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Sample records for biological function electronic

  1. Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules

    Science.gov (United States)

    Zheng, Haoping

    2003-04-01

    The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with unchanged calculation precision. So the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule becomes a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the Ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), are presented. The reactive sites of the inhibitors are determined and explained. The precision of structure determination of inhibitors are tested theoretically.

  2. Wireless Biological Electronic Sensors.

    Science.gov (United States)

    Cui, Yue

    2017-10-09

    The development of wireless biological electronic sensors could open up significant advances for both fundamental studies and practical applications in a variety of areas, including medical diagnosis, environmental monitoring, and defense applications. One of the major challenges in the development of wireless bioelectronic sensors is the successful integration of biosensing units and wireless signal transducers. In recent years, there are a few types of wireless communication systems that have been integrated with biosensing systems to construct wireless bioelectronic sensors. To successfully construct wireless biological electronic sensors, there are several interesting questions: What types of biosensing transducers can be used in wireless bioelectronic sensors? What types of wireless systems can be integrated with biosensing transducers to construct wireless bioelectronic sensors? How are the electrical sensing signals generated and transmitted? This review will highlight the early attempts to address these questions in the development of wireless biological electronic sensors.

  3. Electron Resonance Decay into a Biological Function: Decrease in Viability of E. coli Transformed by Plasmid DNA Irradiated with 0.5-18 eV Electrons.

    Science.gov (United States)

    Kouass Sahbani, S; Cloutier, P; Bass, A D; Hunting, D J; Sanche, L

    2015-10-01

    Transient negative ions (TNIs) are ubiquitous in electron-molecule scattering at low electron impact energies (0-20 eV) and are particularly effective in damaging large biomolecules. Because ionizing radiation generates mostly 0-20 eV electrons, TNIs are expected to play important roles in cell mutagenesis and death during radiotherapeutic cancer treatment, although this hypothesis has never been directly verified. Here, we measure the efficiency of transforming E. coli bacteria by inserting into the cells, pGEM-3ZfL(-) plasmid DNA that confers resistance to the antibiotic ampicillin. Before transformation, plasmids are irradiated with electrons of specific energies between 0.5 and 18 eV. The loss of transformation efficiency plotted as a function of irradiation energy reveals TNIs at 5.5 and 9.5 eV, corresponding to similar states observed in the yields of DNA double strand breaks. We show that TNIs are detectable in the electron-energy dependence of a biological process and can decrease cell viability.

  4. Electron holography of biological samples.

    Science.gov (United States)

    Simon, P; Lichte, H; Formanek, P; Lehmann, M; Huhle, R; Carrillo-Cabrera, W; Harscher, A; Ehrlich, H

    2008-01-01

    In this paper, we summarise the development of off-axis electron holography on biological samples starting in 1986 with the first results on ferritin from the group of Tonomura. In the middle of the 1990s strong interest was evoked, but then stagnation took place because the results obtained at that stage did not reach the contrast and the resolution achieved by conventional electron microscopy. To date, there exist only a few ( approximately 12) publications on electron holography of biological objects, thus this topic is quite small and concise. The reason for this could be that holography is mostly established in materials science by physicists. Therefore, applications for off-axis holography were powerfully pushed forward in the area of imaging, e.g. electric or magnetic micro- and nanofields. Unstained biological systems investigated by means of off-axis electron holography up to now are ferritin, tobacco mosaic virus, a bacterial flagellum, T5 bacteriophage virus, hexagonal packed intermediate layer of bacteria and the Semliki Forest virus. New results of the authors on collagen fibres and surface layer of bacteria, the so-called S-layer 2D crystal lattice are presented in this review. For the sake of completeness, we will shortly discuss in-line holography of biological samples and off-axis holography of materials related to biological systems, such as biomaterial composites or magnetotactic bacteria.

  5. Functions in Biological Kind Classification

    Science.gov (United States)

    Lombrozo, Tania; Rehder, Bob

    2012-01-01

    Biological traits that serve functions, such as a zebra's coloration (for camouflage) or a kangaroo's tail (for balance), seem to have a special role in conceptual representations for biological kinds. In five experiments, we investigate whether and why functional features are privileged in biological kind classification. Experiment 1…

  6. Quantifying electron transfer reactions in biological systems

    DEFF Research Database (Denmark)

    Sjulstok, Emil Sjulstok; Olsen, Jógvan Magnus Haugaard; Solov'yov, Ilia A

    2015-01-01

    to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe...

  7. The relativity of biological function.

    Science.gov (United States)

    Laubichler, Manfred D; Stadler, Peter F; Prohaska, Sonja J; Nowick, Katja

    2015-12-01

    Function is a central concept in biological theories and explanations. Yet discussions about function are often based on a narrow understanding of biological systems and processes, such as idealized molecular systems or simple evolutionary, i.e., selective, dynamics. Conflicting conceptions of function continue to be used in the scientific literature to support certain claims, for instance about the fraction of "functional DNA" in the human genome. Here we argue that all biologically meaningful interpretations of function are necessarily context dependent. This implies that they derive their meaning as well as their range of applicability only within a specific theoretical and measurement context. We use this framework to shed light on the current debate about functional DNA and argue that without considering explicitly the theoretical and measurement contexts all attempts to integrate biological theories are prone to fail.

  8. Biological cryo‐electron microscopy in China

    Science.gov (United States)

    2016-01-01

    Abstract Cryo‐electron microscopy (cryo‐EM) plays an increasingly more important role in structural biology. With the construction of an arm of the Chinese National Protein Science Facility at Tsinghua University, biological cryo‐EM has entered a phase of rapid development in China. This article briefly reviews the history of biological cryo‐EM in China, describes its current status, comments on its impact on the various biological research fields, and presents future outlook. PMID:27534377

  9. e-Biologics: Fabrication of Sustainable Electronics with "Green" Biological Materials.

    Science.gov (United States)

    Lovley, Derek R

    2017-06-27

    The growing ubiquity of electronic devices is increasingly consuming substantial energy and rare resources for materials fabrication, as well as creating expansive volumes of toxic waste. This is not sustainable. Electronic biological materials (e-biologics) that are produced with microbes, or designed with microbial components as the guide for synthesis, are a potential green solution. Some e-biologics can be fabricated from renewable feedstocks with relatively low energy inputs, often while avoiding the harsh chemicals used for synthesizing more traditional electronic materials. Several are completely free of toxic components, can be readily recycled, and offer unique features not found in traditional electronic materials in terms of size, performance, and opportunities for diverse functionalization. An appropriate investment in the concerted multidisciplinary collaborative research required to identify and characterize e-biologics and to engineer materials and devices based on e-biologics could be rewarded with a new "green age" of sustainable electronic materials and devices. Copyright © 2017 Lovley.

  10. Peptide π-Electron Conjugates: Organic Electronics for Biology?

    Science.gov (United States)

    Ardoña, Herdeline Ann M; Tovar, John D

    2015-12-16

    Highly ordered arrays of π-conjugated molecules are often viewed as a prerequisite for effective charge-transporting materials. Studies involving these materials have traditionally focused on organic electronic devices, with more recent emphasis on biological systems. In order to facilitate the transition to biological environments, biomolecules that can promote hierarchical ordering and water solubility are often covalently appended to the π-electron unit. This review highlights recent work on π-conjugated systems bound to peptide moieties that exhibit self-assembly and aims to provide an overview on the development and emerging applications of peptide-based supramolecular π-electron systems.

  11. Molecular ferroelectrics: where electronics meet biology.

    Science.gov (United States)

    Li, Jiangyu; Liu, Yuanming; Zhang, Yanhang; Cai, Hong-Ling; Xiong, Ren-Gen

    2013-12-28

    In the last several years, we have witnessed significant advances in molecular ferroelectrics, with the ferroelectric properties of molecular crystals approaching those of barium titanate. In addition, ferroelectricity has been observed in biological systems, filling an important missing link in bioelectric phenomena. In this perspective, we will present short historical notes on ferroelectrics, followed by an overview of the fundamentals of ferroelectricity. The latest developments in molecular ferroelectrics and biological ferroelectricity will then be highlighted, and their implications and potential applications will be discussed. We close by noting molecular ferroelectric as an exciting frontier between electronics and biology, and a number of challenges ahead are also described.

  12. The biological function of consciousness

    Science.gov (United States)

    Earl, Brian

    2014-01-01

    This research is an investigation of whether consciousness—one's ongoing experience—influences one's behavior and, if so, how. Analysis of the components, structure, properties, and temporal sequences of consciousness has established that, (1) contrary to one's intuitive understanding, consciousness does not have an active, executive role in determining behavior; (2) consciousness does have a biological function; and (3) consciousness is solely information in various forms. Consciousness is associated with a flexible response mechanism (FRM) for decision-making, planning, and generally responding in nonautomatic ways. The FRM generates responses by manipulating information and, to function effectively, its data input must be restricted to task-relevant information. The properties of consciousness correspond to the various input requirements of the FRM; and when important information is missing from consciousness, functions of the FRM are adversely affected; both of which indicate that consciousness is the input data to the FRM. Qualitative and quantitative information (shape, size, location, etc.) are incorporated into the input data by a qualia array of colors, sounds, and so on, which makes the input conscious. This view of the biological function of consciousness provides an explanation why we have experiences; why we have emotional and other feelings, and why their loss is associated with poor decision-making; why blindsight patients do not spontaneously initiate responses to events in their blind field; why counter-habitual actions are only possible when the intended action is in mind; and the reason for inattentional blindness. PMID:25140159

  13. Calculation of X-ray scattering curves and electron distance distribution functions of biological macromolecules in solution using the PROTEIN DATA BANK

    International Nuclear Information System (INIS)

    Mueller, J.J.; Friedrichowicz, E.; Nothnagel, A.; Wunderlich, T.; Ziehlsdorf, E.; Damaschun, G.

    1983-01-01

    The wide angle X-ray scattering curve, the electron distance distribution function and the solvent excluded volume of a macromolecule in solution are calculated from the atomic coordinates contained in the PROTEIN DATA BANK. The structures and the projections of the excluded volumes are depicted using molecule graphic routines. The described computer programs are used to determine the three-dimensional structure of macromolecules in solution from wide angle X-ray scattering data. (author)

  14. Quantum effects in biological electron transfer

    Czech Academy of Sciences Publication Activity Database

    de la Lande, A.; Babcock, N. S.; Řezáč, Jan; Levy, B.; Sanders, B. C.; Salahub, D.

    2012-01-01

    Roč. 14, č. 17 (2012), s. 5902-5918 ISSN 1463-9076 Institutional research plan: CEZ:AV0Z40550506 Keywords : electron transfer * tunnelling * decoherence * semi-classical molecular dynamics * density functional theory Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.829, year: 2012

  15. Quantitative biological measurement in Transmission Electron Tomography

    International Nuclear Information System (INIS)

    Mantell, Judith M; Verkade, Paul; Arkill, Kenton P

    2012-01-01

    It has been known for some time that biological sections shrink in the transmission electron microscope from exposure to the electron beam. This phenomenon is especially important in Electron Tomography (ET). The effect on shrinkage of parameters such as embedding medium or sample type is less well understood. In addition anisotropic area shrinkage has largely been ignored. The intention of this study is to explore the shrinkage on a number of samples ranging in thickness from 200 nm to 500 nm. A protocol was developed to determine the shrinkage in area and thickness using the gold fiducials used in electron tomography. In brief: Using low dose philosophy on the section, a focus area was used prior to a separate virgin study area for a series of known exposures on a tilted sample. The shrinkage was determined by measurements on the gold beads from both sides of the section as determined by a confirmatory tomogram. It was found that the shrinkage in area (approximately to 90-95% of the original) and the thickness (approximately 65% of the original at most) agreed with pervious authors, but that a lmost all the shrinkage was in the first minute and that although the direction of the in-plane shrinkage (in x and y) was sometimes uneven the end result was consistent. It was observed, in general, that thinner samples showed more percentage shrinkage than thicker ones. In conclusion, if direct quantitative measurements are required then the protocol described should be used for all areas studied.

  16. Quantitative biological measurement in Transmission Electron Tomography

    Science.gov (United States)

    Mantell, Judith M.; Verkade, Paul; Arkill, Kenton P.

    2012-07-01

    It has been known for some time that biological sections shrink in the transmission electron microscope from exposure to the electron beam. This phenomenon is especially important in Electron Tomography (ET). The effect on shrinkage of parameters such as embedding medium or sample type is less well understood. In addition anisotropic area shrinkage has largely been ignored. The intention of this study is to explore the shrinkage on a number of samples ranging in thickness from 200 nm to 500 nm. A protocol was developed to determine the shrinkage in area and thickness using the gold fiducials used in electron tomography. In brief: Using low dose philosophy on the section, a focus area was used prior to a separate virgin study area for a series of known exposures on a tilted sample. The shrinkage was determined by measurements on the gold beads from both sides of the section as determined by a confirmatory tomogram. It was found that the shrinkage in area (approximately to 90-95% of the original) and the thickness (approximately 65% of the original at most) agreed with pervious authors, but that a lmost all the shrinkage was in the first minute and that although the direction of the in-plane shrinkage (in x and y) was sometimes uneven the end result was consistent. It was observed, in general, that thinner samples showed more percentage shrinkage than thicker ones. In conclusion, if direct quantitative measurements are required then the protocol described should be used for all areas studied.

  17. Microscopy of electronic wave function

    International Nuclear Information System (INIS)

    Harb, M.

    2010-01-01

    This work of thesis aims to visualize, on a position sensitive detector, the spatial oscillations of slow electrons (∼ meV) emitted by a threshold photoionization in the presence of an external electric field. The interference figure obtained represents the square magnitude of electronic wavefunction. This fundamental work allows us to have access to the electronic dynamics and thus to highlight several quantum mechanisms that occur at the atomic scale (field Coulomb, electron/electron interaction..). Despite the presence an electronic core in Li atom, we have succeeded, experimentally and for the first time, in visualizing the wave function associated with the quasi-discrete Stark states coupled to the ionization continuum. Besides, using simulations of wave packet propagation, based on the 'Split-operator' method, we have conducted a comprehensive study of the H, Li and Cs atoms while revealing the significant effects of the Stark resonances. A very good agreement, on and off resonances, was obtained between simulated and experimental results. In addition, we have developed a generalized analytical model to understand deeply the function of VMI (Velocity-Map Imaging) spectrometer. This model is based on the paraxial approximation; it is based on matrix optics calculation by making an analogy between the electronic trajectory and the light beam. An excellent agreement was obtained between the model predictions and the experimental results. (author)

  18. Integrating Functional, Developmental and Evolutionary Biology into Biology Curricula

    Science.gov (United States)

    Haave, Neil

    2012-01-01

    A complete understanding of life involves how organisms are able to function in their environment and how they arise. Understanding how organisms arise involves both their evolution and development. Thus to completely comprehend living things, biology must study their function, development and evolution. Previous proposals for standardized…

  19. Structure and function in biology

    International Nuclear Information System (INIS)

    Hirs, C.H.W.

    1976-01-01

    A summary is given of the history of the developments of structural chemistry in biology beginning with the work of the bacteriologist Ehrlich leading to a comprehensive examination of the influence of size and configuration on the interaction between specific antibodies and side-chain determinants. Recent developments include the recognition of a higher order of specificity in the interaction of proteins with one another

  20. Electron Bifurcation: Thermodynamics and Kinetics of Two-Electron Brokering in Biological Redox Chemistry.

    Science.gov (United States)

    Zhang, Peng; Yuly, Jonathon L; Lubner, Carolyn E; Mulder, David W; King, Paul W; Peters, John W; Beratan, David N

    2017-09-19

    How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently. This Account provides an exegesis of the biophysical principles that underpin electron bifurcation. Remarkably, bifurcating electron transfer (ET) proteins typically send one electron uphill and one electron downhill by similar energies, such that the overall reaction is spontaneous, but not profligate. Electron bifurcation in the NADH-dependent reduced ferredoxin: NADP + oxidoreductase I (Nfn) is explored in detail here. Recent experimental progress in understanding the structure and function of Nfn allows us to dissect its workings in the framework of modern ET theory. The first electron that leaves the two-electron donor flavin (L-FAD) executes a positive free energy "uphill" reaction, and the departure of this electron switches on a second thermodynamically spontaneous ET reaction from the flavin along a second pathway that moves electrons in the opposite direction and at a very different potential. The singly reduced ET products formed from the bifurcating flavin are more than two nanometers distant from each other. In Nfn, the second electron to leave the flavin is much more reducing than the first: the potentials are said to be "crossed." The eventually reduced cofactors, NADH and ferredoxin in the case of Nfn, perform crucial downstream redox

  1. Electron Transfer in Chemistry and Biology - The Primary Events in ...

    Indian Academy of Sciences (India)

    electron transfer. (PET) is a very important process, with considerable chemical and biological relevance. GENERAL I ARTICLE of electrons, respectively. This has entirely changed the earlier framework of interpreting reactions in chemistry and biology. This shift in emphasis enables one to understand the elementary.

  2. Electron Transfer in Chemistry and Biology - The Primary Events in ...

    Indian Academy of Sciences (India)

    Electron Transfer in Chemistry and Biology -. The Primary Events in Photosynthesis. V Krishnan. One of the most important chemical reactions is electron transfer from one atomic/molecular unit to another. This reaction, accompanied by proton and hydrogen atom transfers, occurs in a cascade in many biological processes,.

  3. Photosynthetic system as a biological functional element

    International Nuclear Information System (INIS)

    Zakhidov, E.A.; Zakhidova, M.A.; Kasymdzhanov, M.A.; Kurbanov, S.S.; Nematov, Sh.K.; Khabibullaev, P.K.

    2005-01-01

    Photosynthetic apparatus of high plants and photosynthetic bacteria is essentially autonomic system in terms of genetics and structural -functional properties located in specific medium, a bio-membrane. Processes of light absorption and exciton migration in light harvesting antenna, separation and further transfer of charges in reaction centers have specific features, which may be used for application of these objects as key elements in construction of future biological functional elements. Progress in study and genetic modification of photosynthetic membranes achieved during the last decade opens great prospects in development biological functional elements and systems. The main characteristics of photosynthetic system for these purposes are: (i) energy conversion processes in the first light phase of the photosynthesis have very short periods, up to picoseconds, which indicates possibility of creation of ultrafast functional elements on their basis; (ii) characteristics sizes of photosynthetic units, 10-100 nm, and possibility to arrange regularly disposed elements in relevant membranes could be prospective point for creation of nano structures and on their basis relevant biologic functional elements; (iii) elements based on modified photosynthetic apparatus and bio-membranes might be efficiently created by methods of gene engineering and manipulation, that open huge opportunities for development of read biological functional systems. In the paper structural-functional properties and characteristics of high plants and purple photosynthetic bacteria, which may be useful for creation of future biological functional elements are considered. (author)

  4. Metacognition: computation, biology and function

    Science.gov (United States)

    Fleming, Stephen M.; Dolan, Raymond J.; Frith, Christopher D.

    2012-01-01

    Many complex systems maintain a self-referential check and balance. In animals, such reflective monitoring and control processes have been grouped under the rubric of metacognition. In this introductory article to a Theme Issue on metacognition, we review recent and rapidly progressing developments from neuroscience, cognitive psychology, computer science and philosophy of mind. While each of these areas is represented in detail by individual contributions to the volume, we take this opportunity to draw links between disciplines, and highlight areas where further integration is needed. Specifically, we cover the definition, measurement, neurobiology and possible functions of metacognition, and assess the relationship between metacognition and consciousness. We propose a framework in which level of representation, order of behaviour and access consciousness are orthogonal dimensions of the conceptual landscape. PMID:22492746

  5. Electron-cyclotron-resonant-heated electron distribution functions

    International Nuclear Information System (INIS)

    Matsuda, Y.; Nevins, W.M.; Cohen, R.H.

    1981-01-01

    Recent studies at Lawrence Livermore National Laboratory (LLNL) with a bounce-averaged Fokker-Planck code indicate that the energetic electron tail formed by electron-cyclotron resonant heating (ECRH) at the second harmonic is not Maxwellian. We present the results of our bounce-averaged Fokker-Planck code along with some simple analytic models of hot-electron distribution functions

  6. Biological applications of ultraviolet free-electron lasers

    International Nuclear Information System (INIS)

    Sutherland, J.C.

    1997-10-01

    This review examines the possibilities for biological research using the three ultraviolet free-electron lasers that are nearing operational status in the US. The projected operating characteristics of major interest in biological research of the free-electron lasers at Brookhaven National Laboratory, the Thomas Jefferson National Accelerator Facility, and Duke University are presented. Experimental applications in the areas of far- and vacuum ultraviolet photophysics and photochemistry, structural biology, environmental photobiology, and medical research are discussed and the prospects for advances in these areas, based upon the characteristics of the new ultraviolet free-electron lasers, are evaluated

  7. Interactions of electrons with biologically important molecules

    International Nuclear Information System (INIS)

    Pisklova, K.; Papp, P.; Stano, M.

    2012-01-01

    For the study of interactions of low-energy electrons with the molecules in the gas phase, the authors used electron-molecule cross-beam apparatus. The experiment is carried out in high vacuum, where molecules of the tested compound are inducted through a capillary. For purposes of this experiment the sample was electrically heated to 180 Deg C., giving a bundle of GlyGly molecules into the gas phase. The resulting signals can be evaluated in two different modes: mass spectrum - at continuous electron energy (e.g. 100 eV) they obtained the signal of intensity of the ions according to their mass to charge ratio; ionization and resonance spectra - for selected ion mass when the authors received the signal of intensity of the ions, depending on the energy of interacting electron.

  8. Functional biology of sympatric krill species

    DEFF Research Database (Denmark)

    Agersted, Mette Dalgaard; Nielsen, Torkel Gissel

    2016-01-01

    Here we compare the functional biology of the sympatric krill species, Meganyctiphanes norvegica and Thysanoessa inermis. For M. norvegica, we investigated functional responses on diatoms and copepods, together with prey size spectra on plankton ,400 mm and copepods in the size range 500–3220 mm...

  9. Connecting Biology to Electronics: Molecular Communication via Redox Modality.

    Science.gov (United States)

    Liu, Yi; Li, Jinyang; Tschirhart, Tanya; Terrell, Jessica L; Kim, Eunkyoung; Tsao, Chen-Yu; Kelly, Deanna L; Bentley, William E; Payne, Gregory F

    2017-12-01

    Biology and electronics are both expert at for accessing, analyzing, and responding to information. Biology uses ions, small molecules, and macromolecules to receive, analyze, store, and transmit information, whereas electronic devices receive input in the form of electromagnetic radiation, process the information using electrons, and then transmit output as electromagnetic waves. Generating the capabilities to connect biology-electronic modalities offers exciting opportunities to shape the future of biosensors, point-of-care medicine, and wearable/implantable devices. Redox reactions offer unique opportunities for bio-device communication that spans the molecular modalities of biology and electrical modality of devices. Here, an approach to search for redox information through an interactive electrochemical probing that is analogous to sonar is adopted. The capabilities of this approach to access global chemical information as well as information of specific redox-active chemical entities are illustrated using recent examples. An example of the use of synthetic biology to recognize external molecular information, process this information through intracellular signal transduction pathways, and generate output responses that can be detected by electrical modalities is also provided. Finally, exciting results in the use of redox reactions to actuate biology are provided to illustrate that synthetic biology offers the potential to guide biological response through electrical cues. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. CMOS biomicrosystems where electronics meets biology

    CERN Document Server

    2011-01-01

    "The book will address the-state-of-the-art in integrated Bio-Microsystems that integrate microelectronics with fluidics, photonics, and mechanics. New exciting opportunities in emerging applications that will take system performance beyond offered by traditional CMOS based circuits are discussed in detail. The book is a must for anyone serious about microelectronics integration possibilities for future technologies. The book is written by top notch international experts in industry and academia. The intended audience is practicing engineers with electronics background that want to learn about integrated microsystems. The book will be also used as a recommended reading and supplementary material in graduate course curriculum"--

  11. Imaging cellular and molecular biological functions

    Energy Technology Data Exchange (ETDEWEB)

    Shorte, S.L. [Institut Pasteur, 75 - Paris (France). Plateforme d' Imagerie Dynamique PFID-Imagopole; Frischknecht, F. (eds.) [Heidelberg Univ. Medical School (Germany). Dept. of Parasitology

    2007-07-01

    'Imaging cellular and molecular biological function' provides a unique selection of essays by leading experts, aiming at scientist and student alike who are interested in all aspects of modern imaging, from its application and up-scaling to its development. Indeed the philosophy of this volume is to provide student, researcher, PI, professional or provost the means to enter this applications field with confidence, and to construct the means to answer their own specific questions. (orig.)

  12. How do electron localization functions describe π-electron delocalization?

    Science.gov (United States)

    Steinmann, Stephan N; Mo, Yirong; Corminboeuf, Clemence

    2011-12-14

    Scalar fields provide an intuitive picture of chemical bonding. In particular, the electron localization function (ELF) has proven to be highly valuable in interpreting a broad range of bonding patterns. The discrimination between enhanced or reduced electron (de)localization within cyclic π-conjugated systems remains, however, challenging for ELF. In order to clearly distinguish between the local properties of ten highly and weakly π-(de)localized prototype systems, we compare the ELFs of both the canonical wave functions and electron-localized states (diabatic) with those of two closely related scalar fields: the electron localizability indicator (ELI-D) and the localized orbital locator (LOL). The simplest LOL function distinguishes enhanced from weak π-(de)localization in an insightful and reliable manner. LOL offers the finest contrast between annulenes with 4n/4n + 2 π electrons and their inorganic analogues as well as between hyperconjugated cyclopentadiene derivatives. LOL(π) also gives an appealing and intuitive picture of the π-bond. In contrast, the most popular ELF fails to capture subtle contrasting local electronic properties and suffers from the arbitrariness of the σ/π dissection. The orbital separation of the most recent ELI-D is clear-cut but the interpretations sometime less straightforward in the present context.

  13. Electron energy-distribution functions in gases

    International Nuclear Information System (INIS)

    Pitchford, L.C.

    1981-01-01

    Numerical calculation of the electron energy distribution functions in the regime of drift tube experiments is discussed. The discussion is limited to constant applied fields and values of E/N (ratio of electric field strength to neutral density) low enough that electron growth due to ionization can be neglected

  14. Dechanneling function for relativistic axially channeled electrons

    International Nuclear Information System (INIS)

    Muralev, V.A.; Telegin, V.I.

    1981-01-01

    Behaviour of the x(t) dechanneling function depending on the depth is theoretically studied. Theoretical consideration of x(t) for axial channeled relativistic electrons in anisotropic medium results in two-dimensional kinetic equation with mixed derivatives of the parabolic type. The kinetic equation in the approximation of the continuous Lindchard model for relativistic axial channeled electrons is numerically solved. The depth dependence of the x(t) dechanneling function is obtained [ru

  15. Advancing Small Satellite Electronics Heritage for Microfluidic Biological Experiments

    Science.gov (United States)

    White, Bruce; Mazmanian, Edward; Tapio, Eric

    2016-01-01

    DLR's Eu:CROPIS (Euglena and Combined Regenerative Organic-Food Production in Space) mission, launching in 2017, will carry multiple biological payloads into a sun-synchronous orbit, including NASA Ames' PowerCell experiment. PowerCell will attempt to characterize the viability of synthetic biology at micro-g, Lunar, and Martian gravity levels. PowerCell experiment requirements demand an electronic system similar to previous microfluidic biology payloads, but with an expanded feature set. As such, the system was based on PharmaSat (Diaz-Aguado et al. 2009), a previous successful biology payload from NASA Ames, and improved upon. Newer, more miniaturized electronics allow for greater capability with a lower part count and smaller size. Two identical PowerCell enclosures will fly. Each enclosure contains two separate and identical experiments with a 48-segment optical density measurement system, grow light system, microfluidic system for nutrient delivery and waste flushing, plus thermal control and environmental sensing/housekeeping including temperature, pressure, humidity, and acceleration. Electronics consist of a single Master PCB that interfaces to the spacecraft bus and regulates power and communication, plus LED, Detector, and Valve Manifold PCBs for each experiment. To facilitate ease of reuse on future missions, experiment electronics were designed to be compatible with a standard 3U small sat form factor and power bus, or to interface with a Master power/comm PCB for use in a larger satellite as in the case of PowerCell's flight on Eu:CROPIS.

  16. Some examples of utilization of electron paramagnetic resonance in biology

    International Nuclear Information System (INIS)

    Bemski, G.

    1982-10-01

    A short outline of the fundamentals of electron paramagnetic resonance (EPR) is presented and is followed by examples of the application of EPR to biology. These include use of spin labels, as well as of ENDOR principally to problems of heme proteins, photosynthesis and lipids. (Author) [pt

  17. Flexible Organic Electronics in Biology: Materials and Devices.

    Science.gov (United States)

    Liao, Caizhi; Zhang, Meng; Yao, Mei Yu; Hua, Tao; Li, Li; Yan, Feng

    2015-12-09

    At the convergence of organic electronics and biology, organic bioelectronics attracts great scientific interest. The potential applications of organic semiconductors to reversibly transmit biological signals or stimulate biological tissues inspires many research groups to explore the use of organic electronics in biological systems. Considering the surfaces of movable living tissues being arbitrarily curved at physiological environments, the flexibility of organic bioelectronic devices is of paramount importance in enabling stable and reliable performances by improving the contact and interaction of the devices with biological systems. Significant advances in flexible organic bio-electronics have been achieved in the areas of flexible organic thin film transistors (OTFTs), polymer electrodes, smart textiles, organic electrochemical ion pumps (OEIPs), ion bipolar junction transistors (IBJTs) and chemiresistors. This review will firstly discuss the materials used in flexible organic bioelectronics, which is followed by an overview on various types of flexible organic bioelectronic devices. The versatility of flexible organic bioelectronics promises a bright future for this emerging area. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Marine Carotenoids: Biological Functions and Commercial Applications

    Directory of Open Access Journals (Sweden)

    José M. Vega

    2011-03-01

    Full Text Available Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functions of carotenoids relevant for life on earth. Biological properties of carotenoids allow for a wide range of commercial applications. Indeed, recent interest in the carotenoids has been mainly for their nutraceutical properties. A large number of scientific studies have confirmed the benefits of carotenoids to health and their use for this purpose is growing rapidly. In addition, carotenoids have traditionally been used in food and animal feed for their color properties. Carotenoids are also known to improve consumer perception of quality; an example is the addition of carotenoids to fish feed to impart color to farmed salmon.

  19. Marine Carotenoids: Biological Functions and Commercial Applications

    Science.gov (United States)

    Vílchez, Carlos; Forján, Eduardo; Cuaresma, María; Bédmar, Francisco; Garbayo, Inés; Vega, José M.

    2011-01-01

    Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functions of carotenoids relevant for life on earth. Biological properties of carotenoids allow for a wide range of commercial applications. Indeed, recent interest in the carotenoids has been mainly for their nutraceutical properties. A large number of scientific studies have confirmed the benefits of carotenoids to health and their use for this purpose is growing rapidly. In addition, carotenoids have traditionally been used in food and animal feed for their color properties. Carotenoids are also known to improve consumer perception of quality; an example is the addition of carotenoids to fish feed to impart color to farmed salmon. PMID:21556162

  20. Advances in cryo-electron tomography for biology and medicine.

    Science.gov (United States)

    Koning, Roman I; Koster, Abraham J; Sharp, Thomas H

    2018-05-01

    Cryo-electron tomography (CET) utilizes a combination of specimen cryo-fixation and multi-angle electron microscopy imaging to produce three-dimensional (3D) volume reconstructions of native-state macromolecular and subcellular biological structures with nanometer-scale resolution. In recent years, cryo-electron microscopy (cryoEM) has experienced a dramatic increase in the attainable resolution of 3D reconstructions, resulting from technical improvements of electron microscopes, improved detector sensitivity, the implementation of phase plates, automated data acquisition schemes, and improved image reconstruction software and hardware. These developments also greatly increased the usability and applicability of CET as a diagnostic and research tool, which is now enabling structural biologists to determine the structure of proteins in their native cellular environment to sub-nanometer resolution. These recent technical developments have stimulated us to update on our previous review (Koning, R.I., Koster, A.J., 2009. Cryo-electron tomography in biology and medicine. Ann Anat 191, 427-445) in which we described the fundamentals of CET. In this follow-up, we extend this basic description in order to explain the aforementioned recent advances, and describe related 3D techniques that can be applied to the anatomy of biological systems that are relevant for medicine. Copyright © 2018 Elsevier GmbH. All rights reserved.

  1. Electron crystallography--the waking beauty of structural biology.

    Science.gov (United States)

    Pope, Christopher R; Unger, Vinzenz M

    2012-08-01

    Since its debut in the mid 1970s, electron crystallography has been a valuable alternative in the structure determination of biological macromolecules. Its reliance on single-layered or double-layered two-dimensionally ordered arrays and the ability to obtain structural information from small and disordered crystals make this approach particularly useful for the study of membrane proteins in a lipid bilayer environment. Despite its unique advantages, technological hurdles have kept electron crystallography from reaching its full potential. Addressing the issues, recent initiatives developed high-throughput pipelines for crystallization and screening. Adding progress in automating data collection, image analysis and phase extension methods, electron crystallography is poised to raise its profile and may lead the way in exploring the structural biology of macromolecular complexes. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Biological pathways and genetic mechanisms involved in social functioning

    NARCIS (Netherlands)

    Ordonana, J.R.; Bartels, M.; Boomsma, D.I.; Cella, D.; Mosing, M.; Oliveira, J.R.; Patrick, D.L.; Veenhoven, R.; Wagner, G.G.; Sprangers, M.A.G.

    2013-01-01

    Purpose: To describe the major findings in the literature regarding associations between biological and genetic factors and social functioning, paying special attention to: (1) heritability studies on social functioning and related concepts; (2) hypothesized biological pathways and genetic variants

  3. Electron Bifurcation: Thermodynamics and Kinetics of Two-Electron Brokering in Biological Redox Chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Peng; Yuly, Jonathon L.; Lubner, Carolyn E. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; Mulder, David W. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; King, Paul W. [National Renewable Energy Laboratory, Golden, Colorado 80401, United States; Peters, John W. [Institute; Beratan, David N. [Department

    2017-08-23

    How can proteins drive two electrons from a redox active donor onto two acceptors at very different potentials and distances? And how can this transaction be conducted without dissipating very much energy or violating the laws of thermodynamics? Nature appears to have addressed these challenges by coupling thermodynamically uphill and downhill electron transfer reactions, using two-electron donor cofactors that have very different potentials for the removal of the first and second electron. Although electron bifurcation is carried out with near perfection from the standpoint of energy conservation and electron delivery yields, it is a biological energy transduction paradigm that has only come into focus recently. This Account provides an exegesis of the biophysical principles that underpin electron bifurcation.

  4. Electron beam irradiation for biological decontamination of Spirulina platensis

    Energy Technology Data Exchange (ETDEWEB)

    Brasoveanu, Mirela [National Institute for Lasers, Plasma and Radiation Physics, Department of Electron Accelerators, 409 Atomistilor Street, P.O. Box MG-36, RO 76 900 Bucharest-Magurele (Romania)]. E-mail: mirela@infim.ro; Nemtanu, Monica [National Institute for Lasers, Plasma and Radiation Physics, Department of Electron Accelerators, 409 Atomistilor Street, P.O. Box MG-36, RO 76 900 Bucharest-Magurele (Romania); Minea, R. [National Institute for Lasers, Plasma and Radiation Physics, Department of Electron Accelerators, 409 Atomistilor Street, P.O. Box MG-36, RO 76 900 Bucharest-Magurele (Romania); Grecu, Maria Nicoleta [National Institute for Materials Physics, Bucharest-Magurele (Romania); Mazilu, Elena [Hofigal SA (Romania); Radulescu, Nora [Hofigal SA (Romania)

    2005-10-15

    The Cyanobacterium Spirulina is commercialized for its use in health foods and for therapeutic purposes due to its valuable constituents particularly proteins and vitamins. The aim of the paper is to study the Spirulina platensis behaviour when it is electron beam irradiated for biological decontamination. Microbial load, antioxidant activity, enzymatic inhibition, electron spin resonance (ESR) and UV-Vis spectra were measured for doses up to 80 kGy. The results were correlated with doses in order to find where decontamination is efficient, keeping the Spirulina qualities.

  5. Electron beam irradiation for biological decontamination of Spirulina platensis

    Science.gov (United States)

    Brasoveanu, Mirela; Nemtanu, Monica; Minea, R.; Grecu, Maria Nicoleta; Mazilu, Elena; Radulescu, Nora

    2005-10-01

    The Cyanobacterium Spirulina is commercialized for its use in health foods and for therapeutic purposes due to its valuable constituents particularly proteins and vitamins. The aim of the paper is to study the Spirulina platensis behaviour when it is electron beam irradiated for biological decontamination. Microbial load, antioxidant activity, enzymatic inhibition, electron spin resonance (ESR) and UV-Vis spectra were measured for doses up to 80 kGy. The results were correlated with doses in order to find where decontamination is efficient, keeping the Spirulina qualities.

  6. Regularity and approximability of electronic wave functions

    CERN Document Server

    Yserentant, Harry

    2010-01-01

    The electronic Schrödinger equation describes the motion of N-electrons under Coulomb interaction forces in a field of clamped nuclei. The solutions of this equation, the electronic wave functions, depend on 3N variables, with three spatial dimensions for each electron. Approximating these solutions is thus inordinately challenging, and it is generally believed that a reduction to simplified models, such as those of the Hartree-Fock method or density functional theory, is the only tenable approach. This book seeks to show readers that this conventional wisdom need not be ironclad: the regularity of the solutions, which increases with the number of electrons, the decay behavior of their mixed derivatives, and the antisymmetry enforced by the Pauli principle contribute properties that allow these functions to be approximated with an order of complexity which comes arbitrarily close to that for a system of one or two electrons. The text is accessible to a mathematical audience at the beginning graduate level as...

  7. Applications of Free Electron Lasers in Biology and Medicine

    International Nuclear Information System (INIS)

    Pelka, J.B.; Tybor, K.R.; Nietubyc, R.; Wrochna, G.

    2010-01-01

    The advent of free electron lasers opens up new opportunities to probe the dynamics of ultrafast processes and the structure of matter with unprecedented spatial and temporal resolution. New methods inaccessible with other known types of radiation sources can be developed, resulting in a breakthrough in deep understanding the fundamentals of life as well as in numerous medical and biological applications. In the present work the properties of free electron laser radiation that make the sources excellent for probing biological matter at an arbitrary wavelength, in a wide range of intensities and pulse durations are briefly discussed. A number of biophysical and biomedical applications of the new sources, currently considered among the most promising in the field, are presented. (author)

  8. Electron scattering from molecules and molecular aggregates of biological relevance

    Science.gov (United States)

    Gorfinkiel, Jimena D.; Ptasinska, Sylwia

    2017-09-01

    In this Topical Review we survey the current state of the art in the study of low energy electron collisions with biologically relevant molecules and molecular clusters. We briefly describe the methods and techniques used in the investigation of these processes and summarise the results obtained so far for DNA constituents and their model compounds, amino acids, peptides and other biomolecules. The applications of the data obtained is briefly described as well as future required developments.

  9. Transmission electron microscopy in molecular structural biology: A historical survey.

    Science.gov (United States)

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. A national facility for biological cryo-electron microscopy

    International Nuclear Information System (INIS)

    Saibil, Helen R.; Grünewald, Kay; Stuart, David I.

    2015-01-01

    This review provides a brief update on the use of cryo-electron microscopy for integrated structural biology, along with an overview of the plans for the UK national facility for electron microscopy being built at the Diamond synchrotron. Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback

  11. Direction, Function, and Signature in Electronic Mail.

    Science.gov (United States)

    Sherblom, John

    1988-01-01

    Presents a content analysis performed on 157 electronic mail files received over the course of several months by a middle level manager in a computer services department of a large organization. Suggests that computer mediated communication changes communication function and context in certain specific ways, which are reflected throughout the…

  12. Structure and biological functions of fungal cerebrosides

    Directory of Open Access Journals (Sweden)

    Barreto-Bergter Eliana

    2004-01-01

    Full Text Available Ceramide monohexosides (CMHs, cerebrosides are glycosphingolipids composed of a hydrophobic ceramide linked to one sugar unit. In fungal cells, CMHs are very conserved molecules consisting of a ceramide moiety containing 9-methyl-4,8-sphingadienine in amidic linkage to 2-hydroxyoctadecanoic or 2-hydroxyhexadecanoic acids, and a carbohydrate portion consisting of one residue of glucose or galactose. 9-Methyl 4,8-sphingadienine-containing ceramides are usually glycosylated to form fungal cerebrosides, but the recent description of a ceramide dihexoside (CDH presenting phytosphingosine in Magnaporthe grisea suggests the existence of alternative pathways of ceramide glycosylation in fungal cells. Along with their unique structural characteristics, fungal CMHs have a peculiar subcellular distribution and striking biological properties. In Pseudallescheria boydii, Candida albicans, Cryptococcus neoformans, Aspergillus nidulans, A. fumigatus, and Schizophyllum commune, CMHs are apparently involved in morphological transitions and fungal growth. The elucidation of structural and functional aspects of fungal cerebrosides may therefore contribute to the design of new antifungal agents inhibiting growth and differentiation of pathogenic species.

