrowband LIBS instrument was used to demonstrate the detection of single simulant (Bg) particles in the size range 1-5 microns. Ca, Mg, and Na, which are present in varying concentrations between 0.3 and 11% (by mass) in the Bg particles, were observed in single particles using LIBS. PMID:14639747

  13. Laser-induced fluorescence-cued, laser-induced breakdown spectroscopy biological-agent detection

    SciTech Connect

    Hybl, John D.; Tysk, Shane M.; Berry, Shaun R.; Jordan, Michael P

    2006-12-01

    Methods for accurately characterizing aerosols are required for detecting biological warfare agents. Currently, fluorescence-based biological agent sensors provide adequate detection sensitivity but suffer from high false-alarm rates. Combining single-particle fluorescence analysis with laser-induced breakdown spectroscopy (LIBS) provides additional discrimination and potentially reduces false-alarm rates. A transportable UV laser-induced fluorescence-cued LIBS test bed has been developed and used to evaluate the utility of LIBS for biological-agent detection. Analysis of these data indicates that LIBS adds discrimination capability to fluorescence-based biological-agent detectors.However, the data also show that LIBS signatures of biological agent simulants are affected by washing. This may limit the specificity of LIBS and narrow the scope of its applicability in biological-agent detection.

  14. Anomalous Diffusion in Polymer Solution as Probed by Fluorescence Correlation Spectroscopy and Its Universal Importance in Biological Systems

    NASA Astrophysics Data System (ADS)

    Ushida, Kiminori

    2008-02-01

    Experimental evidence of anomalous diffusion occurring in an inhomogeneous media (hyaluronan aquous solution) was obtained by use of fluorescence correlation spectroscopy (FCS) combined with other techniques (PFG-NMR and Photochemical reactions). The diffusion coefficient was obtained as a function of diffusion time or diffusion distance. Since this polymer solution can be regarded as a model system of extracellular matrices (ECMs), intercellular communication, which takes part in ECM, is greatly influenced by this anomalous diffusion mode. Therefore universal importance of anomalous diffusion in biological activity is identified in this series of independent experiments to measure diffusion coefficients.

  15. Ultrafast Spectroscopy in Conjugated Organic and Biological Materials

    NASA Astrophysics Data System (ADS)

    Yan, Ming

    The dynamics of two kinds of conjugated materials, the visual pigment rhodopsin and the organic polymer poly(p -phenylene vinylene), have been studied utilizing femtosecond spectroscopy. The 11-cis to all-trans torsional isomerization of the retinal chromophore in rhodopsin for both protonated and deuterated aqueous environments have been studied by time-resolved absorption measurements at room temperature. The kinetic results are well modeled by rate equations based on the scheme which involves the isomerization along the torsional coordinate of the 11-cis bond of the retinal chromophore. A metastable intermediate 90 degree twisted state is formed within 200 fs on the excited state surface by rotation around the C_{11} -C_{12} double bond, and it takes 3 ps to form the fully isomerized all -trans photoproduct known as bathorhodopsin and to repopulate the ground state rhodopsin. These results agree well with the semiempirical energy level and molecular dynamics calculations. The observed dynamics are insensitive to deuteration of the exchangeable protons which suggest that proton translocation is unimportant at physiological temperatures. The conjugated polymer, Poly(p-phenylene vinylene) (PPV) in a stretch oriented film, has been studied using polarized time-resolved absorption with subpicosecond resolution and transient luminescence measurements. Excitations are generated by photoexcitation near the band edge (500nm -540nm) with a 200 fs pulse and the resulting spectral changes are probed with a white light pulse. Lattice stabilized (singlet) self-trapped excitons are formed within 200 fs which are observed by measuring the stimulated gain in their emission band which decay at 10 ps. The agreement of the photoinduced exciton gain spectrum (<1ps), the transient luminescence spectrum (10 ps) and the steady state luminescence spectrum suggest that the singlet excitons are not further trapped after 200fs of their formation time. Excitation wavelength dependence

  16. Feasibility Study of Using Short Wave Infrared Cavity Ringdown Spectroscopy (SWIR-CRDS) for Biological Agent Detection

    SciTech Connect

    Aker, Pam M.; Johnson, Timothy J.; Williams, Richard M.; Valentine, Nancy B.

    2007-10-01

    This project focused on determining the feasibility of using short wave infrared (SWIR) cavity ring down spectroscopy (CRDS) as a means for real-time detection of biological aerosols. The first part of the project involved identifying biological agent signatures that could be detected with SWIR CRDS. After an exhaustive search of the open literature it was determined that whole biological spores and/or cells would not be good candidates for direct SWIR CRDS probing because they have no unique SWIR signatures. It was postulated that while whole cells or spores are not good candidates for SWIR CRDS detection, their pyrolysis break-down products might be. A literature search was then conducted to find biological pyrolysis products with low molecular weights and high symmetry since these species most likely would have overtone and combination vibrational bands that can be detected in the SWIR. It was determined that pyrrole, pyridine and picolinamide were good candidates for evaluation. These molecules are formed when proteins and porphyrins, proteins and dipicolinic acid, and dipicolinic acid are pyrolyzed, respectively. The second part of the project involved measuring quantitative SWIR spectra of pyrrole, pyridine and picolinamide in PNNL’s FTIR Spectroscopy Laboratory. Spectral information about these molecules, in the vapor phase is sparse – there were only a few prior studies that measured line positions and no information on absorption cross sections. Absorption cross sections are needed in order to estimate the SWIR CRDS detection sensitivity, and line position determines what type of laser will be needed for the sensor. The results of the spectroscopy studies allowed us to estimate the SWIR CRDS detection sensitivity for pyrrole to be 3 x 1012 molec cm-3 or 0.1 ppmv, and for pyridine it was 1.5 x 1015 molec cm-3 or 0.6 ppmv. These detection sensitivity limits are close what we have measured for ammonia. Given these detection limits we then estimated the

  17. Strontium: Part II. Chemistry, Biological Aspects and Applications.

    ERIC Educational Resources Information Center

    Britton, G. C.; Johnson, C. H.

    1987-01-01

    Reviews basic information on the Chemistry of strontium and its compounds. Explains biological aspects of strontium and its pharmaceutical applications. Highlights industrial application of strontium and its components. (ML)

  18. Invasion Ecology and School Biology--Part II.

    ERIC Educational Resources Information Center

    Wells, R. V.

    1981-01-01

    Suggests that invasion biology can supply subject matter for teaching evolution, genetics, ecological relationships, and conservation. Describes flowering and non-flowering plant invaders, vertebrates and invertebrates, and two ecological invasions on the southern coast of England. (JN)

  19. Politics & Prejudice: Dissection in Biology Education. Part I.

    ERIC Educational Resources Information Center

    Gilmore, David R.

    1991-01-01

    The ideological basis from which dissection activities spring is discussed. Speciesism, the widely held belief that the human species is entitled to certain rights and privileges, is examined as the cause for dissection activities occurring in biology classrooms. (KR)

  20. Instrumentation: Photodiode Array Detectors in UV-VIS Spectroscopy. Part II.

    ERIC Educational Resources Information Center

    Jones, Dianna G.

    1985-01-01

    A previous part (Analytical Chemistry; v57 n9 p1057A) discussed the theoretical aspects of diode ultraviolet-visual (UV-VIS) spectroscopy. This part describes the applications of diode arrays in analytical chemistry, also considering spectroelectrochemistry, high performance liquid chromatography (HPLC), HPLC data processing, stopped flow, and…

  1. Graphene-based platform for nano-scale infrared near-field spectroscopy of biological materials

    NASA Astrophysics Data System (ADS)

    Khatib, Omar; Wood, Joshua D.; Doidge, Gregory P.; Damhorst, Gregory L.; Rangarajan, Aniruddh; Bashir, Rashid; Pop, Eric; Lyding, Joseph W.; Basov, Dimitri N.

    2014-03-01

    In biological and life sciences, Fourier Transform Infrared (FTIR) spectroscopy serves as a noninvasive probe of vibrational fingerprints used to identify chemical and molecular species. Near-field spectroscopy, based on the illumination of an atomic force microscope (AFM) tip with an infrared laser, allows for determination of IR properties of a material at nanometer length scales. However, application of near-field IR spectroscopy to most biological systems has thus far been elusive. Physiological conditions required for experimentation are incompatible with typical implementations of nano-FTIR. Recently it became possible to trap water and small biomolecules underneath large-area graphene sheets grown by chemical vapor deposition (CVD). The graphene layer serves as an IR-transparent cover that allows for a near-field interrogation of the underlying layers. We present near-field nano-imaging and spectroscopy data of unencapsulated Tobacco Mosaic Viruses (TMV), compared to those sandwiched between two large-area graphene sheets, and discuss the applicability of near-field IR spectroscopy to trapped biomolecules in aqueous environments.

  2. River Pollution: Part II. Biological Methods for Assessing Water Quality.

    ERIC Educational Resources Information Center

    Openshaw, Peter

    1984-01-01

    Discusses methods used in the biological assessment of river quality and such indicators of clean and polluted waters as the Trent Biotic Index, Chandler Score System, and species diversity indexes. Includes a summary of a river classification scheme based on quality criteria related to water use. (JN)

  3. 15 CFR Supplement No. 1 to Part 742 - Nonproliferation of Chemical and Biological Weapons

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Biological Weapons No. Supplement No. 1 to Part 742 Commerce and Foreign Trade Regulations Relating to...—Nonproliferation of Chemical and Biological Weapons Note: Exports and reexports of items in performance of... ECCNs 2B350 and 2B351; (ii) Equipment and materials (for producing biological agents) described in...

  4. Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 1: Identifying Proteins Based on Molecular Mass

    ERIC Educational Resources Information Center

    Arnquist, Isaac J.; Beussman, Douglas J.

    2007-01-01

    Biological mass spectrometry is an important analytical technique in drug discovery, proteomics, and research at the biology-chemistry interface. Currently, few hands-on opportunities exist for undergraduate students to learn about this technique. With the 2002 Nobel Prize being awarded, in part, for the development of biological mass…

  5. LASER BIOLOGY: Laser spectroscopy technique for estimating the efficiency of photosensitisers in biological media

    NASA Astrophysics Data System (ADS)

    Ryabova, A. V.; Stratonnikov, Aleksandr A.; Loshchenov, V. B.

    2006-06-01

    A fast and highly informative method is presented for estimating the photodynamic activity of photosensitisers. The method makes it possible to determine the rate of photodegradation in erythrocyte-containing biological media in nearly in vivo conditions, estimate the degree of irreversible binding of oxygen dissolved in the medium during laser irradiation in the presence of photosensitisers, and determine the nature of degradation of photosensitisers exposed to light (photobleaching).

  6. Method And System For Examining Biological Materials Using Low Power Cw Excitation Raman Spectroscopy.

    DOEpatents

    Alfano, Robert R.; Wang, Wubao

    2003-05-06

    A method and system for examining biological materials using low-power cw excitation Raman spectroscopy. A low-power continuous wave (cw) pump laser beam and a low-power cw Stokes (or anti-Stokes) probe laser beam simultaneously illuminate a biological material and traverse the biological material in collinearity. The pump beam, whose frequency is varied, is used to induce Raman emission from the biological material. The intensity of the probe beam, whose frequency is kept constant, is monitored as it leaves the biological material. When the difference between the pump and probe excitation frequencies is equal to a Raman vibrational mode frequency of the biological material, the weak probe signal becomes amplified by one or more orders of magnitude (typically up to about 10.sup.4 -10.sup.6) due to the Raman emission from the pump beam. In this manner, by monitoring the intensity of the probe beam emitted from the biological material as the pump beam is varied in frequency, one can obtain an excitation Raman spectrum for the biological material tested. The present invention may be applied to in the in vivo and/or in vitro diagnosis of diabetes, heart disease, hepatitis, cancers and other diseases by measuring the characteristic excitation Raman lines of blood glucose, cholesterol, serum glutamic oxalacetic transaminase (SGOT)/serum glutamic pyruvic transaminase (SGPT), tissues and other corresponding Raman-active body constituents, respectively.

  7. Biological capacitance studies of anodes in microbial fuel cells using electrochemical impedance spectroscopy.

    PubMed

    Lu, Zhihao; Girguis, Peter; Liang, Peng; Shi, Haifeng; Huang, Guangtuan; Cai, Lankun; Zhang, Lehua

    2015-07-01

    It is known that cell potential increases while anode resistance decreases during the start-up of microbial fuel cells (MFCs). Biological capacitance, defined as the apparent capacitance attributed to biological activity including biofilm production, plays a role in this phenomenon. In this research, electrochemical impedance spectroscopy was employed to study anode capacitance and resistance during the start-up period of MFCs so that the role of biological capacitance was revealed in electricity generation by MFCs. It was observed that the anode capacitance ranged from 3.29 to 120 mF which increased by 16.8% to 18-20 times over 10-12 days. Notably, lowering the temperature and arresting biological activity via fixation by 4% para formaldehyde resulted in the decrease of biological capacitance by 16.9 and 62.6%, indicating a negative correlation between anode capacitance and anode resistance of MFCs. Thus, biological capacitance of anode should play an important role in power generation by MFCs. We suggest that MFCs are not only biological reactors and/or electrochemical cells, but also biological capacitors, extending the vision on mechanism exploration of electron transfer, reactor structure design and electrode materials development of MFCs. PMID:25656699

  8. Remote time-resolved filament-induced breakdown spectroscopy of biological materials

    NASA Astrophysics Data System (ADS)

    Xu, H. L.; Liu, W.; Chin, S. L.

    2006-05-01

    We report, for what we believe to be the first time, on the feasibility of remote time-resolved filament-induced breakdown spectroscopy (FIBS) of biological materials. The fluorescence from egg white and yeast powder, induced by femtosecond laser pulse filamentation in air, was detected in the backward direction with targets located 3.5 m away from the detection system. The remarkably distinct spectra of egg white and yeast allow us to propose that this technique, time-resolved FIBS, could be potentially useful for remote detection and identification of harmful biological agents.

  9. Application of multivariate analysis and vibrational spectroscopy in classification of biological systems

    NASA Astrophysics Data System (ADS)

    Salman, A.; Shufan, E.; Lapidot, I.; Tsror, L.; Zeiri, L.; Sahu, R. K.; Moreh, R.; Mordechai, S.; Huleihel, M.

    2015-12-01

    Fourier Transform Infrared (FTIR) and Raman spectroscopies have emerged as powerful tools for chemical analysis. This is due to their ability to provide detailed information about the spatial distribution of chemical composition at the molecular level. A biological sample, i.e. bacteria or fungi, has a typical spectrum. This spectral fingerprint, characterizes the sample and can therefore be used for differentiating between biology samples which belong to different groups, i.e., several different isolates of a given fungi. When the spectral differences between the groups are minute, multivariate analysis should be used to provide a good differentiation. We hereby review several results which demonstrate the differentiation success obtained by combining spectroscopy measurements and multivariate analysis.

  10. Damage-free vibrational spectroscopy of biological materials in the electron microscope

    NASA Astrophysics Data System (ADS)

    Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L.; Dellby, Niklas; Lovejoy, Tracy C.; Wolf, Sharon G.; Cohen, Hagai

    2016-03-01

    Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an `aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be `safely' investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C-H, N-H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ~10 nm, simultaneously combined with imaging in the electron microscope.

  11. Damage-free vibrational spectroscopy of biological materials in the electron microscope

    PubMed Central

    Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L.; Dellby, Niklas; Lovejoy, Tracy C.; Wolf, Sharon G.; Cohen, Hagai

    2016-01-01

    Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be ‘safely' investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope. PMID:26961578

  12. [Research under reduced gravity. Part I: bases of gravitational biology].

    PubMed

    Volkmann, D; Sievers, A

    1992-02-01

    The orientation of organisms in space and their morphogenesis in relation to the gravitational field of the Earth are the main topics of research in the field of gravitational biology. For more than 100 years clinostats provided the only possibility to simulate physiological weightlessness. In contrast to animals, plants are characterized by intracellular gravireceptors. Nevertheless, there are some indications, e.g., the minimal energy of approx. 10(-18) J triggering a gravity-dependent response, for similar mechanisms of gravity perception. Stretch-activated ion channels might be the common structural basis. PMID:11536493

  13. Near-infrared spectroscopy and hyperspectral imaging: non-destructive analysis of biological materials.

    PubMed

    Manley, Marena

    2014-12-21

    Near-infrared (NIR) spectroscopy has come of age and is now prominent among major analytical technologies after the NIR region was discovered in 1800, revived and developed in the early 1950s and put into practice in the 1970s. Since its first use in the cereal industry, it has become the quality control method of choice for many more applications due to the advancement in instrumentation, computing power and multivariate data analysis. NIR spectroscopy is also increasingly used during basic research performed to better understand complex biological systems, e.g. by means of studying characteristic water absorption bands. The shorter NIR wavelengths (800-2500 nm), compared to those in the mid-infrared (MIR) range (2500-15 000 nm) enable increased penetration depth and subsequent non-destructive, non-invasive, chemical-free, rapid analysis possibilities for a wide range of biological materials. A disadvantage of NIR spectroscopy is its reliance on reference methods and model development using chemometrics. NIR measurements and predictions are, however, considered more reproducible than the usually more accurate and precise reference methods. The advantages of NIR spectroscopy contribute to it now often being favoured over other spectroscopic (colourimetry and MIR) and analytical methods, using chemicals and producing chemical waste, such as gas chromatography (GC) and high performance liquid chromatography (HPLC). This tutorial review intends to provide a brief overview of the basic theoretical principles and most investigated applications of NIR spectroscopy. In addition, it considers the recent development, principles and applications of NIR hyperspectral imaging. NIR hyperspectral imaging provides NIR spectral data as a set of images, each representing a narrow wavelength range or spectral band. The advantage compared to NIR spectroscopy is that, due to the additional spatial dimension provided by this technology, the images can be analysed and visualised as

  14. Development of a biologically relevant calcium phosphate substrate for sum frequency generation vibrational spectroscopy.

    PubMed

    McGall, Sarah J; Davies, Paul B; Neivandt, David J

    2005-10-01

    A novel biologically relevant composite substrate has been prepared consisting of a calcium phosphate (CaP) layer formed by magnetron sputter-coating from a hydroxyapatite (HA) target onto a gold-coated silicon substrate. The CaP layer is intended to mimic tooth and bone surfaces and allows polymers used in oral care to be deposited in a procedure analogous to that used for dental surfaces. The polymer cetyl dimethicone copolyol (CDC) was deposited onto the CaP surface of the substrate by Langmuir Blodgett deposition, and the structure of the adsorbed layer was investigated by the surface specific technique of sum frequency generation (SFG) vibrational spectroscopy. The gold sublayer provides enhancement of the SFG signal arising from the polymer but plays no part in the adsorption of the polymer. The surface morphology of the substrate was investigated using SEM and AFM. The surface roughness was commensurate with that of the thermally evaporated gold sublayer and uniform over areas of at least 36 mum(2). The chemical composition of the CaP-coated surface was determined by FTIR and TOF-SIMS. It was concluded that the surface is primarily calcium phosphate present as a mixture of amorphous, non-hydroxylated phases rather than solely stoichiometric hydroxyapatite. The SFG spectra from CDC on CaP were closely similar, both in resonance wavenumbers and in their relative intensities, with spectra of thin films of CDC recorded directly on gold. Application of previous analysis of the spectra of CDC on gold therefore enabled interpretation of the polymer orientation and conformation on the CaP substrate. PMID:16834276

  15. Evolving together: the biology of symbiosis, part 2.

    PubMed

    Dimijian, G G

    2000-10-01

    Symbiotic trade-offs dominate the world of biology and medicine in colonist-host relationships and between separate, mutually dependent organisms of different species. Infectious and parasitic diseases can be better understood by exploring the dynamic continuum between pathogenicity and mutualism, between antagonism and cooperation-the sliding scale along which microorganisms can move in a moment's notice with a single nucleotide substitution. Organisms practicing piracy or pastoralism may be close genetic relatives. Mergers occur not only between cells but also between genomes; viruses co-opt host genes and in turn insert themselves into host genomes. Separate organisms, from ants to fungi to plants, establish symbiotic ties with each other that bind over deep time, generating much of the diversity we see in nature. PMID:16389348

  16. Shifted-excitation Raman difference spectroscopy for in vitro and in vivo biological samples analysis.

    PubMed

    da Silva Martins, Mário Augusto; Ribeiro, Dayana Gonçalves; Pereira Dos Santos, Edson Aparecido; Martin, Airton Abrahão; Fontes, Adriana; da Silva Martinho, Herculano

    2010-01-01

    The contamination of the Raman scattering signal with luminescence is a well-known problem when dealing with biological media excited by visible light. The viability of the shifted-excitation Raman difference spectroscopy (SERDS) technique for luminescence suppression on Raman spectra of biological samples was studied in this work. A tunable Lithrow-configuration diode laser (λ = 785 and 830 nm) coupled (directly or by optical fiber) to a dispersive Raman spectrometer was employed to study two sets of human tissues (tooth and skin) in order to determine the set of experimental parameters suitable for luminescence rejection. It was concluded that systematic and reproducible spectra of biological interest can be acquired by SERDS. PMID:21258495

  17. Topics in Chemical Instrumentation: Fourier Transform-Infrared Spectroscopy: Part I. Instrumentation.

    ERIC Educational Resources Information Center

    Perkins, W. D.

    1986-01-01

    Discusses: (1) the design of the Fourier Transform-Infrared Spectroscopy (FT-IR) spectrometer; (2) the computation of the spectrum from the interferogram; and (3) the use of apodization. (Part II will discuss advantages of FT-IR over dispersive techniques and show applications of FT-IR to difficult spectroscopic measurements.) (JN)

  18. Method And System For Examining Biological Materials Using Low Power Cw Excitation Raman Spectroscopy.

    DOEpatents

    Alfano, Robert R.; Wang, Wubao

    2000-11-21

    A method and system for examining biological materials using low-power cw excitation Raman spectroscopy. In accordance with the teachings of the invention, a low-power continuous wave (cw) pump laser beam and a low-power cw Stokes (or anti-Stokes) probe laser beam simultaneously illuminate a biological material and traverse the biological material in collinearity. The pump beam, whose frequency is varied, is used to induce Raman emission from the biological material. The intensity of the probe beam, whose frequency is kept constant, is monitored as it leaves the biological material. When the difference between the pump and probe excitation frequencies is equal to a Raman vibrational mode frequency of the biological material, the weak probe signal becomes amplified by one or more orders of magnitude (typically up to about 10.sup.4 -10.sup.6) due to the Raman emission from the pump beam. In this manner, by monitoring the intensity of the probe beam emitted from the biological material as the pump beam is varied in frequency, one can obtain an excitation Raman spectrum for the biological material tested. The present invention may be applied to in the in vivo and/or in vitro diagnosis of diabetes, heart disease, hepatitis, cancers and other diseases by measuring the characteristic excitation Raman lines of blood glucose, cholesterol, serum glutamic oxalacetic transaminase (SGOT)/serum glutamic pyruvic tansaminase (SGPT), tissues and other corresponding Raman-active body constituents, respectively. For example, it may also be used to diagnose diseases associated with the concentration of Raman-active constituents in urine, lymph and saliva It may be used to identify cancer in the breast, cervix, uterus, ovaries and the like by measuring the fingerprint excitation Raman spectra of these tissues. It may also be used to reveal the growing of tumors or cancers by measuring the levels of nitric oxide in tissue.

  19. Proton MR spectroscopy-detectable major neurotransmitters of the brain: biology and possible clinical applications.

    PubMed

    Agarwal, N; Renshaw, P F

    2012-04-01

    Neurotransmitters are chemical substances that, by definition, allow communication between neurons and permit most neuronal-glial interactions in the CNS. Approximately 80% of all neurons use glutamate, and almost all interneurons use GABA. A third neurotransmitter, NAAG, modulates glutamatergic neurotransmission. Concentration changes in these molecules due to defective synthetic machinery, receptor expression, or errors in their degradation and metabolism are accepted causes of several neurologic disorders. Knowledge of changes in neurotransmitter concentrations in the brain can add useful information in making a diagnosis, helping to pick the right drug of treatment, and monitoring patient response to drugs in a more objective manner. Recent advances in (1)H-MR spectroscopy hold promise in providing a more reliable in vivo detection of these neurotransmitters. In this article, we summarize the essential biology of 3 major neurotransmitters: glutamate, GABA, and NAAG. Finally we illustrate possible applications of (1)H-MR spectroscopy in neuroscience research. PMID:22207303

  20. Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology.