  13. Nodal Structure of the Electronic Wigner Function

    DEFF Research Database (Denmark)

    Schmider, Hartmut; Dahl, Jens Peder

    1996-01-01

    On the example of several atomic and small molecular systems, the regular behavior of nodal patterns in the electronic one-particle reduced Wigner function is demonstrated. An expression found earlier relates the nodal pattern solely to the dot-product of the position and the momentum vector......, if both arguments are large. An argument analogous to the ``bond-oscillatory principle'' for momentum densities links the nuclear framework in a molecule to an additional oscillatory term in momenta parallel to bonds. It is shown that these are visible in the Wigner function in terms of characteristic...

  14. Volume scanning electron microscopy for imaging biological ultrastructure.

    Science.gov (United States)

    Titze, Benjamin; Genoud, Christel

    2016-11-01

    Electron microscopy (EM) has been a key imaging method to investigate biological ultrastructure for over six decades. In recent years, novel volume EM techniques have significantly advanced nanometre-scale imaging of cells and tissues in three dimensions. Previously, this had depended on the slow and error-prone manual tasks of cutting and handling large numbers of sections, and imaging them one-by-one with transmission EM. Now, automated volume imaging methods mostly based on scanning EM (SEM) allow faster and more reliable acquisition of serial images through tissue volumes and achieve higher z-resolution. Various software tools have been developed to manipulate the acquired image stacks and facilitate quantitative analysis. Here, we introduce three volume SEM methods: serial block-face electron microscopy (SBEM), focused ion beam SEM (FIB-SEM) and automated tape-collecting ultramicrotome SEM (ATUM-SEM). We discuss and compare their capabilities, provide an overview of the full volume SEM workflow for obtaining 3D datasets and showcase different applications for biological research. © 2016 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

  15. Electron probe analysis of biological fluids: Possibilities and limitations

    International Nuclear Information System (INIS)

    Roinel, N.

    1984-01-01

    Physical methods of investigation have become essential to investigations at the cellular or subcellular level. Nuclear magnetic resonance is the most recent and striking example, since it is not only a tool for fundamental physicists and organic chemists, but also an extraordinary powerful imaging tool for physicians. The absorption properties of X rays were used immediately after their discovery to image the bones of skeletons. Later, X rays were also found to be extremely efficient in the measurement of the elemental content of microvolumes irradiated by electron probes. The electron probe analyzer (EPA) was immediately adopted by numerous laboratories of metallurgy, geology, and mineral sciences. In the last fifteen years, since the use of this instrument was suggested for liquid analysis, and a preparative technique was developed, the EPA has been used by an increasing number of biological laboratories for measuring the concentrations of the elements contained in subnanoliter volumes of biological fluids. The so-called microdroplet technique has become a routine laboratory method, the only one able to measure the concentrations of an unlimited number of elements in a single 0.1-nl sample. This explains its use in fields as various as renal, reproductive, digestive, and plant physiology, zoology, etc. Several review papers discuss these applications. The possibilities and limitations of the technique are discussed below

  16. Low Voltage Transmission Electron Microscopy in Cell Biology.

    Science.gov (United States)

    Bendayan, Moise; Paransky, Eugene

    2015-07-01

    Low voltage transmission electron microscopy (LVTEM) was employed to examine biological tissues with accelerating voltages as low as 5kV. Tissue preparation was modified to take advantage of the low-voltage techniques. Treatments with heavy metals, such as post-fixation with osmium tetroxide, on block and counterstaining were omitted. Sections (40nm) were thinner than usual and generated highly contrasted images. General appearance of the cells remains similar to that of conventional TEM. New features were however revealed. The matrix of the pancreatic granules displays heterogeneity with partitions that may correspond to the inner-segregation of their secretory proteins. Mitochondria revealed the presence of the ATP synthase granules along their cristea. The nuclear dense chromatin displayed a honeycomb organization while distinct beads, nucleosomes, aligned along thin threads were seen in the dispersed chromatin. Nuclear pore protein complexes revealed their globular nature. The intercalated disks in cardiac muscle displayed their fine structural organization. These features correlate well with data described or predicted by cell and molecular biology. These new aspects are not revealed when thicker and conventionally osmicated tissue sections were examined by LVTEM, indicating that major masking effects are associated with standard TEM techniques. Immunogold was adapted to LVTEM further enhancing its potential in cell biology. Copyright © 2015 Elsevier GmbH. All rights reserved.

  17. Feedback dynamics and cell function: Why systems biology is called Systems Biology.

    Science.gov (United States)

    Wolkenhauer, Olaf; Mesarovic, Mihajlo

    2005-05-01

    A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

  18. Three-Dimensional scanning transmission electron microscopy of biological specimens

    KAUST Repository

    De Jonge, Niels

    2010-01-18

    A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2-3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset. © 2010 Microscopy Society of America.

  19. Marine Carotenoids: Biological Functions and Commercial Applications

    NARCIS (Netherlands)

    Vilchez, C.; Forján, E.; Cuaresma, M.; Bédmar, F.; Garbayo, I.; Vega, J.M.

    2011-01-01

    Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological

  20. Modelling low energy electron and positron tracks in biologically relevant media

    International Nuclear Information System (INIS)

    Blanco, F.; Munoz, A.; Almeida, D.; Ferreira da Silva, F.; Limao-Vieira, P.; Fuss, M.C.; Sanz, A.G.; Garcia, G.

    2013-01-01

    This colloquium describes an approach to incorporate into radiation damage models the effect of low and intermediate energy (0-100 eV) electrons and positrons, slowing down in biologically relevant materials (water and representative biomolecules). The core of the modelling procedure is a C++ computing programme named 'Low Energy Particle Track Simulation (LEPTS)', which is compatible with available general purpose Monte Carlo packages. Input parameters are carefully selected from theoretical and experimental cross section data and energy loss distribution functions. Data sources used for this purpose are reviewed showing examples of electron and positron cross section and energy loss data for interactions with different media of increasing complexity: atoms, molecules, clusters and condense matter. Finally, we show how such a model can be used to develop an effective dosimetric tool at the molecular level (i.e. nanodosimetry). Recent experimental developments to study the fragmentation induced in biologically material by charge transfer from neutrals and negative ions are also included. (authors)

  1. Function-Based Algorithms for Biological Sequences

    Science.gov (United States)

    Mohanty, Pragyan Sheela P.

    2015-01-01

    Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented…

  2. Electron work function of stepped tungsten surfaces

    International Nuclear Information System (INIS)

    Krahl-Urban, B.

    1976-03-01

    The electron work function of tungsten (110) vicinal faces was measured with the aid of thermionic emission, and its dependence on the crystallographic orientation and the surface structure was investigated. The thermionic measurements were evaluated with the aid of the Richardson plot. The real temperature of the emitting tungsten faces was determined with an accuracy of +- 0.5% in the range between 2,200 and 2,800 K. The vicinal faces under investigation have been prepared with an orientation exactness of +- 15'. In the tungsten (110) vicinal faces under investigation, a strong dependence of the temperature coefficient d PHI/dT of the work function on the crystallographic orientation was found. A strong influence of the edge structure as well as of the step density on the temperature coefficient was observed. (orig./HPOE) [de

  3. A national facility for biological cryo-electron microscopy.

    Science.gov (United States)

    Saibil, Helen R; Grünewald, Kay; Stuart, David I

    2015-01-01

    Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback.

  4. A stochastic model of protein conformational dynamics and electronic-conformational coupling in biological energy transduction

    Science.gov (United States)

    Cartling, Bo

    1985-11-01

    The principles of biological energy transduction are discussed by means of a mathematical model of a donor-acceptor system of electron transfer enzymes in which electronic and conformational states are coupled. The internal nuclear motion of the enzymes is considered to be composed of transitions between local potential energy wells, which define conformational states, and vibrations within these. The conformational transitions are treated as a stochastic process of the diffusion type on a conformational potential energy surface. Dissipative processes are avoided by restricting electron transfer with respect to conformational states and molecular mechanisms of such electron gating are discussed. Different types of transient kinetics, determined by the relative rates of electronic and conformational transitions, are demonstrated in terms of probability density functions, which describe the probability for the system to be in different electronic and conformational states as a function of time. The experimental basis for the concepts and mechanisms introduced is discussed and further experiments are proposed. The applicability of the mathematical model to other systems is indicated.

  5. A functional overview of conservation biological control

    DEFF Research Database (Denmark)

    Begg, Graham S; Cook, Samantha M; Dye, Richard

    2017-01-01

    Conservation biological control (CBC) is a sustainable approach to pest management that can contribute to a reduction in pesticide use as part of an Integrated Pest Management (IPM) strategy. CBC is based on the premise that countering habitat loss and environmental disturbance associated...... limitation to the development of effective CBC is due to a failure to adequately direct biological control services to achieve suppression of the target pests. By considering the performance of these and other components of CBC within the context of an integrated system, we believe that the limiting factors...... with intensive crop production will conserve natural enemies, thus contributing to pest suppression. The abundance and diversity of natural enemies increases in response to a variety of conservation measures, including plant and habitat diversification, a reduction in cropping intensity, and increased landscape...

  6. Photo-induced regeneration of hormones by electron transfer processes: Potential biological and medical consequences

    Energy Technology Data Exchange (ETDEWEB)

    Getoff, Nikola, E-mail: nikola.getoff@univie.ac.a [Section of Radiation Biology, Faculty of Life Sciences, University of Vienna, A-1090 Vienna (Austria); Hartmann, Johannes [Department of Gynecologic Endocrinology and Reproduction, Medical University of Vienna, A-1090 Vienna (Austria); Schittl, Heike [Section of Radiation Biology, Faculty of Life Sciences, University of Vienna, A-1090 Vienna (Austria); Gerschpacher, Marion [Department of Gynecologic Endocrinology and Reproduction, Medical University of Vienna, A-1090 Vienna (Austria); Quint, Ruth Maria [Section of Radiation Biology, Faculty of Life Sciences, University of Vienna, A-1090 Vienna (Austria)

    2011-08-15

    Based on the previous results concerning electron transfer processes in biological substances, it was of interest to investigate if hormone transients resulting by e.g. electron emission can be regenerated. The presented results prove for the first time that the hormone transients originating by the electron emission process can be successfully regenerated by the transfer of electrons from a potent electron donor, such as vitamin C (VitC). Investigations were performed using progesterone (PRG), testosterone (TES) and estrone (E1) as representatives of hormones. By irradiation with monochromatic UV light ({lambda}=254 nm) in a media of 40% water and 60% ethanol, the degradation as well as the regeneration of the hormones was studied with each hormone individually and in the mixture with VitC as a function of the absorbed UV dose, using HPLC. Calculated from the obtained initial yields, the determined regeneration of PRG amounted to 52.7%, for TES to 58.6% and for E1 to 90.9%. The consumption of VitC was determined in the same way. The reported results concerning the regeneration of hormones by the transfer of electrons from an electron donor offer a new, promising method for the therapy with hormones. As a consequence of the regeneration of hormones, a decreased formation of carcinogenic metabolites is expected.

  7. Photo-induced regeneration of hormones by electron transfer processes: Potential biological and medical consequences

    International Nuclear Information System (INIS)

    Getoff, Nikola; Hartmann, Johannes; Schittl, Heike; Gerschpacher, Marion; Quint, Ruth Maria

    2011-01-01

    Based on the previous results concerning electron transfer processes in biological substances, it was of interest to investigate if hormone transients resulting by e.g. electron emission can be regenerated. The presented results prove for the first time that the hormone transients originating by the electron emission process can be successfully regenerated by the transfer of electrons from a potent electron donor, such as vitamin C (VitC). Investigations were performed using progesterone (PRG), testosterone (TES) and estrone (E1) as representatives of hormones. By irradiation with monochromatic UV light (λ=254 nm) in a media of 40% water and 60% ethanol, the degradation as well as the regeneration of the hormones was studied with each hormone individually and in the mixture with VitC as a function of the absorbed UV dose, using HPLC. Calculated from the obtained initial yields, the determined regeneration of PRG amounted to 52.7%, for TES to 58.6% and for E1 to 90.9%. The consumption of VitC was determined in the same way. The reported results concerning the regeneration of hormones by the transfer of electrons from an electron donor offer a new, promising method for the therapy with hormones. As a consequence of the regeneration of hormones, a decreased formation of carcinogenic metabolites is expected.

  8. Functionalized apertures for the detection of chemical and biological materials

    Science.gov (United States)

    Letant, Sonia E.; van Buuren, Anthony W.; Terminello, Louis J.; Thelen, Michael P.; Hope-Weeks, Louisa J.; Hart, Bradley R.

    2010-12-14

    Disclosed are nanometer to micron scale functionalized apertures constructed on a substrate made of glass, carbon, semiconductors or polymeric materials that allow for the real time detection of biological materials or chemical moieties. Many apertures can exist on one substrate allowing for the simultaneous detection of numerous chemical and biological molecules. One embodiment features a macrocyclic ring attached to cross-linkers, wherein the macrocyclic ring has a biological or chemical probe extending through the aperture. Another embodiment achieves functionalization by attaching chemical or biological anchors directly to the walls of the apertures via cross-linkers.

  9. Electron reactions in model liquids and biological systems

    International Nuclear Information System (INIS)

    Bakale, G.; Gregg, E.C.

    1982-01-01

    Progress is reported in the following studies: (1) Field-dependent electron attachment; (2) Dependence of electron attachment rate on electron-acceptor dipole moment; (3) Electron attachment in i-octane/TMS mixtures; (4) Electron attachment/detachment equilibria; (5) Electron attachment to reversed micelles; (6) Electron attachment to chemical carcinogens; (7) Radiation-induced bacterial mutagenesis; and (8) Bacterial mutagenicity of nitrobenzene derivatives. 14 references

  10. Electron transfer behaviour of biological macromolecules towards the single-molecule level

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Grubb, Mikala; Hansen, Allan Glargaard

    2003-01-01

    electron transfer (ET) function retained. In situ STM can also address the microscopic mechanisms for electron tunnelling through the biomolecules and offers novel notions such as coherent multi-ET between the substrate and tip via the molecular redox levels. This differs in important respects from...... is combined with state-of-the-art physical electrochemistry with emphasis on single-crystal, atomically planar electrode surfaces, in situ scanning tunnelling microscopy (STM) and other surface techniques. These approaches have brought bioelectrochemistry important steps forward towards the nanoscale...... electrochemical ET at a single metal/electrolyte interface. Similar data for a short oligonucleotide immobilized on Au(111) show that oligonucleotides can be characterized with comparable detail, with novel perspectives for addressing DNA electronic conduction mechanisms and for biological screening towards...

  11. Functionalized Nanodiamonds for Biological and Medical Applications.

    Science.gov (United States)

    Lai, Lin; Barnard, Amanda S

    2015-02-01

    Nanodiamond is a promising material for biological and medical applications, owning to its relatively inexpensive and large-scale synthesis, unique structure, and superior optical properties. However, most biomedical applications, such as drug delivery and bio-imaging, are dependent upon the precise control of the surfaces, and can be significantly affected by the type, distribution and stability of chemical funtionalisations of the nanodiamond surface. In this paper, recent studies on nanodiamonds and their biomedical applications by conjugating with different chemicals are reviewed, while highlighting the critical importance of surface chemical states for various applications.

  12. Electron energy loss spectroscopy microanalysis and imaging in the transmission electron microscope: example of biological applications

    International Nuclear Information System (INIS)

    Diociaiuti, Marco

    2005-01-01

    This paper reports original results obtained in our laboratory over the past few years in the application of both electron energy loss spectroscopy (EELS) and electron spectroscopy imaging (ESI) to biological samples, performed in two transmission electron microscopes (TEM) equipped with high-resolution electron filters and spectrometers: a Gatan model 607 single magnetic sector double focusing EEL serial spectrometer attached to a Philips 430 TEM and a Zeiss EM902 Energy Filtering TEM. The primary interest was on the possibility offered by the combined application of these spectroscopic techniques with those offered by the TEM. In particular, the electron beam focusing available in a TEM allowed us to perform EELS and ESI on very small sample volumes, where high-resolution imaging and electron diffraction techniques can provide important structural information. I show that ESI was able to improve TEM performance, due to the reduced chromatic aberration and the possibility of avoiding the sample staining procedure. Finally, the analysis of the oscillating extended energy loss fine structure (EXELFS) beyond the ionization edges characterizing the EELS spectra allowed me, in a manner very similar to the extended X-ray absorption fine structure (EXAFS) analysis of the X-ray absorption spectra, to obtain short-range structural information for such light elements of biological interest as O or Fe. The Philips EM430 (250-300 keV) TEM was used to perform EELS microanalysis on Ca, P, O, Fe, Al and Si. The assessment of the detection limits of this method was obtained working with well-characterized samples containing Ca and P, and mimicking the actual cellular matrix. I applied EELS microanalysis to Ca detection in bone tissue during the mineralization process and to P detection in the cellular membrane of erythrocytes treated with an anti-tumoral drug, demonstrating that the cellular membrane is a drug target. I applied EELS microanalysis and selected area electron

  13. Free Electron Laser Synthesis of Functional Coatings

    Science.gov (United States)

    Schaaf, Peter; Höche, Daniel

    Functional and smart surfaces and coatings play an increasingly decisive role in the applicability and performance of modern materials. From an industrial point of view, there is a great interest with respect to friction, wear, corrosion, and further properties. Many methods have been developed for the improvement of the respective surface and material properties. Traditionally, these treatments range from simple PVD and CVD processes to complicated plasma and hybrid methods. Recently, it has been established that short laser pulses of high energy can induce a direct laser synthesis of functional coatings if the material's surface is irradiated in a reactive atmosphere. The process is based on a complicated combination of laser plasma - gas - material surface interactions. Tests for steel, aluminum, magnesium, titanium, and silicon in nitrogen, methane, and hydrogen atmospheres have been carried out successfully; with these materials, interesting coatings can be produced by direct laser synthesis, for example, AlN and SiC. Various laser types can be used for this purpose: Excimer, Nd:YAG, CO2 Laser, and even the free electron laser (FEL).

  14. Explaining Biological Functionality: Is Control Theory Enough ...

    African Journals Online (AJOL)

    I argue that the etiological approach, as understood in terms of control theory, suffers from a problem of symmetry, by which function can equally well be placed in the environment as in the organism. Focusing on the autonomy view, I note that it can be understood to some degree in terms of control theory in its version called ...

  15. Towards Integration of Biological and Physiological Functions at Multiple Levels

    Directory of Open Access Journals (Sweden)

    Taishin eNomura

    2010-12-01

    Full Text Available An aim of systems physiology today can be stated as to establish logical and quantitative bridges between phenomenological attributes of physiological entities such as cells and organs and physical attributes of biological entities, i.e., biological molecules, allowing us to describe and better understand physiological functions in terms of underlying biological functions. This article illustrates possible schema that can be used for promoting systems physiology by integrating quantitative knowledge of biological and physiological functions at multiple levels of time and space with the use of information technology infrastructure. Emphasis will be made for systematic, modular, hierarchical, and standardized descriptions of mathematical models of the functions and advantages for the use of them.

  16. Hybrid functional microfibers for textile electronics and biosensors

    Science.gov (United States)

    Nanda Sahoo, Bichitra; Choi, Byungwoo; Seo, Jungmok; Lee, Taeyoon

    2018-01-01

    Fibers are low-cost substrates that are abundantly used in our daily lives. This review highlights recent advances in the fabrication and application of multifunctional fibers to achieve fibers with unique functions for specific applications ranging from textile electronics to biomedical applications. By incorporating various nanomaterials such as carbon nanomaterials, metallic nanomaterials, and hydrogel-based biomaterials, the functions of fibers can be precisely engineered. This review also highlights the performance of the functional fibers and electronic materials incorporated with textiles and demonstrates their practical application in pressure/tensile sensors, chemical/biosensors, and drug delivery. Textile technologies in which fibers containing biological factors and cells are formed and assembled into constructions with biomimetic properties have attracted substantial attention in the field of tissue engineering. We also discuss the current limitations of functional textile-based devices and their prospects for use in various future applications. Project supported by the Priority Research Centers Program (No. 2012-0006689) through the National Research Foundation (NRF) of Korea funded by the Ministry of Education, Science and Technology (MEST) and the R&D program of MOTIE/KEIT [10064081, Development of fiber-based flexible multimodal pressure sensor and algorithm for gesture/posture-recognizable wearable devices]. We gratefully acknowledge partial support from the National Research Foundation of Korea (No. NRF-2017K2A9A2A06013377, NRF-2017M3A7B4049466) and the Yonsei University Future-leading Research Initiative and Implantable artificial electronic skin for an ubiquitous healthcare system of 2016-12-0050. This work is also supported by KIST Project (Nos. 2E26900, 2E27630). Dr. Seo was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (No. 2016R1A6A3A03006491).

  17. Printable Bioelectronics To Investigate Functional Biological Interfaces.

    Science.gov (United States)

    Manoli, Kyriaki; Magliulo, Maria; Mulla, Mohammad Yusuf; Singh, Mandeep; Sabbatini, Luigia; Palazzo, Gerardo; Torsi, Luisa

    2015-10-19

    Thin-film transistors can be used as high-performance bioelectronic devices to accomplish tasks such as sensing or controlling the release of biological species as well as transducing the electrical activity of cells or even organs, such as the brain. Organic, graphene, or zinc oxide are used as convenient printable semiconducting layers and can lead to high-performance low-cost bioelectronic sensing devices that are potentially very useful for point-of-care applications. Among others, electrolyte-gated transistors are of interest as they can be operated as capacitance-modulated devices, because of the high capacitance of their charge double layers. Specifically, it is the capacitance of the biolayer, being lowest in a series of capacitors, which controls the output current of the device. Such an occurrence allows for extremely high sensitivity towards very weak interactions. All the aspects governing these processes are reviewed here. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Genomic Functionalization: The Next Revolution In Biology

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Peter [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Schoeniger, Joseph S. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Imbro, Paula M. [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

    2014-07-01

    We have implemented a ligand-alignment algorithm into our developed computational pipeline for identifying specificity-determining features (SDFs) in protein-ligand complexes. Given a set of protein-ligand complex structures, the algorithm aligns the complexes by ligand rather than by the C -RMSD or standard approach, providing a single reference frame for extracting SDFs. We anticipate that this ligand-alignment capability will be highly useful for protein function prediction. We already have a database containing > 20 K ligand-protein complex crystal structures taken from the Protein Data Bank. By aligning these proteins to single reference frames using ligand alignment, we can submit the complexes to our pipeline for SDF extraction. The SDFs derived from this training procedure can be used as thumbprints that are hallmarks of individual enzyme classes. These SDF thumbprints may then serve as guides to the prediction of function of new unknown proteins.

  19. Biofabricated film with enzymatic and redox-capacitor functionalities to harvest and store electrons

    International Nuclear Information System (INIS)

    Liba, Benjamin D; Kim, Eunkyoung; Martin, Alexandra N; Liu Yi; Bentley, William E; Payne, Gregory F

    2013-01-01

    Exciting opportunities in bioelectronics will be facilitated by materials that can bridge the chemical logic of biology and the digital logic of electronics. Here we report the fabrication of a dual functional hydrogel film that can harvest electrons from its chemical environment and store these electrons by switching the film's redox-state. The hydrogel scaffold was formed by the anodic deposition of the aminopolysaccharide chitosan. Electron-harvesting function was conferred by co-depositing the enzyme glucose dehydrogenase (GDH) with chitosan. GDH catalyzes the transfer of electrons from glucose to the soluble redox-shuttle NADP + . Electron-storage function was conferred by the redox-active food phenolic chlorogenic acid (CA) that was enzymatically grafted to the chitosan scaffold using tyrosinase. The grafted CA undergoes redox-cycling reactions with NADPH resulting in the net transfer of electrons to the film where they are stored in the reduced state of CA. The individual and dual functionalities of these films were demonstrated experimentally. There are three general conclusions from this proof-of-concept study. First, enzymatically-grafted catecholic moieties confer redox-capacitor function to the chitosan scaffold. Second, biological materials (i.e. chitosan and CA) and mechanisms (i.e. tyrosinase-mediated grafting) allow the reagentless fabrication of functional films that should be environmentally-friendly, safe and potentially even edible. Finally, the film's ability to mediate the transfer of electrons from a biological metabolite to an electrode suggests an approach to bridge the chemical logic of biology with the digital logic of electronics. (paper)

  20. Biofabricated film with enzymatic and redox-capacitor functionalities to harvest and store electrons.

    Science.gov (United States)

    Liba, Benjamin D; Kim, Eunkyoung; Martin, Alexandra N; Liu, Yi; Bentley, William E; Payne, Gregory F

    2013-03-01

    Exciting opportunities in bioelectronics will be facilitated by materials that can bridge the chemical logic of biology and the digital logic of electronics. Here we report the fabrication of a dual functional hydrogel film that can harvest electrons from its chemical environment and store these electrons by switching the film's redox-state. The hydrogel scaffold was formed by the anodic deposition of the aminopolysaccharide chitosan. Electron-harvesting function was conferred by co-depositing the enzyme glucose dehydrogenase (GDH) with chitosan. GDH catalyzes the transfer of electrons from glucose to the soluble redox-shuttle NADP(+). Electron-storage function was conferred by the redox-active food phenolic chlorogenic acid (CA) that was enzymatically grafted to the chitosan scaffold using tyrosinase. The grafted CA undergoes redox-cycling reactions with NADPH resulting in the net transfer of electrons to the film where they are stored in the reduced state of CA. The individual and dual functionalities of these films were demonstrated experimentally. There are three general conclusions from this proof-of-concept study. First, enzymatically-grafted catecholic moieties confer redox-capacitor function to the chitosan scaffold. Second, biological materials (i.e. chitosan and CA) and mechanisms (i.e. tyrosinase-mediated grafting) allow the reagentless fabrication of functional films that should be environmentally-friendly, safe and potentially even edible. Finally, the film's ability to mediate the transfer of electrons from a biological metabolite to an electrode suggests an approach to bridge the chemical logic of biology with the digital logic of electronics.

  1. Urban Biomining: Biological Extraction of Metals and Materials from Electronics Waste Using a Synthetic Biology Approach

    Science.gov (United States)

    Urbina-Navarrete, J.; Rothschild, L.

    2016-12-01

    End-of-life electronics waste (e-waste) containing toxic and valuable materials is a rapidly progressing human health and environmental issue. Using synthetic biology tools, we have developed a recycling method for e-waste. Our innovation is to use a recombinant version of a naturally-occurring silica-degrading enzyme to depolymerize the silica in metal- and glass- containing e-waste components, and subsequently, to use engineered bacterial surfaces to bind and separate metals from a solution. The bacteria with bound metals can then be used as "bio-ink" to print new circuits using a novel plasma jet electronics printing technology. Here, we present the results from our initial studies that focus on the specificity of metal-binding motifs for a cognate metal. The candidate motifs that show high affinity and specificity will be engineered into bacterial surfaces for downstream applications in biologically-mediated metal recycling. Since the chemistry and role of Cu in metalloproteins is relatively well-characterized, we are using Cu as a proxy to elucidate metal and biological ligand interactions with various metals in e-waste. We assess the binding parameters of 3 representative classes of Cu-binding motifs using isothermal titration calorimetry; 1) natural motifs found in metalloproteins, 2) consensus motifs, and 3) rationally designed peptides that are predicted, in silico, to bind Cu. Our results indicate that naturally-occurring motifs have relative high affinity and specificity for Cu (association constant for Cu Ka 104 M-1, Zn Ka 103 M-1) when competing ions are present in the aqueous milieu. However, motifs developed through rational design by applying quantum mechanical methods that take into account complexation energies of the elemental binding partners and molecular geometry of the cognate metal, not only show high affinity for the cognate metal (Cu Ka 106 M-1), but they show specificity and discrimination against other metal ions that would be

  2. Electron localization functions and local measures of the covariance

    Indian Academy of Sciences (India)

    The electron localization measure proposed by Becke and Edgecombe is shown to be related to the covariance of the electron pair distribution. Just as with the electron localization function, the local covariance does not seem to be, in and of itself, a useful quantity for elucidating shell structure. A function of the local ...

  3. Mass determination based on electron scattering in electron probe X-ray microanalysis of thin biological specimens

    International Nuclear Information System (INIS)

    Linders, P.W.J.

    1984-01-01

    This thesis describes the development of a method for mass determination of thin biological objects by quantitative electron microscopy. The practical realization of the mass determination consists of photographical recording with subsequent densitometry. (Auth.)

  4. Nano-Bio Electrochemical Interfacing-Linking Cell Biology and Micro-Electronics

    Science.gov (United States)

    Shacham-Diamand, Y.; Popovtzer, R.; Rishpon, Y.

    Integration of biological substance within electronic devices is an innovative and challenging area combining recent progress in molecular biology and micro technology. First, we introduce the concept of integrating living cells with Micro Electro Mechanical Systems (MEMS). Following a brief overview on "whole cell based biosensors" we describe the design, fabrication, and process of a biocompatible electrochemical "Lab-on-a-Chip" system. Demonstrating the application of electrochemical interfacing based whole cell bio chips, we present two different configurations: a. integration of prokaryotic cells (bacteria) for water toxicity detection, and b. integration of eukaryotic cells (human colon cancer cells) for rapid evaluation of the effectiveness of drug treatments. Both applications, with either microbes or mammalian cells integrated onto MEMS based biochips with liquid volume in the range of 100 nL-1 μL, function well and yield a detectable signal much higher than noise level after few minutes.

  5. A dynamic model for functional mapping of biological rhythms.

    Science.gov (United States)

    Fu, Guifang; Luo, Jiangtao; Berg, Arthur; Wang, Zhong; Li, Jiahan; Das, Kiranmoy; Li, Runze; Wu, Rongling

    2011-01-01

    Functional mapping is a statistical method for mapping quantitative trait loci (QTLs) that regulate the dynamic pattern of a biological trait. This method integrates mathematical aspects of biological complexity into a mixture model for genetic mapping and tests the genetic effects of QTLs by comparing genotype-specific curve parameters. As a way of quantitatively specifying the dynamic behavior of a system, differential equations have proven to be powerful for modeling and unraveling the biochemical, molecular, and cellular mechanisms of a biological process, such as biological rhythms. The equipment of functional mapping with biologically meaningful differential equations provides new insights into the genetic control of any dynamic processes. We formulate a new functional mapping framework for a dynamic biological rhythm by incorporating a group of ordinary differential equations (ODE). The Runge-Kutta fourth order algorithm was implemented to estimate the parameters that define the system of ODE. The new model will find its implications for understanding the interplay between gene interactions and developmental pathways in complex biological rhythms.

  6. Evidence for a Role of Executive Functions in Learning Biology

    Science.gov (United States)

    Rhodes, Sinéad M.; Booth, Josephine N.; Campbell, Lorna Elise; Blythe, Richard A.; Wheate, Nial J.; Delibegovic, Mirela

    2014-01-01

    Research examining cognition and science learning has focused on working memory, but evidence implicates a broader set of executive functions. The current study examined executive functions and learning of biology in young adolescents. Fifty-six participants, aged 12-13?years, completed tasks of working memory (Spatial Working Memory), inhibition…

  7. X-rays in the Cryo-Electron Microscopy Era: Structural Biology's Dynamic Future.

    Science.gov (United States)

    Shoemaker, Susannah C; Ando, Nozomi

    2018-01-23

    Over the past several years, single-particle cryo-electron microscopy (cryo-EM) has emerged as a leading method for elucidating macromolecular structures at near-atomic resolution, rivaling even the established technique of X-ray crystallography. Cryo-EM is now able to probe proteins as small as hemoglobin (64 kDa) while avoiding the crystallization bottleneck entirely. The remarkable success of cryo-EM has called into question the continuing relevance of X-ray methods, particularly crystallography. To say that the future of structural biology is either cryo-EM or crystallography, however, would be misguided. Crystallography remains better suited to yield precise atomic coordinates of macromolecules under a few hundred kilodaltons in size, while the ability to probe larger, potentially more disordered assemblies is a distinct advantage of cryo-EM. Likewise, crystallography is better equipped to provide high-resolution dynamic information as a function of time, temperature, pressure, and other perturbations, whereas cryo-EM offers increasing insight into conformational and energy landscapes, particularly as algorithms to deconvolute conformational heterogeneity become more advanced. Ultimately, the future of both techniques depends on how their individual strengths are utilized to tackle questions at the frontiers of structural biology. Structure determination is just one piece of a much larger puzzle: a central challenge of modern structural biology is to relate structural information to biological function. In this perspective, we share insight from several leaders in the field and examine the unique and complementary ways in which X-ray methods and cryo-EM can shape the future of structural biology.

  8. Biological Applications and Transmission Electron Microscopy Investigations of Mesoporous Silica Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Trewyn, Brian G. [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    The research presented and discussed within involves the development of novel biological applications of mesoporous silica nanoparticles (MSN) and an investigation of mesoporous material by transmission electron microscopy (TEM). Mesoporous silica nanoparticles organically functionalized shown to undergo endocytosis in cancer cells and drug release from the pores was controlled intracellularly and intercellularly. Transmission electron microscopy investigations demonstrated the variety of morphologies produced in this field of mesoporous silica nanomaterial synthesis. A series of room-temperature ionic liquid (RTIL) containing mesoporous silica nanoparticle (MSN) materials with various particle morphologies, including spheres, ellipsoids, rods, and tubes, were synthesized. By changing the RTIL template, the pore morphology was tuned from the MCM-41 type of hexagonal mesopores to rotational moire type of helical channels, and to wormhole-like porous structures. These materials were used as controlled release delivery nanodevices to deliver antibacterial ionic liquids against Escherichia coli K12. The involvement of a specific organosiloxane function group, covalently attached to the exterior of fluorescein doped mesoporous silica nanoparticles (FITC-MSN), on the degree and kinetics of endocytosis in cancer and plant cells was investigated. The kinetics of endocystosis of TEG coated FITC-MSN is significantly quicker than FITC-MSN as determined by flow cytometry experiments. The fluorescence confocal microscopy investigation showed the endocytosis of TEG coated-FITC MSN triethylene glycol grafted fluorescein doped MSN (TEG coated-FITC MSN) into both KeLa cells and Tobacco root protoplasts. Once the synthesis of a controlled-release delivery system based on MCM-41-type mesoporous silica nanorods capped by disulfide bonds with superparamagnetic iron oxide nanoparticles was completed. The material was characterized by general methods and the dosage and kinetics of the

  9. Monitoring Chemical and Biological Electron Transfer Reactions with a Fluorogenic Vitamin K Analogue Probe.

    Science.gov (United States)

    Belzile, Mei-Ni; Godin, Robert; Durantini, Andrés M; Cosa, Gonzalo

    2016-12-21

    We report herein the design, synthesis, and characterization of a two-segment fluorogenic analogue of vitamin K, B-VK Q , prepared by coupling vitamin K 3 , also known as menadione (a quinone redox center), to a boron-dipyrromethene (BODIPY) fluorophore (a lipophilic reporter segment). Oxidation-reduction reactions, spectroelectrochemical studies, and enzymatic assays conducted in the presence of DT-diaphorase illustrate that the new probe shows reversible redox behavior on par with that of vitamin K, provides a high-sensitivity fluorescence signal, and is compatible with biological conditions, opening the door to monitor remotely (i.e., via imaging) redox processes in real time. In its oxidized form, B-VK Q is non-emissive, while upon reduction to the hydroquinone form, B-VK QH 2 , BODIPY fluorescence is restored, with emission quantum yield values of ca. 0.54 in toluene. Density functional theory studies validate a photoinduced electron transfer intramolecular switching mechanism, active in the non-emissive quinone form and deactivated upon reduction to the emissive dihydroquinone form. Our results highlight the potential of B-VK Q as a fluorogenic probe to study electron transfer and transport in model systems and biological structures with optimal sensitivity and desirable chemical specificity. Use of such a probe may enable a better understanding of the role that vitamin K plays in biological redox reactions ubiquitous in key cellular processes, and help elucidate the mechanism and pathological significance of these reactions in biological systems.

  10. Relations among several nuclear and electronic density functional reactivity indexes

    Science.gov (United States)

    Torrent-Sucarrat, Miquel; Luis, Josep M.; Duran, Miquel; Toro-Labbé, Alejandro; Solà, Miquel

    2003-11-01

    An expansion of the energy functional in terms of the total number of electrons and the normal coordinates within the canonical ensemble is presented. A comparison of this expansion with the expansion of the energy in terms of the total number of electrons and the external potential leads to new relations among common density functional reactivity descriptors. The formulas obtained provide explicit links between important quantities related to the chemical reactivity of a system. In particular, the relation between the nuclear and the electronic Fukui functions is recovered. The connection between the derivatives of the electronic energy and the nuclear repulsion energy with respect to the external potential offers a proof for the "Quantum Chemical le Chatelier Principle." Finally, the nuclear linear response function is defined and the relation of this function with the electronic linear response function is given.

  11. DFT-based Green's function pathways model for prediction of bridge-mediated electronic coupling.

    Science.gov (United States)

    Berstis, Laura; Baldridge, Kim K

    2015-12-14

    A density functional theory-based Green's function pathway model is developed enabling further advancements towards the long-standing challenge of accurate yet inexpensive prediction of electron transfer rate. Electronic coupling predictions are demonstrated to within 0.1 eV of experiment for organic and biological systems of moderately large size, with modest computational expense. Benchmarking and comparisons are made across density functional type, basis set extent, and orbital localization scheme. The resulting framework is shown to be flexible and to offer quantitative prediction of both electronic coupling and tunneling pathways in covalently bound non-adiabatic donor-bridge-acceptor (D-B-A) systems. A new localized molecular orbital Green's function pathway method (LMO-GFM) adaptation enables intuitive understanding of electron tunneling in terms of through-bond and through-space interactions.

  12. Advances in imaging and electron physics time resolved electron diffraction for chemistry, biology and material science

    CERN Document Server

    Hawkes, Peter W

    2014-01-01

    Advances in Imaging & Electron Physics merges two long-running serials-Advances in Electronics & Electron Physics and Advances in Optical & Electron Microscopy. The series features extended articles on the physics of electron devices (especially semiconductor devices), particle optics at high and low energies, microlithography, image science and digital image processing, electromagnetic wave propagation, electron microscopy, and the computing methods used in all these domains. Contributions from leading authorities Informs and updates on all the latest developments in the field.

  13. Uncovering Biological Network Function via Graphlet Degree Signatures

    Directory of Open Access Journals (Sweden)

    Nataša Pržulj

    2008-01-01

    Full Text Available Motivation: Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker’s yeast. Methods for determining protein function have shifted their focus from targeting specific proteins based solely on sequence homology to analyses of the entire proteome based on protein-protein interaction (PPI networks. Since proteins interact to perform a certain function, analyzing structural properties of PPI networks may provide useful clues about the biological function of individual proteins, protein complexes they participate in, and even larger subcellular machines.Results: We design a sensitive graph theoretic method for comparing local structures of node neighborhoods that demonstrates that in PPI networks, biological function of a node and its local network structure are closely related. The method summarizes a protein’s local topology in a PPI network into the vector of graphlet degrees called the signature of the protein and computes the signature similarities between all protein pairs. We group topologically similar proteins under this measure in a PPI network and show that these protein groups belong to the same protein complexes, perform the same biological functions, are localized in the same subcellular compartments, and have the same tissue expressions. Moreover, we apply our technique on a proteome-scale network data and infer biological function of yet unclassified proteins demonstrating that our method can provide valuable guidelines for future experimental research such as disease protein prediction.Availability: Data is available upon request.

  14. High-Frequency Electron Paramagnetic Resonance Spectroscopy of Nitroxide-Functionalized Nanodiamonds in Aqueous Solution.

    Science.gov (United States)

    Akiel, R D; Stepanov, V; Takahashi, S

    2017-06-01

    Nanodiamond (ND) is an attractive class of nanomaterial for fluorescent labeling, magnetic sensing of biological molecules, and targeted drug delivery. Many of those applications require tethering of target biological molecules on the ND surface. Even though many approaches have been developed to attach macromolecules to the ND surface, it remains challenging to characterize dynamics of tethered molecule. Here, we show high-frequency electron paramagnetic resonance (HF EPR) spectroscopy of nitroxide-functionalized NDs. Nitroxide radical is a commonly used spin label to investigate dynamics of biological molecules. In the investigation, we developed a sample holder to overcome water absorption of HF microwave. Then, we demonstrated HF EPR spectroscopy of nitroxide-functionalized NDs in aqueous solution and showed clear spectral distinction of ND and nitroxide EPR signals. Moreover, through EPR spectral analysis, we investigate dynamics of nitroxide radicals on the ND surface. The demonstration sheds light on the use of HF EPR spectroscopy to investigate biological molecule-functionalized nanoparticles.