    PubMed

    Wang, Yuling; Irudayaraj, Joseph

    2013-02-01

    Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemistry and engineering, along with a significant thrust in applications constituting areas in medicine, biology, environment and agriculture among others. In this review, we will attempt to provide a quick snapshot of the basics of SM-SERS, nanostructures and devices that can enable SM Raman measurement. We will conclude with a discussion on SERS implications in biomedical sciences. PMID:23267180

  1. Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology

    PubMed Central

    Wang, Yuling; Irudayaraj, Joseph

    2013-01-01

    Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemistry and engineering, along with a significant thrust in applications constituting areas in medicine, biology, environment and agriculture among others. In this review, we will attempt to provide a quick snapshot of the basics of SM-SERS, nanostructures and devices that can enable SM Raman measurement. We will conclude with a discussion on SERS implications in biomedical sciences. PMID:23267180

  2. Detection of biological contaminants on foods and food surfaces using laser-induced breakdown spectroscopy (LIBS).

    PubMed

    Multari, Rosalie A; Cremers, David A; Dupre, Jo Anne M; Gustafson, John E

    2013-09-11

    The rapid detection of biological contaminants, such as Escherichia coli O157:H7 and Salmonella enterica , on foods and food-processing surfaces is important to ensure food safety and streamline the food-monitoring process. Laser-induced breakdown spectroscopy (LIBS) is an ideal candidate technology for this application because sample preparation is minimal and results are available rapidly (seconds to minutes). Here, multivariate regression analysis of LIBS data is used to differentiate the live bacterial pathogens E. coli O157:H7 and S. enterica on various foods (eggshell, milk, bologna, ground beef, chicken, and lettuce) and surfaces (metal drain strainer and cutting board). The type (E. coli or S. enterica) of bacteria could be differentiated in all cases studied along with the metabolic state (viable or heat killed). This study provides data showing the potential of LIBS for the rapid identification of biological contaminants using spectra collected directly from foods and surfaces. PMID:23941554

  3. Classification of the biological material with use of FTIR spectroscopy and statistical analysis.

    PubMed

    Bombalska, Aneta; Mularczyk-Oliwa, Monika; Kwaśny, Mirosław; Włodarski, Maksymilian; Kaliszewski, Miron; Kopczyński, Krzysztof; Szpakowska, Małgorzata; Trafny, Elżbieta A

    2011-04-01

    Rapid detection and discrimination of dangerous biological materials such as bacteria and their spores has become a security aim of considerable importance. Various analytical methods, including FTIR spectroscopy combined with statistical analysis have been used to identify vegetative bacteria, bacterial spores and background interferants. The present work discusses the application of FTIR technique performed in reflectance mode using Horizontal Attenuated Total Reflectance accessory (HATR) to the discrimination of biological materials. In comparison with transmission technique the HATR is more rapid and do not require the sample destruction, simultaneously giving similar absorbance bands. HATR-FTIR results combined with statistical analysis PCA and HCA demonstrate that this combination provides novel and accurate microbial identification technique. PMID:21257340

  4. Classification of the biological material with use of FTIR spectroscopy and statistical analysis

    NASA Astrophysics Data System (ADS)

    Bombalska, Aneta; Mularczyk-Oliwa, Monika; Kwaśny, Mirosław; Włodarski, Maksymilian; Kaliszewski, Miron; Kopczyński, Krzysztof; Szpakowska, Małgorzata; Trafny, Elżbieta A.

    2011-04-01

    Rapid detection and discrimination of dangerous biological materials such as bacteria and their spores has become a security aim of considerable importance. Various analytical methods, including FTIR spectroscopy combined with statistical analysis have been used to identify vegetative bacteria, bacterial spores and background interferants. The present work discusses the application of FTIR technique performed in reflectance mode using Horizontal Attenuated Total Reflectance accessory (HATR) to the discrimination of biological materials. In comparison with transmission technique the HATR is more rapid and do not require the sample destruction, simultaneously giving similar absorbance bands. HATR-FTIR results combined with statistical analysis PCA and HCA demonstrate that this combination provides novel and accurate microbial identification technique.

  5. Quantifying Carbon-14 for Biology Using Cavity Ring-Down Spectroscopy.

    PubMed

    McCartt, A Daniel; Ognibene, Ted J; Bench, Graham; Turteltaub, Kenneth W

    2016-09-01

    A cavity ring-down spectroscopy (CRDS) instrument was developed using mature, robust hardware for the measurement of carbon-14 in biological studies. The system was characterized using carbon-14 elevated glucose samples and returned a linear response up to 387 times contemporary carbon-14 concentrations. Carbon-14 free and contemporary carbon-14 samples with varying carbon-13 concentrations were used to assess the method detection limit of approximately one-third contemporary carbon-14 levels. Sources of inaccuracies are presented and discussed, and the capability to measure carbon-14 in biological samples is demonstrated by comparing pharmacokinetics from carbon-14 dosed guinea pigs analyzed by both CRDS and accelerator mass spectrometry. The CRDS approach presented affords easy access to powerful carbon-14 tracer techniques that can characterize complex biochemical systems. PMID:27458740

  6. Nonlinear optical spectroscopy and microscopy of model random and biological media

    NASA Astrophysics Data System (ADS)

    Guo, Yici

    Nonlinear optical (NLO) spectroscopy and microscopy applied to biomedical science are emerging as new and rapidly growing areas which offer important insight into basic phenomena. Ultrafast NLO processes provide temporal, spectral and spatial sensitivities complementary or superior to those achieved through conventional linear optical approaches. The goal of this thesis is to explore the potential of two fundamental NLO processes to produce noninvasive histological maps of biological tissues. Within the goal of the thesis, steady state intensity, polarization and angular measurements of second- and third-harmonic generations (SHG, THG) have been performed on model random scattering and animal tissue samples. The nonlinear optical effects have been evaluated using models. Conversion efficiencies of SHG and THG from animal tissue interfaces have been determined, ranging from 10-7 to 10-10. The changes in the multiharmonic signals were found to depend on both local and overall histological structures of biological samples. The spectral signatures of two photon excitation induced fluorescence from intrinsic fluorophores have been acquired and used to characterize the physical state and types of tissues. Two dimensional scanning SHG and TPF tomographic images have been obtained from in vitro animal tissues, normal and diseased human breast tissues, and resolved subsurface layers and histo-chemical distributions. By combining consecutive 2D maps, a 3D image can be produced. The structure and morphology dependence of the SH signal has been utilized to image and evaluate subsurface tumor progression depth. Second harmonic microscopy in model random and biological cells has been studied using a CCD camera to obtain direct images from subcellular structures. Finally, near infrared (NIR) NLO spectroscopy and microscopy based on SHG and TPF have demonstrated high spatial resolution, deeper penetration depth, low level photo-damaging and enhanced morphological sensitivity for

  7. Damage-free vibrational spectroscopy of biological materials in the electron microscope

    DOE PAGESBeta

    Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L.; Dellby, Niklas; Lovejoy, Tracy C.; Wolf, Sharon G.; Cohen, Hagai

    2016-03-10

    Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof’ electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies o1 eV can be ‘safely’ investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with nomore » observable radiation damage. Furthermore, the technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ~10nm, simultaneously combined with imaging in the electron microscope.« less

  8. Tip-enhanced Raman spectroscopy and related techniques in studies of biological materials

    NASA Astrophysics Data System (ADS)

    Schmid, Thomas; Sebesta, Aleksandar; Stadler, Johannes; Opilik, Lothar; Balabin, Roman M.; Zenobi, Renato

    2010-02-01

    Biological materials can be highly heterogeneous at the nanometer scale. The investigation of nanostructures is often hampered by the low spatial resolution (e.g. spectroscopic techniques) or very little chemical information (e.g. atomic force microscopy (AFM), scanning tunneling microscopy (STM)) provided by analytical techniques. Our research focuses on combined instruments, which allow the analysis of the exactly same area of a sample by complementary techniques, such as AFM and Raman spectroscopy. Tip-enhanced Raman spectroscopy (TERS) combines the high spatial resolution of AFM or STM with the chemical information provided by Raman spectroscopy. The technique is based on enhancement effects known from surface-enhanced Raman scattering (SERS). In TERS the enhancing metallic nanostructure is brought to the sample by an AFM or STM tip. With a TERS-active tip, enhanced Raman signals can be generated from a sample area as small as 10-50 nm in diameter. AFM analysis of bacterial biofilms has demonstrated their heterogeneity at the nanometer scale, revealing a variety of nanostructures such as pili, flagella, and extracelullar polymers. TERS measurements of the biopolymers alginate and cytochrome c have yielded spectroscopic fingerprints even of such weak Raman scatterers, which in future can allow their localization in complex matrices. Furthermore, biofilms of the bacterium Halomonas meridiana were studied, which was found to be involved in the generation of the mineral dolomite. Only combined AFM-Raman analysis was able to identify the nanoglobules found in laboratory cultures of H. meridiana as dolomite nanoparticles. Our combined setups are and will be applied to the investigation of biofilms, fish spermatozoa as well as biological membranes.

  9. 3D Imaging of Nanoparticle Distribution in Biological Tissue by Laser-Induced Breakdown Spectroscopy

    NASA Astrophysics Data System (ADS)

    Gimenez, Y.; Busser, B.; Trichard, F.; Kulesza, A.; Laurent, J. M.; Zaun, V.; Lux, F.; Benoit, J. M.; Panczer, G.; Dugourd, P.; Tillement, O.; Pelascini, F.; Sancey, L.; Motto-Ros, V.

    2016-07-01

    Nanomaterials represent a rapidly expanding area of research with huge potential for future medical applications. Nanotechnology indeed promises to revolutionize diagnostics, drug delivery, gene therapy, and many other areas of research. For any biological investigation involving nanomaterials, it is crucial to study the behavior of such nano-objects within tissues to evaluate both their efficacy and their toxicity. Here, we provide the first account of 3D label-free nanoparticle imaging at the entire-organ scale. The technology used is known as laser-induced breakdown spectroscopy (LIBS) and possesses several advantages such as speed of operation, ease of use and full compatibility with optical microscopy. We then used two different but complementary approaches to achieve 3D elemental imaging with LIBS: a volume reconstruction of a sliced organ and in-depth analysis. This proof-of-concept study demonstrates the quantitative imaging of both endogenous and exogenous elements within entire organs and paves the way for innumerable applications.

  10. Parallel analysis of individual biological cells using multifocal laser tweezers Raman spectroscopy.

    PubMed

    Liu, Rui; Taylor, Douglas S; Matthews, Dennis L; Chan, James W

    2010-11-01

    We report on the development and characterization of a multifocal laser tweezers Raman spectroscopy (M-LTRS) technique for parallel Raman spectral acquisition of individual biological cells. Using a 785-nm diode laser and a time-sharing laser trapping scheme, multiple laser foci are generated to optically trap single polystyrene beads and suspension cells in a linear pattern. Raman signals from the trapped objects are simultaneously projected through the slit of a spectrometer and spatially resolved on a charge-coupled device (CCD) detector with minimal signal crosstalk between neighboring cells. By improving the rate of single-cell analysis, M-LTRS is expected to be a valuable method for studying single-cell dynamics of cell populations and for the development of high-throughput Raman based cytometers. PMID:21073802

  11. Analysis of biological and chemical compounds by remote spectroscopy using IR TeX glass fibers

    NASA Astrophysics Data System (ADS)

    Le Foulgoc, Karine; Le Neindre, Lydia; Guimond, Yann; Ma, Hong Li; Zhang, Xhang H.; Lucas, Jacques

    1995-09-01

    The TeX glasses are attracting much attention as materials for low loss mid-IR optical fibers and are consequently good candidates for thermal imaging, laser power delivery, and more recently remote sensing. The TeX glass fiber, transmitting in a wide optical window, has a minimum attenuation in the 9-10 micrometers region. Fibers with an attenuation of less than 0.5 dB/m have been repeatly obtained. These fibers are coated with a UV curable or thermal plastic, in order to improve their mechanical properites. The IR remote spectroscopy using TeX fibers is one of the most promising applications. This technology allows to perform in situ, real-time, and on-line analysis of chemical and biological compounds. The study of industrial processes such as fermentations has been performed by this method, based on the use of these IR TeX fibers.

  12. Small cantilevers for atomic force microscopy and force spectroscopy of biological molecules

    NASA Astrophysics Data System (ADS)

    Viani, M. B.; Schaffer, T. E.; Chand, A.; Smith, B. L.; Hansma, P. K.; Wendman, M.

    1998-03-01

    Small cantilevers offer new possibilities for high speed/low noise atomic force microscopy of soft, biological samples. We have used a novel process to fabricate metallic cantilevers that should maximize reflectivity and minimize thermal bending. We have fabricated and measured the properties of aluminum, nickel, silver, and 14-karat gold cantilevers that are 3-12 um long, 1-4 um wide, and 60-300 nm thick and have resonant frequencies of 0.5-2 MHz and spring constants of 0.1-3 N/m. We also have fabricated small cantilevers with ultra-low spring constants (1-10 mN/m) out of silicon nitride and used them for force spectroscopy of DNA. This work was supported by grant numbers NSF-DMR9622169 and NSF-DMR9632716 from the Materials Research Division of the National Science Foundation and by grant number DAAH04-96-1-004 from the Army Research Office.

  13. Single-molecule Spectroscopy: Exploring Heterogeneity in Chemical and Biological Systems.

    PubMed

    Ghosh, Shirsendu; Bhattacharyya, Kankan

    2016-04-01

    Many chemical and biological systems are heterogeneous in the molecular length scale (∼ 1 nm). Heterogeneity in many chemical systems and organized assemblies may be monitored using single-molecule spectroscopy (SMS). In SMS, the size of the focal spot (i.e., the smallest region to be probed) is nearly half of the excitation wavelength (λ/2, i.e., 200-375 nm) for visible light (400-750 nm). We discuss how one can get spatial resolutions better than 200 nm using molecules as nanometric probes. We show that polymer hydrogels, lipid vesicles, room temperature ionic liquids (RTILs), and binary liquid mixtures exhibit such heterogeneity. Another important observation is solute-dependent friction in RTILs. In an RTIL, diffusion of an ionic solute is slower than that of a neutral solute. PMID:26814020

  14. Magnetic induction spectroscopy: non-contact measurement of the electrical conductivity spectra of biological samples

    NASA Astrophysics Data System (ADS)

    Barai, A.; Watson, S.; Griffiths, H.; Patz, R.

    2012-08-01

    Measurement of the electrical conductivity of biological tissues as a function of frequency, often termed ‘bioelectrical impedance spectroscopy (BIS)’, provides valuable information on tissue structure and composition. In implementing BIS though, there can be significant practical difficulties arising from the electrode-sample interface which have likely limited its deployment in industrial applications. In magnetic induction spectroscopy (MIS) these difficulties are eliminated through the use of fully non-contacting inductive coupling between the sensors and sample. However, inductive coupling introduces its own set of technical difficulties, primarily related to the small magnitudes of the induced currents and their proportionality with frequency. This paper describes the design of a practical MIS system incorporating new, highly-phase-stable electronics and compares its performance with that of electrode-based BIS in measurements on biological samples including yeast suspensions in saline (concentration 50-400 g l-1) and solid samples of potato, cucumber, tomato, banana and porcine liver. The shapes of the MIS spectra were in good agreement with those for electrode-based BIS, with a residual maximum discrepancy of 28%. The measurement precision of the MIS was 0.05 S m-1 at 200 kHz, improving to 0.01 S m-1 at a frequency of 20 MHz, for a sample volume of 80 ml. The data-acquisition time for each MIS measurement was 52 s. Given the value of spectroscopic conductivity information and the many advantages of obtaining these data in a non-contacting manner, even through electrically-insulating packaging materials if necessary, it is concluded that MIS is a technique with considerable potential for monitoring bio-industrial processes and product quality.

  15. Review of short-wave infrared spectroscopy and imaging methods for biological tissue characterization

    PubMed Central

    Wilson, Robert H.; Nadeau, Kyle P.; Jaworski, Frank B.; Tromberg, Bruce J.; Durkin, Anthony J.

    2015-01-01

    Abstract. We present a review of short-wave infrared (SWIR, defined here as ∼1000 to 2000 nm) spectroscopy and imaging techniques for biological tissue optical property characterization. Studies indicate notable SWIR absorption features of tissue constituents including water (near 1150, 1450, and 1900 nm), lipids (near 1040, 1200, 1400, and 1700 nm), and collagen (near 1200 and 1500 nm) that are much more prominent than corresponding features observed in the visible and near-infrared (VIS-NIR, defined here as ∼400 to 1000 nm). Furthermore, the wavelength dependence of the scattering coefficient has been observed to follow a power-law decay from the VIS-NIR to the SWIR region. Thus, the magnitude of tissue scattering is lower at SWIR wavelengths than that observed at VIS or NIR wavelengths, potentially enabling increased penetration depth of incident light at SWIR wavelengths that are not highly absorbed by the aforementioned chromophores. These aspects of SWIR suggest that the tissue spectroscopy and imaging in this range of wavelengths have the potential to provide enhanced sensitivity (relative to VIS-NIR measurements) to chromophores such as water and lipids, thereby helping to characterize changes in the concentrations of these chromophores due to conditions such as atherosclerotic plaque, breast cancer, and burns. PMID:25803186

  16. Review of short-wave infrared spectroscopy and imaging methods for biological tissue characterization.

    PubMed

    Wilson, Robert H; Nadeau, Kyle P; Jaworski, Frank B; Tromberg, Bruce J; Durkin, Anthony J

    2015-03-01

    We present a review of short-wave infrared (SWIR, defined here as ∼1000 to 2000 nm) spectroscopy and imaging techniques for biological tissue optical property characterization. Studies indicate notable SWIR absorption features of tissue constituents including water (near 1150, 1450, and 1900 nm), lipids (near 1040, 1200, 1400, and 1700 nm), and collagen (near 1200 and 1500 nm) that are much more prominent than corresponding features observed in the visible and near-infrared (VIS-NIR, defined here as ∼400 to 1000 nm). Furthermore, the wavelength dependence of the scattering coefficient has been observed to follow a power-law decay from the VIS-NIR to the SWIR region. Thus, the magnitude of tissue scattering is lower at SWIR wavelengths than that observed at VIS or NIR wavelengths, potentially enabling increased penetration depth of incident light at SWIR wavelengths that are not highly absorbed by the aforementioned chromophores. These aspects of SWIR suggest that the tissue spectroscopy and imaging in this range of wavelengths have the potential to provide enhanced sensitivity (relative to VIS-NIR measurements) to chromophores such as water and lipids, thereby helping to characterize changes in the concentrations of these chromophores due to conditions such as atherosclerotic plaque, breast cancer, and burns. PMID:25803186

  17. Review of short-wave infrared spectroscopy and imaging methods for biological tissue characterization

    NASA Astrophysics Data System (ADS)

    Wilson, Robert H.; Nadeau, Kyle P.; Jaworski, Frank B.; Tromberg, Bruce J.; Durkin, Anthony J.

    2015-03-01

    We present a review of short-wave infrared (SWIR, defined here as ˜1000 to 2000 nm) spectroscopy and imaging techniques for biological tissue optical property characterization. Studies indicate notable SWIR absorption features of tissue constituents including water (near 1150, 1450, and 1900 nm), lipids (near 1040, 1200, 1400, and 1700 nm), and collagen (near 1200 and 1500 nm) that are much more prominent than corresponding features observed in the visible and near-infrared (VIS-NIR, defined here as ˜400 to 1000 nm). Furthermore, the wavelength dependence of the scattering coefficient has been observed to follow a power-law decay from the VIS-NIR to the SWIR region. Thus, the magnitude of tissue scattering is lower at SWIR wavelengths than that observed at VIS or NIR wavelengths, potentially enabling increased penetration depth of incident light at SWIR wavelengths that are not highly absorbed by the aforementioned chromophores. These aspects of SWIR suggest that the tissue spectroscopy and imaging in this range of wavelengths have the potential to provide enhanced sensitivity (relative to VIS-NIR measurements) to chromophores such as water and lipids, thereby helping to characterize changes in the concentrations of these chromophores due to conditions such as atherosclerotic plaque, breast cancer, and burns.

  18. Information theory in systems biology. Part II: protein-protein interaction and signaling networks.

    PubMed

    Mousavian, Zaynab; Díaz, José; Masoudi-Nejad, Ali

    2016-03-01

    By the development of information theory in 1948 by Claude Shannon to address the problems in the field of data storage and data communication over (noisy) communication channel, it has been successfully applied in many other research areas such as bioinformatics and systems biology. In this manuscript, we attempt to review some of the existing literatures in systems biology, which are using the information theory measures in their calculations. As we have reviewed most of the existing information-theoretic methods in gene regulatory and metabolic networks in the first part of the review, so in the second part of our study, the application of information theory in other types of biological networks including protein-protein interaction and signaling networks will be surveyed. PMID:26691180

  19. GenoLIB: a database of biological parts derived from a library of common plasmid features

    PubMed Central

    Adames, Neil R.; Wilson, Mandy L.; Fang, Gang; Lux, Matthew W.; Glick, Benjamin S.; Peccoud, Jean

    2015-01-01

    Synthetic biologists rely on databases of biological parts to design genetic devices and systems. The sequences and descriptions of genetic parts are often derived from features of previously described plasmids using ad hoc, error-prone and time-consuming curation processes because existing databases of plasmids and features are loosely organized. These databases often lack consistency in the way they identify and describe sequences. Furthermore, legacy bioinformatics file formats like GenBank do not provide enough information about the purpose of features. We have analyzed the annotations of a library of ∼2000 widely used plasmids to build a non-redundant database of plasmid features. We looked at the variability of plasmid features, their usage statistics and their distributions by feature type. We segmented the plasmid features by expression hosts. We derived a library of biological parts from the database of plasmid features. The library was formatted using the Synthetic Biology Open Language, an emerging standard developed to better organize libraries of genetic parts to facilitate synthetic biology workflows. As proof, the library was converted into GenoCAD grammar files to allow users to import and customize the library based on the needs of their research projects. PMID:25925571

  20. Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

    PubMed Central

    Bilitchenko, Lesia; Liu, Adam; Cheung, Sherine; Weeding, Emma; Xia, Bing; Leguia, Mariana; Anderson, J. Christopher; Densmore, Douglas

    2011-01-01

    Background Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts. Results We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively. Conclusions Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly. PMID:21559524

  1. Physical Activity: A Tool for Improving Health (Part 1--Biological Health Benefits)

    ERIC Educational Resources Information Center

    Gallaway, Patrick J.; Hongu, Nobuko

    2015-01-01

    Extension educators have been promoting and incorporating physical activities into their community-based programs and improving the health of individuals, particularly those with limited resources. This article is the first of a three-part series describing the benefits of physical activity for human health: 1) biological health benefits of…

  2. GenoLIB: a database of biological parts derived from a library of common plasmid features.

    PubMed

    Adames, Neil R; Wilson, Mandy L; Fang, Gang; Lux, Matthew W; Glick, Benjamin S; Peccoud, Jean

    2015-05-26

    Synthetic biologists rely on databases of biological parts to design genetic devices and systems. The sequences and descriptions of genetic parts are often derived from features of previously described plasmids using ad hoc, error-prone and time-consuming curation processes because existing databases of plasmids and features are loosely organized. These databases often lack consistency in the way they identify and describe sequences. Furthermore, legacy bioinformatics file formats like GenBank do not provide enough information about the purpose of features. We have analyzed the annotations of a library of ∼2000 widely used plasmids to build a non-redundant database of plasmid features. We looked at the variability of plasmid features, their usage statistics and their distributions by feature type. We segmented the plasmid features by expression hosts. We derived a library of biological parts from the database of plasmid features. The library was formatted using the Synthetic Biology Open Language, an emerging standard developed to better organize libraries of genetic parts to facilitate synthetic biology workflows. As proof, the library was converted into GenoCAD grammar files to allow users to import and customize the library based on the needs of their research projects. PMID:25925571

  3. Didactics of Biology. Selected Bibliography for 1982. Parts I and II. Information Bulletin.

    ERIC Educational Resources Information Center

    Altmann, Antonin, Ed.; Lipertova, Paula, Ed.

    Selected articles on various aspects of biology teaching published in 1982 have been annotated in this two-part bibliography. Entries from 25 journals representing 12 countries are presented according to a topic area classification scheme listed in the table of contents. Countries represented include: Australia; Bulgaria; Czechoslovakia; Federal…

  4. Information theory in systems biology. Part I: Gene regulatory and metabolic networks.

    PubMed

    Mousavian, Zaynab; Kavousi, Kaveh; Masoudi-Nejad, Ali

    2016-03-01

    "A Mathematical Theory of Communication", was published in 1948 by Claude Shannon to establish a framework that is now known as information theory. In recent decades, information theory has gained much attention in the area of systems biology. The aim of this paper is to provide a systematic review of those contributions that have applied information theory in inferring or understanding of biological systems. Based on the type of system components and the interactions between them, we classify the biological systems into 4 main classes: gene regulatory, metabolic, protein-protein interaction and signaling networks. In the first part of this review, we attempt to introduce most of the existing studies on two types of biological networks, including gene regulatory and metabolic networks, which are founded on the concepts of information theory. PMID:26701126

  5. Spectroscopic characterization of biological agents using FTIR, normal Raman and surface-enhanced Raman spectroscopies

    NASA Astrophysics Data System (ADS)

    Luna-Pineda, Tatiana; Soto-Feliciano, Kristina; De La Cruz-Montoya, Edwin; Pacheco Londoño, Leonardo C.; Ríos-Velázquez, Carlos; Hernández-Rivera, Samuel P.