  15. The functioning and behaviour of biological parents of children ...

    African Journals Online (AJOL)

    Parenting a child with ADHD may intensify parental stress through functional impairment notwithstanding the diagnosis of ADHD. Methods: Eighty-one biological parents of children diagnosed with attention-deficit/ hyperactivity disorder were screened using self-reporting measurements. ADHD self-report scale (ASRS-V 1.1) ...

  16. Biomaterials-Based Electronics: Polymers and Interfaces for Biology and Medicine

    Science.gov (United States)

    Muskovich, Meredith; Bettinger, Christopher J.

    2012-01-01

    Advanced polymeric biomaterials continue to serve as a cornerstone of new medical technologies and therapies. The vast majority of these materials, both natural and synthetic, interact with biological matter without direct electronic communication. However, biological systems have evolved to synthesize and employ naturally-derived materials for the generation and modulation of electrical potentials, voltage gradients, and ion flows. Bioelectric phenomena can be interpreted as potent signaling cues for intra- and inter-cellular communication. These cues can serve as a gateway to link synthetic devices with biological systems. This progress report will provide an update on advances in the application of electronically active biomaterials for use in organic electronics and bio-interfaces. Specific focus will be granted to the use of natural and synthetic biological materials as integral components in technologies such as thin film electronics, in vitro cell culture models, and implantable medical devices. Future perspectives and emerging challenges will also be highlighted. PMID:23184740

  17. Fundamental Technical Elements of Freeze-fracture/Freeze-etch in Biological Electron Microscopy

    Science.gov (United States)

    Freeze-fracture/freeze-etch describes a process whereby specimens, typically biological or nanomaterial in nature, are frozen, fractured, and replicated to generate a carbon/platinum "cast" intended for examination by transmission electron microscopy. Specimens are subjected to u...

  18. Evolutionary cell biology: functional insight from "endless forms most beautiful".

    Science.gov (United States)

    Richardson, Elisabeth; Zerr, Kelly; Tsaousis, Anastasios; Dorrell, Richard G; Dacks, Joel B

    2015-12-15

    In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking. © 2015 Richardson et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  19. Approaching an experimental electron density model of the biologically active trans -epoxysuccinyl amide group-Substituent effects vs. crystal packing

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Ming W.; Stewart, Scott G.; Sobolev, Alexandre N.; Dittrich, Birger; Schirmeister, Tanja; Luger, Peter; Hesse, Malte; Chen, Yu-Sheng; Spackman, Peter R.; Spackman, Mark A.; Grabowsky, Simon (Heinrich-Heine); (Freie); (UC); (Bremen); (JG-UM); (UWA)

    2017-01-24

    The trans-epoxysuccinyl amide group as a biologically active moiety in cysteine protease inhibitors such as loxistatin acid E64c has been used as a benchmark system for theoretical studies of environmental effects on the electron density of small active ingredients in relation to their biological activity. Here, the synthesis and the electronic properties of the smallest possible active site model compound are reported to close the gap between the unknown experimental electron density of trans-epoxysuccinyl amides and the well-known function of related drugs. Intramolecular substituent effects are separated from intermolecular crystal packing effects on the electron density, which allows us to predict the conditions under which an experimental electron density investigation on trans-epoxysuccinyl amides will be possible. In this context, the special importance of the carboxylic acid function in the model compound for both crystal packing and biological activity is revealed through the novel tool of model energy analysis.

  20. Response function and optimum configuration of semiconductor backscattered-electron detectors for scanning electron microscopes

    International Nuclear Information System (INIS)

    Rau, E. I.; Orlikovskiy, N. A.; Ivanova, E. S.

    2012-01-01

    A new highly efficient design for semiconductor detectors of intermediate-energy electrons (1–50 keV) for application in scanning electron microscopes is proposed. Calculations of the response function of advanced detectors and control experiments show that the efficiency of the developed devices increases on average twofold, which is a significant positive factor in the operation of modern electron microscopes in the mode of low currents and at low primary electron energies.

  1. Electron Transfer Studies of Ruthenium(II) Complexes with Biologically Important Phenolic Acids and Tyrosine.

    Science.gov (United States)

    Rajeswari, Angusamy; Ramdass, Arumugam; Muthu Mareeswaran, Paulpandian; Rajagopal, Seenivasan

    2016-03-01

    The ruthenium(II) complexes having 2,2'-bipyridine and phenanthroline derivatives are synthesized and characterized. The photophysical properties of these complexes at pH 12.5 are studied. The electron transfer reaction of biologically important phenolic acids and tyrosine are studied using absorption, emission and transient absorption spectral techniques. Semiclassical theory is applied to calculate the rate of electron transfer between ruthenium(II) complexes and biologically important phenolic acids.

  2. Venom Proteins from Parasitoid Wasps and Their Biological Functions

    Science.gov (United States)

    Moreau, Sébastien J. M.; Asgari, Sassan

    2015-01-01

    Parasitoid wasps are valuable biological control agents that suppress their host populations. Factors introduced by the female wasp at parasitization play significant roles in facilitating successful development of the parasitoid larva either inside (endoparasitoid) or outside (ectoparasitoid) the host. Wasp venoms consist of a complex cocktail of proteinacious and non-proteinacious components that may offer agrichemicals as well as pharmaceutical components to improve pest management or health related disorders. Undesirably, the constituents of only a small number of wasp venoms are known. In this article, we review the latest research on venom from parasitoid wasps with an emphasis on their biological function, applications and new approaches used in venom studies. PMID:26131769

  3. Neuroscience in the era of functional genomics and systems biology.

    Science.gov (United States)

    Geschwind, Daniel H; Konopka, Genevieve

    2009-10-15

    Advances in genetics and genomics have fuelled a revolution in discovery-based, or hypothesis-generating, research that provides a powerful complement to the more directly hypothesis-driven molecular, cellular and systems neuroscience. Genetic and functional genomic studies have already yielded important insights into neuronal diversity and function, as well as disease. One of the most exciting and challenging frontiers in neuroscience involves harnessing the power of large-scale genetic, genomic and phenotypic data sets, and the development of tools for data integration and mining. Methods for network analysis and systems biology offer the promise of integrating these multiple levels of data, connecting molecular pathways to nervous system function.

  4. Methanol as electron donor for thermophilic biological sulfate and sulfite reduction

    NARCIS (Netherlands)

    Weijma, J.

    2000-01-01

    Sulfur oxyanions (e.g. sulfate, sulfite) can be removed from aqueous waste- and process streams by biological reduction with a suitable electron donor to sulfide, followed by partial chemical or biological oxidation of sulfide to elemental sulfur. The aim of the research described in this

  5. Carbon-Oxygen Hydrogen Bonding in Biological Structure and Function

    Science.gov (United States)

    Horowitz, Scott; Trievel, Raymond C.

    2012-01-01

    Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure. PMID:23048026

  6. Theoretical description of protein field effects on electronic excitations of biological chromophores

    International Nuclear Information System (INIS)

    Varsano, Daniele; Caprasecca, Stefano; Coccia, Emanuele

    2017-01-01

    Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show

  7. Theoretical description of protein field effects on electronic excitations of biological chromophores

    Science.gov (United States)

    Varsano, Daniele; Caprasecca, Stefano; Coccia, Emanuele

    2017-01-01

    Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show

  8. Proximity functions for electrons up to 10 keV

    Energy Technology Data Exchange (ETDEWEB)

    Chmelevsky, D. (Institut fuer Medizinische Strahlenkunde der Universitaet Wuerzburg, Germany); Kellerer, A.M.; Terrissol, M.; Patau, J.P.

    1980-11-01

    Proximity functions for electrons up to 10 keV in water are computed from simulated particle tracks. Numerical results are given for the differential functions t(x) and the integral functions T(x). Basic characteristics of these functions and their connections to other microdosimetric quantities are considered. As an example of the applicability of the proximity functions, the quantity y/sub D/ for spheres is derived from t(x).

  9. Electron localization functions and local measures of the covariance

    Indian Academy of Sciences (India)

    A function of the local covariance, however, is useful for this purpose. A different function, based on the hyperbolic tangent, is proposed to elucidate the shell structure encapsulated by the local covariance; this function also seems to work better for the electron localization measure of Becke and Edgecombe. In addition, we ...

  10. Electronic and Mechanical Properties of Hydrogen Functionalized Carbon Nanotubes

    Science.gov (United States)

    Yang, Liu; Han, Jie; Jaffe, Richard L.; Arnold, Jim (Technical Monitor)

    2001-01-01

    We examined the electronic and mechanical properties of hydrogen functionalized carbon nanotubes. The functionalization pattern covers two extreme groups. One group has randomly selected functionalization sites including one to twenty percent of the carbon atoms. The other group has regularly patterned functional sites parallel to the tube axis. Metallic, small-gap semiconducting and large-gap semiconducting carbon nanotubes are studied. The results reveal that the electronic properties of the tubes are very sensitive to the degree of functionalization, with even one percent functionalization being enough to render metallic tubes semiconducting. On the other hand, the mechanical properties, like tensile modulus, are much less sensitive to functionalization. For carbon nanotubes functionalized with specific patterns, the electric properties depends strongly on the nature of the functionalization pattern.

  11. Correlation function and electronic spectral line broadening in relativistic plasmas

    Directory of Open Access Journals (Sweden)

    Douis S.

    2013-01-01

    Full Text Available The electrons dynamics and the time autocorrelation function Cee(t for the total electric microfield of the electrons on positive charge impurity embedded in a plasma are considered when the relativistic dynamic of the electrons is taken into account. We have, at first, built the effective potential governing the electrons dynamics. This potential obeys a nonlinear integral equation that we have solved numerically. Regarding the electron broadening of the line in plasma, we have found that when the plasma parameters change, the amplitude of the collision operator changes in the same way as the time integral of Cee(t. The electron-impurity interaction is taken at first time as screened Deutsh interaction and at the second time as Kelbg interaction. Comparisons of all interesting quantities are made with respect to the previous interactions as well as between classical and relativistic dynamics of electrons.

  12. Development of functional polymers by electron beam

    International Nuclear Information System (INIS)

    Okamoto, Jiro

    1992-01-01

    Radiation-induced grafting is known as a method for introducing functional groups in a variety of polymers and inorganic substances. Various radiation grafting methods have been extensively developed in the early years and these have been the basis for radiation grafting research and development since that time. These are the preirradiation, the mutual, and the peroxide methods. Most of these methods investigated have been to create active sites on a polymer backbone by irradiation and reacting these with monomer which can then propagate to form grafted side chains of different structure. In this paper, the radiation grafting methods will be described and discussed in some detail together with their advantages and disadvantages. A few typical examples will be discussed with reference to research and development of functional materials such as ion exchange membrane, pervaporation membrane, fibrous ion exchanger and fibrous chelating agent for metal ions. (author)

  13. The Work Function Associated with Ultra-relativistic Electron ...

    Indian Academy of Sciences (India)

    Following an extremely interesting idea (Schieber 1984), published long ago, the work function associated with the emission of ultra-relativistic electrons from magnetically deformed metallic crystal (mainly iron) at the outer crust of a magnetar is obtained using relativistic version of Thomas–Fermi type model for electron ...

  14. Knowledge base and functionality of concepts of some Filipino biology teachers in five biology topics

    Science.gov (United States)

    Barquilla, Manuel B.

    2018-01-01

    This mixed research, is a snapshot of some Filipino Biology teachers' knowledge structure and how their concepts of the five topics in Biology (Photosynthesis, Cellular Respiration, human reproductive system, Mendelian genetics and NonMendelian genetics) functions and develops inside a biology classroom. The study focuses on the six biology teachers and a total of 222 students in their respective classes. Of the Six (6) teachers, three (3) are under the Science curriculum and the other three (3) are under regular curriculum in both public and private schools in Iligan city and Lanao del Norte, Philippines. The study utilized classroom discourses, concept maps, interpretative case-study method, bracketing method, and concept analysis for qualitative part; the quantitative part uses a nonparametric statistical tool, Kendall's tau Coefficient for determining relationship and congruency while measures of central tendencies and dispersion (mean, and standard deviation) for concept maps scores interpretation. Knowledge Base of Biology teachers were evaluated by experts in field of specialization having a doctorate program (e.g. PhD in Genetics) and PhD Biology candidates. The data collection entailed seven (7) months immersion: one (1) month for preliminary phase for the researcher to gain teachers' and students' confidence and the succeeding six (6) months for main observation and data collection. The evaluation of teachers' knowledge base by experts indicated that teachers' knowledge of (65%) is lower than the minimum (75%) recommended by ABD-el-Khalick and Boujaoude (1997). Thus, the experts believe that content knowledge of the teachers is hardly adequate for their teaching assignment. Moreover, the teachers in this study do not systematically use reallife situation to apply the concepts they teach. They can identify concepts too abstract for their student; however, they seldom use innovative ways to bring the discussion to their students' level of readiness and

  15. Using functional genetics to understand breast cancer biology.

    Science.gov (United States)

    Ashworth, Alan; Bernards, Rene

    2010-07-01

    Genetic screens were for long the prerogative of those that studied model organisms. The discovery in 2001 that gene silencing through RNA interference (RNAi) can also be brought about in mammalian cells paved the way for large scale loss-of-function genetic screens in higher organisms. In this article, we describe how functional genetic studies can help us understand the biology of breast cancer, how it can be used to identify novel targets for breast cancer therapy, and how it can help in the identification of those patients that are most likely to respond to a given therapy.

  16. Harnessing systems biology approaches to engineer functional microvascular networks.

    Science.gov (United States)

    Sefcik, Lauren S; Wilson, Jennifer L; Papin, Jason A; Botchwey, Edward A

    2010-06-01

    Microvascular remodeling is a complex process that includes many cell types and molecular signals. Despite a continued growth in the understanding of signaling pathways involved in the formation and maturation of new blood vessels, approximately half of all compounds entering clinical trials will fail, resulting in the loss of much time, money, and resources. Most pro-angiogenic clinical trials to date have focused on increasing neovascularization via the delivery of a single growth factor or gene. Alternatively, a focus on the concerted regulation of whole networks of genes may lead to greater insight into the underlying physiology since the coordinated response is greater than the sum of its parts. Systems biology offers a comprehensive network view of the processes of angiogenesis and arteriogenesis that might enable the prediction of drug targets and whether or not activation of the targets elicits the desired outcome. Systems biology integrates complex biological data from a variety of experimental sources (-omics) and analyzes how the interactions of the system components can give rise to the function and behavior of that system. This review focuses on how systems biology approaches have been applied to microvascular growth and remodeling, and how network analysis tools can be utilized to aid novel pro-angiogenic drug discovery.

  17. Biological denitrification using poly(butanediol succinate) as electron donor.

    Science.gov (United States)

    Shen, Zhiqiang; Yin, Yanan; Wang, Jianlong

    2016-07-01

    Poly(butanediol succinate) (PBS), a biodegradable polymer, was used as both solid carbon source and biofilm carrier for biological nitrate removal process, in which PBS was filled in a packed-bed bioreactor. The denitrification performance and the microbial diversity of biofilm attached on the surface of PBS were investigated. The experimental results showed that the volumetric denitrification rate was 0.60 kg m(-3) day(-1) when NO3-N loading rate was 0.63 kg m(-3) day(-1), and the average NO2-N concentration was below 0.20 mg L(-1). The effluent pH value decreased slightly from a range of 6.98-7.87 to 6.46-7.18. The analysis of microbial community structure of biofilm by pyrosequencing method showed that Proteobacteria was the most abundant phylum (89.87 %), and β-Proteobacteria represented the most abundant class. Among the 76 identified genera, Dechloromonas (10.26 %), Alicycliphilus (9.15 %), Azospira (8.92 %), and Sinobacteraceae-uncultured (8.75 %) were the abundant genera. PBS, as a promising alternative carbon source, is a suitable solid carbon source and biofilm carrier for nitrate removal.

  18. Chitosan to Connect Biology to Electronics: Fabricating the Bio-Device Interface and Communicating Across This Interface

    Directory of Open Access Journals (Sweden)

    Eunkyoung Kim

    2014-12-01

    Full Text Available Individually, advances in microelectronics and biology transformed the way we live our lives. However, there remain few examples in which biology and electronics have been interfaced to create synergistic capabilities. We believe there are two major challenges to the integration of biological components into microelectronic systems: (i assembly of the biological components at an electrode address, and (ii communication between the assembled biological components and the underlying electrode. Chitosan possesses a unique combination of properties to meet these challenges and serve as an effective bio-device interface material. For assembly, chitosan’s pH-responsive film-forming properties allow it to “recognize” electrode-imposed signals and respond by self-assembling as a stable hydrogel film through a cathodic electrodeposition mechanism. A separate anodic electrodeposition mechanism was recently reported and this also allows chitosan hydrogel films to be assembled at an electrode address. Protein-based biofunctionality can be conferred to electrodeposited films through a variety of physical, chemical and biological methods. For communication, we are investigating redox-active catechol-modified chitosan films as an interface to bridge redox-based communication between biology and an electrode. Despite significant progress over the last decade, many questions still remain which warrants even deeper study of chitosan’s structure, properties, and functions.

  19. Probing the Xenopus laevis inner ear transcriptome for biological function

    Directory of Open Access Journals (Sweden)

    Powers TuShun R

    2012-06-01

    Full Text Available Abstract Background The senses of hearing and balance depend upon mechanoreception, a process that originates in the inner ear and shares features across species. Amphibians have been widely used for physiological studies of mechanotransduction by sensory hair cells. In contrast, much less is known of the genetic basis of auditory and vestibular function in this class of animals. Among amphibians, the genus Xenopus is a well-characterized genetic and developmental model that offers unique opportunities for inner ear research because of the amphibian capacity for tissue and organ regeneration. For these reasons, we implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis. Results Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear. The use of gene categories (inner ear tissue; deafness; ion channels; ion transporters; transcription factors facilitated the assignment of functional significance to probe set identifiers. We enhanced the biological relevance of our microarray data by using a variety of curation approaches to increase the annotation of the Affymetrix GeneChip® Xenopus laevis Genome array. In addition, annotation analysis revealed the prevalence of inner ear transcripts represented by probe set identifiers that lack functional characterization. Conclusions We identified an abundance of targets for genetic analysis of auditory and vestibular function. The orthologues to human genes with known inner ear function and the highly expressed transcripts that lack annotation are particularly interesting candidates for future analyses. We used informatics approaches to impart biologically relevant information to the Xenopus inner ear transcriptome

  20. Biological properties of extracellular vesicles and their physiological functions

    Directory of Open Access Journals (Sweden)

    María Yáñez-Mó

    2015-05-01

    Full Text Available In the past decade, extracellular vesicles (EVs have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.

  1. Biological properties of extracellular vesicles and their physiological functions

    Science.gov (United States)

    Yáñez-Mó, María; Siljander, Pia R.-M.; Andreu, Zoraida; Zavec, Apolonija Bedina; Borràs, Francesc E.; Buzas, Edit I.; Buzas, Krisztina; Casal, Enriqueta; Cappello, Francesco; Carvalho, Joana; Colás, Eva; Silva, Anabela Cordeiro-da; Fais, Stefano; Falcon-Perez, Juan M.; Ghobrial, Irene M.; Giebel, Bernd; Gimona, Mario; Graner, Michael; Gursel, Ihsan; Gursel, Mayda; Heegaard, Niels H. H.; Hendrix, An; Kierulf, Peter; Kokubun, Katsutoshi; Kosanovic, Maja; Kralj-Iglic, Veronika; Krämer-Albers, Eva-Maria; Laitinen, Saara; Lässer, Cecilia; Lener, Thomas; Ligeti, Erzsébet; Linē, Aija; Lipps, Georg; Llorente, Alicia; Lötvall, Jan; Manček-Keber, Mateja; Marcilla, Antonio; Mittelbrunn, Maria; Nazarenko, Irina; Hoen, Esther N.M. Nolte-‘t; Nyman, Tuula A.; O'Driscoll, Lorraine; Olivan, Mireia; Oliveira, Carla; Pállinger, Éva; del Portillo, Hernando A.; Reventós, Jaume; Rigau, Marina; Rohde, Eva; Sammar, Marei; Sánchez-Madrid, Francisco; Santarém, N.; Schallmoser, Katharina; Ostenfeld, Marie Stampe; Stoorvogel, Willem; Stukelj, Roman; Van der Grein, Susanne G.; Vasconcelos, M. Helena; Wauben, Marca H. M.; De Wever, Olivier

    2015-01-01

    In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system. PMID:25979354

  2. Transfer function restoration in 3D electron microscopy via iterative data refinement

    International Nuclear Information System (INIS)

    Sorzano, C O S; Marabini, R; Herman, G T; Censor, Y; Carazo, J M

    2004-01-01

    Three-dimensional electron microscopy (3D-EM) is a powerful tool for visualizing complex biological systems. As with any other imaging device, the electron microscope introduces a transfer function (called in this field the contrast transfer function, CTF) into the image acquisition process that modulates the various frequencies of the signal. Thus, the 3D reconstructions performed with these CTF-affected projections are also affected by an implicit 3D transfer function. For high-resolution electron microscopy, the effect of the CTF is quite dramatic and limits severely the achievable resolution. In this work we make use of the iterative data refinement (IDR) technique to ameliorate the effect of the CTF. It is demonstrated that the approach can be successfully applied to noisy data

  3. Electron Beam Induced Functionalization of Fluoropolymers

    International Nuclear Information System (INIS)

    Lappan, U.

    2006-01-01

    Ionizing radiation affects the properties of polymers by chain scission and cross-linking reactions. One process will usually predominate, depending on the chemical structure of the polymer and the irradiation conditions such as temperature and atmosphere. Poly(tetrafluoroethylene) (PTFE) and the perfluorinated copolymers poly(tetrafluoroethylene-co-hexafluoropropylene) (FEP) and poly(tetrafluoroethylene-co-perfluoropropylvinyl ether) (PFA) undergo predominantly chain scission, if the irradiation is performed at room temperature. This shortcoming is exploited by converting PTFE into low molecular weight micropowders. The irradiation of PTFE in the presence of air results in micropowders functionalized with oxygen-containing groups. The concentration of end groups was investigated by FTIR and 19F solid-state NMR. The data were used to calculate number-average molecular weights. It was demonstrated that PTFE can be cross-linked by irradiation above its crystalline melting temperature in an oxygen-free atmosphere. Evidence for cross-links in PTFE was derived directly from structural information using 19 F solid-state NMR. FEP is understood to undergo cross-linking by irradiation above the glass transition temperature. It was found that also PFA can be branched and cross-linked by irradiation under special conditions. Radiation-induced grafting of styrene into fluoropolymer films and subsequent sulfonation offers an attractive way to prepare proton exchange membranes. Recently, radiation-induced grafting into cross-linked PTFE was reported. Modified FEP, PFA and ETFE films have been used as base material in this study. The modified films have been prepared by irradiation in nitrogen atmosphere at different temperatures up to temperatures above the melting temperature of the fluoropolymer

  4. Systemic Modeling of Biological Functions in Consideration of Physiome Project

    Science.gov (United States)

    Minamitani, Haruyuki

    Emerging of the physiome project provides various influences on the medical, biological and pharmaceutical development. In this paper, as an example of physiome research, neural network model analysis providing the conduction mechanisms of pain and tactile sensations was presented, and the functional relations between neural activities of the network cells and stimulus intensity applied on the peripheral receptive fields were described. The modeling presented here is based on the various assumptions made by the results of physiological and anatomical studies reported in the literature. The functional activities of spinothalamic and thalamocortical cells show a good agreement with the physiological and psychophysical functions of somatosensory system that are very instructive for covering the gap between physiologically and psychophysically aspects of pain and tactile sensation.

  5. Biomarkers of Aging: From Function to Molecular Biology

    Directory of Open Access Journals (Sweden)

    Karl-Heinz Wagner

    2016-06-01

    Full Text Available Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a single biomarker or gold standard tool that can monitor successful or healthy aging. Within this short review the current knowledge of putative biomarkers is presented, focusing on their application to the major physiological mechanisms affected by the aging process including physical capability, nutritional status, body composition, endocrine and immune function. This review emphasizes molecular and DNA-based biomarkers, as well as recent advances in other biomarkers such as microRNAs, bilirubin or advanced glycation end products.

  6. Functional annotation of chemical libraries across diverse biological processes.

    Science.gov (United States)

    Piotrowski, Jeff S; Li, Sheena C; Deshpande, Raamesh; Simpkins, Scott W; Nelson, Justin; Yashiroda, Yoko; Barber, Jacqueline M; Safizadeh, Hamid; Wilson, Erin; Okada, Hiroki; Gebre, Abraham A; Kubo, Karen; Torres, Nikko P; LeBlanc, Marissa A; Andrusiak, Kerry; Okamoto, Reika; Yoshimura, Mami; DeRango-Adem, Eva; van Leeuwen, Jolanda; Shirahige, Katsuhiko; Baryshnikova, Anastasia; Brown, Grant W; Hirano, Hiroyuki; Costanzo, Michael; Andrews, Brenda; Ohya, Yoshikazu; Osada, Hiroyuki; Yoshida, Minoru; Myers, Chad L; Boone, Charles

    2017-09-01

    Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound's mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.

  7. Functionalization of polydopamine coated magnetic nanoparticles with biological entities

    Science.gov (United States)

    Mǎgeruşan, Lidia; Mrówczyński, Radosław; Turcu, Rodica

    2015-12-01

    New hybrid materials, obtained through introduction of cysteine, lysine and folic acid as biological entities into polydopamine-coated magnetite nanoparticles, are reported. The syntheses are straight forward and various methods were applied for structural and morphological characterization of the resulting nanoparticles. XPS proved a very powerful tool for surface chemical analysis and it evidences the functionalization of polydopamine coated magnetite nanoparticles. The superparamagnetic behavior and the high values of saturation magnetization recommend all products for further application where magnetism is important for targeting, separation, or heating by alternative magnetic fields.

  8. Electron spin interactions in chemistry and biology fundamentals, methods, reactions mechanisms, magnetic phenomena, structure investigation

    CERN Document Server

    Likhtenshtein, Gertz

    2016-01-01

    This book presents the versatile and pivotal role of electron spin interactions in nature. It provides the background, methodologies and tools for basic areas related to spin interactions, such as spin chemistry and biology, electron transfer, light energy conversion, photochemistry, radical reactions, magneto-chemistry and magneto-biology. The book also includes an overview of designing advanced magnetic materials, optical and spintronic devices and photo catalysts. This monograph appeals to scientists and graduate students working in the areas related to spin interactions physics, biophysics, chemistry and chemical engineering.

  9. Metabolomics for functional genomics, systems biology, and biotechnology.

    Science.gov (United States)

    Saito, Kazuki; Matsuda, Fumio

    2010-01-01

    Metabolomics now plays a significant role in fundamental plant biology and applied biotechnology. Plants collectively produce a huge array of chemicals, far more than are produced by most other organisms; hence, metabolomics is of great importance in plant biology. Although substantial improvements have been made in the field of metabolomics, the uniform annotation of metabolite signals in databases and informatics through international standardization efforts remains a challenge, as does the development of new fields such as fluxome analysis and single cell analysis. The principle of transcript and metabolite cooccurrence, particularly transcriptome coexpression network analysis, is a powerful tool for decoding the function of genes in Arabidopsis thaliana. This strategy can now be used for the identification of genes involved in specific pathways in crops and medicinal plants. Metabolomics has gained importance in biotechnology applications, as exemplified by quantitative loci analysis, prediction of food quality, and evaluation of genetically modified crops. Systems biology driven by metabolome data will aid in deciphering the secrets of plant cell systems and their application to biotechnology.

  10. A short comparison of electron and proton transfer processes in biological systems

    International Nuclear Information System (INIS)

    Bertrand, Patrick

    2005-01-01

    The main differences between electron and proton transfers that take place in biological systems are examined. The relation between the distance dependence of the rate constant and the mass of the transferred particle is analyzed in detail. Differences between the two processes have important consequences at the experimental level, which are discussed. The various mechanisms that ensure the coupling between electron and proton transfers are briefly described

  11. Dynamical "in situ" observation of biological samples using variable pressure scanning electron microscope

    Czech Academy of Sciences Publication Activity Database

    Neděla, Vilém

    2008-01-01

    Roč. 126, - (2008), 012046:1-4 ISSN 1742-6588. [Electron Microscopy and Analysis Group Conference 2007 (EMAG 2007). Glasgow, 03.09.2007-07.09.2007] R&D Projects: GA ČR(CZ) GA102/05/0886; GA AV ČR KJB200650602 Institutional research plan: CEZ:AV0Z20650511 Keywords : biological sample * VP-SEM * dynamical experiments Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering

  12. 2. Brazilian Congress on Cell Biology and 7. Brazilian Colloquium on Electron Microscopy - Abstracts

    International Nuclear Information System (INIS)

    1980-01-01

    Immunology, virology, bacteriology, genetics and protozoology are some of the subjects treated in the 2. Brazilian Congress on Cell Biology. Studies using radioisotopic techniques and ultrastructural cytological studies are presented. Use of optical - and electron microscopy in some of these studies is discussed. In the 7. Brazilian Colloquium on Electron Microscopy, the application of this technique to materials science is discussed (failure analysis in metallurgy, energy dispersion X-ray analysis, etc). (I.C.R.) [pt

  13. Scavenger Receptor CD163 and Its Biological Functions

    Directory of Open Access Journals (Sweden)

    Gabriela Onofre

    2009-01-01

    Full Text Available CD163 is a member of scavenger receptor super family class B of the first subgroup. It is mapped to the region p13 on chromosome 12. Five different isoforms of CD163 have been described, which differ in the structure of their cytoplasmic domains and putative phosporylation sites. This scavenger receptor is selectively expressed on cells of monocytes and macrophages lineage exclusively. CD163 immunological function is essentially homeostatic. It also has other functions because participates in adhesion to endothelial cells, in tolerance induction and tissues regeneration. Other very important function of CD163 is the clearance of hemoglobin in its cell-free form and participation in anti-inflammation in its soluble form, exhibiting cytokine-like functions. We review the biological functions of CD163 which have been discovered until now. It seems apparent from this review that CD163 scavenger receptor can be used as biomarker in different diseases and as a valuable diagnostic parameter for prognosis of many diseases especially inflammatory disorders and sepsis.

  14. Surface Immobilized His-tagged Azurin as a Model Interface for the Investigation of Vectorial Electron Transfer in Biological Systems

    International Nuclear Information System (INIS)

    Casalini, Stefano; Berto, Marcello; Kovtun, Alessandro; Operamolla, Alessandra; Di Rocco, Giulia; Facci, Paolo; Liscio, Andrea; Farinola, Gianluca M.; Borsari, Marco; Bortolotti, Carlo A.

    2015-01-01

    A model system for the electrochemical investigation of vectorial electron transfer in biological systems was designed, assembled and characterized. Gold electrodes, functionalized with a -OCH 3 terminated, aromatic self-assembled monolayer, were used as a substrate for the adsorption of variants of copper-containing, redox metalloprotein azurin. The engineered azurin bears a polyhistidine tag at its C-terminus. Thanks to the presence of the solvent exposed tag, which chelates Cu 2+ ions in solution, we introduced an exogenous redox centre. The different reduction potentials of the two redox centres and their positioning with respect to the surface are such that electron transfer from the exogenous copper centre and the electrode is mediated by the native azurin active site, closely paralleling electron transfer processes in naturally occurring multicentre metalloproteins.

  15. Diffusion of innovations dynamics, biological growth and catenary function

    Science.gov (United States)

    Guseo, Renato

    2016-12-01

    The catenary function has a well-known role in determining the shape of chains and cables supported at their ends under the force of gravity. This enables design using a specific static equilibrium over space. Its reflected version, the catenary arch, allows the construction of bridges and arches exploiting the dual equilibrium property under uniform compression. In this paper, we emphasize a further connection with well-known aggregate biological growth models over time and the related diffusion of innovation key paradigms (e.g., logistic and Bass distributions over time) that determine self-sustaining evolutionary growth dynamics in naturalistic and socio-economic contexts. Moreover, we prove that the 'local entropy function', related to a logistic distribution, is a catenary and vice versa. This special invariance may be explained, at a deeper level, through the Verlinde's conjecture on the origin of gravity as an effect of the entropic force.

  16. STAT6: its role in interleukin 4-mediated biological functions.

    Science.gov (United States)

    Takeda, K; Kishimoto, T; Akira, S

    1997-05-01

    Interleukin (IL) 4 is known to be a cytokine which plays a central role in the regulation of immune response. Studies on cytokine signal transduction have clarified the mechanism by which IL4 exerts its functions. Two cytoplasmic proteins, signal transducer and activator of transcription (STAT) 6 and IL4-induced phosphotyrosine substrate/insulin receptor substrate 2 (4PS/IRS2), are activated in IL4 signal transduction. Recent studies from STAT6-deficient mice have revealed the essential role of STAT6 in IL4-mediated biological actions. In addition, STAT6 has also been demonstrated to be important for the functions mediated by IL13, which is related to IL4. IL4 and IL13 have been shown to induce the production of IgE, which is a major mediator in an allergic response. These findings indicate that STAT6 activation is involved in IL4- and IL13-mediated disorders such as allergy.

  17. Functions of MicroRNAs in Cardiovascular Biology and Disease

    Science.gov (United States)

    Hata, Akiko

    2015-01-01

    In 1993, lin-4 was discovered as a critical modulator of temporal development in Caenorhabditis elegans and, most notably, as the first in the class of small, single-stranded noncoding RNAs now defined as microRNAs (miRNAs). Another eight years elapsed before miRNA expression was detected in mammalian cells. Since then, explosive advancements in the field of miRNA biology have elucidated the basic mechanism of miRNA biogenesis, regulation, and gene-regulatory function. The discovery of this new class of small RNAs has augmented the complexity of gene-regulatory programs as well as the understanding of developmental and pathological processes in the cardiovascular system. Indeed, the contributions of miRNAs in cardiovascular development and function have been widely explored, revealing the extensive role of these small regulatory RNAs in cardiovascular physiology. PMID:23157557

  18. Density-functional method for nonequilibrium electron transport

    DEFF Research Database (Denmark)

    Brandbyge, Mads; Mozos, J.L.; Ordejon, P.

    2002-01-01

    We describe an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density-functional theory (DFT) as implemented...... in the well tested SIESTA approach (which uses nonlocal norm-conserving pseudopotentials to describe the effect of the core electrons, and linear combination of finite-range numerical atomic orbitals to describe the valence states). We fully deal with the atomistic structure of the whole system, treating both...... the contact and the electrodes on the same footing. The effect of the finite bias (including self-consistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. We relate the nonequilibrium Green's function expressions to the more transparent scheme...

  19. Event-based text mining for biology and functional genomics.

    Science.gov (United States)

    Ananiadou, Sophia; Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B

    2015-05-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of 'events', i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. © The Author 2014. Published by Oxford University Press.

  20. Carotenoids from Marine Organisms: Biological Functions and Industrial Applications

    Directory of Open Access Journals (Sweden)

    Christian Galasso

    2017-11-01

    Full Text Available As is the case for terrestrial organisms, carotenoids represent the most common group of pigments in marine environments. They are generally biosynthesized by all autotrophic marine organisms, such as bacteria and archaea, algae and fungi. Some heterotrophic organisms also contain carotenoids probably accumulated from food or partly modified through metabolic reactions. These natural pigments are divided into two chemical classes: carotenes (such as lycopene and α- and β-carotene that are composed of hydrogen and carbon; xanthophylls (such as astaxanthin, fucoxanthin and lutein, which are constituted by hydrogen, carbon and oxygen. Carotenoids, as antioxidant compounds, assume a key role in the protection of cells. In fact, quenching of singlet oxygen, light capture and photosynthesis protection are the most relevant biological functions of carotenoids. The present review aims at describing (i the biological functions of carotenoids and their benefits for human health, (ii the most common carotenoids from marine organisms and (iii carotenoids having large success in pharmaceutical, nutraceutical and cosmeceutical industries, highlighting the scientific progress in marine species cultivation for natural pigments production.

  1. Event-based text mining for biology and functional genomics

    Science.gov (United States)

    Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B.

    2015-01-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of ‘events’, i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. PMID:24907365

  2. Engineered hybrid cardiac patches with multifunctional electronics for online monitoring and regulation of tissue function

    Science.gov (United States)

    Feiner, Ron; Engel, Leeya; Fleischer, Sharon; Malki, Maayan; Gal, Idan; Shapira, Assaf; Shacham-Diamand, Yosi; Dvir, Tal

    2016-01-01

    In cardiac tissue engineering approaches to treat myocardial infarction, cardiac cells are seeded within three-dimensional porous scaffolds to create functional cardiac patches. However, current cardiac patches do not allow for online monitoring and reporting of engineered-tissue performance, and do not interfere to deliver signals for patch activation or to enable its integration with the host. Here, we report an engineered cardiac patch that integrates cardiac cells with flexible, free-standing electronics and a 3D nanocomposite scaffold. The patch exhibited robust electronic properties, enabling the recording of cellular electrical activities and the on-demand provision of electrical stimulation for synchronizing cell contraction. We also show that electroactive polymers containing biological factors can be deposited on designated electrodes to release drugs in the patch microenvironment on-demand. We expect that the integration of complex electronics within cardiac patches will eventually provide therapeutic control and regulation of cardiac function. PMID:26974408

  3. Point-spread functions for backscattered imaging in the scanning electron microscope

    Science.gov (United States)

    Hennig, Philipp; Denk, Winfried

    2007-12-01

    One knows the imaging system's properties are central to the correct interpretation of any image. In a scanning electron microscope regions of different composition generally interact in a highly nonlinear way during signal generation. Using Monte Carlo simulations we found that in resin-embedded, heavy metal-stained biological specimens staining is sufficiently dilute to allow an approximately linear treatment. We then mapped point-spread functions for backscattered-electron contrast, for primary energies of 3 and 7 keV and for different detector specifications. The point-spread functions are surprisingly well confined (both laterally and in depth) compared even to the distribution of only those scattered electrons that leave the sample again.

  4. Engineered hybrid cardiac patches with multifunctional electronics for online monitoring and regulation of tissue function

    Science.gov (United States)

    Feiner, Ron; Engel, Leeya; Fleischer, Sharon; Malki, Maayan; Gal, Idan; Shapira, Assaf; Shacham-Diamand, Yosi; Dvir, Tal

    2016-06-01

    In cardiac tissue engineering approaches to treat myocardial infarction, cardiac cells are seeded within three-dimensional porous scaffolds to create functional cardiac patches. However, current cardiac patches do not allow for online monitoring and reporting of engineered-tissue performance, and do not interfere to deliver signals for patch activation or to enable its integration with the host. Here, we report an engineered cardiac patch that integrates cardiac cells with flexible, freestanding electronics and a 3D nanocomposite scaffold. The patch exhibited robust electronic properties, enabling the recording of cellular electrical activities and the on-demand provision of electrical stimulation for synchronizing cell contraction. We also show that electroactive polymers containing biological factors can be deposited on designated electrodes to release drugs in the patch microenvironment on demand. We expect that the integration of complex electronics within cardiac patches will eventually provide therapeutic control and regulation of cardiac function.

  5. A system to measure suprathermal electron distribution functions in toroidal plasmas by electron cyclotron wave absorption

    International Nuclear Information System (INIS)

    Boyd, D.A.; Skiff, F.; Gulick, S.