    2007-04-01

    FTIR, Raman spectroscopy and Surface Enhanced Raman Scattering (SERS) requires a minimum of sample allows fast identification of microorganisms. The use of this technique for characterizing the spectroscopic signatures of these agents and their stimulants has recently gained considerable attention due to the fact that these techniques can be easily adapted for standoff detection from considerable distances. The techniques also show high sensitivity and selectivity and offer near real time detection duty cycles. This research focuses in laying the grounds for the spectroscopic differentiation of Staphylococcus spp., Pseudomonas spp., Bacillus spp., Salmonella spp., Enterobacter aerogenes, Proteus mirabilis, Klebsiella pneumoniae, and E. coli, together with identification of their subspecies. In order to achieve the proponed objective, protocols to handle, cultivate and analyze the strains have been developed. Spectroscopic similarities and marked differences have been found for Spontaneous or Normal Raman spectra and for SERS using silver nanoparticles have been found. The use of principal component analysis (PCA), discriminate factor analysis (DFA) and a cluster analysis were used to evaluate the efficacy of identifying potential threat bacterial from their spectra collected on single bacteria. The DFA from the bacteria Raman spectra show a little discrimination between the diverse bacterial species however the results obtained from the SERS demonstrate to be high discrimination technique. The spectroscopic study will be extended to examine the spores produced by selected strains since these are more prone to be used as Biological Warfare Agents due to their increased mobility and possibility of airborne transport. Micro infrared spectroscopy as well as fiber coupled FTIR will also be used as possible sensors of target compounds.

  6. Multispectral diode laser based shifted excitation Raman difference spectroscopy for biological sample identification

    NASA Astrophysics Data System (ADS)

    Sowoidnich, Kay; Kronfeldt, Heinz-Detlef

    2012-06-01

    Raman spectroscopy is a well established analytical method with applications in many areas, e.g. analysis of biological samples. To overcome the problem of an undesired fluorescence background masking the Raman signals we present a multi-spectral approach using shifted excitation Raman difference spectroscopy (SERDS). For our investigations we applied microsystem diode lasers which realize two slightly shifted excitation wavelengths required to perform SERDS at 488 nm, 671 nm, and 785 nm. The emission at 488 nm with an optical power of up to 30 mW and a spectral shift of 0.3 nm (12 cm-1) is realized by frequency doubling of a 976 nm distributed feedback (DFB) diode laser. The 671 nm laser diode contains two separate laser cavities (spectral shift: 0.7 nm (13 cm-1)) each incorporating a volume Bragg grating as frequency selective element. In that case, optical powers up to 50 mW can be obtained. For investigations at 785 nm we used a DFB laser with a maximum optical power of 110 mW and a spectral shift of 0.5 nm (7 cm-1). Meat, fat tissue, connective tissue and bones from pork and beef were used as test samples to demonstrate the effective background removal using SERDS. For all three wavelengths integration times of only 5 - 10 seconds were necessary showing the possibility of SERDS for rapid sample identification. A comparison with conventional Raman spectra is given pointing out the improvement of spectral quality. The applicability of SERDS for other analytical applications, e.g. medical diagnosis will be discussed.

  7. Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

    PubMed

    Patron, Nicola J; Orzaez, Diego; Marillonnet, Sylvestre; Warzecha, Heribert; Matthewman, Colette; Youles, Mark; Raitskin, Oleg; Leveau, Aymeric; Farré, Gemma; Rogers, Christian; Smith, Alison; Hibberd, Julian; Webb, Alex A R; Locke, James; Schornack, Sebastian; Ajioka, Jim; Baulcombe, David C; Zipfel, Cyril; Kamoun, Sophien; Jones, Jonathan D G; Kuhn, Hannah; Robatzek, Silke; Van Esse, H Peter; Sanders, Dale; Oldroyd, Giles; Martin, Cathie; Field, Rob; O'Connor, Sarah; Fox, Samantha; Wulff, Brande; Miller, Ben; Breakspear, Andy; Radhakrishnan, Guru; Delaux, Pierre-Marc; Loqué, Dominique; Granell, Antonio; Tissier, Alain; Shih, Patrick; Brutnell, Thomas P; Quick, W Paul; Rischer, Heiko; Fraser, Paul D; Aharoni, Asaph; Raines, Christine; South, Paul F; Ané, Jean-Michel; Hamberger, Björn R; Langdale, Jane; Stougaard, Jens; Bouwmeester, Harro; Udvardi, Michael; Murray, James A H; Ntoukakis, Vardis; Schäfer, Patrick; Denby, Katherine; Edwards, Keith J; Osbourn, Anne; Haseloff, Jim

    2015-10-01

    Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering. PMID:26171760

  8. Technique for examining biological materials using diffuse reflectance spectroscopy and the kubelka-munk function

    DOEpatents

    Alfano, Robert R.; Yang, Yuanlong

    2003-09-02

    Method and apparatus for examining biological materials using diffuse reflectance spectroscopy and the Kubelka-Munk function. In one aspect, the method is used to determine whether a tissue sample is cancerous or not and comprises the steps of (a) measuring the diffuse reflectance from the tissue sample at a first wavelength and at a second wavelength, wherein the first wavelength is a wavelength selected from the group consisting of 255-265 nm and wherein the second wavelength is a wavelength selected from the group consisting of 275-285 nm; (b) using the Kubelka-Munk function to transform the diffuse reflectance measurement obtained at the first and second wavelengths; and (c) comparing a ratio or a difference of the transformed Kubelka-Munk measurements at the first and second wavelengths to appropriate standards determine whether or not the tissue sample is cancerous. One can use the spectral profile of KMF between 250 nm to 300 nm to determine whether or not the tissue sample is cancerous or precancerous. According to the value at the first and second wavelengths determine whether or not the malignant tissue is invasive or mixed invasive and in situ or carcinoma in situ.

  9. 3D Imaging of Nanoparticle Distribution in Biological Tissue by Laser-Induced Breakdown Spectroscopy

    PubMed Central

    Gimenez, Y.; Busser, B.; Trichard, F.; Kulesza, A.; Laurent, J. M.; Zaun, V.; Lux, F.; Benoit, J. M.; Panczer, G.; Dugourd, P.; Tillement, O.; Pelascini, F.; Sancey, L.; Motto-Ros, V.

    2016-01-01

    Nanomaterials represent a rapidly expanding area of research with huge potential for future medical applications. Nanotechnology indeed promises to revolutionize diagnostics, drug delivery, gene therapy, and many other areas of research. For any biological investigation involving nanomaterials, it is crucial to study the behavior of such nano-objects within tissues to evaluate both their efficacy and their toxicity. Here, we provide the first account of 3D label-free nanoparticle imaging at the entire-organ scale. The technology used is known as laser-induced breakdown spectroscopy (LIBS) and possesses several advantages such as speed of operation, ease of use and full compatibility with optical microscopy. We then used two different but complementary approaches to achieve 3D elemental imaging with LIBS: a volume reconstruction of a sliced organ and in-depth analysis. This proof-of-concept study demonstrates the quantitative imaging of both endogenous and exogenous elements within entire organs and paves the way for innumerable applications. PMID:27435424

  10. Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Liang, Chungwen; Jansen, Thomas L. C.; Knoester, Jasper

    2011-01-01

    We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental approaches, describing the whole proton transport process and identifying the rate limiting steps at the molecular level is challenging. In the present paper, we focus on proton transport through the Gramicidin A channel. Using a kinetic PT model derived from all-atom molecular dynamics simulations, we model the amide I region of the 2DIR spectrum of the channel protein to examine its sensitivity to the proton transport process. We demonstrate that the 2DIR spectrum of the isotope-labeled channel contain information on the PT rate, which may be extracted by analyzing the antidiagonal linewidth of the spectral feature related to the labeled site. Such experiments in combination with detailed numerical simulations should allow the extraction of site dependent PT rates, providing a method for identifying possible rate limiting steps for proton channel transfer.

  11. Biological effects and physical safety aspects of NMR imaging and in vivo spectroscopy

    SciTech Connect

    Tenforde, T.S.; Budinger, T.F.

    1985-08-01

    An assessment is made of the biological effects and physical hazards of static and time-varying fields associated with the NMR devices that are being used for clinical imaging and in vivo spectroscopy. A summary is given of the current state of knowledge concerning the mechanisms of interaction and the bioeffects of these fields. Additional topics that are discussed include: (1) physical effects on pacemakers and metallic implants such as aneurysm clips, (2) human health studies related to the effects of exposure to nonionizing electromagnetic radiation, and (3) extant guidelines for limiting exposure of patients and medical personnel to the fields produced by NMR devices. On the basis of information available at the present time, it is concluded that the fields associated with the current generation of NMR devices do not pose a significant health risk in themselves. However, rigorous guidelines must be followed to avoid the physical interaction of these fields with metallic implants and medical electronic devices. 476 refs., 5 figs., 2 tabs.

  12. Diffuse reflectance spectroscopy and optical polarization imaging of in-vivo biological tissue

    NASA Astrophysics Data System (ADS)

    Mora-Núñez, A.; Castillejos, Y.; García-Torales, G.; Martínez-Ponce, G.

    2013-11-01

    A number of optical techniques have been reported in the scientific literature as accomplishable methodologies to diagnose diseases in biological tissue, for instance, diffuse reflectance spectroscopy (DRS) and optical polarization imaging (OPI). The skin is the largest organ in the body and consists of three primary layers, namely, the epidermis (the outermost layer exposed to the world), the dermis, and the hypodermis. The epidermis changes from to site to site, mainly because of difference in hydration. A lower water content increase light scattering and reduce the penetration depth of radiation. In this work, two hairless mice have been selected to evaluate their skin features by using DRS and OPI. Four areas of the specimen body were chosen to realize the comparison: back, abdomen, tail, and head. From DRS, it was possible to distinguish the skin nature because of different blood irrigation at dermis. In the other hand, OPI shows pseudo-depolarizing regions in the measured Mueller images related to a spatially varying propagation of the scattered light. This provides information about the cell size in the irradiated skin.

  13. Next generation techniques in the high resolution spectroscopy of biologically relevant molecules.

    PubMed

    Neill, Justin L; Douglass, Kevin O; Pate, Brooks H; Pratt, David W

    2011-04-28

    Recent advances in the technology of test and measurement equipment driven by the computer and telecommunications industries have made possible the development of a new broadband, Fourier-transform microwave spectrometer that operates on principles similar to FTNMR. This technique uses a high sample-rate arbitrary waveform generator to construct a phase-locked chirped microwave pulse that gives a linear frequency sweep over a wide frequency range in 1 μs. The chirped pulse efficiently polarizes the molecular sample at all frequencies lying within this band. The subsequent free induction decay of this polarization is measured with a high-speed digitizer and then fast Fourier-transformed to yield a broadband, frequency-resolved rotational spectrum, spanning up to 11.5 GHz and containing lines that are as narrow as 100 kHz. This new technique is called chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy. The technique offers the potential to determine the structural and dynamical properties of very large molecules solely from fully resolved pure rotational spectra. FTMW double resonance techniques employing a low-resolution UV laser facilitate an easy assignment of overlapping spectra produced by different conformers in the sample. Of particular interest are the energy landscapes of conformationally flexible molecules of biological importance, including studies of their interaction with solvent and/or other weakly bound molecules. An example is provided from the authors' work on p-methoxyphenethylamine, a neurotransmitter, and its complexes with water. PMID:21394332

  14. Electrical pulse induced biological effects using dielectric spectroscopy and mathematical models

    NASA Astrophysics Data System (ADS)

    Garner, Allen Lawrence

    This dissertation studies the effects of pulsed electric fields (PEFs) on biological cells by measuring the changes in the electrical properties of the pulsed cells and mathematically modeling avascular tumor growth, cell population dynamics, and Ohmic heating. These issues are critical because of the recent use of intense ultrashort PEFs for various biological and medical applications. Recent research using PEFs for tumor treatment motivated an investigation of a simple model for the growth of an avascular tumor. We modeled tumor growth before and after necrotic core formation by incorporating spatial dependence into a one dimensional scaling law. This model emphasized the importance of cell metabolic rate in determining the final steady state size of the tumor. Experimental results showing changes in cell survival and cell cycle due to PEFs led to an investigation of a simple mathematical model for cell population dynamics that considered the cells to be proliferating (dividing) or quiescent (resting). Although some cell populations apparently reached steady state quickly, the proliferating cell population fell below one, meaning that the overall cell population would eventually decay away. This result, which was unaltered by including a transition from the quiescent to proliferating state, emphasized the importance of targeting proliferating cells for successful cancer treatments. Time domain dielectric spectroscopy was used to measure the electrical properties of a biological cell suspension over a wide frequency range with a single pulse following multiple PEFs. Fitting the dielectric properties of a cancer cell (Jurkat) suspension to a double shell model yielded the dielectric parameters of the cell membrane, cytoplasm, nuclear envelope, and nucleoplasm. Decreased cytoplasm and nucleoplasm conductivity and increased suspension conductivity suggestion transport from the cell interior to the exterior consistent with electroporation. Reduced cell membrane

  15. 40 CFR Appendix E to Part 63 - Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment Systems at Kraft Pulp...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Mixed Open Biological Treatment Systems at Kraft Pulp Mills Under Unsafe Sampling Conditions E Appendix..., App. E Appendix E to Part 63—Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment... pollutants (HAP) concentrations from an open biological treatment unit. It is assumed that inlet and...

  16. 9 CFR 381.78 - Condemnation of carcasses and parts: separation of poultry suspected of containing biological...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time of... to be not adulterated. (b) When a lot of poultry suspected of containing biological residues...

  17. 9 CFR 381.78 - Condemnation of carcasses and parts: separation of poultry suspected of containing biological...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time of... to be not adulterated. (b) When a lot of poultry suspected of containing biological residues...

  18. 9 CFR 381.78 - Condemnation of carcasses and parts: separation of poultry suspected of containing biological...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time of... to be not adulterated. (b) When a lot of poultry suspected of containing biological residues...

  19. 9 CFR 381.78 - Condemnation of carcasses and parts: separation of poultry suspected of containing biological...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time of... to be not adulterated. (b) When a lot of poultry suspected of containing biological residues...

  20. 40 CFR Appendix E to Part 63 - Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment Systems at Kraft Pulp...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Mixed Open Biological Treatment Systems at Kraft Pulp Mills Under Unsafe Sampling Conditions E Appendix..., App. E Appendix E to Part 63—Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment... pollutants (HAP) concentrations from an open biological treatment unit. It is assumed that inlet and...

  1. 40 CFR Appendix E to Part 63 - Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment Systems at Kraft Pulp...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Mixed Open Biological Treatment Systems at Kraft Pulp Mills Under Unsafe Sampling Conditions E Appendix..., App. E Appendix E to Part 63—Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment... pollutants (HAP) concentrations from an open biological treatment unit. It is assumed that inlet and...

  2. 40 CFR Appendix E to Part 63 - Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment Systems at Kraft Pulp...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Mixed Open Biological Treatment Systems at Kraft Pulp Mills Under Unsafe Sampling Conditions E Appendix..., App. E Appendix E to Part 63—Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment... pollutants (HAP) concentrations from an open biological treatment unit. It is assumed that inlet and...

  3. 9 CFR 381.78 - Condemnation of carcasses and parts: separation of poultry suspected of containing biological...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time of... to be not adulterated. (b) When a lot of poultry suspected of containing biological residues...

  4. 40 CFR Appendix E to Part 63 - Monitoring Procedure for Nonthoroughly Mixed Open Biological Treatment Systems at Kraft Pulp...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Mixed Open Biological Treatment Systems at Kraft Pulp Mills Under Unsafe Sampling Conditions E Appendix E to Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS..., App. E Appendix E to Part 63—Monitoring Procedure for Nonthoroughly Mixed Open Biological...

  5. Wholes that cause their parts: organic self-reproduction and the reality of biological teleology.

    PubMed

    Teufel, Thomas

    2011-06-01

    A well-rehearsed move among teleological realists in the philosophy of biology is to base the idea of genuinely teleological forms of organic self-reproduction on a type of causality derived from Kant. Teleological realists have long argued for the causal possibility of this form of causality--in which a whole is considered the cause of its parts--as well as formulated a set of teleological criteria of adequacy for it. What is missing, to date, is an account of the mereological principles that govern the envisioned whole-to-part causality. When the latter principles are taken into account, we find that there is no version of whole-to-part causality that is mereologically, causally and teleologically possible all at once, as teleological realism requires. PMID:21486664

  6. Determining enzyme kinetics for systems biology with nuclear magnetic resonance spectroscopy.

    PubMed

    Eicher, Johann J; Snoep, Jacky L; Rohwer, Johann M

    2012-01-01

    Enzyme kinetics for systems biology should ideally yield information about the enzyme's activity under in vivo conditions, including such reaction features as substrate cooperativity, reversibility and allostery, and be applicable to enzymatic reactions with multiple substrates. A large body of enzyme-kinetic data in the literature is based on the uni-substrate Michaelis-Menten equation, which makes unnatural assumptions about enzymatic reactions (e.g., irreversibility), and its application in systems biology models is therefore limited. To overcome this limitation, we have utilised NMR time-course data in a combined theoretical and experimental approach to parameterize the generic reversible Hill equation, which is capable of describing enzymatic reactions in terms of all the properties mentioned above and has fewer parameters than detailed mechanistic kinetic equations; these parameters are moreover defined operationally. Traditionally, enzyme kinetic data have been obtained from initial-rate studies, often using assays coupled to NAD(P)H-producing or NAD(P)H-consuming reactions. However, these assays are very labour-intensive, especially for detailed characterisation of multi-substrate reactions. We here present a cost-effective and relatively rapid method for obtaining enzyme-kinetic parameters from metabolite time-course data generated using NMR spectroscopy. The method requires fewer runs than traditional initial-rate studies and yields more information per experiment, as whole time-courses are analyzed and used for parameter fitting. Additionally, this approach allows real-time simultaneous quantification of all metabolites present in the assay system (including products and allosteric modifiers), which demonstrates the superiority of NMR over traditional spectrophotometric coupled enzyme assays. The methodology presented is applied to the elucidation of kinetic parameters for two coupled glycolytic enzymes from Escherichia coli (phosphoglucose isomerase and

  7. Dynamic nuclear polarization-enhanced 13C NMR spectroscopy of static biological solids

    NASA Astrophysics Data System (ADS)

    Potapov, Alexey; Yau, Wai-Ming; Tycko, Robert

    2013-06-01

    We explore the possibility of using dynamic nuclear polarization (DNP) to enhance signals in structural studies of biological solids by solid state NMR without sample spinning. Specifically, we use 2D 13C-13C exchange spectroscopy to probe the peptide backbone torsion angles (ϕ, ψ) in a series of selectively 13C-labeled 40-residue β-amyloid (Aβ1-40) samples, in both fibrillar and non-fibrillar states. Experiments are carried out at 9.39 T and 8 K, using a static double-resonance NMR probe and low-power microwave irradiation at 264 GHz. In frozen solutions of Aβ1-40 fibrils doped with DOTOPA-TEMPO, we observe DNP signal enhancement factors of 16-21. We show that the orientation- and frequency-dependent spin polarization exchange between sequential backbone carbonyl 13C labels can be simulated accurately using a simple expression for the exchange rate, after experimentally determined homogeneous 13C lineshapes are incorporated in the simulations. The experimental 2D 13C-13C exchange spectra place constraints on the ϕ and ψ angles between the two carbonyl labels. Although the data are not sufficient to determine ϕ and ψ uniquely, the data do provide non-trivial constraints that could be included in structure calculations. With DNP at low temperatures, 2D 13C-13C exchange spectra can be obtained from a 3.5 mg sample of Aβ1-40 fibrils in 4 h or less, despite the broad 13C chemical shift anisotropy line shapes that are observed in static samples.

  8. Dynamic nuclear polarization-enhanced 13C NMR spectroscopy of static biological solids

    PubMed Central

    Potapov, Alexey; Yau, Wai-Ming; Tycko, Robert

    2013-01-01

    We explore the possibility of using dynamic nuclear polarization (DNP) to enhance signals in structural studies of biological solids by solid state NMR without sample spinning. Specifically, we use 2D 13C-13C exchange spectroscopy to probe the peptide backbone torsion angles (ϕ,ψ) in a series of selectively 13C-labeled 40-residue β-amyloid (Aβ1–40) samples, in both fibrillar and non-fibrillar states. Experiments are carried out at 9.39 T and 8 K, using a static double-resonance NMR probe and low-power microwave irradiation at 264 GHz. In frozen solutions of Aβ1–40 fibrils doped with DOTOPA-TEMPO, we observe DNP signal enhancement factors of 16–21. We show that the orientation- and frequency-dependent spin polarization exchange between sequential backbone carbonyl 13C labels can be simulated accurately using a simple expression for the exchange rate, after experimentally determined homogeneous 13C lineshapes are incorporated in the simulations. The experimental 2D 13C-13C exchange spectra place constraints on the ϕ and ψ angles between the two carbonyl labels. Although the data are not sufficient to determine ϕ and ψ uniquely, the data do provide non-trivial constraints that could be included in structure calculations. With DNP at low temperatures, 2D 13C-13C exchange spectra can be obtained from a 3.5 mg sample of Aβ1–40 fibrils in 4 hr or less, despite the broad 13C chemical shift anisotropy line shapes that are observed in static samples. PMID:23562665

  9. Introduction: Andrew Thomson and the Centre for Metalloprotein Spectroscopy and Biology at the University of East Anglia.

    PubMed

    Wilson, Michael T

    2008-12-01

    The present article briefly relates the early history and growth of the Centre for Metalloprotein Spectroscopy and Biology at UEA (University of East Anglia) under the joint directorship of A.J. Thomson and C. Greenwood, and charts the exceptional success that this centre has had in fostering bioinorganic chemistry in the U.K. and the impact that it has had internationally. PMID:19021505

  10. Biological activities and phytochemical profiles of extracts from different parts of bamboo (Phyllostachys pubescens).

    PubMed

    Tanaka, Akinobu; Zhu, Qinchang; Tan, Hui; Horiba, Hiroki; Ohnuki, Koichiro; Mori, Yasuhiro; Yamauchi, Ryoko; Ishikawa, Hiroya; Iwamoto, Akira; Kawahara, Hiroharu; Shimizu, Kuniyoshi

    2014-01-01

    Besides being a useful building material, bamboo also is a potential source of bioactive substances. Although some studies have been performed to examine its use in terms of the biological activity, only certain parts of bamboo, especially the leaves or shoots, have been studied. Comprehensive and comparative studies among different parts of bamboo would contribute to a better understanding and application of this knowledge. In this study, the biological activities of ethanol and water extracts from the leaves, branches, outer culm, inner culm, knots, rhizomes and roots of Phyllostachys pubescens, the major species of bamboo in Japan, were comparatively evaluated. The phytochemical profiles of these extracts were tentatively determined by liquid chromatography-mass spectrometry (LC-MS) analysis. The results showed that extracts from different parts of bamboo had different chemical compositions and different antioxidative, antibacterial and antiallergic activities, as well as on on melanin biosynthesis. Outer culm and inner culm were found to be the most important sources of active compounds. 8-C-Glucosylapigenin, luteolin derivatives and chlorogenic acid were the most probable compounds responsible for the anti-allergy activity of these bamboo extracts. Our study suggests the potential use of bamboo as a functional ingredient in cosmetics or other health-related products. PMID:24945578

  11. Raman Spectroscopy Techniques for the Detection of Biological Samples in Suspensions and as Aerosol Particles: A Review

    NASA Astrophysics Data System (ADS)

    Félix-Rivera, Hilsamar; Hernández-Rivera, Samuel P.

    2012-03-01

    This article reviews current scientific literature focusing on Raman spectroscopy modalities that have been successfully applied to the detection of biological samples in aqueous suspensions and in aerosols. Normal Raman, surface enhanced Raman scattering, coherent anti-stokes Raman scattering, resonance Raman and UV-Raman spectropies, allow the detection of biological samples in situ in the near field and as well as in the far field at standoff distances. Applications span from fundamental studies to applied research in areas of defense and security and in monitoring of environmental pollution. A primary focus has been placed on biological samples including bacteria, pollen, virus, and biological contents in these specimens, in suspensions, and in aerosols. Several Raman spectroscopy studies have been reviewed to show how various modalities can achieve detection in these biosystems. Current data generated by our group is also included. Necessary parameters used to accomplish the detection and data analysis, which could also be used to interpret the results and to render the methodologies robust and reliable, are discussed.

  12. [Nutrition and biological value of food parts of a trade bivalve mollusk Anadara broughtoni].

    PubMed

    Tabakaeva, O V; Tabakaev, A V

    2015-01-01

    Currently, the human diet includes different new products of seafishing, including non-fish--bivalves and gastropods, holothurias, echinoderms, jellyfishes that demands careful studying of their chemical composition. The purpose of the study was to determine the nutritional and biological value of all soft parts of the burrowing bivalve MOLLUSK Anadara broughtoni from the Far East region. It was established thatfood parts of a bivalve were significantly flooded (water content--73.5-84.2%), with the minimum water content in the adductor and maximum in the mantle. Dry solids are presented by organic (89-93%) and mineral (7-11%) components. Organic components consist of protein (14.6-20.7%), lipids (1.8-2.3%), carbohydrates (2.1-2.6%). The analysis of amino-acid composition of proteins of food parts of the mollusk of Anadara broughtonishowed the presence of all essential amino acids with slight differences in their content depending on the localization of the protein. All edible parts have tryptophan as the limiting amino acid. Muscle proteins have maximum level of lysine, methionine, cysteine, phenylalanine and tyrosine; mantle proteins--leucine, isoleucine and threonine; adductor proteins--valine, phenylalanine, tyrosine, methionine and cysteine. Predominant nonessential amino acids forproteins of all food pieces are glycine, aspartic acid, glutamic acid, arginine. The coefficient of amino-acid score differences of adductor protein (31.7%) is less than the same of cloak by 3.7%. The indicator "biological value" is maximal for adductor (68.3%), but the differenceformuscle is only 0.83%. Mantle proteins are characterized by minimum biological value (64.6%). The coefficient of utility of amino acid composition of protein is maximalfor muscle (57.83%), and values for a cloak and an adductor differ slightly (55.81 and 55.96%). Taurine content in food parts of a mollusk Anadara broughtoni is rather high compared to with other bivalve mollusks of the Far East region

  13. [Study on Different Parts of Wild and Cultivated Gentiana Rigescens with Fourier Transform Infrared Spectroscopy].

    PubMed

    Shen, Yun-xia; Zhao, Yan-li; Zhang, Ji; Zuo, Zhi-tian; Wang, Yuan-zhong; Zhang, Qing-zhi

    2016-03-01

    The application of traditional Chinese medicine (TCM) and their preparations have a long history. With the deepening of the research, the market demand is increasing. However, wild resources are so limited that it can not meet the needs of the market. The development of wild and cultivated samples and research on accumulation dynamics of chemical component are of great significance. In order to compare composition difference of different parts (root, stem, and leaf) of wild and cultivated G. rigescens, Fourier infrared spectroscopy (FTIR) and second derivative spectra were used to analyze and evaluate. The second derivative spectra of 60 samples and the rate of affinity (the match values) were measured automatically using the appropriate software (Omnic 8.0). The results showed that the various parts of wild and cultivated G. rigescens. were high similar the peaks at 1732, 1 643, 1 613, 1 510, 1 417, 1 366, 1 322, 1 070 cm(-1) were the characteristic peak of esters, terpenoids and saccharides, respectively. Moreover, the shape and peak intensity were more distinct in the second derivative spectrum of samples. In the second derivative spectrum range of 1 800-600 cm(-1), the fingerprint characteristic peak of samples and gentiopicroside standards were 1 679, 1 613, 1 466, 1 272, 1 204, 1 103, 1 074, 985, 935 cm(-1). The characteristic peak intensity of gentiopicroside of roots of wild and cultivated samples at 1 613 cm(-1) (C-C) was higher than stems and leaves which indicated the higher content of gentiopicroside in root than in stem and leaves. Stems of wild samples at 1 521, 1 462 and 1 452 cm(-1) are the skeletal vibration peak of benzene ring of lignin, and the stem of cultivated sample have stronger peak than other samples which showed that rich lignin in stems. The iInfrared spectrum of samples were similar with the average spectral of root of wild samples, and significant difference was found for the correlation between second derivative spectrum of samples

  14. ATR-FTIR Spectroscopy in the Undergraduate Chemistry Laboratory: Part I--Fundamentals and Examples

    ERIC Educational Resources Information Center

    Schuttlefield, Jennifer D.; Grassian, Vicki H.

    2008-01-01

    Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy is a useful technique for measuring the infrared spectra of solids and liquids as well as probing adsorption on particle surfaces. Several examples of the use of FTIR-ATR spectroscopy in different undergraduate chemistry laboratory courses are presented here. These…

  15. Confocal micro-Raman spectroscopy of single biological cells using optical trapping and shifted excitation difference techniques

    NASA Astrophysics Data System (ADS)

    Xie, Changan; Li, Yong-qing

    2003-03-01

    We report on the study of single biological cells with a confocal micro-Raman spectroscopy system that uses optical trapping and shifted excitation Raman difference technique. A tunable diode laser was used to capture a living cell in solution, confine it in the confocal excitation volume, and then excite the Raman scattering. The optical trapping allows us to lift the cell well off the cover plate so that the fluorescence interference from the plate can be effectively reduced. In order to further remove the interference of the fluorescence and stray light from the trapped cell, we employed a shifted excitation Raman difference technique with slightly tuned laser frequencies. With this system, high-quality Raman spectra were obtained from single optically trapped biological cells including E. coli bacteria, yeast cells, and red blood cells. A significant difference between control and heat-treated E. coli B cells was observed due to the denaturation of biomolecules.

  16. X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples

    PubMed Central

    George, Graham N.; Pickering, Ingrid J.; Pushie, M. Jake; Nienaber, Kurt; Hackett, Mark J.; Ascone, Isabella; Hedman, Britt; Hodgson, Keith O.; Aitken, Jade B.; Levina, Aviva; Glover, Christopher; Lay, Peter A.

    2012-01-01

    As synchrotron light sources and optics deliver greater photon flux on samples, X-ray-induced photo-chemistry is increasingly encountered in X-ray absorption spectroscopy (XAS) experiments. The resulting problems are particularly pronounced for biological XAS experiments. This is because biological samples are very often quite dilute and therefore require signal averaging to achieve adequate signal-to-noise ratios, with correspondingly greater exposures to the X-ray beam. This paper reviews the origins of photo-reduction and photo-oxidation, the impact that they can have on active site structure, and the methods that can be used to provide relief from X-ray-induced photo-chemical artifacts. PMID:23093745

  17. Laser spectroscopy technique for estimating the efficiency of photosensitisers in biological media

    SciTech Connect

    Ryabova, A V; Stratonnikov, Aleksandr A; Loshchenov, V B

    2006-06-30

    A fast and highly informative method is presented for estimating the photodynamic activity of photosensitisers. The method makes it possible to determine the rate of photodegradation in erythrocyte-containing biological media in nearly in vivo conditions, estimate the degree of irreversible binding of oxygen dissolved in the medium during laser irradiation in the presence of photosensitisers, and determine the nature of degradation of photosensitisers exposed to light (photobleaching). (laser biology)

  18. Applications of X-Ray Photoelectron Spectroscopy. Part I. High T(c) Superconductors. Part II. Polymer Degradation.

    NASA Astrophysics Data System (ADS)

    Allan, Kristi Ann

    1990-08-01

    X-ray Photoelectron Spectroscopy (XPS) was applied to two different areas of research: (1) high T _{rm c} cuprate superconductors, (2) X-ray induced polymer degradation. The metallic perovskite LaCuO_3 was synthesized using a high oxygen pressure synthesis. In the XPS spectra of this compound the Cu (2p_ {3/2}) peak exhibited a shift to higher binding energy and the L_3VV Auger kinetic energy is lower than that of CuO. These shifts are representative of Cu(III) in an octahedral site linked to neighboring Cu(III) via a single 180^ circ Cu-O-Cu bridge in a metallic phase similar to copper found in the CuO_2 sheets of the cuprate superconductors. This spectrum is therefore a useful standard for comparison with the XPS spectra of new high T_{rm c} cuprate superconductors. XPS measurements of Tl_{rm 2 - y}Ba_2CuO _{rm 6 - x} as a function of oxygen content to determine the oxidation/reduction mechanism of the CuO_2 sheet. Oxidation/reduction of the CuO_2 sheets beyond or below the formal valence of Cu^{2+} is one of the necessary conditions to induce superconductivity. By employing two new chemical analyses and XPS we determined that the oxidation/reduction mechanism of the CuO _2 sheets is achieved internally by the overlap of the Tl:6s band with the CuO_2 conduction band. Changes in the oxygen content resulted in (1) changes in the phase as evidenced by the appearance or lack of T_{rm c}, (2) changes in the crystal symmetry, and (3) changes in the c axis lattice parameter obtained from X-ray diffraction measurements. Thallium is extruded during the annealing process and this was verified by both the X-ray diffraction and the XPS measurements. Recently, in a study of the anchoring of organometallic compounds on polyvinyl alcohol (PVA, -(CH_2 -HCOH)_{rm n} -), we observed X-ray exposure-dependent changes in the polymer composition. This motivated the detailed study of the X-ray induced compositional modifications of a solvent cast polyvinyl alcohol (PVA) polymer films

  19. The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts.

    PubMed

    Alnahhas, Razan N; Slater, Ben; Huang, Yunle; Mortensen, Catherine; Monk, Jordan W; Okasheh, Yousef; Howard, Marco D; Gottel, Neil R; Hammerling, Michael J; Barrick, Jeffrey E

    2014-01-01

    The Registry of Standard Biological Parts only accepts genetic parts compatible with the RFC 10 BioBrick format. This combined assembly and submission standard requires that four unique restriction enzyme sites must not occur in the DNA sequence encoding a part. We present evidence that this requirement places a nontrivial burden on iGEM teams developing large and novel parts. We further argue that the emergence of inexpensive DNA synthesis and versatile assembly methods reduces the utility of coupling submission and assembly standards and propose a submission standard that is compatible with current quality control strategies while nearly eliminating sequence constraints on submitted parts. PMID:25525459

  20. Polarized Enhanced Backscattering Spectroscopy for Characterization of Biological Tissues at Subdiffusion Length-scales

    PubMed Central

    Radosevich, Andrew J.; Rogers, Jeremy D.; Turzhitsky, Vladimir; Mutyal, Nikhil N.; Yi, Ji; Roy, Hemant K.; Backman, Vadim

    2013-01-01

    Since the early 1980’s, the enhanced backscattering (EBS) phenomenon has been well-studied in a large variety of non-biological materials. Yet, until recently the use of conventional EBS for the characterization of biological tissue has been fairly limited. In this work we detail the unique ability of EBS to provide spectroscopic, polarimetric, and depth-resolved characterization of biological tissue using a simple backscattering instrument. We first explain the experimental and numerical procedures used to accurately measure and model the full azimuthal EBS peak shape in biological tissue. Next we explore the peak shape and height dependencies for different polarization channels and spatial coherence of illumination. We then illustrate the extraordinary sensitivity of EBS to the shape of the scattering phase function using suspensions of latex microspheres. Finally, we apply EBS to biological tissue samples in order to measure optical properties and observe the spatial length-scales at which backscattering is altered in early colon carcinogenesis. PMID:24163574

  1. Gelatin embedding: a novel way to preserve biological samples for terahertz imaging and spectroscopy

    NASA Astrophysics Data System (ADS)

    Fan, Shuting; Ung, Benjamin; Parrott, Edward P. J.; Pickwell-MacPherson, Emma

    2015-04-01

    Sample dehydration has traditionally been a challenging problem in ex vivo terahertz biomedical experiments as water content changes significantly affect the terahertz properties and can diminish important contrast features. In this paper, we propose a novel method to prevent sample dehydration using gelatin embedding. By looking at terahertz image data and calculating the optical properties of the gelatin-embedded sample, we find that our method successfully preserves the sample for at least 35 h, both for imaging and spectroscopy. Our novel preservation method demonstrates for the first time the capability to simultaneously maintain sample structural integrity and prevent dehydration at room temperature. This is particularly relevant for terahertz studies of freshly excised tissues but could be beneficial for other imaging and spectroscopy techniques.

  2. Detection of biological analytes using nanomechanical infrared spectroscopy with a nanoporous microcantilever

    NASA Astrophysics Data System (ADS)

    Lee, Dongkyu; Kim, Seonghwan; Thundat, Thomas

    2013-05-01

    The highly sensitive nanoporous cantilever beam without immobilized receptors was combined with highly selective mid-infrared (IR) spectroscopy for molecular recognition of analytes using characteristic molecular vibrations. Unlike conventional IR spectroscopy, in addition, the detection sensitivity and resolution are drastically enhanced by combining high power tunable quantum cascade laser with a nanoporous cantilever having large surface area, low modulus, and nanowell structures. Further, analytes can be easily loaded on the porous microcantilever without receptor due to nanowells. In addition, orthogonal signals, variations in the mass and IR spectrum, provide more reliable and quantitative results including physical as well as chemical information of samples. We have used this technique to rapidly identify single and double stranded DNA.

  3. FTIR and Raman Spectroscopy Applied to Dementia Diagnosis Through Analysis of Biological Fluids.

    PubMed

    Lopes, Jéssica; Correia, Marta; Martins, Ilka; Henriques, Ana Gabriela; Delgadillo, Ivonne; da Cruz E Silva, Odete; Nunes, Alexandra

    2016-04-01

    To date, it is still difficult to perform an early and accurate diagnosis of dementia, therefore significant research has focused on finding new dementia biomarkers that can aid in this respect. There is an urgent need for non-invasive, rapid, and relatively inexpensive procedures for early diagnostics. Studies have demonstrated that of spectroscopic techniques, such as Fourier Transform Infrared Spectroscopy (FTIR) and Raman Spectroscopy could be a useful and accurate procedure to diagnose dementia. Given that several biochemical mechanisms related to neurodegeneration and dementia can lead to changes in plasma components and others peripheral body fluids; blood-based samples coupled to spectroscopic analyses can be used as a simple and less invasive approach. PMID:27079713

  4. Rapid, noninvasive concentration measurements of aqueous biological analytes by near-infrared Raman spectroscopy.

    PubMed

    Berger, A J; Wang, Y; Feld, M S

    1996-01-01

    Accurate concentration measurements of glucose, lactic acid, and creatinine in saline solution have beena chieved with near-IR Raman spectroscopy and a partial least-squares analysis. The Raman spectra were acquired remotely through optical fibers. A root-mean-squared prediction error of 1.2 mM for glucose concentration was achieved in 100 s. Concentrations of other analytes were predicted with similar accuracy. PMID:21069001

  5. Mode 3 Project-Based O-Level: Part II Biology

    ERIC Educational Resources Information Center

    Greatorex, D.; Lock, R.

    1978-01-01

    Presents a British biology course for the O-level which aims to promote the understanding of broad biological principles through an environmental approach. Results of proper assessment and overall examination performance are also revealed. (HM)

  6. X-ray diffraction and infrared spectroscopy analyses on the crystallinity of engineered biological hydroxyapatite for medical application

    NASA Astrophysics Data System (ADS)

    Poralan, G. M., Jr.; Gambe, J. E.; Alcantara, E. M.; Vequizo, R. M.

    2015-06-01

    Biological hydroxyapatite (BHAp) derived from thermally-treated fish bones was successfully produced. However, the obtained biological HAp was amorphous and thus making it unfavorable for medical application. Consequently, this research exploits and engineers the crystallinity of BHAp powders by addition of CaCO3 and investigates its degree of crystallinity using XRD and IR spectroscopy. On XRD, the HAp powders with [Ca]/[P] ratios 1.42, 1.46, 1.61 and 1.93 have degree of crystallinity equal to 58.08, 72.13, 85.79, 75.85% and crystal size equal to 0.67, 0.74, 0.75, 0.72 nm, respectively. The degree of crystallinity and crystal size of the obtained calcium deficient biological HAp powders increase as their [Ca]/[P] ratio approaches the stoichiometric ratio by addition of CaCO3 as source of Ca2+ ions. These results show the possibility of engineering the crystallinity and crystal size of biological HAp by addition of CaCO3. Moreover, the splitting factor of PO4 vibration matches the result with % crystallinity on XRD. Also, the area of phosphate-substitution site of PO4 vibration shows linear relationship (R2 = 0.994) with crystal size calculated from XRD. It is worth noting that the crystallinity of the biological HAp with [Ca]/[P] ratios 1.42 and 1.48 fall near the range 60-70% for highly resorbable HAp used in the medical application.

  7. Micron surface-enhanced Raman spectroscopy of intact biological organisms and model systems

    SciTech Connect

    Todd, E.A.; Morris, M.D.

    1994-05-01

    Surface-enhanced Raman spectra have been obtained within intact zebrafish embryos and inside the 500-fL pores of a Nucleopore filter membrane with the use of coated microelectrodes with 1-3 {mu}m active silver tip diameters. The spectra obtained demonstrate the microelectrode`s ability to penetrate biological membranes as well as restricted volumes. 8 refs., 5 figs.

  8. Gross boron determination in biological samples by inductively coupled plasma-atomic emission spectroscopy

    SciTech Connect

    Bauer, W.F.; Johnson, D.A.; Steele, S.M.; Messick, K.; Miller, D.L.; Propp, W.A.

    1988-01-01

    This paper describes a method for the analysis of boron in biological samples including urine, blood plasma, and tissues with subsequent boron determinations by ICP-AES. A comparison will be made between results obtained by this method and by the prompt-gamma technique on the same samples. 4 refs., 2 figs., 2 tabs.

  9. Biological and biophysical principles in extracorporal bone tissue engineering. Part I.

    PubMed

    Meyer, U; Joos, U; Wiesmann, H P

    2004-06-01

    Advances in the field of bone tissue engineering have encouraged physicians to introduce these techniques into clinical practice. Bone tissue engineering is the construction, repair or replacement of damaged or missing bone in humans or animals. Engineering of bone can take place within the animal body or extracorporal in a bioreactor for later grafting into the body. Appropriate cell types and non-living substrata are minimal requirements for an extracorporal tissue engineering approach. This review discusses the biological and biophysical background of in vitro bone tissue engineering. Biochemical and biophysical stimuli of cell growth and differentiation are regarded as potent tools to improve bone formation in vitro. The paper focuses on basic principles in extracorporal engineering of bone-like tissues, intended to be implanted in animal experiments and clinical studies. Particular attention is given in this part to the contributions of cell and material science to the development of bone-like tissues. Several approaches are at the level of clinical applicability and it can be expected that widespread use of engineered bone constructs will change the surgeon's work in the near future. PMID:15145032

  10. Modelling of a biologically inspired robotic fish driven by compliant parts.

    PubMed

    El Daou, Hadi; Salumäe, Taavi; Chambers, Lily D; Megill, William M; Kruusmaa, Maarja

    2014-03-01

    Inspired by biological swimmers such as fish, a robot composed of a rigid head, a compliant body and a rigid caudal fin was built. It has the geometrical properties of a subcarangiform swimmer of the same size. The head houses a servo-motor which actuates the compliant body and the caudal fin. It achieves this by applying a concentrated moment on a point near the compliant body base. In this paper, the dynamics of the compliant body driving the robotic fish is modelled and experimentally validated. Lighthill's elongated body theory is used to define the hydrodynamic forces on the compliant part and Rayleigh proportional damping is used to model damping. Based on the assumed modes method, an energetic approach is used to write the equations of motion of the compliant body and to compute the relationship between the applied moment and the resulting lateral deflections. Experiments on the compliant body were carried out to validate the model predictions. The results showed that a good match was achieved between the measured and predicted deformations. A discussion of the swimming motions between the real fish and the robot is presented. PMID:24451164

  11. Retrieving the optical parameters of biological tissues using diffuse reflectance spectroscopy and Fourier series expansions. I. theory and application

    PubMed Central

    Muñoz Morales, Aarón A.; Vázquez y Montiel, Sergio

    2012-01-01

    The determination of optical parameters of biological tissues is essential for the application of optical techniques in the diagnosis and treatment of diseases. Diffuse Reflection Spectroscopy is a widely used technique to analyze the optical characteristics of biological tissues. In this paper we show that by using diffuse reflectance spectra and a new mathematical model we can retrieve the optical parameters by applying an adjustment of the data with nonlinear least squares. In our model we represent the spectra using a Fourier series expansion finding mathematical relations between the polynomial coefficients and the optical parameters. In this first paper we use spectra generated by the Monte Carlo Multilayered Technique to simulate the propagation of photons in turbid media. Using these spectra we determine the behavior of Fourier series coefficients when varying the optical parameters of the medium under study. With this procedure we find mathematical relations between Fourier series coefficients and optical parameters. Finally, the results show that our method can retrieve the optical parameters of biological tissues with accuracy that is adequate for medical applications. PMID:23082281

  12. Micro-FTIR imaging spectroscopy of calcified atheromatous carotid plaques. Part IV

    NASA Astrophysics Data System (ADS)

    Alò, Francesco; Conti, Carla; Ferraris, Paolo; Giorgini, Elisabetta; Rubini, Corrado; Sabbatini, Simona; Tosi, Giorgio

    2009-03-01

    Micro-imaging infrared spectroscopy has been performed on atheromatous plaques in order to localize and characterize substances responsible for the cytotoxic effects that prevent macrophages clearance of lipidic and calcified materials. In plaques with different graded atherosclerotic lesions, infrared determinations allowed to visualize gruel and ceroid toxic components and variously calcified zones. Compare correlations let to visualize the progression of the lesion on going from the lumen to the outer media of the plaque.

  13. Frontiers of Two-Dimensional Correlation Spectroscopy. Part 1. New concepts and noteworthy developments

    NASA Astrophysics Data System (ADS)

    Noda, Isao

    2014-07-01

    A comprehensive survey review of new and noteworthy developments, which are advancing forward the frontiers in the field of 2D correlation spectroscopy during the last four years, is compiled. This review covers books, proceedings, and review articles published on 2D correlation spectroscopy, a number of significant conceptual developments in the field, data pretreatment methods and other pertinent topics, as well as patent and publication trends and citation activities. Developments discussed include projection 2D correlation analysis, concatenated 2D correlation, and correlation under multiple perturbation effects, as well as orthogonal sample design, predicting 2D correlation spectra, manipulating and comparing 2D spectra, correlation strategy based on segmented data blocks, such as moving-window analysis, features like determination of sequential order and enhanced spectral resolution, statistical 2D spectroscopy using covariance and other statistical metrics, hetero-correlation analysis, and sample-sample correlation technique. Data pretreatment operations prior to 2D correlation analysis are discussed, including the correction for physical effects, background and baseline subtraction, selection of reference spectrum, normalization and scaling of data, derivatives spectra and deconvolution technique, and smoothing and noise reduction. Other pertinent topics include chemometrics and statistical considerations, peak position shift phenomena, variable sampling increments, computation and software, display schemes, such as color coded format, slice and power spectra, tabulation, and other schemes.

  14. Biologically active and amidated cecropin produced in a baculovirus expression system from a fusion construct containing the antibody-binding part of protein A.

    PubMed Central

    Andersons, D; Engström, A; Josephson, S; Hansson, L; Steiner, H

    1991-01-01

    A synthetic antibody-binding part derived from protein A from Staphylococcus aureus was used as a fusion partner in a eukaryotic expression system employing Autographa californica nuclear polyhedrosis as a vector. This, in conjunction with an efficient signal sequence, facilitated the purification of the antibacterial peptide cecropin A from the medium of Spodoptera frugiperda cells infected with a recombinant virus. In order to increase further the concentrations of fusion protein, Trichoplusia ni larvae were used as host. Cecropin A could be obtained after cleavage of the fusion protein with CNBr. Biological activity as well as the correct structure including the C-terminal amide group was shown using electrophoresis with detection of antibacterial proteins and mass spectroscopy. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. PMID:1720614

  15. Testing biological liquid samples using modified m-line spectroscopy method

    NASA Astrophysics Data System (ADS)

    Augusciuk, Elzbieta; Rybiński, Grzegorz

    2005-09-01

    Non-chemical method of detection of sugar concentration in biological (animal and plant source) liquids has been investigated. Simplified set was build to show the easy way of carrying out the survey and to make easy to gather multiple measurements for error detecting and statistics. Method is suggested as easy and cheap alternative for chemical methods of measuring sugar concentration, but needing a lot effort to be made precise.