    1997-01-01

    A two-chord, four-beam suprathermal electron diagnostic has been installed on TdeV (B>1.5 T, R=0.86 m, a=0.25 m). Resonant absorption of extraordinary mode electron cyclotron waves is measured to deduce the chordal averaged suprathermal electron distribution function amplitude at the resonant momentum. Simultaneously counterpropagating beams permit good refractive loss cancellation. A nonlinear frequency sweep leads to a concentration of appropriately propagating power in a narrow range of time of flight, thus increasing the signal-to-noise ratio and facilitating the rejection of spurious reflections. Numerous measurements of electron distribution functions have been obtained during lower-hybrid current-drive experiments. copyright 1997 American Institute of Physics

  6. Measurement of the Electron Structure Function at LEP energies

    CERN Document Server

    Abdallah, J; Adam, W; Adzic, P; Albrecht, T; Alemany-Fernandez, R; Allmendinger, T; Allport, P P; Amaldi, U; Amapane, N; Amato, S; Anashkin, E; Andreazza, A; Andringa, S; Anjos, N; Antilogus, P; Apel, W-D; Arnoud, Y; Ask, S; Asman, B; Augustin, J E; Augustinus, A; Baillon, P; Ballestrero, A; Bambade, P; Barbier, R; Bardin, D; Barker, G J; Baroncelli, A; Battaglia, M; Baubillier, M; Becks, K-H; Begalli, M; Behrmann, A; Ben-Haim, E; Benekos, N; Benvenuti, A; Berat, C; Berggren, M; Bertrand, D; Besancon, M; Besson, N; Bloch, D; Blom, M; Bluj, M; Bonesini, M; Boonekamp, M; Booth, P S L; Borisov, G; Botner, O; Bouquet, B; Bowcock, T J V; Boyko, I; Bracko, M; Brenner, R; Brodet, E; Bruckman, P; Brunet, J M; Buschbeck, B; Buschmann, P; Calvi, M; Camporesi, T; Canale, V; Carena, F; Castro, N; Cavallo, F; Chapkin, M; Charpentier, Ph; Checchia, P; Chierici, R; Chliapnikov, P; Chudoba, J; Chung, S U; Cieslik, K; Collins, P; Contri, R; Cosme, G; Cossutti, F; Costa, M J; Crennell, D; Cuevas, J; D'Hondt, J; da Silva, T; Da Silva, W; Della Ricca, G; De Angelis, A; De Boer, W; De Clercq, C; De Lotto, B; De Maria, N; De Min, A; de Paula, L; Di Ciaccio, L; Di Simone, A; Doroba, K; Drees, J; Eigen, G; Ekelof, T; Ellert, M; Elsing, M; Espirito Santo, M C; Fanourakis, G; Fassouliotis, D; Feindt, M; Fernandez, J; Ferrer, A; Ferro, F; Flagmeyer, U; Foeth, H; Fokitis, E; Fulda-Quenzer, F; Fuster, J; Gandelman, M; Garcia, C; Gavillet, Ph; Gazis, E; Gokieli, R; Golob, B; Gomez-Ceballos, G; Goncalves, P; Graziani, E; Grosdidier, G; Grzelak, K; Guy, J; Haag, C; Hallgren, A; Hamacher, K; Hamilton, K; Haug, S; Hauler, F; Hedberg, V; Hennecke, M; Hoffman, J; Holmgren, S-O; Holt, P J; Houlden, M A; Jackson, J N; Jarlskog, G; Jarry, P; Jeans, D; Johansson, E K; Jonsson, P; Joram, C; Jungermann, L; Kapusta, F; Katsanevas, S; Katsoufis, E; Kernel, G; Kersevan, B P; Kerzel, U; King, B T; Kjaer, N J; Kluit, P; Kokkinias, P; Kourkoumelis, C; Kouznetsov, O; Krumstein, Z; Kucharczyk, M; Lamsa, J; Leder, G; Ledroit, F; Leinonen, L; Leitner, R; Lemonne, J; Lepeltier, V; Lesiak, T; Liebig, W; Liko, D; Lipniacka, A; Lopes, J H; Lopez, J M; Loukas, D; Lutz, P; Lyons, L; MacNaughton, J; Malek, A; Maltezos, S; Mandl, F; Marco, J; Marco, R; Marechal, B; Margoni, M; Marin, J-C; Mariotti, C; Markou, A; Martinez-Rivero, C; Masik, J; Mastroyiannopoulos, N; Matorras, F; Matteuzzi, C; Mazzucato, F; Mazzucato, M; Mc Nulty, R; Meroni, C; Migliore, E; Mitaroff, W; Mjoernmark, U; Moa, T; Moch, M; Moenig, K; Monge, R; Montenegro, J; Moraes, D; Moreno, S; Morettini, P; Mueller, U; Muenich, K; Mulders, M; Mundim, L; Murray, W; Muryn, B; Myatt, G; Myklebust, T; Nassiakou, M; Navarria, F; Nawrocki, K; Nemecek, S; Nicolaidou, R; Nikolenko, M; Oblakowska-Mucha, A; Obraztsov, V; Olshevski, A; Onofre, A; Orava, R; Osterberg, K; Ouraou, A; Oyanguren, A; Paganoni, M; Paiano, S; Palacios, J P; Palka, H; Papadopoulou, Th D; Pape, L; Parkes, C; Parodi, F; Parzefall, U; Passeri, A; Passon, O; Peralta, L; Perepelitsa, V; Perrotta, A; Petrolini, A; Piedra, J; Pieri, L; Pierre, F; Pimenta, M; Piotto, E; Podobnik, T; Poireau, V; Pol, M E; Polok, G; Pozdniakov, V; Pukhaeva, N; Pullia, A; Radojicic, D; Rebecchi, P; Rehn, J; Reid, D; Reinhardt, R; Renton, P; Richard, F; Ridky, J; Rivero, M; Rodriguez, D; Romero, A; Ronchese, P; Roudeau, P; Rovelli, T; Ruhlmann-Kleider, V; Ryabtchikov, D; Sadovsky, A; Salmi, L; Salt, J; Sander, C; Savoy-Navarro, A; Schwickerath, U; Sekulin, R; Siebel, M; Sisakian, A; Slominski, W; Smadja, G; Smirnova, O; Sokolov, A; Sopczak, A; Sosnowski, R; Spassov, T; Stanitzki, M; Stocchi, A; Strauss, J; Stugu, B; Szczekowski, M; Szeptycka, M; Szumlak, T; Szwed, J; Tabarelli, T; Tegenfeldt, F; Timmermans, J; Tkatchev, L; Tobin, M; Todorovova, S; Tome, B; Tonazzo, A; Tortosa, P; Travnicek, P; Treille, D; Tristram, G; Trochimczuk, M; Troncon, C; Turluer, M L; Tyapkin, I A; Tyapkin, P; Tzamarias, S; Uvarov, V; Valenti, G; Van Dam, P; Van Eldik, J; van Remortel, N; Van Vulpen, I; Vegni, G; Veloso, F; Venus, W; Verdier, P; Verzi, V; Vilanova, D; Vitale, L; Vrba, V; Wahlen, H; Washbrook, A J; Weiser, C; Wicke, D; Wickens, J; Wilkinson, G; Winter, M; Witek, M; Yushchenko, O; Zalewska, A; Zalewski, P; Zavrtanik, D; Zhuravlov, V; Zimin, N I; Zintchenko, A; Zupan, M

    2010-01-01

    The hadronic part of the Electron Structure Function (ESF) has been measured for the first time, using e+e- data collected by the DELPHI experiment at LEP, at centre-of-mass energies sqrt(s) = 91.2-209.5 GeV. The data analysis is simpler than that of the measurement of the photon structure function. The ESF data are compared to predictions of phenomenological models based on the photon structure function. It is shown that the quasi-real photon virtuality contribution is significant. The presented data can serve as a cross-check of the photon structure function analyses and help in refining existing parametrizations.

  7. Monitoring of biological odour filtration in closed environments with olfactometry and an electronic nose

    NARCIS (Netherlands)

    Willers, H.C.; Gijsel, de P.; Ogink, N.W.M.; Amico, D' A.; Martinelli, E.; Natale, Di C.; Ras, van N.; Waarde, van der J.

    2004-01-01

    Air treatment with a compact biological membrane filter, and air quality monitoring with an electronic nose were tested in the laboratory on air from a cage containing six mice. Additional analyses of air to and from the filter were performed using olfactometry and ammonia and hydrogen sulphide gas

  8. Biomaterials-based electronics: polymers and interfaces for biology and medicine.

    Science.gov (United States)

    Muskovich, Meredith; Bettinger, Christopher J

    2012-05-01

    Advanced polymeric biomaterials continue to serve as a cornerstone for new medical technologies and therapies. The vast majority of these materials, both natural and synthetic, interact with biological matter in the absence of direct electronic communication. However, biological systems have evolved to synthesize and utilize naturally-derived materials for the generation and modulation of electrical potentials, voltage gradients, and ion flows. Bioelectric phenomena can be translated into potent signaling cues for intra- and inter-cellular communication. These cues can serve as a gateway to link synthetic devices with biological systems. This progress report will provide an update on advances in the application of electronically active biomaterials for use in organic electronics and bio-interfaces. Specific focus will be granted to covering technologies where natural and synthetic biological materials serve as integral components such as thin film electronics, in vitro cell culture models, and implantable medical devices. Future perspectives and emerging challenges will also be highlighted. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Electron Transfer in Chemistry and Biology-The Primary Events in ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 12. Electron Transfer in Chemistry and Biology – The Primary Events in Photosynthesis. V Krishnan. General Article Volume 2 Issue 12 December 1997 pp 77-86. Fulltext. Click here to view fulltext PDF. Permanent link:

  10. How to observe small biological objects in low voltage electron microscope

    Czech Academy of Sciences Publication Activity Database

    Nebesářová, Jana; Vancová, Marie

    2007-01-01

    Roč. 13, č. 3 (2007), s. 248-249 ISSN 1431-9276 R&D Projects: GA AV ČR 1QS600220501 Institutional research plan: CEZ:AV0Z60220518 Keywords : low voltage electron microscope * negative staining * flagella * Borrelia burgdorferi Subject RIV: EA - Cell Biology Impact factor: 1.941, year: 2007

  11. Energy-filtered transmission electron microscopy of biological samples on highly transparent carbon nanomembranes

    International Nuclear Information System (INIS)

    Rhinow, Daniel; Bueenfeld, Matthias; Weber, Nils-Eike; Beyer, Andre; Goelzhaeuser, Armin; Kuehlbrandt, Werner; Hampp, Norbert; Turchanin, Andrey

    2011-01-01

    Ultrathin carbon nanomembranes (CNM) comprising crosslinked biphenyl precursors have been tested as support films for energy-filtered transmission electron microscopy (EFTEM) of biological specimens. Due to their high transparency CNM are ideal substrates for electron energy loss spectroscopy (EELS) and electron spectroscopic imaging (ESI) of stained and unstained biological samples. Virtually background-free elemental maps of tobacco mosaic virus (TMV) and ferritin have been obtained from samples supported by ∼1 nm thin CNM. Furthermore, we have tested conductive carbon nanomembranes (cCNM) comprising nanocrystalline graphene, obtained by thermal treatment of CNM, as supports for cryoEM of ice-embedded biological samples. We imaged ice-embedded TMV on cCNM and compared the results with images of ice-embedded TMV on conventional carbon film (CC), thus analyzing the gain in contrast for TMV on cCNM in a quantitative manner. In addition we have developed a method for the preparation of vitrified specimens, suspended over the holes of a conventional holey carbon film, while backed by ultrathin cCNM. -- Research highlights: → We examine ultrathin carbon nanomembranes (CNM) as supports for biological TEM. → CNM comprise crosslinked biphenyl precursors. → CNM supports enable background-free elemental mapping of heavy and light elements. → We perform cryoEM of ice-embedded biological samples on graphene-like conductive CNM.

  12. The ion-electron correlation function in liquid metals

    International Nuclear Information System (INIS)

    Takeda, S.; Tamaki, S.; Waseda, Y.

    1985-01-01

    The structure factors of liquid Zn at 723 K, Sn at 523 K and Bi at 573 K have been determined by neutron diffraction with sufficient accuracy and compared with those of X-ray diffraction. A remarkable difference in the structural information between the two methods is clearly found around the first peak region as well as in the slightly varied peak positions, and it is apparently larger than the experimental errors. With these facts in mind, a new method evaluating the ion-electron correlation function in liquid metals has been proposed by using the measured structural data of X-rays and neutrons, with the help of theoretical values of the electron-electron correlation function by he Utsumi-Ichimaru scheme. This method has been applied to liquid Zn, Sn and Bi, and the radial distribution function of valence electrons around an ion has been estimated, from which the ionic radius and the schematic diagram of the electron distribution map are obtained. The ionic radii evaluated in this work have been found to agree well with those proposed by Pauling. (author)

  13. Distorted wave calculations for electron loss process induced by bare ion impact on biological targets

    International Nuclear Information System (INIS)

    Monti, J.M.; Tachino, C.A.; Hanssen, J.; Fojón, O.A.; Galassi, M.E.; Champion, C.; Rivarola, R.D.

    2014-01-01

    Distorted wave models are employed to investigate the electron loss process induced by bare ions on biological targets. The two main reactions which contribute to this process, namely, the single electron ionization as well as the single electron capture are here studied. In order to further assess the validity of the theoretical descriptions used, the influence of particular mechanisms are studied, like dynamic screening for the case of electron ionization and energy deposition on the target by the impacting projectile for the electron capture one. Results are compared with existing experimental data. - Highlights: ► Distorted wave models are used to investigate ion-molecule collisions. ► Differential and total cross-sections for capture and ionization are evaluated. ► The influence of dynamic screening is determined. ► Capture reaction dominates the mean energy deposited by the projectile on the target

  14. DMPD: Type I interferon receptors: biochemistry and biological functions. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17502368 Type I interferon receptors: biochemistry and biological functions. de Wee...(.html) (.csml) Show Type I interferon receptors: biochemistry and biological functions. PubmedID 17502368 T...itle Type I interferon receptors: biochemistry and biological functions. Authors

  15. Fabricating designed fullerene nanostructures for functional electronic devices

    OpenAIRE

    Larsen, Christian

    2014-01-01

    A long-term goal within the field of organic electronics has been to developflexible and functional devices, which can be processed and patterned withlow-cost and energy-efficient solution-based methods. This thesis presents anumber of functional paths towards the attainment of this goal via thedevelopment and demonstration of novel fabrication and patterningmethods involving the important organic-semiconductor family termedfullerenes.Fullerenes are soccer-shaped small molecules, with two oft...

  16. Correlation between biological activity and electron transferring of bovine liver catalase: Osmolytes effects

    International Nuclear Information System (INIS)

    Tehrani, H. Sepasi; Moosavi-Movahedi, A.A.; Ghourchian, H.

    2013-01-01

    Highlights: • Proline increases ET in Bovine Liver Catalase (BLC) whereas histidine decreases it. • Proline also increased the biological activity, whereas histidine decreased it. • Electron transferring and biological activity for BLC are directly correlated. • Proline causes favorable ET for BLC shown by positive E 1/2 (E°′) and negative ΔG. • Histidine makes ET unfavorable for BLC, manifested by E 1/2 (E°′) 0. -- Abstract: Catalase is a crucial antioxidant enzyme that protects life against detrimental effects of H 2 O 2 by disproportionating it into water and molecular oxygen. Effect of proline as a compatible and histidine as a non compatible osmolyte on the electron transferring and midpoint potential of catalase has been investigated. Proline increases the midpoint potential (ΔE m > 0), therefore causing the ΔG ET to be less positive and making the electron transfer reaction more facile whereas histidine decreases the E m (ΔE m ET , thereby rendering the electron transfer reaction less efficient. These results indicate the inhibitory effect of histidine evident by a −37% decrease in the cathodic peak current compared to 16% increase in the case of proline indicative of activation. The insight paves the tedious way towards our ultimate goal of elucidating a correlation between biological activity and electron transferring

  17. Dawning of a new era in TRP channel structural biology by cryo-electron microscopy.

    Science.gov (United States)

    Madej, M Gregor; Ziegler, Christine M

    2018-02-01

    Cryo-electron microscopy (cryo-EM) permits the determination of atomic protein structures by averaging large numbers of individual projection images recorded at cryogenic temperatures-a method termed single-particle analysis. The cryo-preservation traps proteins within a thin glass-like ice layer, making literally a freeze image of proteins in solution. Projections of randomly adopted orientations are merged to reconstruct a 3D density map. While atomic resolution for highly symmetric viruses was achieved already in 2009, the development of new sensitive and fast electron detectors has enabled cryo-EM for smaller and asymmetrical proteins including fragile membrane proteins. As one of the most important structural biology methods at present, cryo-EM was awarded in October 2017 with the Nobel Prize in Chemistry. The molecular understanding of Transient-Receptor-Potential (TRP) channels has been boosted tremendously by cryo-EM single-particle analysis. Several near-atomic and atomic structures gave important mechanistic insights, e.g., into ion permeation and selectivity, gating, as well as into the activation of this enigmatic and medically important membrane protein family by various chemical and physical stimuli. Lastly, these structures have set the starting point for the rational design of TRP channel-targeted therapeutics to counteract life-threatening channelopathies. Here, we attempt a brief introduction to the method, review the latest advances in cryo-EM structure determination of TRP channels, and discuss molecular insights into the channel function based on the wealth of TRP channel cryo-EM structures.

  18. The Work Function Associated with Ultra-relativistic Electron ...

    Indian Academy of Sciences (India)

    1928), driven by electro-static force at the poles, produced by the strong magnetic field of rotating neutron stars. The work function plays a major role in the emission processes. Moreover, it is interesting to note that electrons are only emitted from the polar region of magnetized neutron stars, but never from some region far ...

  19. The electron-propagator approach to conceptual density-functional ...

    Indian Academy of Sciences (India)

    Unknown

    Abstract. Both electron propagator theory and density-functional theory provide conceptually useful information about chemical reactivity and, most especially, charge transfer. This paper elucidates the qualitative and quantitative links between the two theories, with emphasis on how the reactivity indica- tors of conceptual ...

  20. Current functional theory for multi-electron configuration

    DEFF Research Database (Denmark)

    Bang, Jens N.; Bohr, Henrik

    2010-01-01

    The density functional theory (DFT) formalism is reformulated into a framework of currents so as to give the energy a parameter dependent behaviour, e.g., time. This “current” method is aimed at describing the transition of electrons from one orbital to another and especially from the ground stat...

  1. The electron-propagator approach to conceptual density-functional ...

    Indian Academy of Sciences (India)

    Both electron propagator theory and density-functional theory provide conceptually useful information about chemical reactivity and, most especially, charge transfer. This paper elucidates thequalitative and quantitative links between the two theories, with emphasis on how the reactivity indicators of conceptual ...

  2. Electron processing at low energies: from basics to environmental and biological applications.

    Science.gov (United States)

    Illenberger, Eugen

    2006-10-01

    Electron initiated reactions play a key role in nearly any field of pure and applied sciences, in the gas phase as well as in condensed phases or at interfaces. This include substrate induced photochemistry, radiation damage of biological material (and, accordingly, the molecular mechanisms, how radio sensitizers used in tumour therapy operate), reactions induced by electrons in surface tunnelling microscopy (STM), or any kind of plasma used in industrial plasma processing. In each of these fields the electron-molecule interaction represents a key step within an eventually complex reaction sequence. A particularly interesting field is the interaction of electrons with molecules at energies below the level of electronic excitation. In this range many molecules exhibit large cross sections for resonant electron capture, often followed by the decomposition of the transient negative compound (M^-# ) according to e^- + M --> M^-# --> R + X^-.^ We report on such dissociative electron attachment (DEA) processes studied at different stages of aggregation, namely in single molecules under collision free conditions, in clusters formed by supersonic gas expansion, and on the surface of solids or in molecular nanofilms. In the meantime it has also been recognised that in the damage of living cells by high energy radiation the attachment of low energy secondary electrons to DNA is a key initial process leading to strand breaks. These secondary electrons are created along the ionisation track of the primary high-energy quantum. Apart from that, bio-molecular systems exhibit unique features in DEA, like bond and site selective decompositions.

  3. Biological activity of lactoferrin-functionalized biomimetic hydroxyapatite nanocrystals

    Directory of Open Access Journals (Sweden)

    Nocerino N

    2014-03-01

    Full Text Available Nunzia Nocerino,1 Andrea Fulgione,1 Marco Iannaccone,1 Laura Tomasetta,1 Flora Ianniello,1 Francesca Martora,1 Marco Lelli,2 Norberto Roveri,2 Federico Capuano,3 Rosanna Capparelli1 1Department of Agriculture Special Biotechnology Center Federico II, CeBIOTEC Biotechnology, University of Naples Federico II, Naples, 2Department of Chemistry, G Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, 3Department of Food Inspection IZS ME, Naples, Italy Abstract: The emergence of bacterial strains resistant to antibiotics is a general public health problem. Progress in developing new molecules with antimicrobial properties has been made. In this study, we evaluated the biological activity of a hybrid nanocomposite composed of synthetic biomimetic hydroxyapatite surface-functionalized by lactoferrin (LF-HA. We evaluated the antimicrobial, anti-inflammatory, and antioxidant properties of LF-HA and found that the composite was active against both Gram-positive and Gram-negative bacteria, and that it modulated proinflammatory and anti-inflammatory responses and enhanced antioxidant properties as compared with LF alone. These results indicate the possibility of using LF-HA as an antimicrobial system and biomimetic hydroxyapatite as a candidate for innovative biomedical applications. Keywords: lactoferrin, hydroxyapatite nanocrystals, biomimetism, biological activity, drug delivery

  4. Click Chemistry Mediated Functionalization of Vertical Nanowires for Biological Applications.

    Science.gov (United States)

    Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica; Buch-Månson, Nina; Bovet, Nicolas; Nygård, Jesper; Martinez, Karen L; Meldal, Morten

    2016-01-11

    Semiconductor nanowires (NWs) are gaining significant importance in various biological applications, such as biosensing and drug delivery. Efficient and controlled immobilization of biomolecules on the NW surface is crucial for many of these applications. Here, we present for the first time the use of the Cu(I) -catalyzed alkyne-azide cycloaddition and its strain-promoted variant for the covalent functionalization of vertical NWs with peptides and proteins. The potential of the approach was demonstrated in two complementary applications of measuring enzyme activity and protein binding, which is of general interest for biological studies. The attachment of a peptide substrate provided NW arrays for the detection of protease activity. In addition, green fluorescent protein was immobilized in a site-specific manner and recognized by antibody binding to demonstrate the proof-of-concept for the use of covalently modified NWs for diagnostic purposes using minute amounts of material. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Genome-wide survey for biologically functional pseudogenes.

    Directory of Open Access Journals (Sweden)

    Orjan Svensson

    2006-05-01

    Full Text Available According to current estimates there exist about 20,000 pseudogenes in a mammalian genome. The vast majority of these are disabled and nonfunctional copies of protein-coding genes which, therefore, evolve neutrally. Recent findings that a Makorin1 pseudogene, residing on mouse Chromosome 5, is, indeed, in vivo vital and also evolutionarily preserved, encouraged us to conduct a genome-wide survey for other functional pseudogenes in human, mouse, and chimpanzee. We identify to our knowledge the first examples of conserved pseudogenes common to human and mouse, originating from one duplication predating the human-mouse species split and having evolved as pseudogenes since the species split. Functionality is one possible way to explain the apparently contradictory properties of such pseudogene pairs, i.e., high conservation and ancient origin. The hypothesis of functionality is tested by comparing expression evidence and synteny of the candidates with proper test sets. The tests suggest potential biological function. Our candidate set includes a small set of long-lived pseudogenes whose unknown potential function is retained since before the human-mouse species split, and also a larger group of primate-specific ones found from human-chimpanzee searches. Two processed sequences are notable, their conservation since the human-mouse split being as high as most protein-coding genes; one is derived from the protein Ataxin 7-like 3 (ATX7NL3, and one from the Spinocerebellar ataxia type 1 protein (ATX1. Our approach is comparative and can be applied to any pair of species. It is implemented by a semi-automated pipeline based on cross-species BLAST comparisons and maximum-likelihood phylogeny estimations. To separate pseudogenes from protein-coding genes, we use standard methods, utilizing in-frame disablements, as well as a probabilistic filter based on Ka/Ks ratios.

  6. Biological activity of lactoferrin-functionalized biomimetic hydroxyapatite nanocrystals.

    Science.gov (United States)

    Nocerino, Nunzia; Fulgione, Andrea; Iannaccone, Marco; Tomasetta, Laura; Ianniello, Flora; Martora, Francesca; Lelli, Marco; Roveri, Norberto; Capuano, Federico; Capparelli, Rosanna

    2014-01-01

    The emergence of bacterial strains resistant to antibiotics is a general public health problem. Progress in developing new molecules with antimicrobial properties has been made. In this study, we evaluated the biological activity of a hybrid nanocomposite composed of synthetic biomimetic hydroxyapatite surface-functionalized by lactoferrin (LF-HA). We evaluated the antimicrobial, anti-inflammatory, and antioxidant properties of LF-HA and found that the composite was active against both Gram-positive and Gram-negative bacteria, and that it modulated proinflammatory and anti-inflammatory responses and enhanced antioxidant properties as compared with LF alone. These results indicate the possibility of using LF-HA as an antimicrobial system and biomimetic hydroxyapatite as a candidate for innovative biomedical applications.

  7. Structure, Function, and Biology of the Enterococcus faecalis Cytolysin

    Directory of Open Access Journals (Sweden)

    Daria Van Tyne

    2013-04-01

    Full Text Available Enterococcus faecalis is a Gram-positive commensal member of the gut microbiota of a wide range of organisms. With the advent of antibiotic therapy, it has emerged as a multidrug resistant, hospital-acquired pathogen. Highly virulent strains of E. faecalis express a pore-forming exotoxin, called cytolysin, which lyses both bacterial and eukaryotic cells in response to quorum signals. Originally described in the 1930s, the cytolysin is a member of a large class of lanthionine-containing bacteriocins produced by Gram-positive bacteria. While the cytolysin shares some core features with other lantibiotics, it possesses unique characteristics as well. The current understanding of cytolysin biosynthesis, structure/function relationships, and contribution to the biology of E. faecalis are reviewed, and opportunities for using emerging technologies to advance this understanding are discussed.

  8. Sirtuins in mammals: insights into their biological function

    Science.gov (United States)

    MICHAN, Shaday; SINCLAIR, David

    2009-01-01

    Sirtuins are a conserved family of proteins found in all domains of life. The first known sirtuin, Sir2 (silent information regulator 2) of Saccharomyces cerevisiae, from which the family derives its name, regulates ribosomal DNA recombination, gene silencing, DNA repair, chromosomal stability and longevity. Sir2 homologues also modulate lifespan in worms and flies, and may underlie the beneficial effects of caloric restriction, the only regimen that slows aging and extends lifespan of most classes of organism, including mammals. Sirtuins have gained considerable attention for their impact on mammalian physiology, since they may provide novel targets for treating diseases associated with aging and perhaps extend human lifespan. In this review we describe our current understanding of the biological function of the seven mammalian sirtuins, SIRT1–7, and we will also discuss their potential as mediators of caloric restriction and as pharmacological targets to delay and treat human age-related diseases. PMID:17447894

  9. Development of biological functional material and product from Nelumbo nucifera

    International Nuclear Information System (INIS)

    Jeong, Il Yun; Park, Yong Dae; Jin, Chang Hyun; Choi, Dae Seong

    2008-01-01

    The solvent extracts of Nelumbo nucifera G. were investigated for the activities of antioxidant, whitening, anti-wrinkle and antimicrobial effects to apply as a functional ingredient for cosmetic products. The electron donating ability of irradiated NN-L extract was above 85% at the concentration of 50ppm. The superoxide dismutase(SOD)-like activity of irradiated NN-L extract was about 76% at 1,000ppm concentration. The xanthine oxidase inhibitory effect of irradiated NN-L extract was about 15% at 1,000ppm. The tyrosinase inhibitory effect of irradiated NN-L extract was about 18% at 1,000ppm. Anti-wrinkle effect, the elastase inhibition activity of irradiated NN-L extract was about 45% at 1,000ppm concentration. All these findings suggested that Nelumbo nucifera G. has a great potential as a cosmeceutical ingredient

  10. Development of biological functional material and product from Nelumbo nucifera

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Il Yun; Park, Yong Dae; Jin, Chang Hyun; Choi, Dae Seong

    2008-01-15

    The solvent extracts of Nelumbo nucifera G. were investigated for the activities of antioxidant, whitening, anti-wrinkle and antimicrobial effects to apply as a functional ingredient for cosmetic products. The electron donating ability of irradiated NN-L extract was above 85% at the concentration of 50ppm. The superoxide dismutase(SOD)-like activity of irradiated NN-L extract was about 76% at 1,000ppm concentration. The xanthine oxidase inhibitory effect of irradiated NN-L extract was about 15% at 1,000ppm. The tyrosinase inhibitory effect of irradiated NN-L extract was about 18% at 1,000ppm. Anti-wrinkle effect, the elastase inhibition activity of irradiated NN-L extract was about 45% at 1,000ppm concentration. All these findings suggested that Nelumbo nucifera G. has a great potential as a cosmeceutical ingredient.

  11. Biomimetic self-assembly of a functional asymmetrical electronic device.

    Science.gov (United States)

    Boncheva, Mila; Gracias, David H; Jacobs, Heiko O; Whitesides, George M

    2002-04-16

    This paper introduces a biomimetic strategy for the fabrication of asymmetrical, three-dimensional electronic devices modeled on the folding of a chain of polypeptide structural motifs into a globular protein. Millimeter-size polyhedra-patterned with logic devices, wires, and solder dots-were connected in a linear string by using flexible wire. On self-assembly, the string folded spontaneously into two domains: one functioned as a ring oscillator, and the other one as a shift register. This example demonstrates that biomimetic principles of design and self-organization can be applied to generate multifunctional electronic systems of complex, three-dimensional architecture.

  12. Biosynthesis and biological functions of terpenoids in plants.

    Science.gov (United States)

    Tholl, Dorothea

    2015-01-01

    Terpenoids (isoprenoids) represent the largest and most diverse class of chemicals among the myriad compounds produced by plants. Plants employ terpenoid metabolites for a variety of basic functions in growth and development but use the majority of terpenoids for more specialized chemical interactions and protection in the abiotic and biotic environment. Traditionally, plant-based terpenoids have been used by humans in the food, pharmaceutical, and chemical industries, and more recently have been exploited in the development of biofuel products. Genomic resources and emerging tools in synthetic biology facilitate the metabolic engineering of high-value terpenoid products in plants and microbes. Moreover, the ecological importance of terpenoids has gained increased attention to develop strategies for sustainable pest control and abiotic stress protection. Together, these efforts require a continuous growth in knowledge of the complex metabolic and molecular regulatory networks in terpenoid biosynthesis. This chapter gives an overview and highlights recent advances in our understanding of the organization, regulation, and diversification of core and specialized terpenoid metabolic pathways, and addresses the most important functions of volatile and nonvolatile terpenoid specialized metabolites in plants.

  13. Formation of Autapse Connected to Neuron and Its Biological Function

    Directory of Open Access Journals (Sweden)

    Chunni Wang

    2017-01-01

    Full Text Available Autapse is a specific synapse connected to the neuron via close loop, and its functional adjusting is described by applying time-delayed feedback on the membrane potential of the neuron. This paper discussed the possible formation mechanism and biological function of autapse connection on neurons. We believe that the formation and growth of autapse connected to neuron can be associated with injury on axon and blocking in signal transmission; thus auxiliary loop is developed to form an autapse. When autapse is set up, it can propagate the signals and change the modes of electrical activities under self-adaption. Based on the cable neuron model, the injury on axon is generated by poisoning and blocking in ion channels (of sodium; thus the conductance of ion channels are changed to form injury-associated defects. Furthermore, auxiliary loop with time delay is designed to restore and enhance signal propagation by setting different time delays and feedback gains. The numerical studies confirmed that appropriate time delay and feedback gain in electric or chemical autapse can help signal (or wave generated by external forcing propagation across the blocked area. As a result, formation of autapse could be dependent on the injury of neuron and further enhances the self-adaption to external stimuli.

  14. Electronic and mechanical properties of chemically functionalized nanowires

    Science.gov (United States)

    Bidasaria, Sanjay K.

    2009-12-01

    Organic and inorganic nanostructured materials, nano- and mesoscale objects and devices, and their integration into existing microelectronic technologies have been at the center of recent fundamental and applied research in nanotechnology. One of the critical needs is to develop an enhanced predictive capability of structure-property correlations and enable robust high performance systems by design. My thesis work was concerned with the theoretical and experimental studies of electronic and mechanical properties of chemically functionalized nanowires. I will first describe a theoretical approach for investigating structure-property correlations in atomic-sized metallic wires based on the Density Functional Theory (DFT) for structure calculations and the Non-equilibrium Green's Function (NEGF) technique for electronic transport properties simulations. This synergistic approach is shown to yield the atomic structure of the smallest niobium nanowires. Furthermore, the method was applied to simulate electronic properties of chemically functionalized graphene nanoribbons. Further, I will demonstrate an experimental technique for simultaneous measurements of force and conductance in atomic-size objects based on quartz tuning fork piezoelectric sensors. A peculiar scaling effect, relevant for a broad range of test and measurement applications, namely the squeeze film effect, was observed during the development of the sensors. Using theoretical analysis based on finite element simulations of the hydrodynamic behavior of the sensors in a broad range of ambient conditions, I explain the observed phenomenon.

  15. Electron Correlation from the Adiabatic Connection for Multireference Wave Functions

    Science.gov (United States)

    Pernal, Katarzyna

    2018-01-01

    An adiabatic connection (AC) formula for the electron correlation energy is derived for a broad class of multireference wave functions. The AC expression recovers dynamic correlation energy and assures a balanced treatment of the correlation energy. Coupling the AC formalism with the extended random phase approximation allows one to find the correlation energy only from reference one- and two-electron reduced density matrices. If the generalized valence bond perfect pairing model is employed a simple closed-form expression for the approximate AC formula is obtained. This results in the overall M5 scaling of the computation cost making the method one of the most efficient multireference approaches accounting for dynamic electron correlation also for the strongly correlated systems.

  16. Theoretical characterization of electron energy distribution function in RF plasmas

    International Nuclear Information System (INIS)

    Capitelli, M.; Capriati, G.; Dilonardo, M.; Gorse, C.; Longo, S.

    1993-01-01

    Different methods for the modeling of low-temperature plasmas of both technological and fundamental interest are discussed. The main concept of all these models is the electron energy distribution function (eedf) which is necessary to calculate the rate coefficients for any chemical reaction involving electrons. Results of eedf calculations in homogeneous SF 6 and SiH 4 plasmas are discussed based on solution of the time-dependent Boltzmann equation. The space-dependent eedf in an RF discharge in He is calculated taking into account the sheath oscillations by a Monte Carlo model assuming the plasma heating mechanism and the electric field determined by using a fluid model. The need to take into account the ambipolar diffusion of electrons in RF discharge modeling is stressed. A self-consistent model based on coupling the equations of the fluid model and the chemical kinetics ones is presented. (orig.)

  17. A Feasibility Study of the IMRT Optimization with Pseudo-Biologic Objective Function

    International Nuclear Information System (INIS)

    Yi, Byong Yong; Cho, Sam Ju; Ahn, Seung Do; Kim, Jong Hoon; Choi, Eun Kyung; Chang, Hye Sook; Kwon, Soo Il

    2001-01-01

    The pseudo-biologic objective function has been designed for the IMRT optimization. The RTP Tool Box (RTB) was used for this study. The pseudo-biologic function is similar to the biological objective function in mathematical shape, but uses physical parameters. The concepts of the TCI (Target Coverage Index) and the OSI (Organ Score Index) have been introduced for the target and the normal organs, respectively. The pseudo-biologic objective function s has been defined using these TCI and OSI's. The OSI's from the pseudo-biological function showed better results than from the physical functions, while TCI's showed similar tendency. These results revealed the feasibility of the pseudo-biologic function as an IMRT objective function

  18. Quantum Chemical Topology of the Electron Localization Function in the Field of Attosecond Electron Dynamics.

    Science.gov (United States)

    Parise, Angela; Alvarez-Ibarra, Aurelio; Wu, Xiaojing; Zhao, Xiaodong; Pilmé, Julien; Lande, Aurélien de la

    2018-02-15

    We report original analyses of attosecond electron dynamics of molecules subject to collisions by high energy charged particles based on Real-Time Time-Dependent-Density-Functional-Theory simulations coupled to Topological Analyses of the Electron Localization Function (TA-TD-ELF). We investigate irradiation of water and guanine. TA-TD-ELF enables qualitative and quantitative characterizations of bond breaking and formation, of charge migration within topological basins, or of electron attachment to the colliding particle. Whereas the Lewis-VSEPR structure of gas phase water is blown out within a few attoseconds after collision, that of guanine is far more robust and reconstitutes rapidly after impact even though the molecule remains electronically excited. This difference is accounted by the presence of the electron bath surrounding the impact point which enables energy relaxation within the molecule. Our approach should stimulate future studies to unravel the early steps following irradiation of various types of systems (isolated molecules, biomolecules, nanoclusters, solids, etc.) and is also readily applicable to irradiation by photons of various energies.

  19. Dynamic Processes in Biology, Chemistry, and Materials Science: Opportunities for UltraFast Transmission Electron Microscopy - Workshop Summary Report

    Energy Technology Data Exchange (ETDEWEB)

    Kabius, Bernd C.; Browning, Nigel D.; Thevuthasan, Suntharampillai; Diehl, Barbara L.; Stach, Eric A.

    2012-07-25

    This report summarizes a 2011 workshop that addressed the potential role of rapid, time-resolved electron microscopy measurements in accelerating the solution of important scientific and technical problems. A series of U.S. Department of Energy (DOE) and National Academy of Science workshops have highlighted the critical role advanced research tools play in addressing scientific challenges relevant to biology, sustainable energy, and technologies that will fuel economic development without degrading our environment. Among the specific capability needs for advancing science and technology are tools that extract more detailed information in realistic environments (in situ or operando) at extreme conditions (pressure and temperature) and as a function of time (dynamic and time-dependent). One of the DOE workshops, Future Science Needs and Opportunities for Electron Scattering: Next Generation Instrumentation and Beyond, specifically addressed the importance of electron-based characterization methods for a wide range of energy-relevant Grand Scientific Challenges. Boosted by the electron optical advancement in the last decade, a diversity of in situ capabilities already is available in many laboratories. The obvious remaining major capability gap in electron microscopy is in the ability to make these direct in situ observations over a broad spectrum of fast (µs) to ultrafast (picosecond [ps] and faster) temporal regimes. In an effort to address current capability gaps, EMSL, the Environmental Molecular Sciences Laboratory, organized an Ultrafast Electron Microscopy Workshop, held June 14-15, 2011, with the primary goal to identify the scientific needs that could be met by creating a facility capable of a strongly improved time resolution with integrated in situ capabilities. The workshop brought together more than 40 leading scientists involved in applying and/or advancing electron microscopy to address important scientific problems of relevance to DOE’s research

  20. Cryo-electron tomography-the cell biology that came in from the cold.

    Science.gov (United States)

    Wagner, Jonathan; Schaffer, Miroslava; Fernández-Busnadiego, Rubén

    2017-09-01

    Cryo-electron tomography (cryo-ET) provides high-resolution 3D views into cells pristinely preserved by vitrification. Recent technical advances such as direct electron detectors, the Volta phase plate and cryo-focused ion beam milling have dramatically pushed image quality and expanded the range of cryo-ET applications. Cryo-ET not only allows mapping the positions and interactions of macromolecules within their intact cellular context, but can also reveal their in situ structure at increasing resolution. Here, we review how recent work using cutting-edge cryo-ET technologies is starting to provide fresh views into different aspects of cellular biology at an unprecedented level of detail. We anticipate that these developments will soon make cryo-ET a fundamental technique in cell biology. © 2017 Federation of European Biochemical Societies.

  1. Generalized Fokker-Planck theory for electron and photon transport in biological tissues: application to radiotherapy.

    Science.gov (United States)

    Olbrant, Edgar; Frank, Martin

    2010-12-01

    In this paper, we study a deterministic method for particle transport in biological tissues. The method is specifically developed for dose calculations in cancer therapy and for radiological imaging. Generalized Fokker-Planck (GFP) theory [Leakeas and Larsen, Nucl. Sci. Eng. 137 (2001), pp. 236-250] has been developed to improve the Fokker-Planck (FP) equation in cases where scattering is forward-peaked and where there is a sufficient amount of large-angle scattering. We compare grid-based numerical solutions to FP and GFP in realistic medical applications. First, electron dose calculations in heterogeneous parts of the human body are performed. Therefore, accurate electron scattering cross sections are included and their incorporation into our model is extensively described. Second, we solve GFP approximations of the radiative transport equation to investigate reflectance and transmittance of light in biological tissues. All results are compared with either Monte Carlo or discrete-ordinates transport solutions.

  2. Local electronic and electrical properties of functionalized graphene nano flakes

    International Nuclear Information System (INIS)

    Chutia, Arunabhiram; Sahnoun, Riadh; Deka, Ramesh C.; Zhu, Zhigang; Tsuboi, Hideyuki; Takaba, Hiromitsu; Miyamoto, Akira

    2011-01-01

    Based on experimental findings models of amorphous graphene related carbon materials were generated using graphene nano flakes. On the optimized structures detailed local electronic properties were investigated using density functional theory. The electrical conductivities of all these models were also estimated using an in-house program based on tight-binding method. The calculated electrical conductivity values of all the models agreed well with the trend of calculated energy gap and graphitic character.

  3. Graphene as a transparent conductive support for studying biological molecules by transmission electron microscopy

    International Nuclear Information System (INIS)

    Nair, R. R.; Anissimova, S.; Novoselov, K. S.; Blake, P.; Blake, J. R.; Geim, A. K.; Zan, R.; Bangert, U.; Golovanov, A. P.; Morozov, S. V.; Latychevskaia, T.

    2010-01-01

    We demonstrate the application of graphene as a support for imaging individual biological molecules in transmission electron microscope (TEM). A simple procedure to produce free-standing graphene membranes has been designed. Such membranes are extremely robust and can support practically any submicrometer object. Tobacco mosaic virus has been deposited on graphene samples and observed in a TEM. High contrast has been achieved even though no staining has been applied.