  16. Spectral pre and post processing for infrared and Raman spectroscopy of biological tissues and cells.

    PubMed

    Byrne, Hugh J; Knief, Peter; Keating, Mark E; Bonnier, Franck

    2016-04-01

    Vibrational spectroscopy, both infrared absorption and Raman spectroscopy, have attracted increasing attention for biomedical applications, from in vivo and ex vivo disease diagnostics and screening, to in vitro screening of therapeutics. There remain, however, many challenges related to the accuracy of analysis of physically and chemically inhomogeneous samples, across heterogeneous sample sets. Data preprocessing is required to deal with variations in instrumental responses and intrinsic spectral backgrounds and distortions in order to extract reliable spectral data. Data postprocessing is required to extract the most reliable information from the sample sets, based on often very subtle changes in spectra associated with the targeted pathology or biochemical process. This review presents the current understanding of the factors influencing the quality of spectra recorded and the pre-processing steps commonly employed to improve on spectral quality. It further explores some of the most common techniques which have emerged for classification and analysis of the spectral data for biomedical applications. The importance of sample presentation and measurement conditions to yield the highest quality spectra in the first place is emphasised, as is the potential of model simulated datasets to validate both pre- and post-processing protocols. PMID:26463830

  17. Infrared fiber optic evanescent wave spectroscopy: applications in biology and medicine

    NASA Astrophysics Data System (ADS)

    Afanasyeva, Natalia I.; Bruch, Reinhard F.; Katzir, Abraham

    1999-04-01

    A new powerful and highly sensitive technique for non-invasive biomedical diagnostics in vivo has been developed using Infrared Fiberoptic Evanescent Wave Fourier Transform Spectroscopy (FEW-FTIR). This compact and portable method allows to detect functional chemical groups and bonds via vibrational spectroscopy directly from surfaces including living tissue. Such differences and similarities in molecular structure of tissue and materials can be evaluated online. Operating in the attenuated total reflection (ATR) regime in the middle-infrared (MIR) range, the FEW-FTIR technique provides direct contact between the fiber probe and tissue for non-destructive, non-invasive, fast and remote (few meters) diagnostics and quality control of materials. This method utilizes highly flexible and extremely low loss unclad fibers, for example silver halide fibers. Applications of this method include investigations of normal skin, precancerous and cancerous conditions, monitoring of the process of aging, allergic reactions and radiation damage to the skin. This setup is suitable as well for the detection of the influence of environmental factors (sun, water, pollution, and weather) on skin surfaces. The FEW-FTIR technique is very promising also for fast histological examinations in vitro. In this review, we present recent investigations of skin, breast, lung, stomach, kidney tissues in vivo and ex vivo (during surgery) to define the areas of tumor localization. The main advantages of the FEW-FTIR technique for biomedical, clinical, and environmental applications are discussed.

  18. Recent applications of /sup 13/C NMR spectroscopy to biological systems

    SciTech Connect

    Matwiyoff, N.A.

    1981-01-01

    Carbon-13 nuclear magnetic resonance (NMR) spectroscopy, in conjunction with carbon-13 labelling, is a powerful new analytical technique for the study of metabolic pathways and structural components in intact organelles, cells, and tissues. The technique can provide, rapidly and non-destructively, unique information about: the architecture and dynamics of structural components; the nature of the intracellular environment; and metabolic pathways and relative fluxes of individual carbon atoms. With the aid of results recently obtained by us and those reported by a number of other laboratories, the problems and potentialities of the technique will be reviewed with emphasis on: the viscosities of intracellular fluids; the structure and dynamics of the components of membranes; and the primary and secondary metabolic pathways of carbon in microorganisms, plants, and mammalian cells in culture.

  19. Nanoporous leaky waveguide based chemical and biological sensors with broadband spectroscopy

    NASA Astrophysics Data System (ADS)

    Qi, Zhi-Mei; Honma, Itaru; Zhou, Haoshen

    2007-01-01

    Here the authors demonstrate spectral optical chemical and biological sensors based on a nanoporous thin-film leaky waveguide that were fabricated by dip coating the gold-layer-covered glass substrate from the colloidal TiO2 solution. The sensor operates by interrogating the resonance wavelengths for the leaky modes in a broad bandwidth using the Kretschmann configuration. Sensitivities of the sensor to refractive index of liquid and protein adsorption were investigated and compared with the spectral surface plasmon resonance sensors. The best fitting to the experimental data was carried out with the Fresnel equations, and thickness and porosity of the nanoporous waveguiding layer were determined.

  20. Non-invasive chemically specific measurement of subsurface temperature in biological tissues using surface-enhanced spatially offset Raman spectroscopy.

    PubMed

    Gardner, Benjamin; Stone, Nicholas; Matousek, Pavel

    2016-06-23

    Here we demonstrate for the first time the viability of characterising non-invasively the subsurface temperature of SERS nanoparticles embedded within biological tissues using spatially offset Raman spectroscopy (SORS). The proposed analytical method (T-SESORS) is applicable in general to diffusely scattering (turbid) media and features high sensitivity and high chemical selectivity. The method relies on monitoring the Stokes and anti-Stokes bands of SERS nanoparticles in depth using SORS. The approach has been conceptually demonstrated using a SORS variant, transmission Raman spectroscopy (TRS), by measuring subsurface temperatures within a slab of porcine tissue (5 mm thick). Root-mean-square errors (RMSEs) of 0.20 °C were achieved when measuring temperatures over ranges between 25 and 44 °C. This unique capability complements the array of existing, predominantly surface-based, temperature monitoring techniques. It expands on a previously demonstrated SORS temperature monitoring capability by adding extra sensitivity stemming from SERS to low concentration analytes. The technique paves the way for a wide range of applications including subsurface, chemical-specific, non-invasive temperature analysis within turbid translucent media including: the human body, subsurface monitoring of chemical (e.g. catalytic) processes in manufacture quality and process control and research. Additionally, the method opens prospects for control of thermal treatment of cancer in vivo with direct non-invasive feedback on the temperature of mediating plasmonic nanoparticles. PMID:27049293

  1. 40 CFR Appendix C to Part 63 - Determination of the Fraction Biodegraded (Fbio) in a Biological Treatment Unit

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 14 2010-07-01 2010-07-01 false Determination of the Fraction Biodegraded (Fbio) in a Biological Treatment Unit C Appendix C to Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES...

  2. 40 CFR Appendix C to Part 63 - Determination of the Fraction Biodegraded (Fbio) in a Biological Treatment Unit

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 15 2014-07-01 2014-07-01 false Determination of the Fraction Biodegraded (Fbio) in a Biological Treatment Unit C Appendix C to Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES...

  3. Direct determination and speciation of mercury compounds in environmental and biological samples by carbon bed atomic absorption spectroscopy

    SciTech Connect

    Skelly, E.M.

    1982-01-01

    A method was developed for the direct determination of mercury in water and biological samples using a unique carbon bed atomizer for atomic absorption spectroscopy. The method avoided sources of error such as loss of volatile mercury during sample digestion and contamination of samples through added reagents by eliminating sample pretreatment steps. The design of the atomizer allowed use of the 184.9 nm mercury resonance line in the vacuum ultraviolet region, which increased sensitivity over the commonly used spin-forbidden 253.7 nm line. The carbon bed atomizer method was applied to a study of mercury concentrations in water, hair, sweat, urine, blood, breath and saliva samples from a non-occupationally exposed population. Data were collected on the average concentration, the range and distribution of mercury in the samples. Data were also collected illustrating individual variations in mercury concentrations with time. Concentrations of mercury found were significantly higher than values reported in the literature for a ''normal'' population. This is attributed to the increased accuracy gained by eliminating pretreatment steps and increasing atomization efficiency. Absorption traces were obtained for various solutions of pure and complexed mercury compounds. Absorption traces of biological fluids were also obtained. Differences were observed in the absorption-temperatures traces of various compounds. The utility of this technique for studying complexation was demonstrated.

  4. Surface-enhanced Raman spectroscopy-active substrates: adapting the shape of plasmonic nanoparticles for different biological applications.

    PubMed

    Vitol, Elina A; Friedman, Gary; Gogotsi, Yury

    2014-04-01

    We discuss the relationship between the shape of plasmonic nanoparticles and the biological surface-enhanced Raman spectroscopy (SERS) applications which they can enable. As a step forward in developing SERS-active substrates adapted to a particular application, we demonstrate that a modification of the widely used protocol for the sodium citrate mediated reduction of chloroauric acid, which is typically employed only for obtaining spherical gold nanoparticles, can yield flat polygonal nanoparticles at room temperature and a decreased amount of the reducing agent. The significant advantage of the described approach is that it allows for synthesis of nanoparticles with different geometries using a well-established synthesis protocol without the need for any additional chemicals or special synthesis apparatus. By contrasting spherical and anisotropically shaped nanoparticles, we demonstrate that multifaceted nanoparticles with sharp edges are better suitable for SERS analysis of low concentration analytes requiring strong SERS enhancement. On the other hand, gold nanoparticles with isotropic shapes, while giving a smaller enhancement, can provide a more reproducible SERS signal. This is important for analytical applications of complex biological systems where large SERS enhancement may not always be required, whereas data reproducibility and minimal false positive rate are imperative. Using a SERS-active substrate comprising isotropically shaped gold nanoparticles, we demonstrate the differences between Gram-negative (E. coli) and Gram-positive (S. aureus) bacteria, attributable to the outer membrane and peptidoglycan layer, with the level of detail which has not been previously reported with optical spectroscopic techniques. PMID:24734732

  5. Elemental analysis of biological samples by graphite furnace, inductively coupled plasma - atomic emission spectroscopy (GF-ICP-AES)

    SciTech Connect

    Winge, R.K.; Fassel, V.A.; Grabau, F.; Zu-cheng, J.

    1984-08-01

    The large number of analyses required for monitoring environmental pollution and its ecological impacts suggests that an analytical screening method would be very useful if it could rapidly distinguish those samples containing environmentally significant concentrations of pollutants from those that do not. In the trace elemental analysis of solids the most time consuming step is often the conversion of the sample into a suitable analytical form, usually a digestion and dissolution process. We have addressed these problems by combining a graphite furnace with inductively coupled plasma-atomic emission spectroscopy. With this system solid samples of plant and animal tissue, as well as solutions, can be vaporized and introduced directly into the inductively coupled plasma. A simple standard additions technique was developed for solid samples that yielded acceptable results for a number of elements in biological samples. Powers of detection were not satisfactory for the lowest concentrations of several elements in the NBS biological SRMs and analytical uncertainties were relatively high for quantitative analyses but were generally satisfactory for screening methods. The design of the interface between the graphite furnace and the inductively coupled plasma and the pulse effect caused by the vaporization of the sample are critical factors in the GF-ICP-AES method. 31 references, 21 figures, 4 tables.

  6. High-extinction virtually imaged phased array-based Brillouin spectroscopy of turbid biological media

    PubMed Central

    Zhang, Jitao; Yun, Seok Hyun; Scarcelli, Giuliano

    2016-01-01

    Brillouin microscopy has recently emerged as a powerful technique to characterize the mechanical properties of biological tissue, cell, and biomaterials. However, the potential of Brillouin microscopy is currently limited to transparent samples, because Brillouin spectrometers do not have sufficient spectral extinction to reject the predominant non-Brillouin scattered light of turbid media. To overcome this issue, we combined a multi-pass Fabry-Perot interferometer with a two-stage virtually imaged phased array spectrometer. The Fabry-Perot etalon acts as an ultra-narrow band-pass filter for Brillouin light with high spectral extinction and low loss. We report background-free Brillouin spectra from Intralipid solutions and up to 100 μm deep within chicken muscle tissue. PMID:27274097

  7. High-resolution NMR spectroscopy of biological tissues usingprojected Magic Angle Spinning

    SciTech Connect

    Martin, Rachel W.; Jachmann, Rebecca C.; Sakellariou, Dimitris; Nielsen, Ulla Gro; Pines, Alexander

    2005-01-27

    High-resolution NMR spectra of materials subject toanisotropic broadening are usually obtained by rotating the sample aboutthe magic angle, which is 54.7 degrees to the static magnetic field. Inprojected Magic Angle Spinning (p-MAS), the sample is spun about twoangles, neither of which is the magic angle. This provides a method ofobtaining isotropic spectra while spinning at shallow angles. The p-MASexperiment may be used in situations where spinning the sample at themagic angle is not possible due to geometric or other constraints,allowing the choice of spinning angle to be determined by factors such asthe shape of the sample, rather than by the spin physics. The applicationof this technique to bovine tissue samples is demonstrated as a proof ofprinciple for future biological or medical applications.

  8. High-extinction virtually imaged phased array-based Brillouin spectroscopy of turbid biological media

    NASA Astrophysics Data System (ADS)

    Fiore, Antonio; Zhang, Jitao; Shao, Peng; Yun, Seok Hyun; Scarcelli, Giuliano

    2016-05-01

    Brillouin microscopy has recently emerged as a powerful technique to characterize the mechanical properties of biological tissue, cell, and biomaterials. However, the potential of Brillouin microscopy is currently limited to transparent samples, because Brillouin spectrometers do not have sufficient spectral extinction to reject the predominant non-Brillouin scattered light of turbid media. To overcome this issue, we combined a multi-pass Fabry-Perot interferometer with a two-stage virtually imaged phased array spectrometer. The Fabry-Perot etalon acts as an ultra-narrow band-pass filter for Brillouin light with high spectral extinction and low loss. We report background-free Brillouin spectra from Intralipid solutions and up to 100 μm deep within chicken muscle tissue.

  9. [Bone Cell Biology Assessed by Microscopic Approach. Assessment of bone quality using Raman and infrared spectroscopy].

    PubMed

    Suda, Hiromi Kimura

    2015-10-01

    Bone quality, which was defined as "the sum total of characteristics of the bone that influence the bone's resistance to fracture" at the National Institute of Health (NIH) conference in 2001, contributes to bone strength in combination with bone mass. Bone mass is often measured as bone mineral density (BMD) and, consequently, can be quantified easily. On the other hand, bone quality is composed of several factors such as bone structure, bone matrix, calcification degree, microdamage, and bone turnover, and it is not easy to obtain data for the various factors. Therefore, it is difficult to quantify bone quality. We are eager to develop new measurement methods for bone quality that make it possible to determine several factors associated with bone quality at the same time. Analytic methods based on Raman and FTIR spectroscopy have attracted a good deal of attention as they can provide a good deal of chemical information about hydroxyapatite and collagen, which are the main components of bone. A lot of studies on bone quality using Raman and FTIR imaging have been reported following the development of the two imaging systems. Thus, both Raman and FTIR imaging appear to be promising new bone morphometric techniques. PMID:26412727

  10. Microfluidic impedance spectroscopy as a tool for quantitative biology and biotechnology

    PubMed Central

    Sabuncu, Ahmet C.; Zhuang, Jie; Kolb, Juergen F.; Beskok, Ali

    2012-01-01

    A microfluidic device that is able to perform dielectric spectroscopy is developed. The device consists of a measurement chamber that is 250 μm thick and 750 μm in radius. Around 1000 cells fit inside the chamber assuming average quantities for cell radius and volume fraction. This number is about 1000 folds lower than the capacity of conventional fixtures. A T-cell leukemia cell line Jurkat is tested using the microfluidic device. Measurements of deionized water and salt solutions are utilized to determine parasitic effects and geometric capacitance of the device. Physical models, including Maxwell-Wagner mixture and double shell models, are used to derive quantities for sub-cellular units. Clausius-Mossotti factor of Jurkat cells is extracted from the impedance spectrum. Effects of cellular heterogeneity are discussed and parameterized. Jurkat cells are also tested with a time domain reflectometry system for verification of the microfluidic device. Results indicate good agreement of values obtained with both techniques. The device can be used as a unique cell diagnostic tool to yield information on sub-cellular units. PMID:23853680

  11. Sensing lanthanide metal content in biological tissues with magnetic resonance spectroscopy.

    PubMed

    Hingorani, Dina V; Gonzalez, Sandra I; Li, Jessica F; Pagel, Mark D

    2013-01-01

    The development and validation of MRI contrast agents consisting of a lanthanide chelate often requires a determination of the concentration of the agent in ex vivo tissue. We have developed a protocol that uses 70% nitric acid to completely digest tissue samples that contain Gd(III), Dy(III), Tm(III), Eu(III), or Yb(III) ions, or the MRI contrast agent gadodiamide. NMR spectroscopy of coaxial tubes containing a digested sample and a separate control solution of nitric acid was used to rapidly and easily measure the bulk magnetic susceptibility (BMS) shift caused by each lanthanide ion and gadodiamide. Each BMS shift was shown to be linearly correlated with the concentration of each lanthanide ion and gadodiamide in the 70% nitric acid solution and in digested rat kidney and liver tissues. These concentration measurements had outstanding precision, and also had good accuracy for concentrations ≥10 mM for Tm(III) Eu(III), and Yb(III), and ≥3 mM for Gd(III), gadodiamide, and Dy(III). Improved sample handling methods are needed to improve measurement accuracy for samples with lower concentrations. PMID:24152931

  12. Biological materials: Part A. tuning LCST of raft copolymers and gold/copolymer hybrid nanoparticles and Part B. Biobased nanomaterials

    NASA Astrophysics Data System (ADS)

    Chen, Ning

    The research described in this dissertation is comprised of two major parts. The first part studied the effects of asymmetric amphiphilic end groups on the thermo-response of diblock copolymers of (oligo/di(ethylene glycol) methyl ether (meth)acrylates, OEGA/DEGMA) and the hybrid nanoparticles of these copolymers with a gold nanoparticle core. Placing the more hydrophilic end group on the more hydrophilic block significantly increased the cloud point compared to a similar copolymer composition with the end group placement reversed. For a given composition, the cloud point was shifted by as much as 28 °C depending on the placement of end groups. This is a much stronger effect than either changing the hydrophilic/hydrophobic block ratio or replacing the hydrophilic acrylate monomer with the equivalent methacrylate monomer. The temperature range of the coil-globule transition was also altered. Binding these diblock copolymers to a gold core decreased the cloud point by 5-15 °C and narrowed the temperature range of the coil-globule transition. The effects were more pronounced when the gold core was bound to the less hydrophilic block. Given the limited numbers of monomers that are approved safe for in vivo use, employing amphiphilic end group placement is a useful tool to tune a thermo-response without otherwise changing the copolymer composition. The second part of the dissertation investigated the production of value-added nanomaterials from two biorefinery "wastes": lignin and peptidoglycan. Different solvents and spinning methods (melt-, wet-, and electro-spinning) were tested to make lignin/cellulose blended and carbonized fibers. Only electro-spinning yielded fibers having a small enough diameter for efficient carbonization (≤ 5-10 μm), but it was concluded that cellulose was not a suitable binder. Cellulose lignin fibers before carbonization showed up to 90% decrease in moisture uptake compared to pure cellulose. Peptidoglycan (a bacterial cell wall

  13. Cold Spring Harbor symposia on quantitative biology. Volume XLVII, Part 2. Structures of DNA

    SciTech Connect

    Not Available

    1983-01-01

    This is Volume 2 of the proceedings of the 1982 Cold Springs Harbor Symposium on Quantitative Biology. The volume contains papers on DNA methylation, DNA replication, gene recombination, organization of genes along DNA, molecular structure and enzymology of DNA.

  14. [Topical issues of biological safety under current conditions. Part 3. Scientific provision for the national regulation of the biological safety framework in its broad interpretation].

    PubMed

    Onishchenko, G G; Smolensky, V Yu; Ezhlova, E B; Demina, Yu V; Toporkov, V P; Toporkov, A V; Lyapin, M N; Kutyrev, V V

    2014-01-01

    Consequent of investigation concerned with biological safety (BS) framework development in its broad interpretation, reflected in the Russian Federation State Acts, identified have been conceptual entity parameters of the up-to-date broad interpretation of BS, which have formed a part of the developed by the authors system for surveillance (prophylaxis, localization, indication, identification, and diagnostics) and control (prophylaxis, localization, and response/elimination) over the emergency situations of biological (sanitary-epidemiological) character. The System functionality is activated through supplying the content with information data which are concerned with monitoring and control of specific internal and external threats in the sphere of BS provision fixed in the Supplement 2 of the International Health Regulations (IHR, 2005), and with the previously characterized nomenclature of hazardous biological factors. The system is designed as a network-based research-and-practice tool for evaluation of the situation in the sphere of BS provision, as well as assessment of efficacy of management decision making as regards BS control and proper State policy implementation. Most of the system elements either directly or indirectly relate to the scope of activities conducted by Federal Service for Surveillance in the Sphere of Consumers Rights Protection and Human Welfare, being substantial argument for allocating coordination functions in the sphere of BS provision to this government agency and consistent with its function as the State Coordinator on IHR (2005). The data collected serve as materials to Draft Federal Law "Concerning biological safety provision of the population". PMID:25971137

  15. Applications of High Resolution Laser Induced Breakdown Spectroscopy for Environmental and Biological Samples

    SciTech Connect

    Martin, Madhavi Z; Labbe, Nicole; Wagner, Rebekah J.

    2013-01-01

    This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

  16. Applications of High Resolution Laser: Induced Breakdown Spectroscopy for Environmental and Biological Samples

    NASA Astrophysics Data System (ADS)

    Martin, Madhavi Z.; Labbe, Nicole; Wagner, Rebekah J.

    This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

  17. HNS(+) and HSN(+) cations: Electronic states, spin-rovibronic spectroscopy with planetary and biological implications.

    PubMed

    Trabelsi, Tarek; Ben Yaghlane, Saida; Al Mogren, Muneerah Mogren; Francisco, Joseph S; Hochlaf, Majdi

    2016-08-28

    Ab initio methods in conjunction with a large basis set are used to compute the potential energy surfaces of the 12 lowest electronic states of the HNS(+) and HSN(+) isomeric forms. These potentials are used in discussions of the metastability of these cations and plausible mechanisms for the H(+)/H + SN(+)/SN, S/S(+) + NH(+)/NH, N/N(+) + SH(+)/SH ion-molecule reactions. Interestingly, the low rovibrational levels of HSN(+)(1(2)A″) and HNS(+)(1(2)A″) electronically excited ions are predicted to be long-lived. Both ions are suggested to be a suitable candidate for light-sensitive NO(⋅) donor in vivo and as a possible marker for the detection of intermediates in nitrites + H2S reactions at the cellular level. The full spin rovibronic levels of HNS(+) are presented, which may assist in the experimental identification of HNS(+) and HSN(+) ions and in elucidating their roles in astrophysical and biological media. PMID:27586922

  18. Surface excitations in electron spectroscopy. Part I: dielectric formalism and Monte Carlo algorithm

    PubMed Central

    Salvat-Pujol, F; Werner, W S M

    2013-01-01

    The theory describing energy losses of charged non-relativistic projectiles crossing a planar interface is derived on the basis of the Maxwell equations, outlining the physical assumptions of the model in great detail. The employed approach is very general in that various common models for surface excitations (such as the specular reflection model) can be obtained by an appropriate choice of parameter values. The dynamics of charged projectiles near surfaces is examined by calculations of the induced surface charge and the depth- and direction-dependent differential inelastic inverse mean free path (DIIMFP) and stopping power. The effect of several simplifications frequently encountered in the literature is investigated: differences of up to 100% are found in heights, widths, and positions of peaks in the DIIMFP. The presented model is implemented in a Monte Carlo algorithm for the simulation of the electron transport relevant for surface electron spectroscopy. Simulated reflection electron energy loss spectra are in good agreement with experiment on an absolute scale. Copyright © 2012 John Wiley & Sons, Ltd. PMID:23794766

  19. Mechanism of hydrodenitrogenation (Part 4) infrared spectroscopy of acidic molybdena catalysts

    SciTech Connect

    Miranda, R.

    1990-01-01

    Mo oxide catalysts supported over a complete series of silica-aluminas have been characterized in the oxidic and reduced states, by means of total acidity measurements and by infrared spectroscopy. Ammonia chemisorption was used to titrate the total acidity of the catalysts, and IR absorption of adsorbed pyridine to distinguish Bronsted from Lewis acid sites. The formation of new acidity upon deposition of molybdena on silica-alumina supports was then explained on the basis of a simple surface model. The new acidity is of both Lewis and Bronsted type, the preponderance of one over the other depending on support composition, as well as loading and state of oxidation of Mo. High-alumina supports and low Mo loading favor dispersed Mo species, in particular bidentate and monodentate di-oxo Mo species. The latter is responsible for the new Bronsted acidity. Coordinative unsaturation of polymolybdates is responsible for the new Lewis acidity, which is increased upon reduction of Mo. High-silica supports favor monodentate species (high Bronsted acidity) up to 4 wt % MoO{sub 3}. Beyond that, polymolybdates species and Lewis acidity predominate. 7 refs., 4 figs.

  20. Surface excitations in electron spectroscopy. Part I: dielectric formalism and Monte Carlo algorithm.

    PubMed

    Salvat-Pujol, F; Werner, W S M

    2013-05-01

    The theory describing energy losses of charged non-relativistic projectiles crossing a planar interface is derived on the basis of the Maxwell equations, outlining the physical assumptions of the model in great detail. The employed approach is very general in that various common models for surface excitations (such as the specular reflection model) can be obtained by an appropriate choice of parameter values. The dynamics of charged projectiles near surfaces is examined by calculations of the induced surface charge and the depth- and direction-dependent differential inelastic inverse mean free path (DIIMFP) and stopping power. The effect of several simplifications frequently encountered in the literature is investigated: differences of up to 100% are found in heights, widths, and positions of peaks in the DIIMFP. The presented model is implemented in a Monte Carlo algorithm for the simulation of the electron transport relevant for surface electron spectroscopy. Simulated reflection electron energy loss spectra are in good agreement with experiment on an absolute scale. Copyright © 2012 John Wiley & Sons, Ltd. PMID:23794766

  1. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools

    PubMed Central

    Ham, Timothy S.; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna; Hillson, Nathan J.; Keasling, Jay D.

    2012-01-01

    The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects. PMID:22718978

  2. Scanning laser ultrasound and wavenumber spectroscopy for in-process inspection of additively manufactured parts

    NASA Astrophysics Data System (ADS)

    Koskelo, EliseAnne C.; Flynn, Eric B.

    2016-04-01

    We present a new in-process laser ultrasound inspection technique for additive manufacturing. Ultrasonic energy was introduced to the part by attaching an ultrasonic transducer to the printer build-plate and driving it with a single-tone, harmonic excitation. The full-field response of the part was measured using a scanning laser Doppler vibrometer after each printer layer. For each scan, we analyzed both the local amplitudes and wavenumbers of the response in order to identify defects. For this study, we focused on the detection of delamination between layers in a fused deposition modeling process. Foreign object damage, localized heating damage, and the resulting delamination between layers were detected in using the technique as indicated by increased amplitude and wavenumber responses within the damaged area.

  3. Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 2: 2D NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Deshmukh, Ashish P.; Pacheco, Carlos; Hay, Michael B.; Myneni, Satish C. B.

    2007-07-01

    Carboxyl groups are abundant in natural organic molecules (NOM) and play a major role in their reactivity. The structural environments of carboxyl groups in IHSS soil and river humic samples were investigated using 2D NMR (heteronuclear and homonuclear correlation) spectroscopy. Based on the 1H- 13C heteronuclear multiple-bond correlation (HMBC) spectroscopy results, the carboxyl environments in NOM were categorized as Type I (unsubstituted and alkyl-substituted aliphatic/alicyclic), Type II (functionalized carbon substituted), Type IIIa, b (heteroatom and olefin substituted), and Type IVa, b (5-membered heterocyclic aromatic and 6-membered aromatic). The most intense signal in the HMBC spectra comes from the Type I carboxyl groups, including the 2JCH and 3JCH couplings of unsubstituted aliphatic and alicyclic acids, though this spectral region also includes the 3JCH couplings of Type II and III structures. Type II and III carboxyls have small but detectable 2JCH correlations in all NOM samples except for the Suwannee River humic acid. Signals from carboxyls bonded to 5-membered aromatic heterocyclic fragments (Type IVa) are observed in the soil HA and Suwannee River FA, while correlations to 6-membered aromatics (Type IVb) are only observed in Suwannee River HA. In general, aromatic carboxylic acids may be present at concentrations lower than previously imagined in these samples. Vibrational spectroscopy results for these NOM samples, described in an accompanying paper [Hay M. B. and Myneni S. C. B. (2007) Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy. Geochim. Cosmochim. Acta (in press)], suggest that Type II and Type III carboxylic acids with α substituents (e.g., -OH, -OR, or -CO 2H) constitute the majority of carboxyl structures in all humic substances examined. Furoic and salicylic acid structures (Type IV) are also feasible fragments, albeit as minor constituents. The

  4. Quantitative generalized ratiometric fluorescence spectroscopy for turbid media based on probe encapsulated by biologically localized embedding.

    PubMed

    Yan, Xiu-Fang; Chen, Zeng-Ping; Cui, Yin-Yin; Hu, Yuan-Liang; Yu, Ru-Qin

    2016-05-19

    PEBBLE (probe encapsulated by biologically localized embedding) nanosensor encapsulating an intensity-based fluorescence indicator and an inert reference fluorescence dye inside the pores of stable matrix can be used as a generalized wavelength-ratiometric probe. However, the lack of an efficient quantitative model render the choices of inert reference dyes and intensity-based fluorescence indicators used in PEBBLEs based generalized wavelength-ratiometric probes rather limited. In this contribution, an extended quantitative fluorescence model was derived specifically for generalized wavelength-ratiometric probes based on PEBBLE technique (QFMGRP) with a view to simplify the design of PEBBLEs and hence further extend their application potentials. The effectiveness of QFMGRP has been tested on the quantitative determination of free Ca(2+) in both simulated and real turbid media using a Ca(2+) sensitive PEBBLE nanosensor encapsulating Rhod-2 and eosin B inside the micropores of stable polyacrylamide matrix. Experimental results demonstrated that QFMGRP could realize precise and accurate quantification of free Ca(2+) in turbid samples, even though there is serious overlapping between the fluorescence excitation peaks of eosin B and Ca(2+) bound Rhod-2. The average relative predictive error value of QFMGRP for the test simulated turbid samples was 5.9%, about 2-4 times lower than the corresponding values of partial least squares calibration model and the empirical ratiometric model based on the ratio of fluorescence intensities at the excitation peaks of Ca(2+) bound Rhod-2 and eosin B. The recovery rates of QFMGRP for the real and spiked turbid samples varied from 93.1% to 101%, comparable to the corresponding results of atomic absorption spectrometry. PMID:27126788

  5. High-field EPR spectroscopy applied to biological systems: characterization of molecular switches for electron and ion transfer.

    PubMed

    Möbius, K; Savitsky, A; Schnegg, A; Plato, M; Fuchst, M

    2005-01-01

    -induced electron-transfer intermediates in wild-type and mutant reaction-centre proteins from the photosynthetic bacterium Rhodobacter sphaeroides, (2) light-driven proton-transfer intermediates of site-specifically nitroxide spin-labelled mutants of bacteriorhodopsin proteins from Halobacterium salinarium, (3) refolding intermediates of site-specifically nitroxide spin-labelled mutants of the channel-forming protein domain of Colicin A bacterial toxin produced in Escherichia coli. The detailed information obtained is complementary to that of protein crystallography, solid-state NMR, infrared and optical spectroscopy techniques. A unique strength of high-field EPR is particularly noteworthy: it can provide highly desired detailed information on transient intermediates of proteins in biological action. They can be observed and characterized while staying in their working states on biologically relevant time scales. The review introduces the audience to origins and basic experiments of EPR in relation to NMR, describes the underlying strategies for extending conventional EPR to high-field/high-frequency EPR, and highlights those details of molecular information that are obtained from high-field EPR in conjunction with genetic engineering and that are not accessible by "classical" spectroscopy. The importance of quantum-chemical interpretation of the experimental data by DFT and advanced semiempirical molecular-orbital theory is emphasized. A short description of the laboratory-built 95 GHz and 360 GHz EPR/ENDOR spectrometers at FU Berlin is also presented. The review concludes with an outlook to future opportunities and challenges of advanced bio-EPR in interdisciplinary research. PMID:19785170

  6. Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Hay, Michael B.; Myneni, Satish C. B.

    2007-07-01

    Carboxyls play an important role in the chemistry of natural organic molecules (NOM) in the environment, and their behavior is dependent on local structural environment within the macromolecule. We studied the structural environments of carboxyl groups in dissolved NOM from the Pine Barrens (New Jersey, USA), and IHSS NOM isolates from soils and river waters using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. It is well established that the energies of the asymmetric stretching vibrations of the carboxylate anion (COO -) are sensitive to the structural environment of the carboxyl group. These energies were compiled from previous infrared studies on small organic acids for a wide variety of carboxyl structural environments and compared with the carboxyl spectral features of the NOM samples. We found that the asymmetric stretching peaks for all NOM samples occur within a narrow range centered at 1578 cm -1, suggesting that all NOM samples examined primarily contain very similar carboxyl structures, independent of sample source and isolation techniques employed. The small aliphatic acids containing hydroxyl (e.g., D-lactate, gluconate), ether/ester (methoxyacetate, acetoxyacetate), and carboxylate (malonate) substitutions on the α-carbon, and the aromatic acids salicylate ( ortho-OH) and furancarboxylate ( O-heterocycle), exhibit strong overlap with the NOM range, indicating that similar structures may be common in NOM. The width of the asymmetric peak suggests that the structural heterogeneity among the predominant carboxyl configurations in NOM is small. Changes in peak area with pH at energies distant from the peak at 1578 cm -1, however, may be indicative of a small fraction of other aromatic carboxyls and aliphatic structures lacking α-substitution. This information is important in understanding NOM-metal and mineral-surface complexation, and in building appropriate structural and mechanistic models of humic materials.

  7. Space biology class as part of science education programs for high schools in Japan.

    PubMed

    Kamada, Motoshi; Takaoki, Muneo

    2004-11-01

    Declining incentives and scholastic abilities in science class has been concerned in Japan. The Ministry of Education, Culture, Sports, Science and Technology encourages schools to cooperate with research institutions to raise student's interest in natural sciences. The Science Partnership Program (SPP) and the Super Science High-School (SSH) are among such efforts. Our short SPP course consists of an introductory lecture on space biology in general and a brief laboratory practice on plant gravitropism. Space biology class is popular to students, despite of the absence of flight experiments. We suppose that students are delighted when they find that their own knowledge is not a mere theory, but has very practical applications. Space biology is suitable in science class, since it synthesizes mathematics, physics, chemistry and many other subjects that students might think uninteresting. PMID:15858363

  8. Herpes simplex virus infection: part I--Biology, clinical presentation and latency.

    PubMed

    Yarom, N; Buchner, A; Dayan, D

    2005-01-01

    Oro-facial manifestations of herpes simplex virus (HSV) infections are very common, and include primary herpetic gingivo-stomatitis, recurrent herpes labialis and recurrent intra-oral herpes. Recent research in molecular biology has advanced our knowledge of the HSV pathogenesis and behavior. Understanding the exact mechanism of HSV latency and reactivation enables improvement of drug therapy and prevention strategies of HSV infections. The aim of this review is to update the recent development in the biological and clinical research related to HSV infection, focusing on oral and perioral lesions. PMID:15786655

  9. BIOLOGICAL SIGNIFICANCE OF SOME METALS AS AIR POLLUTANTS. PART II. MERCURY

    EPA Science Inventory

    The study was undertaken in order to elucidate the association between low atmospheric mercury levels and changes in some biological parameters likely to react to such exposures. The study covered four populations believed to be exposed to four different levels of atmospheric mer...

  10. Biology-Chemistry-Physics, Teachers' Guide, a Three-Year Sequence, Parts I and II.

    ERIC Educational Resources Information Center

    Scott, Arthur; And Others

    This is one of two teacher's guides for a three-year integrated biology, chemistry, and physics course being prepared by the Portland Project Committee. This committee reviewed and selected material developed by the national course improvement groups--Physical Science Study Committee, Chemical Bond Approach, Chemical Education Materials Study,…

  11. Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 2: Peptide Identification via Molecular Mass Determination

    ERIC Educational Resources Information Center

    Arnquist, Isaac J.; Beussman, Douglas J.

    2009-01-01

    Mass spectrometry has become a routine analytical tool in the undergraduate curriculum in the form of GC-MS. While relatively few undergraduate programs have incorporated biological mass spectrometry into their programs, the importance of these techniques, as demonstrated by their recognition with the 2002 Nobel Prize, will hopefully lead to…

  12. YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae

    PubMed Central

    Guo, Yakun; Dong, Junkai; Zhou, Tong; Auxillos, Jamie; Li, Tianyi; Zhang, Weimin; Wang, Lihui; Shen, Yue; Luo, Yisha; Zheng, Yijing; Lin, Jiwei; Chen, Guo-Qiang; Wu, Qingyu; Cai, Yizhi; Dai, Junbiao

    2015-01-01

    It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological parts based on the native genes and regulatory elements in Saccharomyces cerevisiae. We have developed highly efficient protocols (termed YeastFab Assembly) to synthesize these genetic elements as standardized biological parts, which can be used to assemble transcriptional units in a single-tube reaction. In addition, standardized characterization assays are developed using reporter constructs to calibrate the function of promoters. Furthermore, the assembled transcription units can be either assayed individually or applied to construct multi-gene metabolic pathways, which targets a genomic locus or a receiving plasmid effectively, through a simple in vitro reaction. Finally, using β-carotene biosynthesis pathway as an example, we demonstrate that our method allows us not only to construct and test a metabolic pathway in several days, but also to optimize the production through combinatorial assembly of a pathway using hundreds of regulatory biological parts. PMID:25956650

  13. Sub-parts-per-billion level detection of dimethyl methyl phosphonate (DMMP) by quantum cascade laser photoacoustic spectroscopy.

    PubMed

    Mukherjee, Anadi; Dunayevskiy, Ilya; Prasanna, Manu; Go, Rowel; Tsekoun, Alexei; Wang, Xiaojun; Fan, Jenyu; Patel, C Kumar N

    2008-04-01

    The need for the detection of chemical warfare agents (CWAs) is no longer confined to battlefield environments because of at least one confirmed terrorist attack, the Tokyo Subway [Emerg. Infect. Dis. 5, 513 (1999)] in 1995, and a suspected, i.e., a false-alarm of a CWA in the Russell Senate Office Building [Washington Post, 9 February 2006, p. B01]. Therefore, detection of CWAs with high sensitivity and low false-alarm rates is considered an important priority for ensuring public safety. We report a minimum detection level for a CWA simulant, dimethyl methyl phosphonate (DMMP), of <0.5 ppb (parts in 10(9)) by use of a widely tunable external grating cavity quantum cascade laser and photoacoustic spectroscopy. With interferents present in Santa Monica, California street air, we demonstrate a false-alarm rate of 1:10(6) at a detection threshold of 1.6 ppb. PMID:18382583

  14. Sensitivity of coded aperture Raman spectroscopy to analytes beneath turbid biological tissue and tissue-simulating phantoms

    PubMed Central

    Maher, Jason R.; Matthews, Thomas E.; Reid, Ashley K.; Katz, David F.; Wax, Adam

    2014-01-01

    Abstract. Traditional slit-based spectrometers have an inherent trade-off between spectral resolution and throughput that can limit their performance when measuring diffuse sources such as light returned from highly scattering biological tissue. Recently, multielement fiber bundles have been used to effectively measure diffuse sources, e.g., in the field of spatially offset Raman spectroscopy, by remapping the source (or some region of the source) into a slit shape for delivery to the spectrometer. Another approach is to change the nature of the instrument by using a coded entrance aperture, which can increase throughput without sacrificing spectral resolution. In this study, two spectrometers, one with a slit-based entrance aperture and the other with a coded aperture, were used to measure Raman spectra of an analyte as a function of the optical properties of an overlying scattering medium. Power-law fits reveal that the analyte signal is approximately proportional to the number of transport mean free paths of the scattering medium raised to a power of −0.47 (coded aperture instrument) or −1.09 (slit-based instrument). These results demonstrate that the attenuation in signal intensity is more pronounced for the slit-based instrument and highlight the scattering regimes where coded aperture instruments can provide an advantage over traditional slit-based spectrometers. PMID:25371979

  15. Identification of antibody isotypes in biological fluids by means of micro-Raman spectroscopy and chemometric methods

    NASA Astrophysics Data System (ADS)

    Araujo-Andrade, C.; Pichardo-Molina, J. L.; Barbosa-Sabanero, G.; Frausto-Reyes, C.

    2008-02-01

    Clinical diagnosis of infections, generally are realized by serological methods, which identifies the antibodies presents in serum or tissue fluids of the patient. Antibodies are proteins present in our bodies that aid in the elimination of pathogens or antigens. Identification of antibodies isotypes is important because can help to predict when and whether patients will recover from infections and are commonly diagnosed by means of indirect methods such as serological test. In the other hand, the majority of these methods requires specific kits for the analysis, special sample preparation, chemical reagents, expensive equipment and require long time for getting results. In this work we show the feasibility to discriminate antibody isotypes in biological fluids like human colostrum by means of Raman spectroscopy and chemometrics. Spectra were obtained using an excitation wavelength of 514 nm over dried samples of human colostrum labeled previously as positives to specific IgG and IgM antibodies against Toxoplasma Gondii by means of ELISA test. Partial least square-discriminant analysis (PLS-DA) was used to discriminate among antibody isotypes by use second derivative of Raman spectra of colostrum samples.

  16. Interaction of Iron II Complexes with B-DNA. Insights from Molecular Modeling, Spectroscopy, and Cellular Biology.

    PubMed

    Gattuso, Hugo; Duchanois, Thibaut; Besancenot, Vanessa; Barbieux, Claire; Assfeld, Xavier; Becuwe, Philippe; Gros, Philippe C; Grandemange, Stephanie; Monari, Antonio

    2015-01-01

    We report the characterization of the interaction between B-DNA and three terpyridin iron II complexes. Relatively long time-scale molecular dynamics (MD) is used in order to characterize the stable interaction modes. By means of molecular modeling and UV-vis spectroscopy, we prove that they may lead to stable interactions with the DNA duplex. Furthermore, the presence of larger π-conjugated moieties also leads to the appearance of intercalation binding mode. Non-covalent stabilizing interactions between the iron complexes and the DNA are also characterized and evidenced by the analysis of the gradient of the electronic density. Finally, the structural deformations induced on the DNA in the different binding modes are also evidenced. The synthesis and chemical characterization of the three complexes is reported, as well as their absorption spectra in presence of DNA duplexes to prove the interaction with DNA. Finally, their effects on human cell cultures have also been evidenced to further enlighten their biological effects. PMID:26734600

  17. Interaction of Iron II Complexes with B-DNA. Insights from Molecular Modeling, Spectroscopy, and Cellular Biology

    PubMed Central

    Gattuso, Hugo; Duchanois, Thibaut; Besancenot, Vanessa; Barbieux, Claire; Assfeld, Xavier; Becuwe, Philippe; Gros, Philippe C.; Grandemange, Stephanie; Monari, Antonio

    2015-01-01

    We report the characterization of the interaction between B-DNA and three terpyridin iron II complexes. Relatively long time-scale molecular dynamics (MD) is used in order to characterize the stable interaction modes. By means of molecular modeling and UV-vis spectroscopy, we prove that they may lead to stable interactions with the DNA duplex. Furthermore, the presence of larger π-conjugated moieties also leads to the appearance of intercalation binding mode. Non-covalent stabilizing interactions between the iron complexes and the DNA are also characterized and evidenced by the analysis of the gradient of the electronic density. Finally, the structural deformations induced on the DNA in the different binding modes are also evidenced. The synthesis and chemical characterization of the three complexes is reported, as well as their absorption spectra in presence of DNA duplexes to prove the interaction with DNA. Finally, their effects on human cell cultures have also been evidenced to further enlighten their biological effects. PMID:26734600

  18. Evaluation of a multi-electrode bioimpedance spectroscopy tensor probe to detect the anisotropic conductivity spectra of biological tissues

    NASA Astrophysics Data System (ADS)

    Karki, Bishal; Wi, Hun; McEwan, Alistair; Kwon, Hyeuknam; In Oh, Tong; Woo, Eung Je; Seo, Jin Keun

    2014-07-01

    This paper presents bioimpedance spectroscopy measurements of anisotropic tissues using a 16 electrode probe and reconstruction method of estimating the anisotropic impedance spectrum in a local region just underneath the center of the probe. This may enable in-vivo surface bioimpedance measurements with similar performance to the ex-vivo gold standard that requires excising and placing the entire tissue sample in a unit measurement cell with uniform electric field. The multiple surface electrodes enable us to create a focused current pattern so that the resulting measured voltage is more sensitive to a local region and less sensitive to other areas. This is exploited in a reconstruction method to provide improved bioimpedance and anisotropy measurements. In this paper, we describe the current pattern for localized electrical energy concentration, performance with the spring loaded pin electrodes, data calibration and experimental results on anisotropic agar phantoms and different tissue types. The anisotropic conductivity spectra are able to differentiate insulating films of different thickness and detect their orientation. Bioimpedance spectra of biological tissues are in agreement with published data and reference instruments. The anisotropy expressed as the ratio of eigenvalues and the orientation of eigenfunctions were reconstructed at 45° intervals. This information is used to predict the underlying anisotropy of the region under the probe. Tissue measurements clearly demonstrate the expected higher anisotropy of muscle tissue compared to liver tissue and spectral changes.

  19. From microbiology to cell biology: when an intracellular bacterium becomes part of its host cell.

    PubMed

    McCutcheon, John P

    2016-08-01

    Mitochondria and chloroplasts are now called organelles, but they used to be bacteria. As they transitioned from endosymbionts to organelles, they became more and more integrated into the biochemistry and cell biology of their hosts. Work over the last 15 years has shown that other symbioses show striking similarities to mitochondria and chloroplasts. In particular, many sap-feeding insects house intracellular bacteria that have genomes that overlap mitochondria and chloroplasts in terms of size and coding capacity. The massive levels of gene loss in some of these bacteria suggest that they, too, are becoming highly integrated with their host cells. Understanding these bacteria will require inspiration from eukaryotic cell biology, because a traditional microbiological framework is insufficient for understanding how they work. PMID:27267617

  20. [Contemporary place of the electroconvulsive therapy Part 1. The historical context arnd the biological basis].

    PubMed

    Zyss, Tomasz; Datka, Wojciech; Rachel, Wojciech; Hese, Robert T; Gorczyca, Piotr; Zięba, Andrzej; Szwajca, Krzysztof; Piekoszewskl, Wojciech

    2014-01-01

    Electroconvulsive therapy (ECT) is a former physical therapy method in psychiatry which is applicable up till today in relation to its high effectiveness and the safety. Centuries of applying nonconvulsive methods of the electric stimulation preceded introducing this method into the clinical practice. ECT is arousing a lot of controversies; populous myths are connected with its applying--that demands explanations. Numerous biological mechanisms explaining the clinical efficacy of ECT action are well-known. PMID:25951704

  1. Bibliographical database of radiation biological dosimetry and risk assessment: Part 1, through June 1988

    SciTech Connect

    Straume, T.; Ricker, Y.; Thut, M.

    1988-08-29

    This database was constructed to support research in radiation biological dosimetry and risk assessment. Relevant publications were identified through detailed searches of national and international electronic databases and through our personal knowledge of the subject. Publications were numbered and key worded, and referenced in an electronic data-retrieval system that permits quick access through computerized searches on publication number, authors, key words, title, year, and journal name. Photocopies of all publications contained in the database are maintained in a file that is numerically arranged by citation number. This report of the database is provided as a useful reference and overview. It should be emphasized that the database will grow as new citations are added to it. With that in mind, we arranged this report in order of ascending citation number so that follow-up reports will simply extend this document. The database cite 1212 publications. Publications are from 119 different scientific journals, 27 of these journals are cited at least 5 times. It also contains reference to 42 books and published symposia, and 129 reports. Information relevant to radiation biological dosimetry and risk assessment is widely distributed among the scientific literature, although a few journals clearly dominate. The four journals publishing the largest number of relevant papers are Health Physics, Mutation Research, Radiation Research, and International Journal of Radiation Biology. Publications in Health Physics make up almost 10% of the current database.

  2. Geometric adaption of biodegradable magnesium alloy scaffolds to stabilise biological myocardial grafts. Part I.

    PubMed

    Bauer, M; Schilling, T; Weidling, M; Hartung, D; Biskup, Ch; Wriggers, P; Wacker, F; Bach, Fr-W; Haverich, A; Hassel, T

    2014-03-01

    Synthetic patch materials currently in use have major limitations, such as high susceptibility to infections and lack of contractility. Biological grafts are a novel approach to overcome these limitations, but do not always offer sufficient mechanical durability in early stages after implantation. Therefore, a stabilising structure based on resorbable magnesium alloys could support the biological graft until its physiologic remodelling. To prevent early breakage in vivo due to stress of non-determined forming, these scaffolds should be preformed according to the geometry of the targeted myocardial region. Thus, the left ventricular geometry of 28 patients was assessed via standard cardiac magnetic resonance imaging (MRI). The resulting data served as a basis for a finite element simulation (FEM). Calculated stresses and strains of flat and preformed scaffolds were evaluated. Afterwards, the structures were manufactured by abrasive waterjet cutting and preformed according to the MRI data. Finally, the mechanical durability of the preformed and flat structures was compared in an in vitro test rig. The FEM predicted higher durability of the preformed scaffolds, which was proven in the in vitro test. In conclusion, preformed scaffolds provide extended durability and will facilitate more widespread use of regenerative biological grafts for surgical left ventricular reconstruction. PMID:24264726

  3. Final report on LDRD project: Semiconductor surface-emitting microcavity laser spectroscopy for analysis of biological cells and microstructures

    SciTech Connect

    Gourley, P.L.; McDonald, A.E.; Gourley, M.F.; Bellum, J.

    1997-08-01

    This article discusses a new intracavity laser technique that uses living or fixed cells as an integral part of the laser. The cells are placed on a GaAs based semiconductor wafer comprising one half of a vertical cavity surface-emitting laser. After placement, the cells are covered with a dielectric mirror to close the laser cavity. When photo-pumped with an external laser, this hybrid laser emits coherent light images and spectra that depend sensitively on the cell size, shape, and dielectric properties. The light spectra can be used to identify different cell types and distinguish normal and abnormal cells. The laser can be used to study single cells in real time as a cell-biology lab-on-a-chip, or to study large populations of cells by scanning the pump laser at high speed. The laser is well-suited to be integrated with other micro-optical or micro-fluidic components to lead to micro-optical-mechanical systems for analysis of fluids, particulates, and biological cells.