  4. Direct Electron Transfer of Enzymes in a Biologically Assembled Conductive Nanomesh Enzyme Platform.

    Science.gov (United States)

    Lee, Seung-Woo; Lee, Ki-Young; Song, Yong-Won; Choi, Won Kook; Chang, Joonyeon; Yi, Hyunjung

    2016-02-24

    Nondestructive assembly of a nanostructured enzyme platform is developed in combination of the specific biomolecular attraction and electrostatic coupling for highly efficient direct electron transfer (DET) of enzymes with unprecedented applicability and versatility. The biologically assembled conductive nanomesh enzyme platform enables DET-based flexible integrated biosensors and DET of eight different enzyme with various catalytic activities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. RGB color coded images in scanning electron microscopy of biological surfaces

    Czech Academy of Sciences Publication Activity Database

    Kofroňová, Olga; Benada, Oldřich

    2017-01-01

    Roč. 61, č. 3 (2017), s. 349-352 ISSN 0001-723X R&D Projects: GA MŠk(CZ) LO1509; GA ČR(CZ) GA16-20229S Institutional support: RVO:61388971 Keywords : Biological surfaces * Color image s * Scanning electron microscopy Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 0.673, year: 2016

  6. A generalized electron energy probability function for inductively coupled plasmas under conditions of nonlocal electron kinetics

    Science.gov (United States)

    Mouchtouris, S.; Kokkoris, G.

    2018-01-01

    A generalized equation for the electron energy probability function (EEPF) of inductively coupled Ar plasmas is proposed under conditions of nonlocal electron kinetics and diffusive cooling. The proposed equation describes the local EEPF in a discharge and the independent variable is the kinetic energy of electrons. The EEPF consists of a bulk and a depleted tail part and incorporates the effect of the plasma potential, Vp, and pressure. Due to diffusive cooling, the break point of the EEPF is eVp. The pressure alters the shape of the bulk and the slope of the tail part. The parameters of the proposed EEPF are extracted by fitting to measure EEPFs (at one point in the reactor) at different pressures. By coupling the proposed EEPF with a hybrid plasma model, measurements in the gaseous electronics conference reference reactor concerning (a) the electron density and temperature and the plasma potential, either spatially resolved or at different pressure (10-50 mTorr) and power, and (b) the ion current density of the electrode, are well reproduced. The effect of the choice of the EEPF on the results is investigated by a comparison to an EEPF coming from the Boltzmann equation (local electron kinetics approach) and to a Maxwellian EEPF. The accuracy of the results and the fact that the proposed EEPF is predefined renders its use a reliable alternative with a low computational cost compared to stochastic electron kinetic models at low pressure conditions, which can be extended to other gases and/or different electron heating mechanisms.

  7. hCG: Biological Functions and Clinical Applications.

    Science.gov (United States)

    Nwabuobi, Chinedu; Arlier, Sefa; Schatz, Frederick; Guzeloglu-Kayisli, Ozlem; Lockwood, Charles Joseph; Kayisli, Umit Ali

    2017-09-22

    Human chorionic gonadotropin (hCG) is produced primarily by differentiated syncytiotrophoblasts, and represents a key embryonic signal that is essential for the maintenance of pregnancy. hCG can activate various signaling cascades including mothers against decapentaplegic homolog 2 (Smad2), protein kinase C (PKC), and/or protein kinase A (PKA) in several cells types by binding to luteinizing hormone/chorionic gonadotropin receptor (LHCGR) or potentially by direct/indirect interaction with transforming growth factor beta receptor (TGFβR). The molecule displays specialized roles in promoting angiogenesis in the uterine endothelium, maintaining myometrial quiescence, as well as fostering immunomodulation at the maternal-fetal interface. It is a member of the glycoprotein hormone family that includes luteinizing hormone (LH), thyroid-stimulating hormone (TSH), and follicle-stimulating hormone (FSH). The α-subunit of hCG displays homologies with TSH, LH, and FSH, whereas the β subunit is 80-85% homologous to LH. The hCG molecule is produced by a variety of organs, exists in various forms, exerts vital biological functions, and has various clinical roles ranging from diagnosis and monitoring of pregnancy and pregnancy-related disorders to cancer surveillance. This review presents a detailed examination of hCG and its various clinical applications.

  8. Functional synchronization of biological rhythms in a tritrophic system.

    Science.gov (United States)

    Zhang, Sufang; Wei, Jianing; Guo, Xiaojiao; Liu, Tong-Xian; Kang, Le

    2010-06-10

    In a tritrophic system formed by a plant, an herbivore and a natural enemy, each component has its own biological rhythm. However, the rhythm correlations among the three levels and the underlying mechanisms in any tritrophic system are largely unknown. Here, we report that the rhythms exhibited bidirectional correlations in a model tritrophic system involving a lima bean, a pea leafminer and a parasitoid. From the bottom-up perspective, the rhythm was initiated from herbivore feeding, which triggered the rhythms of volatile emissions; then the rhythmic pattern of parasitoid activities was affected, and these rhythms were synchronized by a light switch signal. Increased volatile concentration can enhance the intensity of parasitoid locomotion and oviposition only under light. From the top-down perspective, naive and oviposition-experienced parasitoids were able to utilize the different volatile rhythm information from the damaged plant to locate host leafminers respectively. Our results indicated that the three interacting organisms in this system can achieve rhythmic functional synchronization under a natural light-dark photoperiod, but not under constant light or darkness. These findings provide new insight into the rhythm synchronization of three key players that contribute to the utilization of light and chemical signals, and our results may be used as potential approaches for manipulating natural enemies.

  9. Functional synchronization of biological rhythms in a tritrophic system.

    Directory of Open Access Journals (Sweden)

    Sufang Zhang

    Full Text Available In a tritrophic system formed by a plant, an herbivore and a natural enemy, each component has its own biological rhythm. However, the rhythm correlations among the three levels and the underlying mechanisms in any tritrophic system are largely unknown. Here, we report that the rhythms exhibited bidirectional correlations in a model tritrophic system involving a lima bean, a pea leafminer and a parasitoid. From the bottom-up perspective, the rhythm was initiated from herbivore feeding, which triggered the rhythms of volatile emissions; then the rhythmic pattern of parasitoid activities was affected, and these rhythms were synchronized by a light switch signal. Increased volatile concentration can enhance the intensity of parasitoid locomotion and oviposition only under light. From the top-down perspective, naive and oviposition-experienced parasitoids were able to utilize the different volatile rhythm information from the damaged plant to locate host leafminers respectively. Our results indicated that the three interacting organisms in this system can achieve rhythmic functional synchronization under a natural light-dark photoperiod, but not under constant light or darkness. These findings provide new insight into the rhythm synchronization of three key players that contribute to the utilization of light and chemical signals, and our results may be used as potential approaches for manipulating natural enemies.

  10. Function and regulation of lipid biology in Caenorhabditis elegans aging

    Directory of Open Access Journals (Sweden)

    Nicole Shangming Hou

    2012-05-01

    Full Text Available Rapidly expanding aging populations and a concomitant increase in the prevalence of age-related diseases are global health problems today. Over the past three decades, a large body of work has led to the identification of genes and regulatory networks that affect longevity and health span, often benefitting from the tremendous power of genetics in vertebrate and invertebrate model organisms. Interestingly, many of these factors appear linked to lipids, important molecules that participate in cellular signaling, energy metabolism, and structural compartmentalization. Despite the putative link between lipids and longevity, the role of lipids in aging remains poorly understood. Emerging data from the model organism Caenorhabditis elegans suggest that lipid composition may change during aging, as several pathways that influence aging also regulate lipid metabolism enzymes; moreover, some of these enzymes apparently play key roles in the pathways that affect the rate of aging. By understanding how lipid biology is regulated during C. elegans aging, and how it impacts molecular, cellular and organismal function, we may gain insight into novel ways to delay aging using genetic or pharmacological interventions. In the present review we discuss recent insights into the roles of lipids in C. elegans aging, including regulatory roles played by lipids themselves, the regulation of lipid metabolic enzymes, and the roles of lipid metabolism genes in the pathways that affect aging.

  11. Information Functional Theory: Electronic Properties as Functionals of Information for Atoms and Molecules.

    Science.gov (United States)

    Zhou, Xia-Yu; Rong, Chunying; Lu, Tian; Zhou, Panpan; Liu, Shubin

    2016-05-26

    How to accurately predict electronic properties of a Columbic system with the electron density obtained from experiments such as X-ray crystallography is still an unresolved problem. The information-theoretic approach recently developed in the framework of density functional reactivity theory is one of the efforts to address the issue. In this work, using 27 atoms and 41 molecules as illustrative examples, we present a study to demonstrate that one is able to satisfactorily describe such electronic properties as the total energy and its components with information-theoretic quantities like Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, and Onicescu information energy. Closely related to the earlier attempt of expanding density functionals using simple homogeneous functionals, this work not only confirms Nagy's proof that Shannon entropy alone should contain all the information needed to adequately describe an electronic system but also provides a feasible pathway to map the relationship between the experimentally available electron density and various electronic properties for Columbic systems such as atoms and molecules. Extensions to other electronic properties are straightforward.

  12. Direct observation of unstained wet biological samples by scanning-electron generation X-ray microscopy

    International Nuclear Information System (INIS)

    Ogura, Toshihiko

    2010-01-01

    Analytical tools of nanometre-scale resolution are indispensable in the fields of biology, physics and chemistry. One suitable tool, the soft X-ray microscope, provides high spatial resolution of visible light for wet specimens. For biological specimens, X-rays of water-window wavelength between carbon (284 eV; 4.3 nm) and oxygen (540 eV; 2.3 nm) absorption edges provide high-contrast imaging of biological samples in water. Among types of X-ray microscope, the transmission X-ray microscope using a synchrotron radiation source with diffractive zone plates offers the highest spatial resolution, approaching 15-10 nm. However, even higher resolution is required to measure proteins and protein complexes in biological specimens; therefore, a new type of X-ray microscope with higher resolution that uses a simple light source is desirable. Here we report a novel scanning-electron generation X-ray microscope (SGXM) that demonstrates direct imaging of unstained wet biological specimens. We deposited wet yeasts in the space between two silicon nitride (Si 3 N 4 ) films. A scanning electron beam of accelerating voltage 5 keV and current 1.6 nA irradiates the titanium (Ti)-coated Si 3 N 4 film, and the soft X-ray signal from it is detected by an X-ray photodiode (PD) placed below the sample. The SGXM can theoretically achieve better than 5 nm resolution. Our method can be utilized easily for various wet biological samples of bacteria, viruses, and protein complexes.

  13. Density functional theory and an experimentally-designed energy functional of electron density.

    Science.gov (United States)

    Miranda, David A; Bueno, Paulo R

    2016-09-21

    We herein demonstrate that capacitance spectroscopy (CS) experimentally allows access to the energy associated with the quantum mechanical ground state of many-electron systems. Priorly, electrochemical capacitance, C [small mu, Greek, macron] [ρ], was previously understood from conceptual and computational density functional theory (DFT) calculations. Thus, we herein propose a quantum mechanical experiment-based variational method for electron charging processes based on an experimentally-designed functional of the ground state electron density. In this methodology, the electron state density, ρ, and an energy functional of the electron density, E [small mu, Greek, macron] [ρ], can be obtained from CS data. CS allows the derivative of the electrochemical potential with respect to the electron density, (δ[small mu, Greek, macron][ρ]/δρ), to be obtained as a unique functional of the energetically minimised system, i.e., β/C [small mu, Greek, macron] [ρ], where β is a constant (associated with the size of the system) and C [small mu, Greek, macron] [ρ] is an experimentally observable quantity. Thus the ground state energy (at a given fixed external potential) can be obtained simply as E [small mu, Greek, macron] [ρ], from the experimental measurement of C [small mu, Greek, macron] [ρ]. An experimental data-set was interpreted to demonstrate the potential of this quantum mechanical experiment-based variational principle.

  14. Characterization of functional LB films using electron spin resonance spectroscopy

    International Nuclear Information System (INIS)

    Kuroda, Shin-ichi

    1995-01-01

    The role of ESR spectroscopy in the characterization of functional LB films is discussed. Unpaired electrons in LB films are associated with isolated radical molecules produced by charge transfer, paramagnetic metallic ions such as Cu 2+ , strongly interacting spins in the mixed valence states in charge-transfer salts, and so on. These spins often manifest the functions of materials. They can also act as microscopic probes in the ESR analysis devoted for the elucidation of characteristic properties of LB films. In structural studies, ESR is of particular importance in the analysis of molecular orientation of LB films. ESR can unambiguously determine the orientation of molecules through g-value anisotropy: different g value, different resonance field. Two types of new control methods of molecular orientation in LB films originated from the ESR analysis: study of in-plane orientation in dye LB films which led to the discovery of flow-orientation effect, and observation of drastic change of orientation of Cu-porphyrin in LB films using the trigger molecule, n-hexatriacontane. In the studies of electronic properties, hyperfine interactions between electron and nuclear spins provide information about molecular orbitals and local structures. Stable isotopes have been successfully applied to the stable radicals in merocyanine LB films to identify hyperfine couplings. In conducting LB films composed of charge-transfer salts, quasi-one-dimensional antiferromagnetism in semiconducting films and spin resonance of conduction electrons in metallic films are observed. Results provide microscopic evidence for the development of columnar structures of constituent molecules. Development of new functional LB films may provide more cases where ESR spectroscopy will clarify the nature of such films. (author)

  15. Functionalized diamond nanopowder for phosphopeptides enrichment from complex biological fluids

    Energy Technology Data Exchange (ETDEWEB)

    Hussain, Dilshad [Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800 (Pakistan); Najam-ul-Haq, Muhammad, E-mail: najamulhaq@bzu.edu.pk [Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800 (Pakistan); Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, A-6020 Innsbruck (Austria); Jabeen, Fahmida; Ashiq, Muhammad N.; Athar, Muhammad [Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800 (Pakistan); Rainer, Matthias; Huck, Christian W.; Bonn, Guenther K. [Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, A-6020 Innsbruck (Austria)

    2013-05-02

    Graphical abstract: -- Highlights: •Derivatization of diamond nanopowder as IMAC and RP. •Characterization with SEM, EDX and FT-IR. •Phosphopeptide enrichment from standard as well as real samples. •Desalting and human serum profiling with reproducible results. •MALDI-MS analysis with database identification. -- Abstract: Diamond is known for its high affinity and biocompatibility towards biomolecules and is used exclusively in separation sciences and life science research. In present study, diamond nanopowder is derivatized as Immobilized Metal Ion Affinity Chromatographic (IMAC) material for the phosphopeptides enrichment and as Reversed Phase (C-18) media for the desalting of complex mixtures and human serum profiling through MALDI-TOF-MS. Functionalized diamond nanopowder is characterized by Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy. Diamond-IMAC is applied to the standard protein (β-casein), spiked human serum, egg yolk and non-fat milk for the phosphopeptides enrichment. Results show the selectivity of synthesized IMAC-diamond immobilized with Fe{sup 3+} and La{sup 3+} ions. To comprehend the elaborated use, diamond-IMAC is also applied to the serum samples from gall bladder carcinoma for the potential biomarkers. Database search is carried out by the Mascot program ( (www.matrixscience.com)) for the assignment of phosphorylation sites. Diamond nanopowder is thus a separation media with multifunctional use and can be applied to cancer protein profiling for the diagnosis and biomarker identification.

  16. Functional Requirements for an Electronic Work Package System

    Energy Technology Data Exchange (ETDEWEB)

    Oxstrand, Johanna H. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2016-12-01

    This document provides a set of high level functional requirements for a generic electronic work package (eWP) system. The requirements have been identified by the U.S. nuclear industry as a part of the Nuclear Electronic Work Packages - Enterprise Requirements (NEWPER) initiative. The functional requirements are mainly applied to eWP system supporting Basic and Moderate types of smart documents, i.e., documents that have fields for recording input such as text, dates, numbers, and equipment status, and documents which incorporate additional functionalities such as form field data “type“ validation (e.g. date, text, number, and signature) of data entered and/or self-populate basic document information (usually from existing host application meta data) on the form when the user first opens it. All the requirements are categorized by the roles; Planner, Supervisor, Craft, Work Package Approval Reviewer, Operations, Scheduling/Work Control, and Supporting Functions. The categories Statistics, Records, Information Technology are also included used to group the requirements. All requirements are presented in Section 2 through Section 11. Examples of more detailed requirements are provided for the majority of high level requirements. These examples are meant as an inspiration to be used as each utility goes through the process of identifying their specific requirements. The report’s table of contents provides a summary of the high level requirements.

  17. Phytochrome from Green Plants: Properties and biological Function

    Energy Technology Data Exchange (ETDEWEB)

    Quail, Peter H.

    2014-07-25

    Pfr conformer reverses this activity upon initial light exposure, inducing the switch to photomorphogenic development. This reversal involves light-triggered translocation of the photoactivated phy molecule into the nucleus where it interacts with PIF-family members, inducing rapid phosphorylation and degradation of the PIFs via the ubiquitin-proteasome system. This degradation in turn elicits rapid alterations in gene expression that drive the deetiolation transition. This project has made considerable progress in defining phy-PIF signaling activity in controlling the SAR. The biological functions of the multiple PIF-family members in controlling the SAR, including dissection of the relative contributions of the individual PIFs to this process, as well as to diurnal growth-control oscillations, have been investigated using higher-order pif-mutant combinations. Using microarray analysis of a quadruple pif mutant we have defined the shade-induced, PIF-regulated transcriptional network genome-wide. This has revealed that a dynamic antagonism between the phys and PIFs generates selective reciprocal responses during deetiolation and the SAR in a rapidly light-responsive transcriptional network. Using integrated RNA-seq and ChIP-seq analysis of higher order pif-mutant combinations, we have defined the direct gene-targets of PIF transcriptional regulation, and have obtained evidence that this regulation involves differential direct targeting of rapidly light-responsive genes by the individual PIF-family members. This project has provided significant advances in our understanding of the molecular mechanisms by which the phy-PIF photosensory signaling pathway regulates an important bioenergy-related plant response to the light environment. The identification of molecular targets in the primary transcriptional-regulatory circuitry of this pathway has the potential to enable genetic or reverse-genetic manipulation of the partitioning of carbon between reproductive and

  18. The electronic work function of the different faces of tungsten

    International Nuclear Information System (INIS)

    Modinos, A.

    1978-01-01

    A semi-empirical theory of the electronic work function of the different faces of tungsten is presented. All the parameters entering the theory, except one, are estimated independently. The one adjustable parameter relates to the isotropic contribution to the work function, and, can, in principle, be determined from a self-consistent calculation of the band-structure of the energy levels in the bulk of the metal. The calculated values for the work function are in reasonably good agreement with available experimental data for practically all of the crystallographic planes with the exception of the (100) plane. For the latter, the calculated value is 0.3 eV above the experimental value. It is suggested that a negative contribution to the surface dipole potential from surface states, that exist on this plane, may be the reason of this discrepancy. (Auth.)

  19. Existence of time-dependent density-functional theory for open electronic systems: time-dependent holographic electron density theorem.

    Science.gov (United States)

    Zheng, Xiao; Yam, ChiYung; Wang, Fan; Chen, GuanHua

    2011-08-28

    We present the time-dependent holographic electron density theorem (TD-HEDT), which lays the foundation of time-dependent density-functional theory (TDDFT) for open electronic systems. For any finite electronic system, the TD-HEDT formally establishes a one-to-one correspondence between the electron density inside any finite subsystem and the time-dependent external potential. As a result, any electronic property of an open system in principle can be determined uniquely by the electron density function inside the open region. Implications of the TD-HEDT on the practicality of TDDFT are also discussed.

  20. Cryo-electron microscopy for structural analysis of dynamic biological macromolecules.

    Science.gov (United States)

    Murata, Kazuyoshi; Wolf, Matthias

    2018-02-01

    Since the introduction of what became today's standard for cryo-embedding of biological macromolecules at native conditions more than 30years ago, techniques and equipment have been drastically improved and the structure of biomolecules can now be studied at near atomic resolution by cryo-electron microscopy (cryo-EM) while capturing multiple dynamic states. Here we review the recent progress in cryo-EM for structural studies of dynamic biological macromolecules. We provide an overview of the cryo-EM method and introduce contemporary studies to investigate biomolecular structure and dynamics, including examples from the recent literature. Cryo-EM is a powerful tool for the investigation of biological macromolecular structures including analysis of their dynamics by using advanced image-processing algorithms. The method has become even more widely applicable with present-day single particle analysis and electron tomography. The cryo-EM method can be used to determine the three-dimensional structure of biomacromolecules in near native condition at close to atomic resolution, and has the potential to reveal conformations of dynamic molecular complexes. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  1. The integrative role of cryo electron microscopy in molecular and cellular structural biology.

    Science.gov (United States)

    Orlov, Igor; Myasnikov, Alexander G; Andronov, Leonid; Natchiar, S Kundhavai; Khatter, Heena; Beinsteiner, Brice; Ménétret, Jean-François; Hazemann, Isabelle; Mohideen, Kareem; Tazibt, Karima; Tabaroni, Rachel; Kratzat, Hanna; Djabeur, Nadia; Bruxelles, Tatiana; Raivoniaina, Finaritra; Pompeo, Lorenza di; Torchy, Morgan; Billas, Isabelle; Urzhumtsev, Alexandre; Klaholz, Bruno P

    2017-02-01

    After gradually moving away from preparation methods prone to artefacts such as plastic embedding and negative staining for cell sections and single particles, the field of cryo electron microscopy (cryo-EM) is now heading off at unprecedented speed towards high-resolution analysis of biological objects of various sizes. This 'revolution in resolution' is happening largely thanks to new developments of new-generation cameras used for recording the images in the cryo electron microscope which have much increased sensitivity being based on complementary metal oxide semiconductor devices. Combined with advanced image processing and 3D reconstruction, the cryo-EM analysis of nucleoprotein complexes can provide unprecedented insights at molecular and atomic levels and address regulatory mechanisms in the cell. These advances reinforce the integrative role of cryo-EM in synergy with other methods such as X-ray crystallography, fluorescence imaging or focussed-ion beam milling as exemplified here by some recent studies from our laboratory on ribosomes, viruses, chromatin and nuclear receptors. Such multi-scale and multi-resolution approaches allow integrating molecular and cellular levels when applied to purified or in situ macromolecular complexes, thus illustrating the trend of the field towards cellular structural biology. © 2016 The Authors. Biology of the Cell published by Wiley-VCH Verlag GmbH & Co. KGaA on behalf of Société Française des Microscopies and Société de Biologie Cellulaire de France.

  2. IMPLEMENTATION OF FUNCTIONS OF ELECTRONIC DEAN'S OFFICE USING PLATFORM MOODLE

    Directory of Open Access Journals (Sweden)

    Oleksandr A. Shcherbyna

    2016-01-01

    Full Text Available The introduction of information and communication technologies (ICT allows to more effectively and efficiently solve planning and organization tasks, as well as implementation and monitoring of educational process, which are usually handled by the dean's office. The article shows how the functions of electronic dean's office can be implemented in Moodle learning management system using public plugins. In particular, the methods for collection, processing and generalization of operational information about students’ performance are considered. A method of students’ enrollment is offered. The method uses the meta courses and cohorts mechanisms, which allow significantly reduce the amount of work for site administration.

  3. Membrane Binding of Recoverin: From Mechanistic Understanding to Biological Functionality

    Czech Academy of Sciences Publication Activity Database

    Timr, S.; Pleskot, Roman; Kadlec, J.; Kohagen, M.; Magarkar, A.; Jungwirth, P.

    2017-01-01

    Roč. 3, č. 8 (2017), s. 868-874 ISSN 2374-7943 Institutional support: RVO:61389030 Keywords : recoverin * membrane * myristoyl Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Cell biology Impact factor: 7.481, year: 2016

  4. Electron energy distribution function, effective electron temperature, and dust charge in the temporal afterglow of a plasma

    Energy Technology Data Exchange (ETDEWEB)

    Denysenko, I. B.; Azarenkov, N. A. [School of Physics and Technology, V. N. Karazin Kharkiv National University, Svobody sq. 4, 61022 Kharkiv (Ukraine); Kersten, H. [Institut für Experimentelle und Angewandte Physik, Leibnizstr. 19, Kiel D-24098 (Germany)

    2016-05-15

    Analytical expressions describing the variation of electron energy distribution function (EEDF) in an afterglow of a plasma are obtained. Especially, the case when the electron energy loss is mainly due to momentum-transfer electron-neutral collisions is considered. The study is carried out for different EEDFs in the steady state, including Maxwellian and Druyvesteyn distributions. The analytical results are not only obtained for the case when the rate for momentum-transfer electron-neutral collisions is independent on electron energy but also for the case when the collisions are a power function of electron energy. Using analytical expressions for the EEDF, the effective electron temperature and charge of the dust particles, which are assumed to be present in plasma, are calculated for different afterglow durations. An analytical expression for the rate describing collection of electrons by dust particles for the case when the rate for momentum-transfer electron-neutral collisions is independent on electron energy is also derived. The EEDF profile and, as a result, the effective electron temperature and dust charge are sufficiently different in the cases when the rate for momentum-transfer electron-neutral collisions is independent on electron energy and when the rate is a power function of electron energy.

  5. Electron Bio-Imaging Centre (eBIC): the UK national research facility for biological electron microscopy.

    Science.gov (United States)

    Clare, Daniel K; Siebert, C Alistair; Hecksel, Corey; Hagen, Christoph; Mordhorst, Valerie; Grange, Michael; Ashton, Alun W; Walsh, Martin A; Grünewald, Kay; Saibil, Helen R; Stuart, David I; Zhang, Peijun

    2017-06-01

    The recent resolution revolution in cryo-EM has led to a massive increase in demand for both time on high-end cryo-electron microscopes and access to cryo-electron microscopy expertise. In anticipation of this demand, eBIC was set up at Diamond Light Source in collaboration with Birkbeck College London and the University of Oxford, and funded by the Wellcome Trust, the UK Medical Research Council (MRC) and the Biotechnology and Biological Sciences Research Council (BBSRC) to provide access to high-end equipment through peer review. eBIC is currently in its start-up phase and began by offering time on a single FEI Titan Krios microscope equipped with the latest generation of direct electron detectors from two manufacturers. Here, the current status and modes of access for potential users of eBIC are outlined. In the first year of operation, 222 d of microscope time were delivered to external research groups, with 95 visits in total, of which 53 were from unique groups. The data collected have generated multiple high- to intermediate-resolution structures (2.8-8 Å), ten of which have been published. A second Krios microscope is now in operation, with two more due to come online in 2017. In the next phase of growth of eBIC, in addition to more microscope time, new data-collection strategies and sample-preparation techniques will be made available to external user groups. Finally, all raw data are archived, and a metadata catalogue and automated pipelines for data analysis are being developed.

  6. Electronic properties of graphene nanoribbons: A density functional investigation

    International Nuclear Information System (INIS)

    Kumar, Sandeep; Sharma, Hitesh

    2015-01-01

    Density functional theory calculations have been performed on graphene nano ribbons (GNRs) to investigate the electronic properties as a function of chirality, size and hydrogenation on the edges. The calculations were performed on GNRs with armchair and zigzag configurations with 28, 34, 36, 40, 50, 56, 62, 66 carbon atoms. The structural stability of AGNR and ZGNR increases with the size of nanoribbon where as hydrogenation of GNR tends to lowers their structural stability. All GNRs considered have shown semiconducting behavior with HOMO-LUMO gap decreasing with the increase in the GNR size. The hydrogenation of GNR decreases its HOMO-LUMO gap significantly. The results are in agreement with the available experimental and theoretical results

  7. Removal of diclofenac from surface water by electron beam irradiation combined with a biological aerated filter

    Science.gov (United States)

    He, Shijun; Wang, Jianlong; Ye, Longfei; Zhang, Youxue; Yu, Jiang

    2014-12-01

    The degradation of DCF was investigated in aqueous solution by using electron beam (EB) technology. When the initial concentration was between 10 and 40 mg/L, almost 100% of the DCF was degraded at a dose of 0.5 kGy. However, only about 6.5% of DCF was mineralized even at 2 kGy according to total organic carbon (TOC) measurements. A combined process of EB and biological aerated filter (BAF) was therefore developed to enhance the treatment of DCF contaminated surface water. The effluent quality of combined process was substantially improved by EB pretreatment due to the degradation of DCF and related intermediates. Both irradiation and biological treatment reduced the toxicity of the treated water. The experimental results showed that EB is effective for removing DCF from artificial aqueous solution and real surface water.

  8. Emerging opportunities in structural biology with X-ray free-electron lasers

    Science.gov (United States)

    Schlichting, Ilme; Miao, Jianwei

    2012-01-01

    X-ray free-electron lasers (X-FELs) produce X-ray pulses with extremely brilliant peak intensity and ultrashort pulse duration. It has been proposed that radiation damage can be “outrun” by using an ultra intense and short X-FEL pulse that passes a biological sample before the onset of significant radiation damage. The concept of “diffraction-before-destruction” has been demonstrated recently at the Linac Coherent Light Source, the first operational hard X-ray FEL, for protein nanocrystals and giant virus particles. The continuous diffraction patterns from single particles allow solving the classical “phase problem” by the oversampling method with iterative algorithms. If enough data are collected from many identical copies of a (biological) particle, its three-dimensional structure can be reconstructed. We review the current status and future prospects of serial femtosecond crystallography (SFX) and single-particle coherent diffraction imaging (CDI) with X-FELs. PMID:22922042

  9. A geometric initial guess for localized electronic orbitals in modular biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Beckman, P. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of Chicago, IL (United States); Fattebert, J. L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lau, E. Y. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Osei-Kuffuor, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-09-11

    Recent first-principles molecular dynamics algorithms using localized electronic orbitals have achieved O(N) complexity and controlled accuracy in simulating systems with finite band gaps. However, accurately deter- mining the centers of these localized orbitals during simulation setup may require O(N3) operations, which is computationally infeasible for many biological systems. We present an O(N) approach for approximating orbital centers in proteins, DNA, and RNA which uses non-localized solutions for a set of fixed-size subproblems to create a set of geometric maps applicable to larger systems. This scalable approach, used as an initial guess in the O(N) first-principles molecular dynamics code MGmol, facilitates first-principles simulations in biological systems of sizes which were previously impossible.

  10. The BIOSCI electronic newsgroup network for the biological sciences. Final report, October 1, 1992--June 30, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Kristofferson, D.; Mack, D.

    1996-10-01

    This is the final report for a DOE funded project on BIOSCI Electronic Newsgroup Network for the biological sciences. A usable network for scientific discussion, major announcements, problem solving, etc. has been created.

  11. THREE-DIMENSIONAL OBSERVATIONS ON THICK BIOLOGICAL SPECIMENS BY HIGH VOLTAGE ELECTRON MICROSCOPY

    Directory of Open Access Journals (Sweden)

    Tetsuji Nagata

    2011-05-01

    Full Text Available Thick biological specimens prepared as whole mount cultured cells or thick sections from embedded tissues were stained with histochemical reactions, such as thiamine pyrophosphatase, glucose-6-phosphatase, cytochrome oxidase, acid phosphatase, DAB reactions and radioautography, to observe 3-D ultrastructures of cell organelles producing stereo-pairs by high voltage electron microscopy at accerelating voltages of 400-1000 kV. The organelles demonstrated were Golgi apparatus, endoplasmic reticulum, mitochondria, lysosomes, peroxisomes, pinocytotic vesicles and incorporations of radioactive compounds. As the results, those cell organelles were observed 3- dimensionally and the relative relationships between these organelles were demonstrated.

  12. Wavelets as basis functions in electronic structure calculations

    International Nuclear Information System (INIS)

    Chauvin, C.

    2005-11-01

    This thesis is devoted to the definition and the implementation of a multi-resolution method to determine the fundamental state of a system composed of nuclei and electrons. In this work, we are interested in the Density Functional Theory (DFT), which allows to express the Hamiltonian operator with the electronic density only, by a Coulomb potential and a non-linear potential. This operator acts on orbitals, which are solutions of the so-called Kohn-Sham equations. Their resolution needs to express orbitals and density on a set of functions owing both physical and numerical properties, as explained in the second chapter. One can hardly satisfy these two properties simultaneously, that is why we are interested in orthogonal and bi-orthogonal wavelets basis, whose properties of interpolation are presented in the third chapter. We present in the fourth chapter three dimensional solvers for the Coulomb's potential, using not only the preconditioning property of wavelets, but also a multigrid algorithm. Determining this potential allows us to solve the self-consistent Kohn-Sham equations, by an algorithm presented in chapter five. The originality of our method consists in the construction of the stiffness matrix, combining a Galerkin formulation and a collocation scheme. We analyse the approximation properties of this method in case of linear Hamiltonian, such as harmonic oscillator and hydrogen, and present convergence results of the DFT for small electrons. Finally we show how orbital compression reduces considerably the number of coefficients to keep, while preserving a good accuracy of the fundamental energy. (author)

  13. Quantitative analysis of biological fluids by electron probe and X ray spectrometry

    International Nuclear Information System (INIS)

    Girod, Chantal

    1986-01-01

    In order to know the kidney normal operation and to have an insight on cellular transport mechanisms and hormonal regulations at the nephron level, a technique based on the use of an electron probe has been developed for the elemental analysis of micro-volumes of biological fluids. This academic document reports applications of this technique on animals on which such fluids have been sampled at different levels of the nephron. As these samples are available in too small volumes to be dosed by conventional methods, they have been quantitatively analysed by using an electronic probe based analyser in order to determine concentrations of all elements with an atomic number greater than that of carbon. After a presentation of the implemented method and hardware, the author thus describes how an analysis is performed, and reports and discusses an example (analysis conditions, data acquisition, data processing, minimum detectable concentration, reasons for measurement scattering)

  14. Ultrastable gold substrates: Properties of a support for high-resolution electron cryomicroscopy of biological specimens

    Science.gov (United States)

    Russo, Christopher J.; Passmore, Lori A.

    2016-01-01

    Electron cryomicroscopy (cryo-EM) allows structure determination of a wide range of biological molecules and specimens. All-gold supports improve cryo-EM images by reducing radiation-induced motion and image blurring. Here we compare the mechanical and electrical properties of all-gold supports to amorphous carbon foils. Gold supports are more conductive, and have suspended foils that are not compressed by differential contraction when cooled to liquid nitrogen temperatures. These measurements show how the choice of support material and geometry can reduce specimen movement by more than an order of magnitude during low-dose imaging. We provide methods for fabrication of all-gold supports and preparation of vitrified specimens. We also analyse illumination geometry for optimal collection of high resolution, low-dose data. Together, the support structures and methods herein can improve the resolution and quality of images from any electron cryomicroscope. PMID:26592474

  15. FIVA : Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes

    NARCIS (Netherlands)

    Blom, E.J.; Bosman, D.W.; van Hijum, S.A F T; Breitling, R.; Tijsma, L.; Silvis, R.; Roerdink, J.B.T.M.; Kuipers, O.P.

    2007-01-01

    FIVA (Function Information Viewer and Analyzer) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software assists in functional profiling of large sets of genes and generates a comprehensive overview of affected

  16. Nuclear structure functions at a future electron-ion collider

    Science.gov (United States)

    Aschenauer, E. C.; Fazio, S.; Lamont, M. A. C.; Paukkunen, H.; Zurita, P.

    2017-12-01

    The quantitative knowledge of heavy nuclei's partonic structure is currently limited to rather large values of momentum fraction x —robust experimental constraints below x ˜10-2 at low resolution scale Q2 are particularly scarce. This is in sharp contrast to the free proton's structure which has been probed in Deep Inelastic Scattering (DIS) measurements down to x ˜10-5 at perturbative resolution scales. The construction of an electron-ion collider (EIC) with a possibility to operate with a wide variety of nuclei, will allow one to explore the low-x region in much greater detail. In the present paper we simulate the extraction of the nuclear structure functions from measurements of inclusive and charm reduced cross sections at an EIC. The potential constraints are studied by analyzing simulated data directly in a next-to-leading order global fit of nuclear Parton Distribution Functions based on the recent EPPS16 analysis. A special emphasis is placed on studying the impact an EIC would have on extracting the nuclear gluon parton distribution function, the partonic component most prone to nonlinear effects at low Q2. In comparison to the current knowledge, we find that the gluon parton distribution function can be measured at an EIC with significantly reduced uncertainties.

  17. Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation.

    Science.gov (United States)

    Martin, William F

    2012-03-09

    Life is a persistent, self-specified set of far from equilibrium chemical reactions. In modern microbes, core carbon and energy metabolism are what keep cells alive. In very early chemical evolution, the forerunners of carbon and energy metabolism were the processes of generating reduced carbon compounds from CO(2) and the mechanisms of harnessing energy as compounds capable of doing some chemical work. The process of serpentinization at alkaline hydrothermal vents holds promise as a model for the origin of early reducing power, because Fe(2+) in the Earth's crust reduces water to H(2) and inorganic carbon to methane. The overall geochemical process of serpentinization is similar to the biochemical process of methanogenesis, and methanogenesis is similar to acetogenesis in that both physiologies allow energy conservation from the reduction of CO(2) with electrons from H(2). Electron bifurcation is a newly recognized cytosolic process that anaerobes use generate low potential electrons, it plays an important role in some forms of methanogenesis and, via speculation, possibly in acetogenesis. Electron bifurcation likely figures into the early evolution of biological energy conservation. Copyright © 2011. Published by Elsevier B.V.

  18. Decacyclene Trianhydride at Functional Interfaces: An Ideal Electron Acceptor Material for Organic Electronics

    DEFF Research Database (Denmark)

    de Oteyza, Dimas G.; García Lastra, Juan Maria; Toma, Francesca M.

    2016-01-01

    We report the interface energetics of decacyclene trianhydride (DTA) monolayers on top of two distinct model surfaces, namely, Au(111) and Ag(111). On the latter, combined valence band photoemission and X-ray absorption measurements that access the occupied and unoccupied molecular orbitals......, respectively, reveal that electron transfer from substrate to surface sets in. Density functional theory calculations confirm our experimental findings and provide an understanding not only of the photoemission and X-ray absorption spectral features of this promising organic semiconductor but also...

  19. Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Maria Simak

    Full Text Available The great amount of gene expression data has brought a big challenge for the discovery of Gene Regulatory Network (GRN. For network reconstruction and the investigation of regulatory relations, it is desirable to ensure directness of links between genes on a map, infer their directionality and explore candidate biological functions from high-throughput transcriptomic data. To address these problems, we introduce a Boolean Function Network (BFN model based on techniques of hidden Markov model (HMM, likelihood ratio test and Boolean logic functions. BFN consists of two consecutive tests to establish links between pairs of genes and check their directness. We evaluate the performance of BFN through the application to S. cerevisiae time course data. BFN produces regulatory relations which show consistency with succession of cell cycle phases. Furthermore, it also improves sensitivity and specificity when compared with alternative methods of genetic network reverse engineering. Moreover, we demonstrate that BFN can provide proper resolution for GO enrichment of gene sets. Finally, the Boolean functions discovered by BFN can provide useful insights for the identification of control mechanisms of regulatory processes, which is the special advantage of the proposed approach. In combination with low computational complexity, BFN can serve as an efficient screening tool to reconstruct genes relations on the whole genome level. In addition, the BFN approach is also feasible to a wide range of time course datasets.

  20. Lipid polymorphism and the functional roles of lipids in biological membranes

    NARCIS (Netherlands)

    Cullis, P.R.; Kruijff, B. de

    1979-01-01

    The reasons for the great variety of lipids found in biological membranes, and the relations between lipid composition and membrane function pose major unsolved problems in membrane biology. Perhaps the only major functional role of lipids which may be regarded as firmly established involves the

  1. Long shelf-life streptavidin support-films suitable for electron microscopy of biological macromolecules

    OpenAIRE

    Han, Bong-Gyoon; Watson, Zoe; Kang, Hannah; Pulk, Arto; Downing, Kenneth H.; Cate, Jamie; Glaeser, Robert M.

    2016-01-01

    © 2016 Elsevier Inc. We describe a rapid and convenient method of growing streptavidin (SA) monolayer crystals directly on holey-carbon EM grids. As expected, these SA monolayer crystals retain their biotin-binding function and crystalline order through a cycle of embedding in trehalose and, later, its removal. This fact allows one to prepare, and store for later use, EM grids on which SA monolayer crystals serve as an affinity substrate for preparing specimens of biological macromolecules. I...

  2. Click chemistry mediated functionalization of vertical nanowires for biological applications

    DEFF Research Database (Denmark)

    Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica

    2016-01-01

    is of general interest for biological studies. The attachment of a peptide substrate provided NW arrays for the detection of protease activity. In addition, green fluorescent protein was immobilized in a site-specific manner and recognized by antibody binding to demonstrate the proof-of-concept for the use...