  4. Unique nucleotide sequence (UNS)-guided assembly of repetitive DNA parts for synthetic biology applications

    PubMed Central

    Torella, Joseph P.; Lienert, Florian; Boehm, Christian R.; Chen, Jan-Hung; Way, Jeffrey C.; Silver, Pamela A.

    2016-01-01

    Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts and hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies — for example repeated terminator and insulator sequences — that complicate recombination-based assembly. We and others have recently developed DNA assembly methods that we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly-assembled constructs, or into high-quality combinatorial libraries in only 2–3 days. If the DNA parts must be generated from scratch, an additional 2–5 days are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques. PMID:25101822

  5. Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications

    SciTech Connect

    Torella, JP; Lienert, F; Boehm, CR; Chen, JH; Way, JC; Silver, PA

    2014-08-07

    Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies-for example, repeated terminator and insulator sequences-that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.

  6. Endobiogeny: A Global Approach to Systems Biology (Part 2 of 2)

    PubMed Central

    Lapraz, Jean-Claude; Pauly, Patrice

    2013-01-01

    Endobiogeny and the biology of functions are based on four scientific concepts that are known and generally accepted: (1) human physiology is complex and multifactorial and exhibits the properties of a system; (2) the endocrine system manages metabolism, which is the basis of the continuity of life; (3) the metabolic activity managed by the endocrine system results in the output of biomarkers that reflect the functional achievement of specific aspects of metabolism; and (4) when biomarkers are related to each other in ratios, it contextualizes one type of function relative to another to which is it linked anatomically, sequentially, chronologically, biochemically, etc. PMID:24416662

  7. Endobiogeny: A Global Approach to Systems Biology (Part 1 of 2)

    PubMed Central

    Lapraz, Jean-Claude

    2013-01-01

    Endobiogeny is a global systems approach to human biology that may offer an advancement in clinical medicine based in scientific principles of rigor and experimentation and the humanistic principles of individualization of care and alleviation of suffering with minimization of harm. Endobiogeny is neither a movement away from modern science nor an uncritical embracing of pre-rational methods of inquiry but a synthesis of quantitative and qualitative relationships reflected in a systems-approach to life and based on new mathematical paradigms of pattern recognition. PMID:24381827

  8. Endobiogeny: a global approach to systems biology (part 1 of 2).

    PubMed

    Lapraz, Jean-Claude; Hedayat, Kamyar M

    2013-01-01

    Endobiogeny is a global systems approach to human biology that may offer an advancement in clinical medicine based in scientific principles of rigor and experimentation and the humanistic principles of individualization of care and alleviation of suffering with minimization of harm. Endobiogeny is neither a movement away from modern science nor an uncritical embracing of pre-rational methods of inquiry but a synthesis of quantitative and qualitative relationships reflected in a systems-approach to life and based on new mathematical paradigms of pattern recognition. PMID:24381827

  9. Surface functionalization of bioactive glasses with natural molecules of biological significance, part II: Grafting of polyphenols extracted from grape skin

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

    2013-12-01

    Polyphenols, as one of the most important family of phytochemicals protective substances from grape fruit, possess various biological activities and health-promoting benefits, for example: inhibition of some degenerative diseases, cardiovascular diseases and certain types of cancers, reduction of plasma oxidative stress and slowing aging. The combination of polyphenols and biomaterials may have good potential to reach good bioavailability and controlled release, as well as to give biological signaling properties to the biomaterial surfaces. In this research, conventional solvent extraction was developed for obtaining polyphenols from dry grape skins. The Folin&Ciocalteu method was used to determine the amount of total polyphenols in the extracts. Surface functionalization of two bioactive glasses (SCNA and CEL2) was performed by grafting the extracted polyphenols on their surfaces. The effectiveness of the functionalization was tested by UV spectroscopy, which analyzes the amount of polyphenols in the uptake solution (before and after functionalization) and on solid samples, and XPS, which analyzes the presence of phenols on the material surface.

  10. On the effect of experimental noise on the classification of biological samples using Raman micro-spectroscopy

    NASA Astrophysics Data System (ADS)

    Barton, Sinead J.; Kerr, Laura T.; Domijan, Katarina; Hennelly, Bryan M.

    2016-04-01

    Raman micro-spectroscopy is an optoelectronic technique that can be used to evaluate the chemical composition of biological samples and has been shown to be a powerful diagnostic tool for the investigation of various cancer related diseases including bladder, breast, and cervical cancer. Raman scattering is an inherently weak process with approximately 1 in 107 photons undergoing scattering and for this reason, noise from the recording system can have a significant impact on the quality of the signal, and its suitability for diagnostic classification. The main sources of noise in the recorded signal are shot noise, CCD dark current, and CCD readout noise. Shot noise results from the low signal photon count while dark current results from thermally generated electrons in the semiconductor pixels. Both of these noise sources are time dependent; readout noise is time independent but is inherent in each individual recording and results in the fundamental limit of measurement, arising from the internal electronics of the camera. In this paper, each of the aforementioned noise sources are analysed in isolation, and used to experimentally validate a mathematical model. This model is then used to simulate spectra that might be acquired under various experimental conditions including the use of different cameras, different source wavelength, and power etc. Simulated noisy datasets of T24 and RT112 cell line spectra are generated based on true cell Raman spectrum irradiance values (recorded using very long exposure times) and the addition of simulated noise. These datasets are then input to multivariate classification using Principal Components Analysis and Linear Discriminant Analysis. This method enables an investigation into the effect of noise on the sensitivity and specificity of Raman based classification under various experimental conditions and using different equipment.

  11. Analysis of poly-β-hydroxyalkonates (PHA) during the enhanced biological phosphorus removal process using FTIR spectroscopy.

    PubMed

    Li, Wei-hua; Mao, Qin-yan; Liu, Yi-xin; Sheng, Guo-ping; Yu, Han-qing; Huang, Xian-huai; Liu, Shao-geng; Ling, Qi; Yan, Guo-bing

    2014-06-01

    Enhanced biological phosphorus removal (EBPR) is the main phosphorus removal technique for wastewater treatment. During the anaerobic-aerobic alternative process, the activated sludge experienced the anaerobic storage of polyhydroxy-β-alkonates (PHA) and aerobic degradation, corresponding the infrared peak intensity of sludge at 1 740 cm(-1) increased in the aerobic phase and declined in the anaerobic phase. Compared with PHA standard, this peak was indentified to attribute the carbonyl of PHA. The overlapping peaks of PHA, protein I and II bands were separated using Gaussian peak fitting method. The infrared peak area ratios of PHA versus protein I had a good relationship with the PHA contents measured by gas chromatography, and the correlation coefficient was 0.873. Thus, the ratio of the peak area of PHA versus protein I can be considered as the indicator of the PHA content in the sludge. The infrared spectra of 1 480-1 780 cm(-1) was selected, normalized and transferred to the absorption data. Combined with the chromatography analysis of PHA content in the sludge sample, a model between the Fourier-transform infrared spectroscopy (ETIR) spectra of the sludge and PHA content was established, which could be used for the prediction of the PHA content in the unknown sample. The PHA content in the sludge sample could be acquired by the infrared spectra of the sludge sample and the established model, and the values fitted well with the results obtained from chromatograph. The results would provide a novel analysis method for the rapid characterization and quantitative determination of the intracellular PHA content in the activated sludge. PMID:25358156

  12. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps.

    PubMed

    Greenbury, S F; Ahnert, S E

    2015-12-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype-phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into 'constrained' and 'unconstrained' sequences, in the broadest possible sense. As 'constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. 'Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with 'coding' and 'non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps. PMID:26609063

  13. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

    PubMed Central

    Greenbury, S. F.; Ahnert, S. E.

    2015-01-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained' and ‘unconstrained' sequences, in the broadest possible sense. As ‘constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding' and ‘non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps. PMID:26609063

  14. A steady-state model for aerobic biological treatment: Part 1

    SciTech Connect

    McHarg, W.H. )

    1993-12-01

    In the aerobic biological treatment of wastewater, microorganisms use oxygen to decompose organic contaminants. Carbon dioxide, water and biosolids -- or sludge -- are the primary products. After a predetermined time in the reactor or aeration basin, the sludge is either removed from the process or sent to a clarifier, where it settles. Some of this sludge is recycled back to the aeration basin to initiate further oxidation, and some is removed from the process. In many aerobic processes, the average retention time of the sludge in the aeration basin -- called the sludge age -- is the main design parameter. However, other parameters, such as the rate of oxygen transfer rates and the capacity of the clarifier can affect the quality of the effluent. A simple mathematical model can be used to calculate these parameters.

  15. Impact of Two Ant Species on Egg Parasitoids Released as Part of a Biological Control Program

    PubMed Central

    Kergunteuil, Alan; Basso, César; Pintureau, Bernard

    2013-01-01

    Biological control using Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae), an egg parasitoid wasp, was tested in Uruguay to reduce populations of lepidopteran pests on soybeans. It was observed that the commercial parasitoid dispensers, which were made of cardboard, were vulnerable to small predators that succeeded in entering and emptying the containers of all the eggs parasitized by T. pretiosum. Observations in a soybean crop showed that the only small, common predators present were two ant species. The species responsible for the above mentioned predation was determined from the results of a laboratory experiment in which the behavior of the two common ants was tested. A modification of the dispensers to prevent introduction of this ant has been proposed and successfully tested in the laboratory and in the field. PMID:24738954

  16. Study of cardiovascular disease biomarkers among tobacco consumers, part 2: biomarkers of biological effect

    PubMed Central

    Nordskog, Brian K.; Brown, Buddy G.; Marano, Kristin M.; Campell, Leanne R.; Jones, Bobbette A.; Borgerding, Michael F.

    2015-01-01

    Abstract An age-stratified, cross-sectional study was conducted in the US among healthy adult male cigarette smokers, moist snuff consumers, and non-tobacco consumers to evaluate cardiovascular biomarkers of biological effect (BoBE). Physiological assessments included flow-mediated dilation, ankle-brachial index, carotid intima-media thickness and expired carbon monoxide. Approximately one-half of the measured serum BoBE showed statistically significant differences; IL-12(p70), sICAM-1 and IL-8 were the BoBE that best differentiated among the three groups. A significant difference in ABI was observed between the cigarette smokers and non-tobacco consumer groups. Significant group and age effect differences in select biomarkers were identified. PMID:25787701

  17. Study of cardiovascular disease biomarkers among tobacco consumers, part 2: biomarkers of biological effect.

    PubMed

    Nordskog, Brian K; Brown, Buddy G; Marano, Kristin M; Campell, Leanne R; Jones, Bobbette A; Borgerding, Michael F

    2015-02-01

    An age-stratified, cross-sectional study was conducted in the US among healthy adult male cigarette smokers, moist snuff consumers, and non-tobacco consumers to evaluate cardiovascular biomarkers of biological effect (BoBE). Physiological assessments included flow-mediated dilation, ankle-brachial index, carotid intima-media thickness and expired carbon monoxide. Approximately one-half of the measured serum BoBE showed statistically significant differences; IL-12(p70), sICAM-1 and IL-8 were the BoBE that best differentiated among the three groups. A significant difference in ABI was observed between the cigarette smokers and non-tobacco consumer groups. Significant group and age effect differences in select biomarkers were identified. PMID:25787701

  18. Biological methods for archiving and maintaining mutant laboratory mice. Part I: conserving mutant strains.

    PubMed

    Fray, Martin D

    2009-01-01

    The mouse is now firmly established as the model organism of choice for scientists studying mammalian biology and human disease. Consequently, a plethora of novel, genetically altered (GA) mouse lines have been created. In addition, the output from the large scale mutagenesis programmes currently under way around the world will increase the collection of GA mouse strains still further. Because of the implications for animal welfare and the constraints on resources, it would be unreasonable to expect anything other than those strains essential for ongoing research programmes to be maintained as breeding colonies. Unfortunately, unless the redundant strains are preserved using robust procedures, which guarantee their recovery, they will be lost to future generations of researchers.This chapter describes some of the preservation methods currently used in laboratories around the world to archive novel mouse strains. PMID:19504080

  19. The BioCAT undulator beamline 18ID: A facility for biological non-crystalline diffraction and x-ray absorption spectroscopy at the APS

    SciTech Connect

    Fischetti, R.; Stepanov, S.; Rosenbaum, G.; Barrea, R.; Black, E.; Gore, D.; Heurich, R.; Kondrashkina, E.; Kropf, A.J.; Wang, S.; Zhang, K.; Irving, T.C.; Bunker, G.B.

    2008-07-02

    The 18ID undulator beamline of the Biophysics Collaborative Access Team at the Advanced Photon Source, Argonne, IL, USA, is a high-performance instrument designed for, and dedicated to, the study of partially ordered and disordered biological materials using the techniques of small-angle X-ray scattering, fiber diffraction, and X-ray absorption spectroscopy. The beamline and associated instrumentation are described in detail and examples of the representative experimental results are presented.

  20. Raman Spectroscopy.

    ERIC Educational Resources Information Center

    Gerrard, Donald L.

    1984-01-01

    Reviews literature on Raman spectroscopy from late 1981 to late 1983. Topic areas include: instrumentation and sampling; liquids and solutions; gases and matrix isolation; biological molecules; polymers; high-temperature and high-pressure studies; Raman microscopy; thin films and surfaces; resonance-enhanced and surface-enhanced spectroscopy; and…

  1. Observations on the biology of Afrotropical Hesperiidae (Lepidoptera). Part 6. Hesperiinae incertae sedis: palm feeders.

    PubMed

    Cock, Matthew J W; Congdon, T Colin E; Collins, Steve C

    2014-01-01

    Partial life histories for 12 Hesperiinae incertae sedis that feed on palms (Arecaceae) are described and illustrated. The genera dealt with are: Perrotia (part), Ploetzia, Zophopetes, Gretna (part), Pteroteinon, Leona, and Caenides (part) (all from Evans' Ploetzia genera group). Although Gamia spp. have been reported to feed on palms, these records are considered to be in error, as caterpillars of this genus feed on Dracaena spp. (Asparagaceae). The life histories of the species documented are fairly uniform, in that caterpillars of most species have rounded brown heads, wider basally, with or without limited black markings, smooth bodies and make simple shelters by rolling leaves. Variation in caterpillar markings and male genitalia of Zophopetes dysmephila (Trimen) and caterpillar and adult markings of Gretna carmen Evans merit further study. In G. carmen, G. waga (Plötz) and G. balenge (Holland), the caterpillars' head and body are covered with hair-like setae, and develop an extensive covering of white waxy powder, which in G. balenge also covers the long setae. Furthermore, the pupa of G. balenge is unusual in having a pair of large, elaborate processes frontally on the head; when disturbed, the pupa vibrates violently and rattles noisily against the sides of the shelter. Ploetzia amygdalis (Mabille) and Pteroteinon laufella (Hewitson) have gregarious caterpillars, whereas the remaining species are solitary. After eclosion, the first instar caterpillars of Gretna spp. moult to the second instar without feeding. The implications of a palm-feeding life-style are discussed, and economic damage and plant quarantine risks to coconut, oil palm and ornamental palms pointed out. The known life histories suggest that all Afrotropical palm-feeding Hesperiidae will belong in the same tribe when the incertae sedis section is further elucidated, although the affinities of Gretna deserve further consideration.  PMID:25081274

  2. Water Complexes Take Part in Biological Effect Created by Weak Combined Magnetic Field

    NASA Astrophysics Data System (ADS)

    Sheykina, Nadiia

    2016-07-01

    It was revealed experimentally that at small level of magnetic field's noise (less than 4µT/Hz0.5) the dependence of gravitropc reaction of cress roots on frequency had a fine structure/ The peak that corresponded to the cyclotron frequency of Ca2+ ions for the static component of combined magnetic field that was equal to 40µT became split up into three peaks ( f1 = 31/3Hz, f2 = 32.5Hz i f3 = 34 Hz./ . The frequency f1 corresponded to the Ca2+ ion (theoretical value 31.6 Hz), the frequency f2 corresponded to the hydronium ion H3O+ (theoretical value 32.9 Hz), the frequency f3 corresponded to OH- ion (theoretical value 35 Hz). Taking into account the influence of combined magnetic field on hydronium ions and Del Giudice' hypothesis one may throw away doubts about the possibility of ion cyclotron resonance. The hydronium ions are unusual because they have a long free path length. It was revealed that pH of the distillated water changed under the treatment in combined magnetic field tuned to cyclotron frequency of hydronium ion. Such changes in pH had to lead to the biological effects on the molecular ,cell and organism levels.

  3. Fixed-wing MAV attitude stability in atmospheric turbulence-Part 2: Investigating biologically-inspired sensors

    NASA Astrophysics Data System (ADS)

    Mohamed, A.; Watkins, S.; Clothier, R.; Abdulrahim, M.; Massey, K.; Sabatini, R.

    2014-11-01

    Challenges associated with flight control of agile fixed-wing Micro Air Vehicles (MAVs) operating in complex environments is significantly different to any larger scale vehicle. The micro-scale of MAVs can make them particularly sensitive to atmospheric disturbances thus limiting their operation. As described in Part 1, current conventional reactive attitude sensing systems lack the necessary response times for attitude control in high turbulence environments. This paper reviews in greater detail novel and emerging biologically inspired sensors, which can sense the disturbances before a perturbation is induced. A number of biological mechanoreceptors used by flying animals are explored for their utility in MAVs. Man-made attempts of replicating mechanoreceptors have thus been reviewed. Bio-inspired flow and pressure-based sensors were found to be the most promising for complementing or replacing current inertial-based reactive attitude sensors. Achieving practical implementations that meet the size, weight and power constraints of MAVs remains a significant challenge. Biological systems were found to rely on multiple sensors, potentially implying a number of research opportunities in the exploration of heterogeneous bio-inspired sensing solutions.

  4. Concentration and temperature measurements in a laser-induced high explosive ignition zone. Part 1: LIF spectroscopy measurements

    SciTech Connect

    Oestmark, H.; Carlson, M.; Ekvall, E.

    1996-05-01

    This paper describes a method that combines a laser ignition technique with laser-induced fluorescence (LIF) spectroscopy for studying the gas-phase products in a laser-induced subignition zone and the reactions that lead to a self-sustained ignition. The experiment comprises a tunable 180 W CO{sub 2}-laser as ignition source, an excimer pumped dye-laser for inducing the fluorescence, and a spectrometer equipped with an optical multichannel analyzer. This technique was used for measurements of relative NO and CN concentrations in the subignition zone of RDX (1,3,5-Trinitrohexahydro-s-triazine) in pseudo-real time (time resolution better than 1 {micro}s). By using LIF technique for measuring the relative population of different vibrational levels, the authors were able to calculate the vibrational temperature in the gas phase reaction zone in front of the sample at subignition to approximately 3,100 K. The measurements show clearly that the chemical reactions and the diffusion in the subignition zone play an important part long before a self-sustained reaction occurs, and thus influence the sensitivity of an explosive. By using LIF imaging technique, two-dimensional images of the NO concentration were registered at different times in the ignition pulse, and the wavelength dependence of the ignition source was also studied. The results correspond to a model for fast radiative ignition where Lambert-Beer absorption is the main energy interaction mechanism between the energetic material and the laser beam.

  5. Development and evaluation of a pliable biological valved conduit. Part II: Functional and hemodynamic evaluation.

    PubMed

    Sung, H W; Witzel, T H; Hata, C; Tu, R; Shen, S H; Lin, D; Noishiki, Y; Tomizawa, Y; Quijano, R C

    1993-04-01

    Many congenital cardiac malformations may require a valved conduit for the reconstruction of the right ventricular outflow tract. In spite of many endeavors made in the last 25 years, the clinical results of right ventricular outflow tract reconstruction with currently available valved conduits are still not satisfactory. Specific problems encountered clinically include suboptimal hemodynamic performance, conduit kinking or compression, and fibrous peeling from the luminal surface. To address these deficiencies, we undertook the development of a biological valved conduit: a bovine external jugular vein graft with a retained native valve cross-linked with a diglycidyl ether (DE). This study, using a canine model, was to evaluate the functional and hemodynamic performance of this newly developed valved conduit. Three 14 mm conduits, implanted as bypass grafts, right ventricle to pulmonary artery, were evaluated. The evaluation was conducted with a noninvasive color Doppler flow mapping system at pre-implantation, immediately post implantation, one- and three-months post implantation, and prior to retrieval (five-months post implantation). The two-dimensional tomographic inspection of the leaflet motion at various periods post implantation showed that the valvular leaflets in the DE treated conduit was quite pliable. No cardiac failure or valvular dysfunction was observed in any of the studied cases. The color Doppler flow mapping study demonstrated that the valve in the DE treated conduit was competent, with no conduit kinking or compression observed in any of the three cases. The spectral Doppler velocity study evidenced that the transvalvular pressure gradients of the DE treated conduit were minimal as compared to those of the currently available conduits. In conclusion, from the functional and hemodynamic performance points of view, this newly developed valved conduit is superior to those currently available. PMID:8325697

  6. Surface analysis of commercially pure titanium implant retrieved from rat bone. Part 1: initial biological response of sandblasted surface.

    PubMed

    Watanabe, Kouichi; Okawa, Seigo; Kanatani, Mitugu; Homma, Kikuo

    2009-03-01

    To gain insight on the early biological response to commercial pure titanium (cpTi), the surface properties of cpTi implants retrieved from rat bone were examined by X-ray photoelectron spectroscopy (XPS). To this end, semi-cylindrical bullets, 1.1 mm in diameter and 3.5 mm in length, were implanted into the femurs of Wistar rats and then retrieved after either 3 hours or 7 days. Regardless of implantation interval, elements of Ti, O, C, and N were observed on the retrieved implants and that the thickness of the adsorbed film (mainly protein) was estimated to be about 2.5 nm. Small amounts of both Ca and P were also detected, whereby the Ca/P atomic ratios after 3 hours and 7 days were very small compared to that of hydroxyapatite. Furthermore, no correlation was found between the Ca and P distributions in the element maps. In conclusion, no calcium phosphate compounds were formed on the implant in vivo after 7 days. PMID:19496397

  7. ATR-FTIR Spectroscopy in the Undergraduate Chemistry Laboratory: Part II--A Physical Chemistry Laboratory Experiment on Surface Adsorption

    ERIC Educational Resources Information Center

    Schuttlefield, Jennifer D.; Larsen, Sarah C.; Grassian, Vicki H.

    2008-01-01

    Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy is a useful technique for measuring the infrared spectra of solids and liquids as well as probing adsorption on particle surfaces. The use of FTIR-ATR spectroscopy in organic and inorganic chemistry laboratory courses as well as in undergraduate research was presented…

  8. Biological materials: (Part A): Temperature-responsive polymers and drug delivery, and, (Part B): Polymer modification of fish scale and their nano-mechanical properties

    NASA Astrophysics Data System (ADS)

    Xiang, Xu

    This research has three parts. Two parts deal with novel nanoparticle assemblies for drug delivery, and are described in Part A, while the third part looks at properties of fish scales, an abundant and little-used waste resource, that can be modified to have value in medical and other areas. Part A describes fundamental research into the affects of block sequence of amphiphilic block copolymers prepared from on a new and versatile class of monomers, oligo(ethylene glycol) methyl ether acrylate (OEGA) and the more hydrophobic di(ethylene glycol) methyl ether methacrylate (DEGMA). Polymers from these monomers are biologically safe and give polymers with thermoresponsive properties that can be manipulated over a broader temperature range than the more researched N-isopropylacrylamide polymers. Using RAFT polymerization and different Chain Transfer Agents (CTAs) amphiphilic block copolymers were prepared to study the effect of block sequence (hydrophilic OEGA and more hydrophobic DEGMA) on their thermo-responsive properties. Pairing hydrophilic chain ends to a hydrophobic DEGMA block and hydrophobic chain ends to hydrophilic blocks ("mis-matched polarity") significantly affected thermoresponsive properties for linear and star diblock copolymers, but little affected symmetric triblock copolymers. Specifically matching polarity in diblock copolymers yielded nanoparticles with higher cloud points (CP), narrow temperature ranges for coil collapse above CP, and smaller hydrodynamic diameter than mis-matched polarity. Using this knowledge two linear OEGA/DEGMA diblock copolymers were prepared with thiol end groups and assembled into hybrid nanoparticles with a gold nanoparticle core (GNP-polymer hybrids). This design was made using the hypothesis that a hybrid polymer drug carrier with a high CP (50-60 °C) and a diblock structure could be designed with low levels of drug release below 37 °C (body temperature) allowing the drug carrier to reach a target (tumor) site with

  9. Characterizing the Biological and Geochemical Architecture of Hydrothermally Derived Sedimentary Deposits: Coupling Micro Raman Spectroscopy with Noble Gas Spectrometry

    NASA Astrophysics Data System (ADS)

    Bower, D. M.; Conrad, P. G.; Steele, A.; Fries, M. D.