  3. Taming Membranes : Functional Immobilization of Biological Membranes in Hydrogels

    NARCIS (Netherlands)

    Kusters, Ilja; Mukherjee, Nobina; de Jong, Menno R.; Tans, Sander; Kocer, Armagan; Driessen, Arnold J. M.

    2011-01-01

    Single molecule studies on membrane proteins embedded in their native environment are hampered by the intrinsic difficulty of immobilizing elastic and sensitive biological membranes without interfering with protein activity. Here, we present hydrogels composed of nano-scaled fibers as a generally

  4. Cell biology and functional dynamics of the mammalian sperm surface

    NARCIS (Netherlands)

    Gadella, B.M.|info:eu-repo/dai/nl/115389873; Luna, C.

    2014-01-01

    Theriogenology has now a 40-year rich history on covering sperm biological aspects with a special emphasis on farm and husbandry animals. The major and most influential of these contributions will be placed into an evolutionary perspective of ongoing and intriguing progresses made in this field.

  5. Electron and Proton Transfer by the Grotthuss Mechanism in Aqueous Solution and in Biological Systems

    International Nuclear Information System (INIS)

    Horne, R.A.; Courant, R.A.; Johnson, D.S.

    1965-01-01

    TheFe ll -Fe III electron-exchange reaction and certain long-range biological redox reactions involve the transfer of electrons by a Grotthuss-type mechanism over water bridges. The Grotthuss mechanism is also responsible for the anomalously great electrical conductivity of acidic aqueous solutions. At ordinary pressures the rate-determining step of the Grotthuss mechanism is the rotation of H 2 O, or possibly H 3 O+, and not the actual proton flip itself. The Grotthuss mechanism is confined to the ''free'' rotatable monomeric water between the Frank-Wen clusters in liquid water and avoids areas of relative order. The concentration dependence of protonic conduction can be represented by an equation based upon a cube root of concentration extrapolation and containing Arrhenius terms in which the activation energies are those for the rotation of and the formation of ''holes'' in the solvent water. Thus chemical energy and/or electrical energy can be transmitted rapidly over relatively great distances by the Grotthuss mechanism. Such processes are involved in a variety of phenomena of biological significance, examples being muscular contraction and the chemistry of the respiratory pigments. (author) [fr

  6. Biological shielding design and qualification of concreting process for construction of electron beam irradiation facility

    International Nuclear Information System (INIS)

    Petwal, V.C.; Kumar, P.; Suresh, N.; Parchani, G.; Dwivedi, J.; Thakurta, A.C.

    2011-01-01

    A technology demonstration facility for irradiation of food and agricultural products is being set-up by RRCAT at Indore. The facility design is based on linear electron accelerator with maximum beam power of 10 kW and can be operated either in electron mode at 10 MeV or photon modes at 5/7.5 MeV. Biological shielding has been designed in accordance with NCRP 51 to achieve dose rate at all accessible points outside the irradiation vault less than the permissible limit of 0.1 mR/hr. In addition to radiation attenuation property, concrete must have satisfactory mechanical properties to meet the structural requirements. There are number of site specific variables which affect the structural, thermal and radiological properties of concrete, leading to considerable difference in actual values and design values. Hence it is essential to establish a suitable site and environmental specific process to cast the concrete and qualify the process by experimental measurement. For process qualification we have cast concrete test blocks of different thicknesses up to 3.25 m and evaluated the radiological and mechanical properties by radiometry, ultrasonic and mechanical tests. In this paper we describe the biological shielding design of the facility and analyse the results of tests carried out for qualification of the process. (author)

  7. New versatile staining reagents for biological transmission electron microscopy that substitute for uranyl acetate.

    Science.gov (United States)

    Nakakoshi, Masamichi; Nishioka, Hideo; Katayama, Eisaku

    2011-12-01

    Aqueous uranyl acetate has been extensively used as a superb staining reagent for transmission electron microscopy of biological materials. However, recent regulation of nuclear fuel material severely restricts its use even for purely scientific purposes. Since uranyl salts are hazardous due to biological toxicity and remaining radioactivity, development of safe and non-radioactive substitutes is greatly anticipated. We examined two lanthanide salts, samarium triacetate and gadolinium triacetate, and found that 1-10% solution of these reagents was safe but still possess excellent capability for staining thin sections of plastic-embedded materials of animal and plant origin. Although post-fixation with osmium tetroxide was essential for high-contrast staining, post-staining with lead citrate could be eliminated if a slow-scan CCD camera is available for observation. These lanthanide salts can also be utilized as good negative-staining reagents to study supramolecular architecture of biological macromolecules. They were not as effective as a fixative of protein assembly, reflecting the non-hazardous nature of the reagents.

  8. Recent Advances in Momordica charantia: Functional Components and Biological Activities.

    Science.gov (United States)

    Jia, Shuo; Shen, Mingyue; Zhang, Fan; Xie, Jianhua

    2017-11-28

    Momordica charantia L. ( M. charantia ), a member of the Cucurbitaceae family, is widely distributed in tropical and subtropical regions of the world. It has been used in folk medicine for the treatment of diabetes mellitus, and its fruit has been used as a vegetable for thousands of years. Phytochemicals including proteins, polysaccharides, flavonoids, triterpenes, saponins, ascorbic acid and steroids have been found in this plant. Various biological activities of M. charantia have been reported, such as antihyperglycemic, antibacterial, antiviral, antitumor, immunomodulation, antioxidant, antidiabetic, anthelmintic, antimutagenic, antiulcer, antilipolytic, antifertility, hepatoprotective, anticancer and anti-inflammatory activities. However, both in vitro and in vivo studies have also demonstrated that M. charantia may also exert toxic or adverse effects under different conditions. This review addresses the chemical constituents of M. charantia and discusses their pharmacological activities as well as their adverse effects, aimed at providing a comprehensive overview of the phytochemistry and biological activities of M. charantia .

  9. Recent Advances in Momordica charantia: Functional Components and Biological Activities

    Directory of Open Access Journals (Sweden)

    Shuo Jia

    2017-11-01

    Full Text Available Momordica charantia L. (M. charantia, a member of the Cucurbitaceae family, is widely distributed in tropical and subtropical regions of the world. It has been used in folk medicine for the treatment of diabetes mellitus, and its fruit has been used as a vegetable for thousands of years. Phytochemicals including proteins, polysaccharides, flavonoids, triterpenes, saponins, ascorbic acid and steroids have been found in this plant. Various biological activities of M. charantia have been reported, such as antihyperglycemic, antibacterial, antiviral, antitumor, immunomodulation, antioxidant, antidiabetic, anthelmintic, antimutagenic, antiulcer, antilipolytic, antifertility, hepatoprotective, anticancer and anti-inflammatory activities. However, both in vitro and in vivo studies have also demonstrated that M. charantia may also exert toxic or adverse effects under different conditions. This review addresses the chemical constituents of M. charantia and discusses their pharmacological activities as well as their adverse effects, aimed at providing a comprehensive overview of the phytochemistry and biological activities of M. charantia.

  10. Recent Advances in Momordica charantia: Functional Components and Biological Activities

    OpenAIRE

    Jia, Shuo; Shen, Mingyue; Zhang, Fan; Xie, Jianhua

    2017-01-01

    Momordica charantia L. (M. charantia), a member of the Cucurbitaceae family, is widely distributed in tropical and subtropical regions of the world. It has been used in folk medicine for the treatment of diabetes mellitus, and its fruit has been used as a vegetable for thousands of years. Phytochemicals including proteins, polysaccharides, flavonoids, triterpenes, saponins, ascorbic acid and steroids have been found in this plant. Various biological activities of M. charantia have been report...

  11. Avoiding artefacts during electron microscopy of silver nanomaterials exposed to biological environments.

    Science.gov (United States)

    Chen, S; Goode, A E; Skepper, J N; Thorley, A J; Seiffert, J M; Chung, K F; Tetley, T D; Shaffer, M S P; Ryan, M P; Porter, A E

    2016-02-01

    Electron microscopy has been applied widely to study the interaction of nanomaterials with proteins, cells and tissues at nanometre scale. Biological material is most commonly embedded in thermoset resins to make it compatible with the high vacuum in the electron microscope. Room temperature sample preparation protocols developed over decades provide contrast by staining cell organelles, and aim to preserve the native cell structure. However, the effect of these complex protocols on the nanomaterials in the system is seldom considered. Any artefacts generated during sample preparation may ultimately interfere with the accurate prediction of the stability and reactivity of the nanomaterials. As a case study, we review steps in the room temperature preparation of cells exposed to silver nanomaterials (AgNMs) for transmission electron microscopy imaging and analysis. In particular, embedding and staining protocols, which can alter the physicochemical properties of AgNMs and introduce artefacts thereby leading to a misinterpretation of silver bioreactivity, are scrutinized. Recommendations are given for the application of cryogenic sample preparation protocols, which simultaneously fix both particles and diffusible ions. By being aware of the advantages and limitations of different sample preparation methods, compromises or selection of different correlative techniques can be made to draw more accurate conclusions about the data. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  12. An overview of the applicability of functional diversity in Biological Conservation

    OpenAIRE

    Freitas, J. R.; Mantovani, W.

    2017-01-01

    Abstract Functional diversity is increasingly pointed as a useful approach to reach Biological Conservation goals. Here, we provide an overview of the functional diversity approach status in the Biological Conservation field. We sought for peer-reviewed papers published over a period of twenty years (from 1994 to 2014). First we used the general topic “functional diversity” and then refined our search using the key-word “conservation”. We have identified the conservation strategies addressed,...

  13. Inferring biological functions of guanylyl cyclases with computational methods

    KAUST Repository

    Alquraishi, May Majed

    2013-09-03

    A number of studies have shown that functionally related genes are often co-expressed and that computational based co-expression analysis can be used to accurately identify functional relationships between genes and by inference, their encoded proteins. Here we describe how a computational based co-expression analysis can be used to link the function of a specific gene of interest to a defined cellular response. Using a worked example we demonstrate how this methodology is used to link the function of the Arabidopsis Wall-Associated Kinase-Like 10 gene, which encodes a functional guanylyl cyclase, to host responses to pathogens. © Springer Science+Business Media New York 2013.

  14. Experimental measurement of the electron energy distribution function in the radio frequency electron cyclotron resonance inductive discharge

    International Nuclear Information System (INIS)

    Chung, ChinWook; Kim, S.S.; Chang, H.Y.

    2004-01-01

    Recently, the existence of electron cyclotron resonance (ECR) in a weakly magnetized inductively coupled plasma (MICP) has been evidenced [ChinWook Chung et al., Phys. Rev. Lett. 80, 095002 (2002)]. The distinctive feature of the ECR effect in the MICP is efficacious heating of low-energy electrons. In the present paper, electron heating characteristics in the MICP have been investigated by observing electron energy distribution function dependencies on various external parameters such as gas pressure, driving frequency, and rf power (electron density). It is found that the ECR effect on electron heating becomes enhanced with decreasing pressure or increasing driving frequency. The ECR heating becomes weak at high rf power due to the electron-electron collisions

  15. Quantum chemical calculations predict biological function: The case of T cell receptor interaction with a peptide/MHC class I

    Science.gov (United States)

    Antipas, Georgios S. E.; Germenis, Anastasios

    2015-02-01

    A combination of atomic correlation statistics and quantum chemical calculations are shown to predict biological function. In the present study, various antigenic peptide-Major Histocompatibility Complex (pMHC) ligands with near-identical stereochemistries, in complexation with the same T cell receptor (TCR), were found to consistently induce distinctly different quantum chemical behavior, directly dependent on the peptide’s electron spin density and intrinsically expressed by the protonation state of the peptide’s N-terminus. Furthermore, the cumulative coordination difference of any variant in respect to the native peptide was found to accurately reflect peptide biological function and immerges as the physical observable which is directly related to the immunological end-effect of pMHC-TCR interaction.

  16. Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope

    Science.gov (United States)

    Wu, J.S.; Kim, A. M.; Bleher, R.; Myers, B.D.; Marvin, R. G.; Inada, H.; Nakamura, K.; Zhang, X.F.; Roth, E.; Li, S.Y.; Woodruff, T. K.; O'Halloran, T. V.; Dravid, Vinayak P.

    2013-01-01

    A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room- and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. PMID:23500508

  17. Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach.

    Science.gov (United States)

    Li, Jun; Zhao, Patrick X

    2016-01-01

    Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

  18. Interfacial electronic effects in functional biolayers integrated into organic field-effect transistors

    Science.gov (United States)

    Angione, Maria Daniela; Cotrone, Serafina; Magliulo, Maria; Mallardi, Antonia; Altamura, Davide; Giannini, Cinzia; Cioffi, Nicola; Sabbatini, Luigia; Fratini, Emiliano; Baglioni, Piero; Scamarcio, Gaetano; Palazzo, Gerardo; Torsi, Luisa

    2012-01-01

    Biosystems integration into an organic field-effect transistor (OFET) structure is achieved by spin coating phospholipid or protein layers between the gate dielectric and the organic semiconductor. An architecture directly interfacing supported biological layers to the OFET channel is proposed and, strikingly, both the electronic properties and the biointerlayer functionality are fully retained. The platform bench tests involved OFETs integrating phospholipids and bacteriorhodopsin exposed to 1–5% anesthetic doses that reveal drug-induced changes in the lipid membrane. This result challenges the current anesthetic action model relying on the so far provided evidence that doses much higher than clinically relevant ones (2.4%) do not alter lipid bilayers’ structure significantly. Furthermore, a streptavidin embedding OFET shows label-free biotin electronic detection at 10 parts-per-trillion concentration level, reaching state-of-the-art fluorescent assay performances. These examples show how the proposed bioelectronic platform, besides resulting in extremely performing biosensors, can open insights into biologically relevant phenomena involving membrane weak interfacial modifications. PMID:22493224

  19. The lectins: properties, functions, and applications in biology and medicine

    National Research Council Canada - National Science Library

    Liener, Irvin E; Sharon, Nathan; Goldstein, Irwin J

    1986-01-01

    ... (Editors). The Enzymology of Post-Translational Modification of Proteins, Volume 1, 1980. Volume 2, 1985 W A I YIU CHEUNG (Editor). Calcium and Cell Function, Volume I: Calmodulin, 1980. Volume II, ...

  20. The Lectins: properties, functions, and applications in biology and medicine

    National Research Council Canada - National Science Library

    Liener, Irvin E; Sharon, Nathan; Goldstein, Irwin J; Goldstein, Irwin Joseph

    1986-01-01

    ... (Editors). The Enzymology of Post-Translational Modification of Proteins, Volume 1, 1980. Volume 2, 1985 W A I YIU CHEUNG (Editor). Calcium and Cell Function, Volume I: Calmodulin, 1980. Volume II, ...

  1. An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology

    Science.gov (United States)

    Thompson, Rebecca F.; Walker, Matt; Siebert, C. Alistair; Muench, Stephen P.; Ranson, Neil A.

    2016-01-01

    Transmission electron microscopy (EM) is a versatile technique that can be used to image biological specimens ranging from intact eukaryotic cells to individual proteins >150 kDa. There are several strategies for preparing samples for imaging by EM, including negative staining and cryogenic freezing. In the last few years, cryo-EM has undergone a ‘resolution revolution’, owing to both advances in imaging hardware, image processing software, and improvements in sample preparation, leading to growing number of researchers using cryo-EM as a research tool. However, cryo-EM is still a rapidly growing field, with unique challenges. Here, we summarise considerations for imaging of a range of specimens from macromolecular complexes to cells using EM. PMID:26931652

  2. Particle Accelerator Applications: Ion and Electron Irradiation in Materials Science, Biology and Medicine

    Science.gov (United States)

    Rodríguez-Fernández, Luis

    2010-09-01

    Although the developments of particle accelerators are devoted to basic study of matter constituents, since the beginning these machines have been applied with different purposes in many areas also. Today particle accelerators are essential instruments for science and technology. This work presents an overview of the main application for direct particle irradiation with accelerator in material science, biology and medicine. They are used for material synthesis by ion implantation and charged particle irradiation; to make coatings and micromachining; to characterize broad kind of samples by ion beam analysis techniques; as mass spectrometers for atomic isotopes determination. In biomedicine the accelerators are applied for the study of effects by charged particles on cells. In medicine the radiotherapy by electron irradiation is widely used, while hadrontherapy is still under development. Also, they are necessary for short life radioisotopes production required in radiodiagnostic.

  3. Do-it-yourself biology and electronic waste hacking: A politics of demonstration in precarious times.

    Science.gov (United States)

    Delgado, Ana; Callén, Blanca

    2017-02-01

    In recent years, there has been an explosion of do it yourself, maker and hacker spaces in Europe. Through makers and do-it-yourself initiatives, 'hacking' is moving into the everyday life of citizens. This article explores the collective and political nature of those hacks by reporting on empirical work on electronic waste and do-it-yourself biology hacking. Using Dewey's experimental approach to politics, we analyse hacks as 'inquiry' to see how they serve to articulate public and political action. We argue that do-it-yourself and makers' hacks are technical and political demonstrations. What do-it-yourself and makers' hacks ultimately demonstrate is that things can be done otherwise and that 'you' can also do it. In this sense, they have a potential viral effect. The final part of the article explores some potential shortcomings of such politics of demonstration.

  4. Reconstructing Regional Ionospheric Electron Density: A Combined Spherical Slepian Function and Empirical Orthogonal Function Approach

    Science.gov (United States)

    Farzaneh, Saeed; Forootan, Ehsan

    2018-03-01

    The computerized ionospheric tomography is a method for imaging the Earth's ionosphere using a sounding technique and computing the slant total electron content (STEC) values from data of the global positioning system (GPS). The most common approach for ionospheric tomography is the voxel-based model, in which (1) the ionosphere is divided into voxels, (2) the STEC is then measured along (many) satellite signal paths, and finally (3) an inversion procedure is applied to reconstruct the electron density distribution of the ionosphere. In this study, a computationally efficient approach is introduced, which improves the inversion procedure of step 3. Our proposed method combines the empirical orthogonal function and the spherical Slepian base functions to describe the vertical and horizontal distribution of electron density, respectively. Thus, it can be applied on regional and global case studies. Numerical application is demonstrated using the ground-based GPS data over South America. Our results are validated against ionospheric tomography obtained from the constellation observing system for meteorology, ionosphere, and climate (COSMIC) observations and the global ionosphere map estimated by international centers, as well as by comparison with STEC derived from independent GPS stations. Using the proposed approach, we find that while using 30 GPS measurements in South America, one can achieve comparable accuracy with those from COSMIC data within the reported accuracy (1 × 1011 el/cm3) of the product. Comparisons with real observations of two GPS stations indicate an absolute difference is less than 2 TECU (where 1 total electron content unit, TECU, is 1016 electrons/m2).

  5. Scanning transmission electron microscopy through-focal tilt-series on biological specimens.

    Science.gov (United States)

    Trepout, Sylvain; Messaoudi, Cédric; Perrot, Sylvie; Bastin, Philippe; Marco, Sergio

    2015-10-01

    Since scanning transmission electron microscopy can produce high signal-to-noise ratio bright-field images of thick (≥500 nm) specimens, this tool is emerging as the method of choice to study thick biological samples via tomographic approaches. However, in a convergent-beam configuration, the depth of field is limited because only a thin portion of the specimen (from a few nanometres to tens of nanometres depending on the convergence angle) can be imaged in focus. A method known as through-focal imaging enables recovery of the full depth of information by combining images acquired at different levels of focus. In this work, we compare tomographic reconstruction with the through-focal tilt-series approach (a multifocal series of images per tilt angle) with reconstruction with the classic tilt-series acquisition scheme (one single-focus image per tilt angle). We visualised the base of the flagellum in the protist Trypanosoma brucei via an acquisition and image-processing method tailored to obtain quantitative and qualitative descriptors of reconstruction volumes. Reconstructions using through-focal imaging contained more contrast and more details for thick (≥500 nm) biological samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. iBET: Immersive visualization of biological electron-transfer dynamics.

    Science.gov (United States)

    Nakano, C Masato; Moen, Erick; Byun, Hye Suk; Ma, Heng; Newman, Bradley; McDowell, Alexander; Wei, Tao; El-Naggar, Mohamed Y

    2016-04-01

    Recently, we presented a computational framework named VizBET to simulate and visualize biological electron-transfer (ET) dynamics. The visualization process was encapsulated as a plugin to the Visual Molecular Dynamics (VMD) software. However, the user's ability to understand complex, multidimensional ET pathways was severely limited when visualized in 2D on traditional computer monitors. To provide a more accurate representation with enhanced depth perception, we here present an extension of VizBET named iBET to render the VMD model of ET dynamics in a commodity virtual reality (VR) platform. The paper describes detailed procedures to export VMD models into the Unity game engine and render it in an Oculus Rift head mounted display. With the increasing availability of low-cost VR systems like the Rift and rich programmability of game engines, the iBET framework provides a powerful means to explore and understand not only biological ET processes but also a unique experiential tool for broad scientific communities. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Engineered hybrid cardiac patches with multifunctional electronics for online monitoring and regulation of tissue function.

    Science.gov (United States)

    Feiner, Ron; Engel, Leeya; Fleischer, Sharon; Malki, Maayan; Gal, Idan; Shapira, Assaf; Shacham-Diamand, Yosi; Dvir, Tal

    2016-06-01

    In cardiac tissue engineering approaches to treat myocardial infarction, cardiac cells are seeded within three-dimensional porous scaffolds to create functional cardiac patches. However, current cardiac patches do not allow for online monitoring and reporting of engineered-tissue performance, and do not interfere to deliver signals for patch activation or to enable its integration with the host. Here, we report an engineered cardiac patch that integrates cardiac cells with flexible, freestanding electronics and a 3D nanocomposite scaffold. The patch exhibited robust electronic properties, enabling the recording of cellular electrical activities and the on-demand provision of electrical stimulation for synchronizing cell contraction. We also show that electroactive polymers containing biological factors can be deposited on designated electrodes to release drugs in the patch microenvironment on demand. We expect that the integration of complex electronics within cardiac patches will eventually provide therapeutic control and regulation of cardiac function.

  8. Chemically-functionalized microcantilevers for detection of chemical, biological and explosive material

    Science.gov (United States)

    Pinnaduwage, Lal A [Knoxville, TN; Thundat, Thomas G [Knoxville, TN; Brown, Gilbert M [Knoxville, TN; Hawk, John Eric [Olive Branch, MS; Boiadjiev, Vassil I [Knoxville, TN

    2007-04-24

    A chemically functionalized cantilever system has a cantilever coated on one side thereof with a reagent or biological species which binds to an analyte. The system is of particular value when the analyte is a toxic chemical biological warfare agent or an explosive.

  9. Biological markers for kidney injury and renal function in the intensive care unit

    NARCIS (Netherlands)

    Royakkers, A.A.N.M.

    2014-01-01

    The purpose of the investigations described in this thesis was to seek for answers to two relevant questions in ICUs in resource-rich settings, i.e., can new biological markers play a role in early recognition of AKI, and can new biological markers predict recovery of renal function in patients who

  10. Thermodynamics of electron transfer and its coupling to vectorial processes in biological membranes.

    Science.gov (United States)

    Arata, H; Nishimura, M

    1980-11-01

    A method is developed to express the flux of an electron transfer reaction as a function of the conjugate force, the redox potential difference, throughout the nonlinear region. The flux can be expressed by a product of the hyperbolic sine of the force, a factor ("redox-poising parameter") determined by the redox potentials of subsystem (in certain cases by local pH's and pK's of subsystems), and some constants. This is analogous to the expression of the flux of a diffusion process by the product of its force and the concentration of the diffusing species. The redox-poising parameter corresponds to the concentration term. The expression is applied to redox chains in which electron transfers are coupled to vectorial processes such as proton translocation or electric current.

  11. Electron transfer behaviour of biological macromolecules towards the single-molecule level

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Grubb, Mikala; Hansen, Allan Glargaard

    2003-01-01

    is combined with state-of-the-art physical electrochemistry with emphasis on single-crystal, atomically planar electrode surfaces, in situ scanning tunnelling microscopy (STM) and other surface techniques. These approaches have brought bioelectrochemistry important steps forward towards the nanoscale...... and single-molecule levels.We discuss here these advances with reference to two specific redox metalloproteins, the blue single-copper protein Pseudomonas aeruginosa azurin and the single-haem protein Saccharomyces cerevisiae yeast cytochrome c, and a short oligonucleotide. Both proteins can be immobilized...... electron transfer (ET) function retained. In situ STM can also address the microscopic mechanisms for electron tunnelling through the biomolecules and offers novel notions such as coherent multi-ET between the substrate and tip via the molecular redox levels. This differs in important respects from...

  12. Modulation transfer function and detective quantum efficiency of electron bombarded charge coupled device detector for low energy electrons

    Czech Academy of Sciences Publication Activity Database

    Horáček, Miroslav

    2005-01-01

    Roč. 76, č. 9 (2005), 093704:1-6 ISSN 0034-6748 R&D Projects: GA ČR(CZ) GA202/03/1575 Keywords : electron bombarded CCD * modulation transfer function * detective quantum efficiency Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.235, year: 2005

  13. Functional response of Xylocoris falvipes , a biological control agent ...

    African Journals Online (AJOL)

    The warehouse pirate bug Xylocoris falvipes is an opportunist predator of many stored product insect pests. Its functional response in relationship with variable densities of prey appears as the Holling\\'s type II model. The predator X. falvipes, collected within small holder granaries in Mayo Danay division in the far North ...

  14. Measuring the functional redundancy of biological communities: a quantitative guide

    Czech Academy of Sciences Publication Activity Database

    Ricotta, C.; de Bello, Francesco; Moretti, M.; Caccianiga, M.; Cerabolini, B. E. L.; Pavoine, S.

    2016-01-01

    Roč. 7, č. 11 (2016), s. 1386-1395 ISSN 2041-210X Institutional support: RVO:67985939 Keywords : absolute vs. relative measures * community structure * functional uniqueness Subject RIV: EH - Ecology, Behaviour Impact factor: 5.708, year: 2016

  15. Enhanced Physicochemical and Biological Properties of Ion-Implanted Titanium Using Electron Cyclotron Resonance Ion Sources

    Directory of Open Access Journals (Sweden)

    Csaba Hegedűs

    2016-01-01

    Full Text Available The surface properties of metallic implants play an important role in their clinical success. Improving upon the inherent shortcomings of Ti implants, such as poor bioactivity, is imperative for achieving clinical use. In this study, we have developed a Ti implant modified with Ca or dual Ca + Si ions on the surface using an electron cyclotron resonance ion source (ECRIS. The physicochemical and biological properties of ion-implanted Ti surfaces were analyzed using various analytical techniques, such as surface analyses, potentiodynamic polarization and cell culture. Experimental results indicated that a rough morphology was observed on the Ti substrate surface modified by ECRIS plasma ions. The in vitro electrochemical measurement results also indicated that the Ca + Si ion-implanted surface had a more beneficial and desired behavior than the pristine Ti substrate. Compared to the pristine Ti substrate, all ion-implanted samples had a lower hemolysis ratio. MG63 cells cultured on the high Ca and dual Ca + Si ion-implanted surfaces revealed significantly greater cell viability in comparison to the pristine Ti substrate. In conclusion, surface modification by electron cyclotron resonance Ca and Si ion sources could be an effective method for Ti implants.

  16. Mimicking Biological Synaptic Functionality with an Indium Phosphide Synaptic Device on Silicon for Scalable Neuromorphic Computing.

    Science.gov (United States)

    Sarkar, Debarghya; Tao, Jun; Wang, Wei; Lin, Qingfeng; Yeung, Matthew; Ren, Chenhao; Kapadia, Rehan

    2018-02-27

    Neuromorphic or "brain-like" computation is a leading candidate for efficient, fault-tolerant processing of large-scale data as well as real-time sensing and transduction of complex multivariate systems and networks such as self-driving vehicles or Internet of Things applications. In biology, the synapse serves as an active memory unit in the neural system and is the component responsible for learning and memory. Electronically emulating this element via a compact, scalable technology which can be integrated in a three-dimensional (3-D) architecture is critical for future implementations of neuromorphic processors. However, present day 3-D transistor implementations of synapses are typically based on low-mobility semiconductor channels or technologies that are not scalable. Here, we demonstrate a crystalline indium phosphide (InP)-based artificial synapse for spiking neural networks that exhibits elasticity, short-term plasticity, long-term plasticity, metaplasticity, and spike timing-dependent plasticity, emulating the critical behaviors exhibited by biological synapses. Critically, we show that this crystalline InP device can be directly integrated via back-end processing on a Si wafer using a SiO 2 buffer without the need for a crystalline seed, enabling neuromorphic devices that can be implemented in a scalable and 3-D architecture. Specifically, the device is a crystalline InP channel field-effect transistor that interacts with neuron spikes by modification of the population of filled traps in the MOS structure itself. Unlike other transistor-based implementations, we show that it is possible to mimic these biological functions without the use of external factors (e.g., surface adsorption of gas molecules) and without the need for the high electric fields necessary for traditional flash-based implementations. Finally, when exposed to neuronal spikes with a waveform similar to that observed in the brain, these devices exhibit the ability to learn without the

  17. Flexible biological arsenite oxidation utilizing NOxand O2as alternative electron acceptors.

    Science.gov (United States)

    Wang, Jie; Wan, Junfeng; Wu, Zihao; Li, Hongli; Li, Haisong; Dagot, Christophe; Wang, Yan

    2017-07-01

    The feasibility of flexible microbial arsenite (As III ) oxidation coupled with the reduction of different electron acceptors was investigated. The results indicated the acclimated microorganisms could oxidize As III with oxygen, nitrate and nitrite as the alternative electron acceptors. A series of batch tests were conducted to measure the kinetic parameters of As III oxidation and to evaluate the effects of environmental conditions including pH and temperature on the activity of biological As III oxidation dependent on different electron acceptors. Kinetic results showed that oxygen-dependent As III oxidation had the highest oxidation rate (0.59 mg As g -1  VSS min -1 ), followed by nitrate- (0.40 mg As g -1  VSS min -1 ) and nitrite-dependent As III oxidation (0.32 mg As g -1  VSS min -1 ). The kinetic data of aerobic As III oxidation were fitted well with the Monod kinetic model, while the Haldane substrate inhibition model was better applicable to describe the inhibition of anoxic As III oxidation. Both aerobic and anoxic As III oxidation performed the optimal activity at the near neutral pH. Besides, the optimal temperature for oxygen-, nitrate- and nitrite-dependent As III oxidation was 30 ± 1 °C, 40 ± 1 °C and 20 ± 1 °C, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Influence of Bicarbonate, Sulfate, and Electron Donors on Biological reduction of Uranium and Microbial Community Composition

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Wensui [ORNL; Zhou, Jizhong [ORNL; Wu, Weimin [ORNL; Yan, Tingfen [ORNL; Criddle, Craig [ORNL; Jardine, Philip M [ORNL; Gu, Baohua [ORNL

    2007-01-01

    A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 mM or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonate (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and geoundwater geochemistry alter microbial communities responsible for U(VI) reduction.

  19. Influence of bicarbonate, sulfate, and electron donors on biological reduction of uranium and microbial community composition

    Energy Technology Data Exchange (ETDEWEB)

    Luo Wensui [Oak Ridge Inst. for Science and Education, TN (United States); Oak Ridge National Lab., TN (United States). Environmental Sciences Div.; Wu Wei-Min; Criddle, C.S. [Stanford Univ., CA (United States). Dept. of Civil and Environmental Engineering; Yan Tingfen [Oak Ridge Inst. for Science and Education, TN (United States); Jardine, P.M.; Gu Baohua [Oak Ridge National Lab., TN (United States). Environmental Sciences Div.; Zhou Jizhong [Oklahoma Univ., Norman, OK (United States). Dept. of Botany and Microbiology

    2007-12-15

    A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonate (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low-bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high-bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and groundwater geochemistry alter microbial communities responsible for U(VI) reduction. (orig.)

  20. 3D Printing Polymers with Supramolecular Functionality for Biological Applications.

    Science.gov (United States)

    Pekkanen, Allison M; Mondschein, Ryan J; Williams, Christopher B; Long, Timothy E

    2017-09-11

    Supramolecular chemistry continues to experience widespread growth, as fine-tuned chemical structures lead to well-defined bulk materials. Previous literature described the roles of hydrogen bonding, ionic aggregation, guest/host interactions, and π-π stacking to tune mechanical, viscoelastic, and processing performance. The versatility of reversible interactions enables the more facile manufacturing of molded parts with tailored hierarchical structures such as tissue engineered scaffolds for biological applications. Recently, supramolecular polymers and additive manufacturing processes merged to provide parts with control of the molecular, macromolecular, and feature length scales. Additive manufacturing, or 3D printing, generates customizable constructs desirable for many applications, and the introduction of supramolecular interactions will potentially increase production speed, offer a tunable surface structure for controlling cell/scaffold interactions, and impart desired mechanical properties through reinforcing interlayer adhesion and introducing gradients or self-assembled structures. This review details the synthesis and characterization of supramolecular polymers suitable for additive manufacture and biomedical applications as well as the use of supramolecular polymers in additive manufacturing for drug delivery and complex tissue scaffold formation. The effect of supramolecular assembly and its dynamic behavior offers potential for controlling the anisotropy of the printed objects with exquisite geometrical control. The potential for supramolecular polymers to generate well-defined parts, hierarchical structures, and scaffolds with gradient properties/tuned surfaces provides an avenue for developing next-generation biomedical devices and tissue scaffolds.

  1. Biological Rhythms Workshop IB: neurophysiology of SCN pacemaker function.

    Science.gov (United States)

    Kuhlman, S J

    2007-01-01

    Pacemakers are functional units capable of generating oscillations that synchronize downstream rhythms. In mammals, the suprachiasmatic nucleus (SCN) of the hypothalamus is a circadian pacemaker composed of individual neurons that intrinsically express a near 24-hour rhythm in gene expression. Rhythmic gene expression is tightly coupled to a rhythm in spontaneous firing rate via intrinsic daily regulation of potassium current. Recent progress in the field indicates that SCN pacemaking is a specialized property that emerges from intrinsic features of single cells, structural connectivity among cells, and activity dynamics within the SCN. The focus of this chapter is on how Nature built a functional pacemaker from many individual oscillators that is capable of coordinating the daily timing of essential brain and physiological processes.

  2. Functional nanostructured platforms for chemical and biological sensing

    Science.gov (United States)

    Létant, S. E.

    2006-05-01

    The central goal of our work is to combine semiconductor nanotechnology and surface functionalization in order to build platforms for the selective detection of bio-organisms ranging in size from bacteria (micron range) down to viruses, as well as for the detection of chemical agents (nanometer range). We will show on three porous silicon platforms how pore geometry and pore wall chemistry can be combined and optimized to capture and detect specific targets. We developed a synthetic route allowing to directly anchor proteins on silicon surfaces and illustrated the relevance of this technique by immobilizing live enzymes onto electrochemically etched luminescent nano-porous silicon. The powerful association of the specific enzymes with the transducing matrix led to a selective hybrid platform for chemical sensing. We also used light-assisted electrochemistry to produce periodic arrays of through pores on pre-patterned silicon membranes with controlled diameters ranging from many microns down to tens of nanometers. We demonstrated the first covalently functionalized silicon membranes and illustrated their selective capture abilities with antibody-coated micro-beads. These engineered membranes are extremely versatile and could be adapted to specifically recognize the external fingerprints (size and coat composition) of target bio-organisms. Finally, we fabricated locally functionalized single nanopores using a combination of focused ion beam drilling and ion beam assisted oxide deposition. We showed how a silicon oxide ring can be grown around a single nanopore and how it can be functionalized with DNA probes to detect single viral-sized beads. The next step for this platform is the detection of whole viruses and bacteria.

  3. Biological factors of natural and artificial ecosystems stable (unstable) functioning

    Science.gov (United States)

    Pechurkin, Nikolai S.

    The problem of sustainable development of humanity on Earth and the problem of supporting human life in space have the same scientific and methodological bases. The key to solve both problems is a long term maintenance of balanced material cycle. As a whole, natural or artificial ecosystems are to be more closed than open, but their elements (links of systems) are to be substantially open in interactions with each other. Prolonged stable interactions of different links have to have unique joint results - closed material cycling or biotic turnover. It is necessary to include, at least, three types of main links into any system to support real material cycling: producers, consumers, reducers. Producer links are now under studies in many laboratories. It is evident that the higher productivity of link, the lower link stability. Especially, it concerns with parasite impact to plants. As usual, artificial ecosystems are more simple (incomplete) than natural ecosystems, sometimes, they have not enough links for prolonged stable functioning. For example, life support system for space flight can be incomplete in consumer link, having only some crew persons, instead of interacting populations of consumers. As for reducer link, it is necessary to "organize" a special coordinated work of microbial biocenoses to fulfill proper cycling. Possible evolution of links, their self development is a matter of special attention for the maintenance of prolonged stable functioning. It's the most danger for systems with populations of quickly reproducing, so-called, R - strategists, according to symbols of logistic equation. From another side, quick reproduction of R - strategists is able to increase artificial ecosystems and their links functioning. After some damages of system, R - strategist's link can be quickly "self repaired" up to level of normal functioning. Some experimental data of this kind and mathematical models are to be discussed in the paper. This work is supported by

  4. Thermodynamics of electron transfer and its coupling to vectorial processes in biological membranes

    OpenAIRE

    Arata, H.; Nishimura, M.

    1980-01-01

    A method is developed to express the flux of an electron transfer reaction as a function of the conjugate force, the redox potential difference, throughout the nonlinear region. The flux can be expressed by a product of the hyperbolic sine of the force, a factor ("redox-poising parameter") determined by the redox potentials of subsystem (in certain cases by local pH's and pK's of subsystems), and some constants. This is analogous to the expression of the flux of a diffusion process by the pro...

  5. The functions of biological diversity in an age of extinction.

    Science.gov (United States)

    Naeem, Shahid; Duffy, J Emmett; Zavaleta, Erika

    2012-06-15

    Ecosystems worldwide are rapidly losing taxonomic, phylogenetic, genetic, and functional diversity as a result of human appropriation of natural resources, modification of habitats and climate, and the spread of pathogenic, exotic, and domestic plants and animals. Twenty years of intense theoretical and empirical research have shown that such biotic impoverishment can markedly alter the biogeochemical and dynamic properties of ecosystems, but frontiers remain in linking this research to the complexity of wild nature, and in applying it to pressing environmental issues such as food, water, energy, and biosecurity. The question before us is whether these advances can take us beyond merely invoking the precautionary principle of conserving biodiversity to a predictive science that informs practical and specific solutions to mitigate and adapt to its loss.

  6. Biological function of activation-induced cytidine deaminase (AID

    Directory of Open Access Journals (Sweden)

    Ritu Kumar

    2014-10-01

    Full Text Available Activation-induced Cytidine Deaminase (AID is an essential regulator of B cell diversification, but its full range of action has until recently been an enigma. Based on homology, it was originally proposed to be an RNA-editing enzyme, but so far, no RNA substrates are known. Rather, it functions by deaminating cytidine, and in this manner, coupled with base-excision repair or mismatch repair machinery, it is a natural mutator. This allows it to play a central role in adaptive immunity, whereby it initiates the processes of class switch recombination and somatic hypermutation to help generate a diverse and high-affinity repertoire of immunoglobulin isotypes. More recently, it has been appreciated that methylated cytidine, already known as a key epigenetic mark on DNA controlling gene expression, can also be a target for AID modification. Coupled with repair machinery, this can facilitate the active removal of methylated DNA. This activity can impact the process of cellular reprogramming, including transition of a somatic cell to pluripotency, which requires major reshuffling of epigenetic memory. Thus, seemingly disparate roles for AID in controlling immune diversity and epigenetic memory have a common mechanistic basis. However, the very activity that is so useful for B cell diversity and cellular reprogramming is dangerous for the integrity of the genome. Thus, AID expression and activity is tightly regulated, and deregulation is associated with diseases including cancer. Here, we review the range of AID functions with a focus on its mechanisms of action and regulation. Major questions remain to be answered concerning how and when AID is targeted to specific loci and how this impacts development and disease.

  7. EDF: Computing electron number probability distribution functions in real space from molecular wave functions

    Science.gov (United States)

    Francisco, E.; Pendás, A. Martín; Blanco, M. A.

    2008-04-01

    Given an N-electron molecule and an exhaustive partition of the real space ( R) into m arbitrary regions Ω,Ω,…,Ω ( ⋃i=1mΩ=R), the edf program computes all the probabilities P(n,n,…,n) of having exactly n electrons in Ω, n electrons in Ω,…, and n electrons ( n+n+⋯+n=N) in Ω. Each Ω may correspond to a single basin (atomic domain) or several such basins (functional group). In the later case, each atomic domain must belong to a single Ω. The program can manage both single- and multi-determinant wave functions which are read in from an aimpac-like wave function description ( .wfn) file (T.A. Keith et al., The AIMPAC95 programs, http://www.chemistry.mcmaster.ca/aimpac, 1995). For multi-determinantal wave functions a generalization of the original .wfn file has been introduced. The new format is completely backwards compatible, adding to the previous structure a description of the configuration interaction (CI) coefficients and the determinants of correlated wave functions. Besides the .wfn file, edf only needs the overlap integrals over all the atomic domains between the molecular orbitals (MO). After the P(n,n,…,n) probabilities are computed, edf obtains from them several magnitudes relevant to chemical bonding theory, such as average electronic populations and localization/delocalization indices. Regarding spin, edf may be used in two ways: with or without a splitting of the P(n,n,…,n) probabilities into α and β spin components. Program summaryProgram title: edf Catalogue identifier: AEAJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5387 No. of bytes in distributed program, including test data, etc.: 52 381 Distribution format: tar.gz Programming language: Fortran 77 Computer

  8. Biological catalysis of the hydrological cycle: life's thermodynamic function

    Science.gov (United States)

    Michaelian, K.

    2011-01-01

    Darwinian theory depicts life as being overwhelmingly consumed by a fight for survival in a hostile environment. However, from a thermodynamic perspective, life is a dynamic out of equilibrium process, stabilizing and coevolving in concert with its abiotic environment. The living component of the biosphere on the surface of the Earth of greatest biomass, the plants and cyanobacteria, are involved in the transpiration of a vast amount of water. Transpiration is part of the global water cycle, and it is this cycle that distinguishes Earth from its apparently life barren neighboring planets, Venus and Mars. The dissipation of sunlight into heat by organic molecules in the biosphere and its coupling to the water cycle (as well as other abiotic processes), is by far the greatest entropy producing process occurring on Earth. Life, from this perspective, can be viewed as performing an important thermodynamic function; acting as a dynamic catalyst by aiding irreversible abiotic process such as the water cycle, hurricanes, and ocean and wind currents to produce entropy. The role of animals in this view is that of unwitting but dedicated servants of the plants and cyanobacteria, helping them to grow and to spread into initially inhospitable areas.

  9. Biological Functions of the Secretome of Neisseria meningitidis

    Directory of Open Access Journals (Sweden)

    Jan Tommassen

    2017-06-01

    Full Text Available Neisseria meningitidis is a Gram-negative bacterial pathogen that normally resides as a commensal in the human nasopharynx but occasionally causes disease with high mortality and morbidity. To interact with its environment, it transports many proteins across the outer membrane to the bacterial cell surface and into the extracellular medium for which it deploys the common and well-characterized autotransporter, two-partner and type I secretion mechanisms, as well as a recently discovered pathway for the surface exposure of lipoproteins. The surface-exposed and secreted proteins serve roles in host-pathogen interactions, including adhesion to host cells and extracellular matrix proteins, evasion of nutritional immunity imposed by iron-binding proteins of the host, prevention of complement activation, neutralization of antimicrobial peptides, degradation of immunoglobulins, and permeabilization of epithelial layers. Furthermore, they have roles in interbacterial interactions, including the formation and dispersal of biofilms and the suppression of the growth of bacteria competing for the same niche. Here, we will review the protein secretion systems of N. meningitidis and focus on the functions of the secreted proteins.

  10. Full momentum- and energy-resolved spectral function of a 2D electronic system

    Science.gov (United States)

    Jang, Joonho; Yoo, Heun Mo; Pfeiffer, L. N.; West, K. W.; Baldwin, K. W.; Ashoori, Raymond C.

    2017-11-01

    The single-particle spectral function measures the density of electronic states in a material as a function of both momentum and energy, providing central insights into strongly correlated electron phenomena. Here we demonstrate a high-resolution method for measuring the full momentum- and energy-resolved electronic spectral function of a two-dimensional (2D) electronic system embedded in a semiconductor. The technique remains operational in the presence of large externally applied magnetic fields and functions even for electronic systems with zero electrical conductivity or with zero electron density. Using the technique on a prototypical 2D system, a GaAs quantum well, we uncover signatures of many-body effects involving electron-phonon interactions, plasmons, polarons, and a phonon analog of the vacuum Rabi splitting in atomic systems.

  11. Distinguishing Biologically Controlled Calcareous Biomineralization in Fossil Organisms Using Electron Backscatter Diffraction (EBSD)

    Science.gov (United States)

    Päßler, Jan-Filip; Jarochowska, Emilia; Bestmann, Michel; Munnecke, Axel

    2018-02-01

    Although carbonate-precipitating cyanobacteria are ubiquitous in aquatic ecosystems today, the criteria used to identify them in the geological record are subjective and rarely testable. Differences in the mode of biomineralization between cyanobacteria and eukaryotes, i.e. biologically induced calcification (BIM) vs. biologically controlled calcification (BCM), result in different crystallographic structures which might be used as a criterion to test cyanobacterial affinities. Cyanobacteria are often used as a ‘wastebasket taxon’, to which various microfossils are assigned. The lack of a testable criterion for the identification of cyanobacteria may bias their fossil record severely. We employed electron backscatter diffraction (EBSD) to investigate the structure of calcareous skeletons in two microproblematica widespread in Palaeozoic marine ecosystems: Rothpletzella, hypothesized to be a cyanobacterium, and an incertae sedis microorganism Allonema. We used a calcareous trilobite shell as a BCM reference. The mineralized structure of Allonema has a simple single-layered structure of acicular crystals perpendicular to the surface of the organism. The c-axes of these crystals are parallel to the elongation and thereby normal to the surface of the organism. EBSD pole figures and misorientation axes distribution reveal a fibre texture around the c-axis with a small degree of variation (up to 30°), indicating a highly ordered structure. A comparable pattern was found in the trilobite shell. This structure allows excluding biologically induced mineralization as the mechanism of shell formation in Allonema. In Rothpletzella, the c-axes of the microcrystalline sheath show a broader clustering compared to Allonema, but still reveal crystals tending to be perpendicular to the surface of the organism. The misorientation axes of adjacent crystals show an approximately random distribution. Rothpletzella also shares morphological similarities with extant cyanobacteria. We

  12. Distinguishing Biologically Controlled Calcareous Biomineralization in Fossil Organisms Using Electron Backscatter Diffraction (EBSD

    Directory of Open Access Journals (Sweden)

    Jan-Filip Päßler

    2018-02-01

    Full Text Available Although carbonate-precipitating cyanobacteria are ubiquitous in aquatic ecosystems today, the criteria used to identify them in the geological record are subjective and rarely testable. Differences in the mode of biomineralization between cyanobacteria and eukaryotes, i.e., biologically induced calcification (BIM vs. biologically controlled calcification (BCM, result in different crystallographic structures which might be used as a criterion to test cyanobacterial affinities. Cyanobacteria are often used as a “wastebasket taxon,” to which various microfossils are assigned. The lack of a testable criterion for the identification of cyanobacteria may bias their fossil record severely. We employed electron backscatter diffraction (EBSD to investigate the structure of calcareous skeletons in two microproblematica widespread in Palaeozoic marine ecosystems: Rothpletzella, hypothesized to be a cyanobacterium, and an incertae sedis microorganism Allonema. We used a calcareous trilobite shell as a BCM reference. The mineralized structure of Allonema has a simple single-layered structure of acicular crystals perpendicular to the surface of the organism. The c-axes of these crystals are parallel to the elongation and thereby normal to the surface of the organism. EBSD pole figures and misorientation axes distribution reveal a fiber texture around the c-axis with a small degree of variation (up to 30°, indicating a highly ordered structure. A comparable pattern was found in the trilobite shell. This structure allows excluding biologically induced mineralization as the mechanism of shell formation in Allonema. In Rothpletzella, the c-axes of the microcrystalline sheath show a broader clustering compared to Allonema, but still reveal crystals tending to be perpendicular to the surface of the organism. The misorientation axes of adjacent crystals show an approximately random distribution. Rothpletzella also shares morphological similarities with extant

  13. The reflection of life functional entailment and imminence in relational biology

    CERN Document Server

    Louie, A H

    2013-01-01

    A. H. Louie’s The Reflection of Life: Functional Entailment and Imminence in Relational Biology is a continuation of the exploratory journey in relational biology which began with his 2009 monograph More Than Life Itself: A Synthetic Continuation in Relational Biology. The theme of his first book was ‘What is life?’; the theme of this sequel is “How do two life forms interact?” Biology is a subject concerned with organization of relations. Relational biology is the approach that advocates ‘function dictates structure”, rather than ‘structure implies function’. It is mathematics decoded into biological realizations. The book demonstrates some of the powers of the approach of relational biology, and illustrates how pertinent problems in biology can be better addressed this way. In the first volume the theory was developed by using partially ordered sets, lattices, simulations, models, Aristotle’s four causes, graphs, categories, simple and complex systems, anticipatory systems, and metabolis...

  14. [Comparison of biological functional assessment in intensity-modulated radiotherapy: two-dimensional study].

    Science.gov (United States)

    Dejean, C; Lemosquet, A; Lefkopoulos, D; Touboul, E

    2001-12-01

    Modulated intensity dose distributions are obtained by inverse planning. It requires an inversion algorithm and an objective function that can be physical or biological. The biological objective functions aim at quantifying the probability of the favourable end of the treatment. The inversion algorithm used is analytical and is based on the mathematical analysis of the singular values decomposition. It proposes as many solutions as there are elementary beams. From the Tumour Control Probability, Normal Tissue Complication Probabilities and complication free tumour control, three biological assessment functions of the proposed solutions are compared with the least square difference between the prescribed and obtained dose distributions. We used a simplified irradiation configuration: Brahme's dose prescription (2D modelling of a prostate) and 9 beams (1D). The choice by mean of biological criterion of the optimal solution makes it possible to increase the average dose in the tumour, so as its homogeneity compared to physical optimisation. Conversely, the organs at risk are then less protected. The laying down of relevant constraints makes it possible to obtain satisfactory dose distributions. Concerning the validity of the models and data used, some limitations appear. At present time, it seems to exclude the use in clinical routine of an only biological optimisation. The future availability of new biological data will allow the development and in particular the clinical use of biological optimisation.

  15. Are Prompts Provided by Electronic Books as Effective for Teaching Preschoolers a Biological Concept as Those Provided by Adults?

    Science.gov (United States)

    Strouse, Gabrielle A.; Ganea, Patricia A.

    2016-01-01

    Research Findings: Prior research indicates that shared book reading is an effective method for teaching biological concepts to young children. Adult questioning during reading enhances children's comprehension. We investigated whether adult prompting during the reading of an electronic book enhanced children's understanding of a biological…

  16. Electron Cryo-Tomography of Vitreous Cryo-Sections : Towards Imaging Biological Nanomachines in their Cellular Environment

    NARCIS (Netherlands)

    Pierson, J.

    2011-01-01

    The field of biological electron microcopy (EM) has evolved into a reliable imaging technique for examining the ultrastructure of cells and their constituents at molecular, and, in some cases, atomic1, 2 resolution. Conventional EM techniques are being overshadowed by cryo-techniques, which ensure a

  17. Electron Green's Function of Graphene in the Aharonov-Bohm Potential

    International Nuclear Information System (INIS)

    Slobodenyuk, A.O.

    2011-01-01

    The dynamics of electron excitations, which are described by the Dirac equation, in the Aharonov-Bohm field has been studied. The eigenfunctions and the spectrum of the Hamiltonian of a system have been used to construct the integral formula for the electron Green's function. Possible applications of the results obtained to numerically calculate the electronic properties of graphene have been discussed.

  18. Correlation functions of electronic and nuclear spins in a Heisenberg antiferromagnet semi-infinite medium

    International Nuclear Information System (INIS)

    Sarmento, E.F.

    1981-01-01

    Results are found for the dynamical correlation functions (or its corresponding Green's functions) among any combination including operator pairs of electronic and nuclear spins in an antiferromagnet semi-infinite medium, at low temperatures T [pt

  19. Sharing Structure and Function in Biological Design with SBOL 2.0.

    Science.gov (United States)

    Roehner, Nicholas; Beal, Jacob; Clancy, Kevin; Bartley, Bryan; Misirli, Goksel; Grünberg, Raik; Oberortner, Ernst; Pocock, Matthew; Bissell, Michael; Madsen, Curtis; Nguyen, Tramy; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Densmore, Douglas; Gennari, John H; Wipat, Anil; Sauro, Herbert M; Myers, Chris J

    2016-06-17

    The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and members of commercial biotechnology enterprises. We demonstrate and discuss how a set of SBOL-enabled software tools can form an integrated, cross-organizational workflow to recapitulate the design of one of the largest published genetic circuits to date, a 4-input AND sensor. This design encompasses the structural components of the system, such as its DNA, RNA, small molecules, and proteins, as well as the interactions between these components that determine the system's behavior/function. The demonstrated workflow and resulting circuit design illustrate the utility of SBOL 2.0 in automating the exchange of structural and functional specifications for genetic parts, devices, and the biological systems in which they operate.

  20. Evolutionary cell biology: functional insight from “endless forms most beautiful”

    Science.gov (United States)

    Richardson, Elisabeth; Zerr, Kelly; Tsaousis, Anastasios; Dorrell, Richard G.; Dacks, Joel B.

    2015-01-01

    In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking. PMID:26668171

  1. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

    Science.gov (United States)

    Farré, Jean-Claude; Kramer, Michael; Ideker, Trey; Subramani, Suresh

    2017-07-03

    Increasingly, various 'omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new 'omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.

  2. Bioactive components and functional properties of biologically activated cereal grains: A bibliographic review.

    Science.gov (United States)

    Singh, Arashdeep; Sharma, Savita

    2017-09-22

    Whole grains provide energy, nutrients, fibers, and bioactive compounds that may synergistically contribute to their protective effects. A wide range of these compounds is affected by germination. While some compounds, such as β-glucans are degraded, others, like antioxidants and total phenolics are increased by means of biological activation of grains. The water and oil absorption capacity as well as emulsion and foaming capacity of biologically activated grains are also improved. Application of biological activation of grains is of emerging interest, which may significantly enhance the nutritional, functional, and bioactive content of grains, as well as improve palatability of grain foods in a natural way. Therefore, biological activation of cereals can be a way to produce food grains enriched with health-promoting compounds and enhanced functional attributes.

  3. Diurnal rhythmicity in biological processes involved in bioavailability of functional food factors.

    Science.gov (United States)

    Tsurusaki, Takashi; Sakakibara, Hiroyuki; Aoshima, Yoshiki; Yamazaki, Shunsuke; Sakono, Masanobu; Shimoi, Kayoko

    2013-05-01

    In the past few decades, many types of functional factors have been identified in dietary foods; for example, flavonoids are major groups widely distributed in the plant kingdom. However, the absorption rates of the functional food factors are usually low, and many of these are difficult to be absorbed in the intact forms because of metabolization by biological processes during absorption. To gain adequate beneficial effects, it is therefore mandatory to know whether functional food factors are absorbed in sufficient quantity, and then reach target organs while maintaining beneficial effects. These are the reasons why the bioavailability of functional food factors has been well investigated using rodent models. Recently, many of the biological processes have been reported to follow diurnal rhythms recurring every 24 h. Therefore, absorption and metabolism of functional food factors influenced by the biological processes may vary with time of day. Consequently, the evaluation of the bioavailability of functional food factors using rodent models should take into consideration the timing of consumption. In this review, we provide a perspective overview of the diurnal rhythm of biological processes involved in the bioavailability of functional food factors, particularly flavonoids.

  4. Bio-templated CdSe quantum dots green synthesis in the functional protein, lysozyme, and biological activity investigation

    International Nuclear Information System (INIS)

    Wang, Qisui; Li, Song; Liu, Peng; Min, Xinmin

    2012-01-01

    Bifunctional fluorescence (CdSe Quantum Dots) – protein (Lysozyme) nanocomposites were synthesized at room temperature by a protein-directed, solution-phase, green-synthetic method. Fluorescence (FL) and absorption spectra showed that CdSe QDs were prepared successfully with Lyz. The average particle size and crystalline structure of QDs were investigated by high-resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD), respectively. With attenuated total reflection-fourier transform infrared (ATR-FTIR) spectra and thermogravimetric (TG) analysis, it was confirmed that there is interaction between QDs and amide I, amide II groups in Lyz. FL polarization was measured and FL imaging was done to monitor whether QDs could be responsible for possible changes in the conformation and activity of Lyz. Interestingly, the results showed Lyz still retain the biological activity after formation of QDs, but the secondary structure of the Lyz was changed. And the advantage of this synthesis method is producing excellent fluorescent QDs with specifically biological function. -- Highlights: ► Lysozyme-directed green synthesis of CdSe quantum dots. ► Lysozyme still retain the biological activity after formation of CdSe. ► The method is the production of fluorescent QDs with highly specific and functions.

  5. Electron energy probability function in the temporal afterglow of a dusty plasma

    Science.gov (United States)

    Denysenko, I. B.; Azarenkov, N. A.; Ostrikov, K.; Yu, M. Y.

    2018-01-01

    The kinetic description of the electron energy probability function (EEPF) in a dusty afterglow plasma is considered for two typical cases: when the rate of electron-neutral momentum-transfer collisions is independent of the electron energy and when it is a power function of the electron energy. The electron Boltzmann equation is solved using the method of characteristics and analytical expressions for the EEPF are obtained for different initial EEPFs (including both Maxwellian and Druyvesteyn distributions) at electron energies larger than the dust-surface potential. The analytical EEPF functions are then used to analyze several experimental parameter regimes of the dust radius and density, the dust-charge decay time, the afterglow duration, etc. It is also found that absorption of electrons by the dust particles plays an important role in determining the EEPF in a dusty afterglow.

  6. The effect of electron range on electron beam induced current collection and a simple method to extract an electron range for any generation function

    International Nuclear Information System (INIS)

    Lahreche, A.; Beggah, Y.; Corkish, R.

    2011-01-01

    The effect of electron range on electron beam induced current (EBIC) is demonstrated and the problem of the choice of the optimal electron ranges to use with simple uniform and point generation function models is resolved by proposing a method to extract an electron range-energy relationship (ERER). The results show that the use of these extracted electron ranges remove the previous disagreement between the EBIC curves computed with simple forms of generation model and those based on a more realistic generation model. The impact of these extracted electron ranges on the extraction of diffusion length, surface recombination velocity and EBIC contrast of defects is discussed. It is also demonstrated that, for the case of uniform generation, the computed EBIC current is independent of the assumed shape of the generation volume. -- Highlights: → Effect of electron ranges on modeling electron beam induced current is shown. → A method to extract an electron range for simple form of generation is proposed. → For uniform generation the EBIC current is independent of the choice of it shape. → Uses of the extracted electron ranges remove some existing literature ambiguity.

  7. An overview of the applicability of functional diversity in Biological Conservation.

    Science.gov (United States)

    Freitas, J R; Mantovani, W

    2017-10-23

    Functional diversity is increasingly pointed as a useful approach to reach Biological Conservation goals. Here, we provide an overview of the functional diversity approach status in the Biological Conservation field. We sought for peer-reviewed papers published over a period of twenty years (from 1994 to 2014). First we used the general topic "functional diversity" and then refined our search using the key-word "conservation". We have identified the conservation strategies addressed, the organism studied, and the continent of study site in each paper. Thirteen classes of conservation strategies were identified. Plants were the most commonly studied organism group and most study-sites were located in Europe. The functional diversity approach was introduced in the Biological Conservation field in the early 2000's and its inclusion in conservation strategies is broadly advised. However, the number of papers that operationalise such inclusion by developing models and systems is still low. Functional diversity responds differently and eventually better than other measures to changes in land use and management, which suggests that this approach can potentially better predict the impacts. More studies are needed to corroborate this hypothesis. We pointed out knowledge gaps regarding identification of the responses for functional diversity about urban impacts and in research on the level of management intensity of land needed to maintain functional diversity. We recommend the use of functional diversity measures to find ecological indicators. Future studies should focus on the development of functional diversity measures of other taxa beyond plants as well as test hypothesis in tropical ecosystems.

  8. Biology

    Indian Academy of Sciences (India)

    I am particularly happy that the Academy is bringing out this document by Professor M S. Valiathan on Ayurvedic Biology. It is an effort to place before the scientific community, especially that of India, the unique scientific opportunities that arise out of viewing Ayurveda from the perspective of contemporary science, its tools ...

  9. Superclusters : a search for novel structures and functions of biological iron-sulfur clusters

    NARCIS (Netherlands)

    Arendsen, A.F.

    1996-01-01


    Iron sulfur (Fe-S) proteins are found in a variety of organisms. They usually function in electron transport, but they may also be involved in other functions like gene regulation and Lewis acid catalysis. The structure and spectroscopic properties of Fe-S clusters holding one, two,

  10. Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

    Science.gov (United States)

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

  11. Multifunctional Electronics Core Substrate Configurable Electronics Functionality with Stacked Silicon and Multi-Chip Modules

    Data.gov (United States)

    National Aeronautics and Space Administration — Integration of a mix of heterogeneous electronic device technologies (silicon, III-V, passive, etc.) into a single multifunctional substrate core. Based on the...

  12. Density functional theory study of structure, electronic and magnetic ...

    Indian Academy of Sciences (India)

    Keywords. Rhodium; boron; aluminium; gallium; methanol activation. Abstract. Rhodium clusters are very important finite size materials because of their unique electronic, magneticand catalytic properties. Tuning the physical and chemical properties of rhodium clusters by incorporatingdifferent metal and non-metal atoms ...

  13. Density functional study of : Electronic and optical properties

    Indian Academy of Sciences (India)

    K C Bhamu

    2017-06-20

    Jun 20, 2017 ... used as an inner layer of solar cells for electricity gen- eration. This peculiar characteristic has established a benchmark in invisible electronics and opened a new era in solar cell technology [5–9]. Dietrich and Jansen [10] synthesized and reported the 3R phase of AgScO2. Shannon et al [11] reported.

  14. Electron localization functions and local measures of the covariance ∑

    Indian Academy of Sciences (India)

    Unknown

    Bader and Stephens have noted that, despite its intuitive appeal, in many molecules the minimal fluctuation remains quite large and so this criterion sometimes fails to yield intuitive electron dot diagrams.9 The recent proposal by Savin and coworkers to define molecular regions be defined so that the probability of observing ...

  15. Electron transfer flavoprotein deficiency: Functional and molecular aspects

    DEFF Research Database (Denmark)

    Schiff, M; Froissart, R; Olsen, Rikke Katrine Jentoft

    2006-01-01

    Multiple acyl-CoA dehydrogenase deficiency (MADD) is a recessively inherited metabolic disorder that can be due to a deficiency of electron transfer flavoprotein (ETF) or its dehydrogenase (ETF-ubiquinone oxidoreductase). ETF is a mitochondrial matrix protein consisting of alpha- (30kDa) and beta...

  16. Density functional theory study of structure, electronic and magnetic ...

    Indian Academy of Sciences (India)

    ABHIJIT DUTTA

    2018-01-30

    Jan 30, 2018 ... Abstract. Rhodium clusters are very important finite size materials because of their unique electronic, magnetic and catalytic properties. Tuning the physical and chemical properties of rhodium clusters by incorporating different metal and non-metal atoms have found a great research interest in recent years.

  17. K-shell Analysis Reveals Distinct Functional Parts in an Electron Transfer Network and Its Implications for Extracellular Electron Transfer.

    Science.gov (United States)

    Ding, Dewu; Li, Ling; Shu, Chuanjun; Sun, Xiao

    2016-01-01

    Shewanella oneidensis MR-1 is capable of extracellular electron transfer (EET) and hence has attracted considerable attention. The EET pathways mainly consist of c-type cytochromes, along with some other proteins involved in electron transfer processes. By whole genome study and protein interactions inquisition, we constructed a large-scale electron transfer network containing 2276 interactions among 454 electron transfer related proteins in S. oneidensis MR-1. Using the k-shell decomposition method, we identified and analyzed distinct parts of the electron transfer network. We found that there was a negative correlation between the k s (k-shell values) and the average DR_100 (disordered regions per 100 amino acids) in every shell, which suggested that disordered regions of proteins played an important role during the formation and extension of the electron transfer network. Furthermore, proteins in the top three shells of the network are mainly located in the cytoplasm and inner membrane; these proteins can be responsible for transfer of electrons into the quinone pool in a wide variety of environmental conditions. In most of the other shells, proteins are broadly located throughout the five cellular compartments (cytoplasm, inner membrane, periplasm, outer membrane, and extracellular), which ensures the important EET ability of S. oneidensis MR-1. Specifically, the fourth shell was responsible for EET and the c-type cytochromes in the remaining shells of the electron transfer network were involved in aiding EET. Taken together, these results show that there are distinct functional parts in the electron transfer network of S. oneidensis MR-1, and the EET processes could achieve high efficiency through cooperation through such an electron transfer network.

  18. Wood-Derived Materials for Green Electronics, Biological Devices, and Energy Applications.

    Science.gov (United States)

    Zhu, Hongli; Luo, Wei; Ciesielski, Peter N; Fang, Zhiqiang; Zhu, J Y; Henriksson, Gunnar; Himmel, Michael E; Hu, Liangbing

    2016-08-24

    goal of this study is to review the fundamental structures and chemistries of wood and wood-derived materials, which are essential for a wide range of existing and new enabling technologies. The scope of the review covers multiscale materials and assemblies of cellulose, hemicellulose, and lignin as well as other biomaterials derived from wood, in regard to their major emerging applications. Structure-properties-application relationships will be investigated in detail. Understanding the fundamental properties of these structures is crucial for designing and manufacturing products for emerging applications. Today, a more holistic understanding of the interplay between the structure, chemistry, and performance of wood and wood-derived materials is advancing historical applications of these materials. This new level of understanding also enables a myriad of new and exciting applications, which motivate this review. There are excellent reviews already on the classical topic of woody materials, and some recent reviews also cover new understanding of these materials as well as potential applications. This review will focus on the uniqueness of woody materials for three critical applications: green electronics, biological devices, and energy storage and bioenergy.

  19. Wood-Derived Materials for Green Electronics, Biological Devices, and Energy Applications

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Hongli; Luo, Wei; Ciesielski, Peter N.; Fang, Zhiqiang; Zhu, J. Y.; Henriksson, Gunnar; Himmel, Michael E.; Hu, Liangbing

    2016-08-24

    goal of this study is to review the fundamental structures and chemistries of wood and wood-derived materials, which are essential for a wide range of existing and new enabling technologies. The scope of the review covers multiscale materials and assemblies of cellulose, hemicellulose, and lignin as well as other biomaterials derived from wood, in regard to their major emerging applications. Structure-properties-application relationships will be investigated in detail. Understanding the fundamental properties of these structures is crucial for designing and manufacturing products for emerging applications. Today, a more holistic understanding of the interplay between the structure, chemistry, and performance of wood and wood-derived materials is advancing historical applications of these materials. This new level of understanding also enables a myriad of new and exciting applications, which motivate this review. There are excellent reviews already on the classical topic of woody materials, and some recent reviews also cover new understanding of these materials as well as potential applications. This review will focus on the uniqueness of woody materials for three critical applications: green electronics, biological devices, and energy storage and bioenergy.

  20. Urban biomining meets printable electronics: end-to-end at destination biological recycling and reprinting

    Data.gov (United States)

    National Aeronautics and Space Administration — Space missions rely utterly on metallic components, from the spacecraft to electronics. Yet, metals add mass, and electronics have the additional problem of a...

  1. The Work Function Associated with Ultra-relativistic Electron ...

    Indian Academy of Sciences (India)

    the study of anisotropic nature of work function in the presence of strong quantizing magnetic field, relevant for strongly magnetized neutron star crustal region, has not been studied earlier. Of course, a completely different approach, popularly known as density functional theory (DFT) has been used by Medin & Lai (2006, ...

  2. Effects of a kappa distribution function of electrons on incoherent scatter spectra

    Directory of Open Access Journals (Sweden)

    S. Saito

    2000-09-01

    Full Text Available In usual incoherent scatter data analysis, the plasma distribution function is assumed to be Maxwellian. In space plasmas, however, distribution functions with a high energy tail which can be well modeled by a generalized Lorentzian distribution function with spectral index kappa (kappa distribution have been observed. We have theoretically calculated incoherent scatter spectra for a plasma that consists of electrons with kappa distribution function and ions with Maxwellian neglecting the effects of the magnetic field and collisions. The ion line spectra have a double-humped shape similar to those from a Maxwellian plasma. The electron temperatures are underestimated, however, by up to 40% when interpreted assuming Maxwellian distribution. Ion temperatures and electron densities are affected little. Accordingly, actual electron temperatures might be underestimated when an energy input maintaining a high energy tail exists. We have also calculated plasma lines with the kappa distribution function. They are enhanced in total strength, and the peak frequencies appear to be slightly shifted to the transmitter frequency compared to the peak frequencies for a Maxwellian distribution. The damping rate depends on the electron temperature. For lower electron temperatures, plasma lines for electrons with a κ distribution function are more strongly damped than for a Maxwellian distribution. For higher electron temperatures, however, they have a relatively sharp peak.Key words: Ionosphere (auroral ionosphere; plasma waves and instabilities – Space plasma physics (kinetic and MHD theory

  3. Myocardial function and effects of biologic therapy in patients with severe psoriasis

    DEFF Research Database (Denmark)

    Ahlehoff, O.; Hansen, P. R.; Gislason, G. H.

    2016-01-01

    function in patients with severe psoriasis who initiated biologic therapy. Methods Between November 1 2013 and May 31 2014 the study subjects underwent physical, laboratory and comprehensive echocardiographic examination at baseline and after 3 months of treatment. Pearson correlation coefficients...... and Student's t-test were applied to assess changes in diastolic function (defined as the E/e' ratio) and global longitudinal strain (GLS). Results Eighteen patients with severe psoriasis treated with biologic therapy with a mean follow-up of 85.6 ± 18.2 days were included. The patients had a baseline.......74). Likewise, no changes were seen in total cholesterol, low density lipoprotein cholesterol, high density lipoprotein cholesterol, estimated glomerular filtration rate and glycosylated haemoglobin. Conclusion In patients with severe psoriasis treatment with biologic therapy was associated with improved PASI...

  4. Improvement of functioning of executive devices of radio electronic facilities

    OpenAIRE

    V. G. Smolyaninov; A. N. Sukhopara

    2012-01-01

    Efficiency of functioning of RES which electromagnetic executive devices (EIU), mechanisms and engines, enter in the complement of, determined their power and dynamic descriptions which provide of the continuous mode of operations of RES with maximal KPD. Possibility of improvement of functioning of EIU is rotined by a construct effektive managements without additional sensors, due to control of electromagnetic procesov in the own construction of EIU through control of size of current i...

  5. Finite element analysis (FEA): applying an engineering method to functional morphology in anthropology and human biology.

    Science.gov (United States)

    Panagiotopoulou, O

    2009-01-01

    A fundamental research question for morphologists is how morphological variation in the skeleton relates to function. Traditional approaches have advanced our understanding of form-function relationships considerably but have limitations. Strain gauges can only record strains on a surface, and the geometry of the structure can limit where they can be bonded. Theoretical approaches, such as geometric abstractions, work well on problems with simple geometries and material properties but biological structures typically have neither of these. Finite element analysis (FEA) is a method that overcomes these problems by reducing a complex geometry into a finite number of elements with simple geometries. In addition, FEA allows strain to be modelled across the entire surface of the structure and throughout the internal structure. With advances in the processing power of computers, FEA has become more accessible and as such is becoming an increasingly popular tool to address questions about form-function relationships in development and evolution, as well as human biology generally. This paper provides an introduction to FEA including a review of the sequence of steps needed for the generation of biologically accurate finite element models that can be used for the testing of biological and functional morphology hypotheses.

  6. Biological interpretation of genome-wide association studies using predicted gene functions

    NARCIS (Netherlands)

    Pers, Tune H.; Karjalainen, Juha M.; Chan, Yingleong; Westra, Harm-Jan; Wood, Andrew R.; Yang, Jian; Lui, Julian C.; Vedantam, Sailaja; Gustafsson, Stefan; Esko, Tonu; Frayling, Tim; Speliotes, Elizabeth K.; Boehnke, Michael; Raychaudhuri, Soumya; Fehrmann, Rudolf S. N.; Hirschhorn, Joel N.; Franke, Lude; Chu, Audrey Y.; Estrada, Karol; Luan, Jian'an; Kutalik, Zoltán; Amin, Najaf; Buchkovich, Martin L.; Croteau-Chonka, Damien C.; Day, Felix R.; Duan, Yanan; Fall, Tove; Fehrmann, Rudolf; Ferreira, Teresa; Jackson, Anne U.; Karjalainen, Juha; Lo, Ken Sin; Locke, Adam E.; Mägi, Reedik; Mihailov, Evelin; Porcu, Eleonora; Randall, Joshua C.; Scherag, André; Vinkhuyzen, Anna A. E.; Winkler, Thomas W.; Workalemahu, Tsegaselassie; Zhao, Jing Hua; Absher, Devin; Albrecht, Eva; Anderson, Denise; Baron, Jeffrey; Beekman, Marian; Demirkan, Ayse; Ehret, Georg B.; Feenstra, Bjarke; Feitosa, Mary F.; Fischer, Krista; Fraser, Ross M.; Goel, Anuj; Gong, Jian; Justice, E.; Kanoni, Stavroula; Kleber, Marcus E.; Kristiansson, Kati; Lim, Unhee; Lotay, Vaneet; Mangino, Massimo; Mateo Leach, Irene; Medina-Gomez, Carolina; Nalls, Michael A.; Nyholt, Dale R.; Palmer, Cameron D.; Pasko, Dorota; Pechlivanis, Sonali; Prokopenko, Inga; Ried, Janina S.; Ripke, Stephan; Shungin, Dmitry; Stancáková, Alena; Strawbridge, Rona J.; Sung, Yun Ju; Tanaka, Toshiko; Teumer, Alexander; Trompet, Stella; van der Laan, Sander W.; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V.; Wang, Zhaoming; Yengo, Loïc; Zhang, Weihua; Afzal, Uzma; Ärnlöv, Johan; Arscott, Gillian M.; Bandinelli, Stefania; Barrett, Amy; Bellis, Claire; Bennett, Amanda J.; Berne, Christian; Blüher, Matthias; Bolton, Jennifer L.; Böttcher, Yvonne; Boyd, Heather A.; Bruinenberg, Marcel; Buckley, Brendan M.; Buyske, Steven; Caspersen, Ida H.; Chines, Peter S.; Clarke, Robert; Claudi-Boehm, Simone; Cooper, Matthew; Daw, E. Warwick; de Jong, A.; Deelen, Joris; Delgado, Graciela; Denny, Josh C.; Dhonukshe-Rutten, Rosalie; Dimitriou, Maria; Doney, Alex S. F.; Dörr, Marcus; Eklund, Niina; Eury, Elodie; Folkersen, Lasse; Garcia, Melissa E.; Geller, Frank; Giedraitis, Vilmantas; Go, Alan S.; Grallert, Harald; Grammer, Tanja B.; Gräßler, Jürgen; Grönberg, Henrik; de Groot, Lisette C. P. G. M.; Groves, Christopher J.; Haessler, Jeffrey; Haller, Toomas; Hallmans, Goran; Hannemann, Anke; Hartman, Catharina A.; Hassinen, Maija; Hayward, Caroline; Heard-Costa, Nancy L.; Helmer, Quinta; Hemani, Gibran; Henders, Anjali K.; Hillege, Hans L.; Hlatky, Mark A.; Hoffmann, Wolfgang; Hoffmann, Per; Holmen, Oddgeir; Houwing-Duistermaat, Jeanine J.; Illig, Thomas; Isaacs, Aaron; James, Alan L.; Jeff, Janina; Johansen, Berit; Johansson, Åsa; Jolley, Jennifer; Juliusdottir, Thorhildur; Junttila, Juhani; Kho, Abel N.; Kinnunen, Leena; Klopp, Norman; Kocher, Thomas; Kratzer, Wolfgang; Lichtner, Peter; Lind, Lars; Lindström, Jaana; Lobbens, Stéphane; Lorentzon, Mattias; Lu, Yingchang; Lyssenko, Valeriya; Magnusson, Patrik K. E.; Mahajan, Anubha; Maillard, Marc; McArdle, Wendy L.; McKenzie, Colin A.; McLachlan, Stela; McLaren, Paul J.; Menni, Cristina; Merger, Sigrun; Milani, Lili; Moayyeri, Alireza; Monda, Keri L.; Morken, Mario A.; Müller, Gabriele; Müller-Nurasyid, Martina; Musk, Arthur W.; Narisu, Narisu; Nauck, Matthias; Nolte, Ilja M.; Nöthen, Markus M.; Oozageer, Laticia; Pilz, Stefan; Rayner, Nigel W.; Renstrom, Frida; Robertson, Neil R.; Rose, Lynda M.; Roussel, Ronan; Sanna, Serena; Scharnagl, Hubert; Scholtens, Salome; Schumacher, Fredrick R.; Schunkert, Heribert; Scott, Robert A.; Sehmi, Joban; Seufferlein, Thomas; Shi, Jianxin; Silventoinen, Karri; Smit, Johannes H.; Smith, Albert Vernon; Smolonska, Joanna; Stanton, Alice V.; Stirrups, Kathleen; Stott, David J.; Stringham, Heather M.; Sundström, Johan; Swertz, Morris A.; Syvänen, Ann-Christine; Tayo, Bamidele O.; Thorleifsson, Gudmar; Tyrer, Jonathan P.; van Dijk, Suzanne; van Schoor, Natasja M.; van der Velde, Nathalie; van Heemst, Diana; van Oort, Floor V. A.; Vermeulen, Sita H.; Verweij, Niek; Vonk, Judith M.; Waite, Lindsay L.; Waldenberger, Melanie; Wennauer, Roman; Wilkens, Lynne R.; Willenborg, Christina; Wilsgaard, Tom; Wojczynski, Mary K.; Wong, Andrew; Wright, Alan F.; Zhang, Qunyuan; Arveiler, Dominique; Bakker, Stephan J. L.; Beilby, John; Bergman, Richard N.; Bergmann, Sven; Biffar, Reiner; Blangero, John; Boomsma, I.; Bornstein, Stefan R.; Bovet, Pascal; Brambilla, Paolo; Brown, Morris J.; Campbell, Harry; Caulfield, Mark J.; Chakravarti, Aravinda; Collins, Rory; Collins, Francis S.; Crawford, Dana C.; Cupples, L. Adrienne; Danesh, John; de Faire, Ulf; den Ruijter, Hester M.; Erbel, Raimund; Erdmann, Jeanette; Eriksson, Johan G.; Farrall, Martin; Ferrannini, Ele; Ferrières, Jean; Ford, Ian; Forouhi, Nita G.; Forrester, Terrence; Gansevoort, Ron T.; Gejman, Pablo V.; Gieger, Christian; Golay, Alain; Gottesman, Omri; Gudnason, Vilmundur; Gyllensten, Ulf; Haas, David W.; Hall, Alistair S.; Harris, Tamara B.; Hattersley, Andrew T.; Heath, Andrew C.; Hengstenberg, Christian; Hicks, Andrew A.; Hindorff, Lucia A.; Hingorani, Aroon D.; Hofman, Albert; Hovingh, G. Kees; Humphries, Steve E.; Hunt, Steven C.; Hypponen, Elina; Jacobs, Kevin B.; Jarvelin, Marjo-Riitta; Jousilahti, Pekka; Jula, Antti M.; Kaprio, Jaakko; Kastelein, John J. P.; Kayser, Manfred; Kee, Frank; Keinanen-Kiukaanniemi, Sirkka M.; Kiemeney, Lambertus A.; Kooner, Jaspal S.; Kooperberg, Charles; Koskinen, Seppo; Kovacs, Peter; Kraja, Aldi T.; Kumari, Meena; Kuusisto, Johanna; Lakka, Timo A.; Langenberg, Claudia; Le Marchand, Loic; Lehtimäki, Terho; Lupoli, Sara; Madden, Pamela A. F.; Männistö, Satu; Manunta, Paolo; Marette, André; Matise, Tara C.; McKnight, Barbara; Meitinger, Thomas; Moll, Frans L.; Montgomery, Grant W.; Morris, Andrew D.; Morris, Andrew P.; Murray, Jeffrey C.; Nelis, Mari; Ohlsson, Claes; Oldehinkel, Albertine J.; Ong, Ken K.; Ouwehand, Willem H.; Pasterkamp, Gerard; Peters, Annette; Pramstaller, Peter P.; Price, Jackie F.; Qi, Lu; Raitakari, Olli T.; Rankinen, Tuomo; Rao, D. C.; Rice, Treva K.; Ritchie, Marylyn; Rudan, Igor; Salomaa, Veikko; Samani, Nilesh J.; Saramies, Jouko; Sarzynski, Mark A.; Schwarz, Peter E. H.; Sebert, Sylvain; Sever, Peter; Shuldiner, Alan R.; Sinisalo, Juha; Steinthorsdottir, Valgerdur; Stolk, Ronald P.; Tardif, Jean-Claude; Tönjes, Anke; Tremblay, Angelo; Tremoli, Elena; Virtamo, Jarmo; Vohl, Marie-Claude; Amouyel, Philippe; Asselbergs, Folkert W.; Assimes, Themistocles L.; Bochud, Murielle; Boehm, Bernhard O.; Boerwinkle, Eric; Bottinger, Erwin P.; Bouchard, Claude; Cauchi, Stéphane; Chambers, John C.; Chanock, Stephen J.; Cooper, Richard S.; de Bakker, Paul I. W.; Dedoussis, George; Ferrucci, Luigi; Franks, Paul W.; Froguel, Philippe; Groop, Leif C.; Haiman, Christopher A.; Hamsten, Anders; Hayes, M. Geoffrey; Hui, Jennie; Hunter, David J.; Hveem, Kristian; Jukema, J. Wouter; Kaplan, Robert C.; Kivimaki, Mika; Kuh, Diana; Laakso, Markku; Liu, Yongmei; Martin, Nicholas G.; März, Winfried; Melbye, Mads; Moebus, Susanne; Munroe, Patricia B.; Njølstad, Inger; Oostra, Ben A.; Palmer, Colin N. A.; Pedersen, Nancy L.; Perola, Markus; Pérusse, Louis; Peters, Ulrike; Powell, Joseph E.; Power, Chris; Quertermous, Thomas; Rauramaa, Rainer; Reinmaa, Eva; Ridker, Paul M.; Rivadeneira, Fernando; Rotter, Jerome I.; Saaristo, Timo E.; Saleheen, Danish; Schlessinger, David; Slagboom, P. Eline; Snieder, Harold; Spector, Tim D.; Strauch, Konstantin; Stumvoll, Michael; Tuomilehto, Jaakko; Uusitupa, Matti; van der Harst, Pim; Völzke, Henry; Walker, Mark; Wareham, Nicholas J.; Watkins, Hugh; Wichmann, H.-Erich; Wilson, James F.; Zanen, Pieter; Deloukas, Panos; Heid, Iris M.; Lindgren, Cecilia M.; Mohlke, Karen L.; Thorsteinsdottir, Unnur; Barroso, Inês; Fox, Caroline S.; North, Kari E.; Strachan, David P.; Beckmann, Jacques S.; Berndt, Sonja I.; Borecki, Ingrid B.; McCarthy, Mark I.; Metspalu, Andres; Stefansson, Kari; Uitterlinden, André G.; van Duijn, Cornelia M.; Willer, Cristen J.; Price, Alkes L.; Lettre, Guillaume; Loos, Ruth J. F.; Weedon, Michael N.; Ingelsson, Erik; O'Connell, Jeffrey R.; Abecasis, Goncalo R.; Chasman, Daniel I.; Goddard, Michael E.; Visscher, Peter M.; Frayling, Timothy M.