    2016-05-01

    The chemical species in cherts and glass fragments were analyzed using micro Raman spectroscopy in conjunction with measurements of heavy noble gas isotopes to characterize hydrothermally derived sedimentary environments.

  10. Gaseous VOCs rapidly modify particulate matter and its biological effects - Part 1: Simple VOCs and model PM

    NASA Astrophysics Data System (ADS)

    Ebersviller, S.; Lichtveld, K.; Sexton, K. G.; Zavala, J.; Lin, Y.-H.; Jaspers, I.; Jeffries, H. E.

    2012-12-01

    This is the first of a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOC), particulate matter (PM), and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of biological effects, using cultured human lung cells as model indicators. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects) from cells exposed to chamber air relative to cells exposed to clean air. The exposure systems permit virtually gas-only- or PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure. Our simple experiments in this part of the study were designed to eliminate many competing atmospheric processes to reduce ambiguity in our results. Simple volatile and semi-volatile organic gases that have inherent cellular toxic properties were tested individually for biological effect in the dark (at constant humidity). Airborne mixtures were then created with each compound to which we added PM that has no inherent cellular toxic properties for another cellular exposure. Acrolein and p-tolualdehyde were used as model VOCs and mineral oil aerosol (MOA) was selected as a surrogate for organic-containing PM. MOA is appropriately complex in composition to represent ambient PM, and exhibits no inherent cellular toxic effects and thus did not contribute any biological detrimental effects on its own. Chemical measurements, combined with the responses of our biological exposures, clearly demonstrate that gas-phase pollutants can modify the composition of PM (and its resulting detrimental effects on lung cells). We observed that, even if the gas-phase pollutants are not

  11. Gaseous VOCs rapidly modify particulate matter and its biological effects - Part 1: Simple VOCs and model PM

    NASA Astrophysics Data System (ADS)

    Ebersviller, S.; Lichtveld, K.; Sexton, K. G.; Zavala, J.; Lin, Y.-H.; Jaspers, I.; Jeffries, H. E.

    2012-02-01

    This is the first of a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOC), particulate matter (PM), and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of gas-only- and PM-only-biological effects, using cultured human lung cells as model indicators. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects) from cells exposed to chamber air relative to cells exposed to clean air. The exposure systems permit gas-only- or PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure. Our simple experiments in this part of the study were designed to eliminate many competing atmospheric processes to reduce ambiguity in our results. Simple volatile and semi-volatile organic gases that have inherent cellular toxic properties were tested individually for biological effect in the dark (at constant humidity). Airborne mixtures were then created with each compound and PM that has no inherent cellular toxic properties for another cellular exposure. Acrolein and p-tolualdehyde were used as model VOCs and mineral oil aerosol (MOA) was selected as a surrogate for organic-containing PM. MOA is appropriately complex in composition to represent ambient PM, and it exhibits no inherent cellular toxic effects and thus did not contribute any biological detrimental effects on its own. Chemical measurements, combined with the responses of our biological exposures, clearly demonstrate that gas-phase pollutants can modify the composition of PM (and its resulting detrimental effects on lung cells) - even if the gas-phase pollutants are not considered likely to

  12. Photoacoustic detection and optical spectroscopy of high-intensity focused ultrasound-induced thermal lesions in biologic tissue

    SciTech Connect

    Alhamami, Mosa; Kolios, Michael C.; Tavakkoli, Jahan

    2014-05-15

    Purpose: The aims of this study are: (a) to investigate the capability of photoacoustic (PA) method in detecting high-intensity focused ultrasound (HIFU) treatments in muscle tissuesin vitro; and (b) to determine the optical properties of HIFU-treated and native tissues in order to assist in the interpretation of the observed contrast in PA detection of HIFU treatments. Methods: A single-element, spherically concaved HIFU transducer with a centre frequency of 1 MHz was utilized to create thermal lesions in chicken breast tissuesin vitro. To investigate the detectability of HIFU treatments photoacoustically, PA detection was performed at 720 and 845 nm on seven HIFU-treated tissue samples. Within each tissue sample, PA signals were acquired from 22 locations equally divided between two regions of interest within two volumes in tissue – a HIFU-treated volume and an untreated volume. Optical spectroscopy was then carried out on 10 HIFU-treated chicken breast specimens in the wavelength range of 500–900 nm, in 1-nm increments, using a spectrophotometer with an integrating sphere attachment. The authors’ optical spectroscopy raw data (total transmittance and diffuse reflectance) were used to obtain the optical absorption and reduced scattering coefficients of HIFU-induced thermal lesions and native tissues by employing the inverse adding-doubling method. The aforementioned interaction coefficients were subsequently used to calculate the effective attenuation coefficient and light penetration depth of HIFU-treated and native tissues in the wavelength range of 500–900 nm. Results: HIFU-treated tissues produced greater PA signals than native tissues at 720 and 845 nm. At 720 nm, the averaged ratio of the peak-to-peak PA signal amplitude of HIFU-treated tissue to that of native tissue was 3.68 ± 0.25 (mean ± standard error of the mean). At 845 nm, the averaged ratio of the peak-to-peak PA signal amplitude of HIFU-treated tissue to that of native tissue was 3.75

  13. Near-field Raman spectroscopy of biological nanomaterials by in situ laser-induced synthesis of tip-enhanced Raman spectroscopy tips.

    PubMed

    Sinjab, Faris; Lekprasert, Banyat; Woolley, Richard A J; Roberts, Clive J; Tendler, Saul J B; Notingher, Ioan

    2012-06-15

    We report a new approach in tip-enhanced Raman spectroscopy (TERS) in which TERS-active tips with enhancement factors of ∼10(-5)× can be rapidly (1-3 min) produced in situ by laser-induced synthesis of silver nanoparticles at the tip apex. The technique minimizes the risks of tip contamination and damage during handling and provides in situ feedback control, which allows the prediction of the tip performance. We show that TERS tips produced by this technique enable the measurement of spatially resolved TERS spectra of self-assembled peptide nanotubes with a spatial resolution of ∼20  nm. PMID:22739873

  14. Implementation and evaluation of a training program as part of the Cooperative Biological Engagement Program in Azerbaijan

    PubMed Central

    Johnson, April; Akhundova, Gulshan; Aliyeva, Saida; Strelow, Lisa

    2015-01-01

    A training program for animal and human health professionals has been implemented in Azerbaijan through a joint agreement between the United States Defense Threat Reduction Agency and the Government of Azerbaijan. The training program is administered as part of the Cooperative Biological Engagement Program, and targets key employees in Azerbaijan's disease surveillance system including physicians, veterinarians, epidemiologists, and laboratory personnel. Training is aimed at improving detection, diagnosis, and response to especially dangerous pathogens (EDPs), although the techniques and methodologies can be applied to other pathogens and diseases of concern. Biosafety and biosecurity training is provided to all trainees within the program. Prior to 2014, a variety of international agencies and organizations provided training, which resulted in gaps related to lack of coordination of training materials and content. In 2014 a new training program was implemented in order to address those gaps. This paper provides an overview of the Cooperative Biological Engagement Program training program in Azerbaijan, a description of how the program fits into existing national training infrastructure, and an evaluation of the new program's effectiveness to date. Long-term sustainability of the program is also discussed. PMID:26501051

  15. Insight into the Local Solvent Environment of Biologically Relevant Iron-nitroysl Systems through Two-Dimensional Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Brookes, Jennifer Faith

    Iron-nitrosyl systems, particularly in the form of heme proteins, with their iron metal active sites play an important role in biological systems. Heme proteins act as storage, transporters, and receptors for nitric oxide (NO), a signaling molecule that is important in immune, nervous, and cardiovascular systems of mammals. By better understanding the local environment of the active site of NO binding heme proteins we can gain insight into disease in which the NO pathways have been implicated. This is an important step to being able to develop pharmaceuticals targeting NO pathways in humans. Sodium nitroprusside ((SNP, Na2[Fe(CN)5is NO]·2H 2O) investigated as a model system for the active site of nitric oxide binding heme proteins. Using two-dimensional infrared spectroscopy (2D IR) to obtain dephasing dynamics of the nitrosyl stretch (nuNO) in a series of solvents we are able to better understand the local environment of the more complicated metalloproteins. Rigorous line shape analysis is performed by using nonlinear response theory to simulate 2D IR spectra which are then fit to experimental data in an iterative process to extract frequency-frequency correlation functions (FFCFs). The time scales obtained are then correlated to empirical solvent polarity parameters. The analysis of the 2D IR lineshapes reveal that the spectral diffusion timescale of the nuNO in SNP varies from 0.8 -- 4 ps and is negatively correlated with the empirical solvent polarity scales. We continue to investigate NO binding of metalloproteins through 2D IR experiments on nitrophorin 4 (NP4). NP4 is a pH-sensitive NO transporter protein present in the salivary gland of the blood sucking insect Rhodius prolixus which undergoes a pH sensitive structural change between a closed and open conformation allowing for the storage and delivery of NO. The two structures are observed spectroscopically as two distinct pH-dependent nu NO frequencies at ~1904 and ~1917 cm-1. We obtain FFCFs by globally

  16. Nitric Oxide and Redox Regulation in the Liver: Part I General Considerations and Redox biology in Hepatitis

    PubMed Central

    Diesen, Diana L.; Kuo, Paul C.

    2010-01-01

    Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are created in normal hepatocytes and are critical for normal physiological processes including oxidative respiration, growth, regeneration, apoptosis, and microsomal defense. When the levels of oxidation products exceed the capacity of normal antioxidant systems, oxidative stress occurs. This type of stress, in the form of ROS and RNS, can be damaging to all liver cells, including hepatocytes, Kupffer cells, stellate cells, and endothelial cells, through induction of inflammation, ischemia, fibrosis, necrosis, apoptosis, or through malignant transformation by damaging lipids, proteins, and/or DNA. In part I of this review, we will discuss basic redox biology in the liver, including a review of ROS, RNS, and antioxidants, with a focus on nitric oxide as a common source of RNS. We will then review the evidence for oxidative stress as a mechanism of liver injury in hepatitis (alcoholic, viral, non-alcoholic). In part II of this review, we will review oxidative stress in common pathophysiological conditions including ischemia/reperfusion injury, fibrosis, hepatocellular carcinoma, iron overload, Wilson's disease, sepsis and acetaminophen overdose. Finally, biomarkers, proteomic, and antioxidant therapies will be discussed as areas for future therapeutic interventions. PMID:20444470

  17. Nitric Oxide and Redox Regulation in the Liver: Part II Redox biology in Pathologic Hepatocytes and Implications for intervention

    PubMed Central

    Diesen, Diana L.; Kuo, Paul C.

    2009-01-01

    Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are created in normal hepatocytes and are critical for normal physiological processes including oxidative respiration, growth, regeneration, apoptosis, and microsomal defense. When the levels of oxidation products exceed the capacity of normal antioxidant systems, oxidative stress occurs. This type of stress, in the form of ROS and RNS, can be damaging to all liver cells, including hepatocytes, Kupffer cells, stellate cells, and endothelial cells, through induction of inflammation, ischemia, fibrosis, necrosis, apoptosis, or through malignant transformation by damaging lipids, proteins, and/or DNA. In part I of this review, we will discuss basic redox biology in the liver, including a review of ROS, RNS, and antioxidants, with a focus on nitric oxide as a common source of RNS. We will then review the evidence for oxidative stress as a mechanism of liver injury in hepatitis (alcoholic, viral, non-alcoholic). In part II of this review, we will review oxidative stress in common pathophysiological conditions including ischemia/reperfusion injury, fibrosis, hepatocellular carcinoma, iron overload, Wilson’s disease, sepsis and acetaminophen overdose. Finally, biomarkers, proteomic, and antioxidant therapies will be discussed as areas for future therapeutic interventions. PMID:20400112

  18. Gaseous VOCs rapidly modify particulate matter and its biological effects - Part 2: Complex urban VOCs and model PM

    NASA Astrophysics Data System (ADS)

    Ebersviller, S.; Lichtveld, K.; Sexton, K. G.; Zavala, J.; Lin, Y.-H.; Jaspers, I.; Jeffries, H. E.

    2012-12-01

    This is the second study in a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOCs), particulate matter (PM), and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber, both in the dark and in sunlight. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of gas-only- and PM-only-biological effects, using cultured human lung cells as model living receptors. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects) from cells exposed to chamber air relative to cells exposed to clean air. Our exposure systems permit side-by-side, gas-only- and PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure for either gases or PM. In Part 1 (Ebersviller et al., 2012a), we demonstrated the existence of PM "effect modification" (NAS, 2004) for the case of a single gas-phase toxicant and an inherently non-toxic PM (mineral oil aerosol, MOA). That is, in the presence of the single gas-phase toxicant in the dark, the initially non-toxic PM became toxic to lung cells in the PM-only-biological exposure system. In this Part 2 study, we used sunlit-reactive systems to create a large variety of gas-phase toxicants from a complex mixture of oxides of nitrogen and 54 VOCs representative of those measured in US city air. In these mostly day-long experiments, we have designated the period in the dark just after injection (but before sunrise) as the "Fresh" condition and the period in the dark after sunset as the "Aged" condition. These two conditions were used to expose cells and to collect chemical characterization samples. We used the same inherently non-toxic PM from the Part 1 study as the target PM for "effect

  19. Gaseous VOCs rapidly modify particulate matter and its biological effects - Part 2: Complex urban VOCs and model PM

    NASA Astrophysics Data System (ADS)

    Ebersviller, S.; Lichtveld, K.; Sexton, K. G.; Zavala, J.; Lin, Y.-H.; Jaspers, I.; Jeffries, H. E.

    2012-03-01

    This is the second study in a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOCs), particulate matter (PM), and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber, both in the dark and in sunlight. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of gas-only- and PM-only-biological effects, using cultured human lung cells as model living receptors. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects) from cells exposed to chamber air relative to cells exposed to clean air. Our exposure systems permit side-by-side, gas-only- and PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure for either gases or PM. In Part 1 (Ebersviller et al., 2012a), we demonstrated the existence of PM "effect modification" (NAS, 2004) for the case of a single gas-phase toxicant and an inherently non-toxic PM (mineral oil aerosol, MOA). That is, in the presence of the single gas-phase toxicant in the dark, the initially non-toxic PM became toxic to lung cells in the PM-only-biological exposure system. In this Part 2 study, we used sunlit-reactive systems to create a large variety of gas-phase toxicants from a complex mixture of oxides of nitrogen and 54 VOCs representative of those measured in US city air. In these mostly day-long experiments, we have designated the period in the dark just after injection (but before sunrise) as the "Fresh" condition and the period in the dark after sunset as the "Aged" condition. These two conditions were used to expose cells and to collect chemical characterization samples. We used the same inherently non-toxic PM from the Part 1 study as the target PM for "effect

  20. Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy.

    PubMed

    Sun, Shiyu; Zhao, Guangxu; Huang, Yibing; Cai, Mingjun; Shan, Yuping; Wang, Hongda; Chen, Yuxin

    2016-01-01

    In this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers. PMID:27363513

  1. Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy

    PubMed Central

    Sun, Shiyu; Zhao, Guangxu; Huang, Yibing; Cai, Mingjun; Shan, Yuping; Wang, Hongda; Chen, Yuxin

    2016-01-01

    In this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers. PMID:27363513

  2. Study of energetic-particle-irradiation induced biological effect on Rhizopus oryzae through synchrotron-FTIR micro-spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, Jinghua; Qi, Zeming; Huang, Qing; Wei, Xiaoli; Ke, Zhigang; Fang, Yusheng; Tian, Yangchao; Yu, Zengliang

    2013-01-01

    Energetic particles exist ubiquitously and cause varied biological effects such as DNA strand breaks, lipid peroxidation, protein modification, cell apoptosis or death. An emerging biotechnology based on ion-beam technique has been developed to serve as an effective tool for mutation breeding of crops and microbes. In order to improve the effectiveness of ion-beam biotechnology for mutation breeding, it is indispensible to gain a better understanding of the mechanism of the interactions between the energetic ions and biological systems which is still elusive. A new trend is to conduct more comprehensive research which is based on micro-scaled observation of the changes of the cellular structures and compositions under the interactions. For this purpose, advanced synchrotron FTIR (s-FTIR) microscopy was employed to monitor the cellular changes of single fungal hyphae under irradiation of α-particles from 241Am. Intracellular contents of ROS, MDA, GSSG/GSH and activities of CAT and SOD were measured via biochemical assay. Ion-irradiation on Rhizopus oryzae causes localized vacuolation, autolysis of cell wall and membrane, lipid peroxidation, DNA damage and conformational changes of proteins, which have been clearly revealed by the s-FTIR microspectroscopy. The different changes of cell viability, SOD and CAT activities can be explained by the ROS-involved chemical reactions. Evidently, the elevated level of ROS in hyphal cells upon irradiation plays the key role in the caused biological effect. This study demonstrates that s-FTIR microspectroscopy is an effective tool to study the damage of fungal hyphae caused by ionizing radiation and it facilitates the exploit of the mechanism for the interactions between the energetic ions and biological systems.

  3. The AstroBiology Explorer (ABE) MIDEX Mission: Using Infrared Spectroscopy to Identify Organic Molecules in Space

    NASA Technical Reports Server (NTRS)

    Sandford, S. A.

    2002-01-01

    The AstroBiology Explorer (ABE) mission is one of four selected for Phase A Concept Study in NASA's current call for MIDEX class missions. ABE is a cooled space telescope equipped with spectrographs covering the 2.5-20 micron spectral range. The ABE mission is devoted to the detection and identification of organic and related molecular species in space. ABE is currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace.

  4. Individuals at the center of biology: Rudolf Leuckart's Polymorphismus der Individuen and the ongoing narrative of parts and wholes. With an annotated translation.

    PubMed

    Nyhart, Lynn K; Lidgard, Scott

    2011-01-01

    Rudolf Leuckart's 1851 pamphlet Ueber den Polymorphismus der Individuen (On the polymorphism of individuals) stood at the heart of naturalists' discussions on biological individuals, parts and wholes in mid-nineteenth-century Britain and Europe. Our analysis, which accompanies the first translation of this pamphlet into English, situates Leuckart's contribution to these discussions in two ways. First, we present it as part of a complex conceptual knot involving not only individuality and the understanding of compound organisms, but also the alternation of generations, the division of labor in nature, and the possibility of finding general laws of the organic world. Leuckart's pamphlet is important as a novel attempt to give order to the strands of this knot. It also solved a set of key biological problems in a way that avoided some of the drawbacks of an earlier teleological tradition. Second, we situate the pamphlet within a longer trajectory of inquiry into part-whole relations in biology from the mid-eighteenth century to the present. We argue that biological individuality, along with the problem-complexes with which it engaged, was as central a problem to naturalists before 1859 as evolution, and that Leuckart's contributions to it left a long legacy that persisted well into the twentieth century. As biologists' interests in part-whole relations are once again on the upswing, the longue durée of this problem merits renewed consideration. PMID:21308403

  5. An assessment of the potential of laser-induced breakdown spectroscopy (LIBS) for the analysis of cesium in liquid samples of biological origin.

    PubMed

    Metzinger, Anikó; Kovács-Széles, Eva; Almási, István; Galbács, Gábor

    2014-01-01

    The present study describes the development of an analytical method for the determination of cesium in biological fluid samples (human urine and blood samples) by laser-induced breakdown spectroscopy (LIBS). The developed method is based on sample presentation by liquid-to-solid conversion, enhancing the emission signal by drying the liquid into small "pockets" created in a metal support (zinc plate), and allows the analysis to be carried out on as little as 1 μL of sample volume, in a closed sample cell. Absolute detection limits on the Cs I 852.1 nm spectral line were calculated by the IUPAC 3σ method to be 6 ng in the urine sample and 27 ng in the blood serum sample. It is estimated that LIBS may be used to detect highly elevated concentration levels of Cs in fluid samples taken from people potentially exposed to surges of Cs from non-natural sources. PMID:25014845

  6. Mapping the metal uptake in plants from Jasper Ridge Biological Preserve using synchrotron micro-focused X-ray fluorescence spectroscopy

    SciTech Connect

    Lo, Allison

    2015-08-20

    Serpentine soil originates in the Earth’s mantle and contains high concentrations of potentially toxic transition metals. Although serpentine soil limits plant growth, endemic and adapted plants at Jasper Ridge Biological Preserve, located behind SLAC National Accelerator Laboratory, can tolerate these conditions. Serpentine soil and seeds belonging to native California and invasive plants were collected at Jasper Ridge. The seeds were grown hydroponically and on serpentine and potting soil to examine the uptake and distribution of ions in the roots and shoots using synchrotron micro-focused X-ray fluorescence spectroscopy. The results were used to determine differences between serpentine-tolerant plants. Rye grown on potting soil was enriched in Ni, Fe, Mn, and Cr compared to purple needlegrass grown on serpentine soil. Serpentine vegetation equally suppressed the uptake of Mn, Ni, and Fe in the roots and shoots. The uptake of Ca and Mg affected the uptake of other elements such as K, S, and P.

  7. Elucidation of molecular structures at buried polymer interfaces and biological interfaces using sum frequency generation vibrational spectroscopy

    PubMed Central

    Zhang, Chi; Myers, John; Chen, Zhan

    2013-01-01

    Sum frequency generation (SFG) vibrational spectroscopy has been developed into an important technique to study surfaces and interfaces. It can probe buried interfaces in situ and provide molecular level structural information such as the presence of various chemical moieties, quantitative molecular functional group orientation, and time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the recent progress in SFG studies on interfaces related to polymer materials and biomolecules. The results discussed here demonstrate that SFG can provide important molecular structural information of buried interfaces in situ and in real time, which is difficult to obtain by other surface sensitive analytical techniques. PMID:23710244

  8. Modeling the effect of cell-associated polymeric fluid layers on force spectroscopy measurements. Part I: model development.

    PubMed

    Coldren, Faith M; Foteinopoulou, Katerina; Carroll, David L; Laso, Manuel

    2008-09-01

    The mechanical response, the force-indentation relationship, in normal force spectroscopy measurements carried out on individual polysaccharide encapsulated bacteria is modeled using three increasingly refined approaches that consider the elastic response of the bacterium and cantilever in combination with a fluid (hydrodynamic) model for the polysaccharide layer. For the hydrodynamic description of the polysaccharide layer, several increasingly realistic models are described in detail, together with numerical solution techniques. These models range from one-dimensional, Newtonian, to two-dimensional, axisymmetric, fully viscoelastic (Phan-Thien/Tanner). In all cases, the models rigorously consider the time-dependent rheological-mechanical coupling between the elastic and fluid viscoelastic physical components of the experimental setup. Effects of inherent variability in geometrical and material properties of the bacterium and polysaccharide layer on the measurable response are quantified. A parametric investigation of the force-indentation relationship highlights the importance of accurate knowledge of the rheology of the extracellular polysaccharides. We also draw conclusions about the design and evaluation of force spectroscopy experiments on single encapsulated bacteria. Supported by model calculations, we also point the way to methods of in vivo rheological characterization of the extracellular polysaccharide as a preferable alternative to characterization after its removal from the native environment. PMID:18666790

  9. Transient absorption spectroscopy in biology using the Super-ACO storage ring FEL and the synchrotron radiation combination

    NASA Astrophysics Data System (ADS)

    Renault, Eric; Nahon, Laurent; Garzella, David; Nutarelli, Daniele; De Ninno, Giovanni; Hirsch, Matthias; Couprie, Marie Emmanuelle

    2001-12-01

    The Super-ACO storage ring FEL, covering the UV range down to 300 nm with a high average power (300 mW at 350 nm) together with a high stability and long lifetime, is a unique tool for the performance of users applications. We present here the first pump-probe two color experiments on biological species using a storage ring FEL coupled to the synchrotron radiation. The intense UV pulse of the Super-ACO FEL is used to prepare a high initial concentration of chromophores in their first singlet electronic excited state. The nearby bending magnet synchrotron radiation provides, on the other hand a pulsed, white light continuum (UV-IR), naturally synchronized with the FEL pulses and used to probe the photochemical subsequent events and the associated transient species. We have demonstrated the feasibility with a dye molecule (POPOP) observing a two-color effect, signature of excited state absorption and a temporal signature with Acridine. Applications on various chromophores of biological interest are carried out, such as the time-resolved absorption study of the first excited state of Acridine.

  10. BIOLOGICAL MONITORING OF TOXIC TRACE METALS. VOLUME 2. TOXIC TRACE METALS IN PLANTS AND ANIMALS OF THE WORLD. PART III

    EPA Science Inventory

    The needs and priorities in using biological accumulator organisms for monitoring toxic trace metals in plants and animals are analyzed. The toxic trace metals selected for study are antimony, arsenic, beryllium, boron, cadmium, chromium, cobalt, copper, lead, mercury, nickel, se...