    2015-01-01

    The main challenge for gaining biological insights from genetic associations is identifying which genes and pathways explain the associations. Here we present DEPICT, an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated

  7. Application and Optimization of Biolog EcoPlates in Functional Diversity Studies of Soil Microbial Communities

    Directory of Open Access Journals (Sweden)

    Xu Wenhuan

    2015-01-01

    Full Text Available The biological diversity contributes to many aspects of human well-being and ecosystem function, however, we have known very little about microbial diversity due to the limitations of appropriate methodology underneath it. The development of biotech have brought revolutionary progress in the study of microbial diversity in which Biolog required to pay a lot of attention due to its ability of reflecting the metabolic situation of living microbial communities and have used widely in the study of soil microbial communities. However, there are some controversies during its operation procedure and incubation process, handling large data during the analysis might have also caused trouble in the overall process. The approach based on uses of “absolute used”, “INDIRECT” function in Excel could greatly optimize the data analysis, and the increase of principle components in Principle Component Analysis (PCA were able to extract more information from original data. Besides, the method that through “Taylor” and “logic” transformation for original data before PCA analysis could achieve data analysis optimization. This paper have presented the applications and optimization of Biolog EcoPlates in studies of functional diversity of microbial communities, presented its inherent biases and prospects, provided some reference for the applications and popularization of Biolog EcoPlates for microbial study and finally, the results imply improving the knowledge of biotech in study of soil microbial functional diversity.

  8. Fungal secretomics to probe the biological functions of lytic polysaccharide monooxygenases

    DEFF Research Database (Denmark)

    Berrin, Jean-Guy; Rosso, Marie-Noëlle; Abou Hachem, Maher

    2017-01-01

    to starch, the main carbon storage reservoir. In this review, we focus on the identification of lytic polysaccharide monooxygenases (LPMOs) and their redox partners in fungal secretomes to highlight the biological functions of these remarkable enzyme systems and we discuss future trends related to LPMO...

  9. Determining the impacts of trawling on benthic function in European waters : a biological traits approach

    DEFF Research Database (Denmark)

    Bolam, Stefan; Kenny, Andrew; Garcia, Clement

    on benthic ecosystem functioning over much larger spatial scales than previously undertaken. Biological traits information from 887 stations across European waters (Norwegian, UK, Belgian, Dutch, Danish waters, the Mediterranean and Black Sea) were analysed to: i) quantify the relationships between infaunal...

  10. MicroRNA functional network in pancreatic cancer: From biology to ...

    Indian Academy of Sciences (India)

    malignancy. [Wang J and Sen S 2011 MicroRNA functional network in pancreatic cancer: From biology to biomarkers of disease. J. Biosci. 36 481–491] ... aid in improving clinical management and therapeutic outcome for the patients. ..... 133a is a characteristic of pancreatic tissue and that a total of. 26 miRs are aberrantly ...

  11. Investigations in space-related molecular biology. [cryo-electron microscopic and diffraction studies on terrestrial and extraterrestrial specimens

    Science.gov (United States)

    Fernandez-Moran, H.; Pritzker, A. N.

    1974-01-01

    Improved instrumentation and preparation techniques for high resolution, high voltage cryo-electron microscopic and diffraction studies on terrestrial and extraterrestrial specimens are reported. Computer correlated ultrastructural and biochemical work on hydrated and dried cell membranes and related biological systems provided information on membrane organization, ice crystal formation and ordered water, RNA virus linked to cancer, lunar rock samples, and organometallic superconducting compounds. Apollo 11, 12, 14, and 15 specimens were analyzed

  12. Electron Bifurcation

    Energy Technology Data Exchange (ETDEWEB)

    Peters, John W.; Miller, Anne-Frances; Jones, Anne K.; King, Paul W.; Adams, Michael W. W.

    2016-04-01

    Electron bifurcation is the recently recognized third mechanism of biological energy conservation. It simultaneously couples exergonic and endergonic oxidation-reduction reactions to circumvent thermodynamic barriers and minimize free energy loss. Little is known about the details of how electron bifurcating enzymes function, but specifics are beginning to emerge for several bifurcating enzymes. To date, those characterized contain a collection of redox cofactors including flavins and iron-sulfur clusters. Here we discuss the current understanding of bifurcating enzymes and the mechanistic features required to reversibly partition multiple electrons from a single redox site into exergonic and endergonic electron transfer paths.

  13. Enhanced biological phosphorus removal. Carbon sources, nitrate as electron acceptor, and characterization of the sludge community

    Energy Technology Data Exchange (ETDEWEB)

    Christensson, M.

    1997-10-01

    Enhanced biological phosphorus removal (EBPR) was studied in laboratory scale experiments as well as in a full scale EBPR process. The studies were focused on carbon source transformations, the use of nitrate as an electron acceptor and characterisation of the microflora. A continuous anaerobic/aerobic laboratory system was operated on synthetic wastewater with acetate as sole carbon source. An efficient EBPR was obtained and mass balances over the anaerobic reactor showed a production of 1.45 g poly-{beta}-hydroxyalcanoic acids (PHA), measured as chemical oxygen demand (COD), per g of acetic acid (as COD) taken up. Furthermore, phosphate was released in the anaerobic reactor in a ratio of 0.33 g phosphorus (P) per g PHA (COD) formed and 0.64 g of glycogen (COD) was consumed per g of acetic acid (COD) taken up. Microscopic investigations revealed a high amount of polyphosphate accumulating organisms (PAO) in the sludge. Isolation and characterisation of bacteria indicated Acinetobacter spp. to be abundant in the sludge, while sequencing of clones obtained in a 16S rDNA clone library showed a large part of the bacteria to be related to the high mole % G+C Gram-positive bacteria and only a minor fraction to be related to the gamma-subclass of proteobacteria to which Acinetobacter belongs. Operation of a similar anaerobic/aerobic laboratory system with ethanol as sole carbon source showed that a high EBPR can be achieved with this compound as carbon source. However, a prolonged detention time in the anaerobic reactor was required. PHA were produced in the anaerobic reactor in an amount of 1.24 g COD per g of soluble DOC taken up, phosphate was released in an amount of 0.4-0.6 g P per g PHA (COD) produced and 0.46 g glycogen (COD) was consumed per g of soluble COD taken up. Studies of the EBPR in the UCT process at the sewage treatment plant in Helsingborg, Sweden, showed the amount of volatile fatty acids (VFA) available to the PAO in the anaerobic stage to be

  14. Electronic Biosensing with Functionalized rGO FETs

    Directory of Open Access Journals (Sweden)

    Ciril Reiner-Rozman

    2016-04-01

    Full Text Available In the following we give a short summary of examples for biosensor concepts in areas in which reduced graphene oxide-based electronic devices can be developed into new classes of biosensors, which are highly sensitive, label-free, disposable and cheap, with electronic signals that are easy to analyze and interpret, suitable for multiplexed operation and for remote control, compatible with NFC technology, etc., and in many cases a clear and promising alternative to optical sensors. The presented areas concern sensing challenges in medical diagnostics with an example for detecting general antibody-antigen interactions, for the monitoring of toxins and pathogens in food and feed stuff, exemplified by the detection of aflatoxins, and the area of smell sensors, which are certainly the most exciting development as there are very few existing examples in which the typically small and hydrophobic odorant molecules can be detected by other means. The example given here concerns the recording of a honey flavor (and a cancer marker for neuroblastoma, homovanillic acid, by the odorant binding protein OBP 14 from the honey bee, immobilized on the reduced graphene oxide gate of an FET sensor.

  15. Determination of many-electron basis functions for a quantum Hall ground state using Schur polynomials

    Science.gov (United States)

    Mandal, Sudhansu S.; Mukherjee, Sutirtha; Ray, Koushik

    2018-03-01

    A method for determining the ground state of a planar interacting many-electron system in a magnetic field perpendicular to the plane is described. The ground state wave-function is expressed as a linear combination of a set of basis functions. Given only the flux and the number of electrons describing an incompressible state, we use the combinatorics of partitioning the flux among the electrons to derive the basis wave-functions as linear combinations of Schur polynomials. The procedure ensures that the basis wave-functions form representations of the angular momentum algebra. We exemplify the method by deriving the basis functions for the 5/2 quantum Hall state with a few particles. We find that one of the basis functions is precisely the Moore-Read Pfaffian wave function.

  16. Slow electron distribution function in a cylindrical hollow-cathode discharge

    International Nuclear Information System (INIS)

    Arslanbekov, R.R.; Kudryavtsev, A.A.; Movchan, I.A.

    1992-01-01

    The formation of the electron distribution function in a cylindrical hollow cathode at energies up to the threshold for inelastic processes is examined. It is shown that the distribution function is a Maxwellian distribution in the thermal region plus a step determined by the sources of fast electrons. The distribution develops nonlocally, and the distinctive feature of this regime is the absence of a radial dependence when scaled to the total energy. The derived formulas can be used to calculate the electron distribution function simply from a given current and geometrical dimensions of the discharge. 14 refs., 3 figs

  17. Digital technique for inverse function obtaining and electron emission power distribution calculation

    International Nuclear Information System (INIS)

    Sorokin, O.M.

    1984-01-01

    The way to obtain energy distribution of electron emission using the method of the inverse function, in which two amplitude pulse analyzers are Used, has been improved. One of them, the flowsheet of which is somewhat changed, is used to obtain the inverse function in the regime of tracing search of channel address of the set ordinate of voltammetric characteristics distribution, and second one - to obtain amplitude distribution of standard pulses, discriminated according to the law of inverse voltammetric characteristics. The distribution function as to the energy which is obtained as a result can have a statistical error of 1-2% at emission currents up to 10-100 electron/s

  18. A parity function for studying the molecular electronic structure

    DEFF Research Database (Denmark)

    Schmider, Hartmut

    1996-01-01

    Sections through the molecular Wigner function with zero momentum variable are shown to provide important information about the off-diagonal regions of the spinless one-particle reduced density matrix. Since these regions are characteristic for the bonding situation in molecules, the sections...... are qualitatively even more affected by the presence of chemical bonds than a complementary projection, the reciprocal form factor. In this paper we discuss, on the grounds of a variety of examples, how this rather simple function may aid the understanding of the chemical bond on a one-particle level. (C) 1996...

  19. Electronic energy distribution function at high electron swarm energies in neon

    International Nuclear Information System (INIS)

    Brown, K.L.; Fletcher, J.

    1995-01-01

    Electron swarms moving through a gas under the influence of an applied electric field have been extensively investigated. Swarms at high energies, as measured by the ratio of the applied field to the gas number density, E/N, which are predominant in many applications have, in general, been neglected. Discharges at E/N in the range 300 0 < 133 Pa using a differentially pumped vacuum system in which the swarm electrons are extracted from the discharge and energy analysed in both a parallel plate retarded potential analyser and a cylindrical electrostatic analyser. Both pre-breakdown and post-breakdown discharges have been studied. Initial results indicate that as the discharge traverses breakdown no sudden change in the nature of the discharge occurs and that the discharge can be described by both a Monte Carlo simulation and by a Boltzmann treatment given by Phelps et al. (1987). 18 refs., 8 figs

  20. Titanium coated with functionalized carbon nanotubes — A promising novel material for biomedical application as an implantable orthopaedic electronic device

    Energy Technology Data Exchange (ETDEWEB)

    Przekora, Agata, E-mail: agata.przekora@umlub.pl [Department of Biochemistry and Biotechnology, Medical University of Lublin, Faculty of Pharmacy with Medical Analytics Division, Chodzki 1, 20-093 Lublin (Poland); Benko, Aleksandra; Nocun, Marek; Wyrwa, Jan; Blazewicz, Marta [Faculty of Materials Science and Ceramics, AGH-Univ. of Science and Technology, A. Mickiewicz 30 Ave., 30-059 Cracow (Poland); Ginalska, Grazyna [Department of Biochemistry and Biotechnology, Medical University of Lublin, Faculty of Pharmacy with Medical Analytics Division, Chodzki 1, 20-093 Lublin (Poland)

    2014-12-01

    The aim of the study was to fabricate titanium (Ti) material coated with functionalized carbon nanotubes (f-CNTs) that would have potential medical application in orthopaedics as an implantable electronic device. The novel biomedical material (Ti-CNTs-H{sub 2}O) would possess specific set of properties, such as: electrical conductivity, non-toxicity, and ability to inhibit connective tissue cell growth and proliferation protecting the Ti-CNTs-H{sub 2}O surface against covering by cells. The novel material was obtained via an electrophoretic deposition of CNTs-H{sub 2}O on the Ti surface. Then, physicochemical, electrical, and biological properties were evaluated. Electrical property evaluation revealed that a Ti-CNTs-H{sub 2}O material is highly conductive and X-ray photoelectron spectroscopy analysis demonstrated that there are mainly COOH groups on the Ti-CNTs-H{sub 2}O surface that are found to inhibit cell growth. Biological properties were assessed using normal human foetal osteoblast cell line (hFOB 1.19). Conducted cytotoxicity tests and live/dead fluorescent staining demonstrated that Ti-CNTs-H{sub 2}O does not exert toxic effect on hFOB cells. Moreover, fluorescence laser scanning microscope observation demonstrated that Ti-CNTs-H{sub 2}O surface retards to a great extent cell proliferation. The study resulted in successful fabrication of highly conductive, non-toxic Ti-CNTs-H{sub 2}O material that possesses ability to inhibit osteoblast proliferation and thus has a great potential as an orthopaedic implantable electronic device. - Highlights: • Functionalized carbon nanotubes were electrophoretically deposited on Ti surface. • Physicochemical, electrical, and biological properties were evaluated. • Ti-CNTs-H{sub 2}O is highly conductive and there are mainly COOH groups on its surface. • Novel material is non-toxic and retards to a great extent osteoblast proliferation. • Ti-CNTs-H{sub 2}O has a promising potential as implantable orthopaedic

  1. The electron-propagator approach to conceptual density-functional ...

    Indian Academy of Sciences (India)

    Unknown

    (4), the external potential is fixed by identity of the molecular system and is thus treated as a parameter and not a variable. Equation (4) is an exact expres- sion for the ...... the virtual spin-orbitals, and {χp} is a set of ortho- normal basis functions. The expression for the third- order correction is more complicated. Because the.

  2. Density functional study of : Electronic and optical properties

    Indian Academy of Sciences (India)

    K C Bhamu

    2017-06-20

    Jun 20, 2017 ... the refractive index in zero frequency limits is 2.42. The absorption coefficient predicts the applicability of AgScO2 in solar cells and flat panel liquid crystal display as a transparent top window layer. Keywords. Density functional theory; band structure; optical properties. PACS Nos 71.15.Mb; 71.20.−b; 78.20.

  3. Heme isomers substantially affect heme's electronic structure and function

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2017-01-01

    Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as due...

  4. Develop Infrared Structural Biology for Probing Structural Dynamics of Protein Functions

    Science.gov (United States)

    Xie, Aihua; Kang, Zhouyang; Causey, Oliver; Liu, Charle

    2015-03-01

    Protein functions are carried out through a series of structural transitions. Lack of knowledge on functionally important structural motions of proteins impedes our understanding of protein functions. Infrared structural biology is an emerging technology with powerful applications for protein structural dynamics. One key element of infrared structural biology is the development of vibrational structural marker (VSM) database library that translates infrared spectroscopic signals into specific structural information. We report the development of VSM for probing the type, geometry and strength of hydrogen bonding interactions of buried COO- side chains of Asp and Glu in proteins. Quantum theory based first principle computational studies combined with bioinformatic hydrogen bond analysis are employed in this study. We will discuss the applications of VSM in mechanistic studies of protein functions. Infrared structural biology is expected to emerge as a powerful technique for elucidating the functional mechanism of a broad range of proteins, including water soluble and membrane proteins. This work is supported by OCAST HR10-078 and NSF DBI1338097.

  5. Holography and coherent diffraction with low-energy electrons: A route towards structural biology at the single molecule level

    Energy Technology Data Exchange (ETDEWEB)

    Latychevskaia, Tatiana; Longchamp, Jean-Nicolas; Escher, Conrad; Fink, Hans-Werner, E-mail: hwfink@physik.uzh.ch

    2015-12-15

    The current state of the art in structural biology is led by NMR, X-ray crystallography and TEM investigations. These powerful tools however all rely on averaging over a large ensemble of molecules. Here, we present an alternative concept aiming at structural analysis at the single molecule level. We show that by combining electron holography and coherent diffraction imaging estimations concerning the phase of the scattered wave become needless as the phase information is extracted from the data directly and unambiguously. Performed with low-energy electrons the resolution of this lens-less microscope is just limited by the De Broglie wavelength of the electron wave and the numerical aperture, given by detector geometry. In imaging freestanding graphene, a resolution of 2 Å has been achieved revealing the 660.000 unit cells of the graphene sheet from a single data set. Once applied to individual biomolecules the method shall ultimately allow for non-destructive imaging and imports the potential to distinguish between different conformations of proteins with atomic resolution. - Highlights: • Structural biology of single proteins. • Radiation damage-free imaging of individual biomolecules. • Holography. • Low-energy electrons. • Coherent diffraction and phase retrieval.

  6. Application of Advanced Functional Maps to the Radiation Treatment Plan for Biological Clinical Target Volumes

    International Nuclear Information System (INIS)

    Park, Ji Yeon; Jung, Won Gyun; Suh, Tae Suk; Lee, Jeong Woo; Ahn, Kook Jin

    2010-01-01

    Anatomical images including computerized tomography (CT) and T1-weighted magnetic resonance (T1-MR) images have been generally used to determine target volumes in radiation treatment plan (RTP). As only conventional images were referenced, tumors have tendency not to be enhanced by administrating agents depending on the tumor grade and patients. Recent advanced MR images, however, could guide physiologically and pathologically significant tumor characteristics. Furthermore, if the multi-functional images are employed, errors from using only one type of image will be complemented and distinct biological parameters can be applied as histological activity index. In this study, biological clinical target volumes (bCTVs) considered vascularity and cellularity can be determined based on multifunctional parametric maps using the in-house software for image registration and analysis. Using the developed software, rCBV and ADC maps were analyzed and bCTVs can be resolved considering vascularity and cellularity. In result, the bCTVs are exported on conventional images for biological RTP using image registration. Based on the multi-functional parametric maps of overlapped tumor regions, malignant sub-volumes can be determined. Multi-functional parametric maps would contribute to the detection of physiological and pathological tumor characteristics which are not be found in conventional images. They would reflect individual tumor biological characteristics to RTP for local tumor control.

  7. The energy distribution function of excess electrons trapped in the pulse irradiated low density polyethylene (LDPE)

    International Nuclear Information System (INIS)

    Wysocki, S.; Mazurek, L.; Karolczak, S.; Kroh, J.

    1995-01-01

    Distribution function D (E) of electrons trapped in irradiated LDPE was calculated on the basis of time resolved absorption spectra recorded at temperatures of 20-250 K. Variation of absorption spectra with time and temperature were observed and discussed in terms of simultaneous decay and relocation of electrons from shallow to deeper traps. Results obtained imply domination of trap limited transport for shallowly trapped electrons. For deeper traps, hopping mechanism is prevailing. (author)

  8. Calculating the SnS(010) surface electronic structure using the green function method

    Science.gov (United States)

    Jahangirli, Z. A.

    2011-08-01

    The electronic structure of the (010) surface in a layered SnS semiconductor terminating with Sn and S atomic planes is calculated by the Green function method. The electronic structure of a perfect crystal is calculated according to the linear combination of atomic orbitals (LCAO) using Slater s-, p-, and d-orbitals. Defect-induced changes in the density of states and the origin and orbital composition of electronic states in the band gap are discussed.

  9. Transmission microscopy of unmodified biological materials: comparative radiation dosages with electrons and ultrasoft X-ray photons

    International Nuclear Information System (INIS)

    Sayre, D.; Feder, R.; Spiller, E.; Kirz, J.; Kim, D.M.

    1977-01-01

    The minimum radiation dosage in a specimen consistent with transmission microscopy at resolution d and specimen thickness t is calculated for model specimens resembling biological materials in their natural state. The calculations cover 10 4 -10 7 eV electrons and 1.3-90 A photons in a number of microscopy modes. The results indicate that over a considerable part of the (t,d)-plane transmission microscopy on such specimens can be carried out at lower dosage with photons than with electrons. Estimates of the maximum resolutions obtainable with electrons and photons, consistent with structural survival of the specimen, are obtained, as are data on optimal operating conditions for microscopy with the two particles

  10. Cryo-electron microscopy and X-ray crystallography: complementary approaches to structural biology and drug discovery.

    Science.gov (United States)

    Vénien-Bryan, Catherine; Li, Zhuolun; Vuillard, Laurent; Boutin, Jean Albert

    2017-04-01

    The invention of the electron microscope has greatly enhanced the view scientists have of small structural details. Since its implementation, this technology has undergone considerable evolution and the resolution that can be obtained for biological objects has been extended. In addition, the latest generation of cryo-electron microscopes equipped with direct electron detectors and software for the automated collection of images, in combination with the use of advanced image-analysis methods, has dramatically improved the performance of this technique in terms of resolution. While calculating a sub-10 Å resolution structure was an accomplishment less than a decade ago, it is now common to generate structures at sub-5 Å resolution and even better. It is becoming possible to relatively quickly obtain high-resolution structures of biological molecules, in particular large ones (>500 kDa) which, in some cases, have resisted more conventional methods such as X-ray crystallography or nuclear magnetic resonance (NMR). Such newly resolved structures may, for the first time, shed light on the precise mechanisms that are essential for cellular physiological processes. The ability to attain atomic resolution may support the development of new drugs that target these proteins, allowing medicinal chemists to understand the intimacy of the relationship between their molecules and targets. In addition, recent developments in cryo-electron microscopy combined with image analysis can provide unique information on the conformational variability of macromolecular complexes. Conformational flexibility of macromolecular complexes can be investigated using cryo-electron microscopy and multiconformation reconstruction methods. However, the biochemical quality of the sample remains the major bottleneck to routine cryo-electron microscopy-based determination of structures at very high resolution.

  11. ELECTRONIC EQUIPMENT TO MONITORIZE SOME BIOLOGICAL PROCESS OF ECONOMIC IMPORTANCE IN HONEYBEE COLONY AND ITS ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    A. SICEANU

    2007-10-01

    Full Text Available The electronic hive is the result of the scientific researches carried out between2003-2006 by a research project funded by MEdC through the National ProgramRELANSIN, being accomplished by Institute for Beekeeping Research andDevelopment –Bucharest in cooperation with the Polytechnics University fromBucharest –The Center for Electronic Technology and Interconnection Techniquesand the Radio Consult CompanyTo achieve the great complexity of the electronic model adapted to the hive –the“smart” hive, it was necessary to establish the all electronic details which to makepossible to monitorize some very important information from the bee colony andits environment with the help of the honeybees and which to eliminate the errorsthat may occur in the information collection process.Thus, the project aimed to conceive the electronic system in order to collectinformation from inside the hive and from environment too, to storage andtransmit it to a data basis by GSM network in order to be analyzed and processedby users.By this complex electronic system, composed by electronic equipment and thehoney bee colony, which is dynamic and strong related with natural evolution ofvegetation correlated with the climate factors, is possible to identify instantaneousor periodically a large palette of aggression factors as well naturals (acids rains,extreme temperatures, calamities as anthropic factors –accidental chemical orbiologic pollution. The obtained data, electronically quantified and taken out intothe data basis, could offer accurate information about the moisturized areas atdifferent time intervals.

  12. Electron-nuclear coupling in time-dependent multicomponent density functional theory

    NARCIS (Netherlands)

    Butriy, Olena O.

    2008-01-01

    In this thesis we developed the time-dependent version of the multicomponent density functional approach to treat time-dependent electron-nuclear systems. The method enables to describe the electron-nuclear coupling fully quantum mechanically. No Born-Oppenheimer approximation is involved in the

  13. Anisotropy of electron work function and reticular compacting of friable faces of metallic crystals

    International Nuclear Information System (INIS)

    Vladimirov, A.F.

    1999-01-01

    The review and statistical estimate of experimental data on work functions for BCC-, FCC- and HCP - metals (W, Mo, Ta, Nb, Cr, V, Ni, Y) as well as the earlier developed quantum-mechanical statistical model of double electrical layer formation at metal surface and the calculation of an electron work function dipole constituent serve as a basis for the development of a semi-empirical theory of electron work function anisotropy. A coefficient of reticular compacting of friable crystal faces is introduced and statistically estimated. A coefficient of crystal emission anisotropy is also introduced and estimated both theoretically and empirically. The theory permits calculating work functions for all crystal faces and a volumetric constituent of the work function from the measured value of electron work function for a single face [ru

  14. A biologically inspired psychometric function for accuracy of visual identification as a function of exposure duration

    DEFF Research Database (Denmark)

    Petersen, Anders; Andersen, Tobias

    in modelling human performance in whole and partial report tasks in which multiple simultaneously presented letters are to be reported (Shibuya & Bundesen, 1988). Therefore, we investigated visual letter identification as a function of exposure duration. On each trial, a single randomly chosen letter (A...... rising from zero, then peaking, and finally decaying to a somewhat sustained plateau, mimicking closely observed instantaneous firing rates of monkey visual cortex neurons. The new psychometric function fits well to experimental data in both the present study and in a previous study of single...... into Bundesen’s Theory of Visual Attention (Bundesen, 1990), the new psychometric function enables closer fits to data from a previous whole and partial report experiment....

  15. Electron Transfer in Chemistry and Biology – The Primary Events in ...

    Indian Academy of Sciences (India)

    molecular unit to another. This reaction, accompanied by proton and hydrogen atom trans- fers, occurs in a cascade in many biological processes, includ- ing photosynthesis. The key chemical steps involved in photo- synthesis and the many ...

  16. The Structural Characterisation of Risk in the R&D Process of Functional Raw Materials for Electronic Devices

    OpenAIRE

    Chikamori, Yoji; Nasu, Seigo

    2017-01-01

    The electronic materials and electronics device industries remain important to Japan in spite of the general decline of the Japanese electronics industry. There is risk and uncertainty when developing functional materials in the electronics industry. However, studies examining the uncertainty and risk variables in the development of functional materials are scarce. This study examines incremental research and development (R&D) developed for raw functional materials for electronics. Our analys...

  17. Dynamical 'in situ' observation of biological samples using variable pressure scanning electron microscope

    International Nuclear Information System (INIS)

    Nedela, V

    2008-01-01

    Possibilities of 'in-situ' observation of non-conductive biological samples free of charging artefacts in dynamically changed surrounding conditions are the topic of this work. The observed biological sample, the tongue of a rat, was placed on a cooled Peltier stage. We studied the visibility of topographical structure depending on transition between liquid and gas state of water in the specimen chamber of VP SEM.

  18. Electron work function and composition of gallium-indium alloy surface

    International Nuclear Information System (INIS)

    Egorova, E.M.

    1979-01-01

    The dependences of electron work functions on the composition for gallium-indium alloy obtained under different conditions are compared. An attempt is made to estimate a change in the alloy surface composition caused by a change in temperature and in the boundary phase nature. For the case under consideration it has been shown to be reasonable to compare the dependences of the electron work functions not on the alloy volumetric composition but on the composition of its surface

  19. An electron-boson glue function derived from electronic Raman scattering.

    Science.gov (United States)

    Muschler, B; Prestel, W; Schachinger, E; Carbotte, J P; Hackl, R; Ono, Shimpei; Ando, Yoichi

    2010-09-22

    Raman scattering cross sections depend on photon polarization. In the cuprates, nodal and antinodal directions are weighted more strongly in B(2g) and B(1g) symmetries, respectively. On the other hand, in angle-resolved photoemission spectroscopy (ARPES), electronic properties are measured along well-defined directions in momentum space rather than their weighted averages being taken. In contrast, the optical conductivity involves a momentum average over the entire Brillouin zone. Newly measured Raman response data on high-quality Bi(2)Sr(2)CaCu(2)O(8 + δ) single crystals up to high energies have been inverted using a modified maximum entropy inversion technique to extract from B(1g) and B(2g) Raman data corresponding electron-boson spectral densities (glue), and these are compared to the results obtained with known ARPES and optical inversions. We find that the B(2g) spectrum agrees qualitatively with nodal direction ARPES while the B(1g) results look more like the optical spectrum. A large peak around 30-40 meV in B(1g) and a much less prominent one in B(2g) are taken as support for the importance of (π, π) scattering at this frequency.

  20. Immune function parameters as markers of biological age and predictors of longevity

    Science.gov (United States)

    de Toda, Irene Martínez; Maté, Ianire; Vida, Carmen; Cruces, Julia; De la Fuente, Mónica

    2016-01-01

    Chronological age is not a good indicator of how each individual ages and thus how to maintain good health. Due to the long lifespan in humans and the consequent difficulty of carrying out longitudinal studies, finding valid biomarkers of the biological age has been a challenge both for research and clinical studies. The aim was to identify and validate several immune cell function parameters as markers of biological age. Adult, mature, elderly and long-lived human volunteers were used. The chemotaxis, phagocytosis, natural killer activity and lymphoproliferation in neutrophils and lymphocytes of peripheral blood were analyzed. The same functions were measured in peritoneal immune cells from mice, at the corresponding ages (adult, mature, old and long lived) in a longitudinal study. The results showed that the evolution of these functions was similar in humans and mice, with a decrease in old subjects. However, the long-lived individuals maintained values similar to those in adults. In addition, the values of these functions in adult prematurely aging mice were similar to those in chronologically old animals, and they died before their non-prematurely aging mice counterparts. Thus, the parameters studied are good markers of the rate of aging, allowing the determination of biological age. PMID:27899767

  1. Electron polarization function and plasmons in metallic armchair graphene nanoribbons

    DEFF Research Database (Denmark)

    Shylau, A. A.; Badalyan, S. M.; Peeters, F. M.

    2015-01-01

    Plasmon excitations in metallic armchair graphene nanoribbons are investigated using the random phase approximation. An exact analytical expression for the polarization function of Dirac fermions is obtained, valid for arbitrary temperature and doping. We find that at finite temperatures, due...... mode whose energy dispersion is determined by the graphene's fine structure constant. In the case of two Coulomb-coupled nanoribbons, this plasmon splits into in-phase and out-of-phase plasmon modes with splitting energy determined by the inter-ribbon spacing....

  2. Physical characterization of functionalized spider silk: electronic and sensing properties

    Directory of Open Access Journals (Sweden)

    Eden Steven, Jin Gyu Park, Anant Paravastu, Elsa Branco Lopes, James S Brooks, Ongi Englander, Theo Siegrist, Papatya Kaner and Rufina G Alamo

    2011-01-01

    Full Text Available This work explores functional, fundamental and applied aspects of naturally harvested spider silk fibers. Natural silk is a protein polymer where different amino acids control the physical properties of fibroin bundles, producing, for example, combinations of β-sheet (crystalline and amorphous (helical structural regions. This complexity presents opportunities for functional modification to obtain new types of material properties. Electrical conductivity is the starting point of this investigation, where the insulating nature of neat silk under ambient conditions is described first. Modification of the conductivity by humidity, exposure to polar solvents, iodine doping, pyrolization and deposition of a thin metallic film are explored next. The conductivity increases exponentially with relative humidity and/or solvent, whereas only an incremental increase occurs after iodine doping. In contrast, iodine doping, optimal at 70 °C, has a strong effect on the morphology of silk bundles (increasing their size, on the process of pyrolization (suppressing mass loss rates and on the resulting carbonized fiber structure (that becomes more robust against bending and strain. The effects of iodine doping and other functional parameters (vacuum and thin film coating motivated an investigation with magic angle spinning nuclear magnetic resonance (MAS-NMR to monitor doping-induced changes in the amino acid-protein backbone signature. MAS-NMR revealed a moderate effect of iodine on the helical and β-sheet structures, and a lesser effect of gold sputtering. The effects of iodine doping were further probed by Fourier transform infrared (FTIR spectroscopy, revealing a partial transformation of β-sheet-to-amorphous constituency. A model is proposed, based on the findings from the MAS-NMR and FTIR, which involves iodine-induced changes in the silk fibroin bundle environment that can account for the altered physical properties. Finally, proof

  3. The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

    Directory of Open Access Journals (Sweden)

    Carmel McDougall

    Full Text Available In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the

  4. TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions.

    Science.gov (United States)

    Martínez-Reyes, Inmaculada; Diebold, Lauren P; Kong, Hyewon; Schieber, Michael; Huang, He; Hensley, Christopher T; Mehta, Manan M; Wang, Tianyuan; Santos, Janine H; Woychik, Richard; Dufour, Eric; Spelbrink, Johannes N; Weinberg, Samuel E; Zhao, Yingming; DeBerardinis, Ralph J; Chandel, Navdeep S

    2016-01-21

    Mitochondrial metabolism is necessary for the maintenance of oxidative TCA cycle function and mitochondrial membrane potential. Previous attempts to decipher whether mitochondria are necessary for biological outcomes have been hampered by genetic and pharmacologic methods that simultaneously disrupt multiple functions linked to mitochondrial metabolism. Here, we report that inducible depletion of mitochondrial DNA (ρ(ο) cells) diminished respiration, oxidative TCA cycle function, and the mitochondrial membrane potential, resulting in diminished cell proliferation, hypoxic activation of HIF-1, and specific histone acetylation marks. Genetic reconstitution only of the oxidative TCA cycle function specifically in these inducible ρ(ο) cells restored metabolites, resulting in re-establishment of histone acetylation. In contrast, genetic reconstitution of the mitochondrial membrane potential restored ROS, which were necessary for hypoxic activation of HIF-1 and cell proliferation. These results indicate that distinct mitochondrial functions associated with respiration are necessary for cell proliferation, epigenetics, and HIF-1 activation. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. A Multi-Functional Power Electronic Converter in Distributed Generation Power Systems

    DEFF Research Database (Denmark)

    Chen, Zhe; Blaabjerg, Frede; Pedersen, John Kim

    2005-01-01

    This paper presents a power electronic converter which is used as an interface for a distributed generation unit/energy storage device, and also functioned as an active power compensator in a hybrid compensation system. The operation and control of the converter have been described. An example...... of the converter interfacing a wind power generation unit is also given. The power electronic interface performs the optimal operation in the wind turbine system to extract the maximum wind power, while it also plays a key role in a hybrid compensation system that consists of the active power electronic converter...... of the system where the power electronic converter is connected....

  6. The electronic fine structure of 4-nitrophenyl functionalized single-walled carbon nanotubes

    International Nuclear Information System (INIS)

    Chakraborty, Amit K; Coleman, Karl S; Dhanak, Vinod R

    2009-01-01

    Controlling the electronic structure of carbon nanotubes (CNTs) is of great importance to various CNT based applications. Herein the electronic fine structure of single-walled carbon nanotube films modified with 4-nitrophenyl groups, produced following reaction with 4-nitrobenzenediazonium tetrafluoroborate, was investigated for the first time. Various techniques such as x-ray and ultra-violet photoelectron spectroscopy, and near edge x-ray absorption fine structure studies were used to explore the electronic structure, and the results were compared with the measured electrical resistances. A reduction in number of the π electronic states in the valence band consistent with the increased resistance of the functionalized nanotube films was observed.

  7. Expansion of a plasma into vacuum with a bi-Maxwellian electron distribution function

    Directory of Open Access Journals (Sweden)

    Diaw A.

    2013-11-01

    Full Text Available A comprehensive theory is developped to describe the expansion of a plasma into a vacuum with a two-temperature electron distribution function. The characteristics of the rarefaction shock which occurs in the plasma when the hot- to the cold-electron temperature ratio is larger than 9.9 are investigated with a semi-infinite plasma. Furthermore by using a finite plasma foil, a possible heating of the cold electrons population is evidenced, for a sufficiently large hot- to the cold-electron density ratio.

  8. Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective.

    Science.gov (United States)

    Davidsen, Peter K; Turan, Nil; Egginton, Stuart; Falciani, Francesco

    2016-02-01

    The overall aim of physiological research is to understand how living systems function in an integrative manner. Consequently, the discipline of physiology has since its infancy attempted to link multiple levels of biological organization. Increasingly this has involved mathematical and computational approaches, typically to model a small number of components spanning several levels of biological organization. With the advent of "omics" technologies, which can characterize the molecular state of a cell or tissue (intended as the level of expression and/or activity of its molecular components), the number of molecular components we can quantify has increased exponentially. Paradoxically, the unprecedented amount of experimental data has made it more difficult to derive conceptual models underlying essential mechanisms regulating mammalian physiology. We present an overview of state-of-the-art methods currently used to identifying biological networks underlying genomewide responses. These are based on a data-driven approach that relies on advanced computational methods designed to "learn" biology from observational data. In this review, we illustrate an application of these computational methodologies using a case study integrating an in vivo model representing the transcriptional state of hypoxic skeletal muscle with a clinical study representing muscle wasting in chronic obstructive pulmonary disease patients. The broader application of these approaches to modeling multiple levels of biological data in the context of modern physiology is discussed. Copyright © 2016 the American Physiological Society.

  9. Teleology then and now: the question of Kant's relevance for contemporary controversies over function in biology.

    Science.gov (United States)

    Zammito, John

    2006-12-01

    'Naturalism' is the aspiration of contemporary philosophy of biology, and Kant simply cannot be refashioned into a naturalist. Instead, epistemological 'deflation' was the decisive feature of Kant's treatment of the 'biomedical' science in his day, so it is not surprising that this might attract some philosophers of science to him today. A certain sense of impasse in the contemporary 'function talk' seems to motivate renewed interest in Kant. Kant--drawing on his eighteenth-century predecessors-provided a discerning and powerful characterization of what biologists had to explain in organic form. His difference from the rest is that he opined that it was impossible to explain it. Its 'inscrutability' was intrinsic. The third Critique essentially proposed the reduction of biology to a kind of pre-scientific descriptivism, doomed never to attain authentic scientificity, to have its 'Newton of the blade of grass'. By contrast, for Locke, and a fortiori for Buffon and his followers, 'intrinsic purposiveness' was a fact of the matter about concrete biological phenomena; the features of internal self-regulation were hypotheses arising out of actual research practice. The difference comes most vividly to light once we recognize Kant's distinction of the concept of organism from the concept of life. If biology must conceptualize self-organization as actual in the world, Kant's regulative/constitutive distinction is pointless in practice and the (naturalist) philosophy of biology has urgent work to undertake for which Kant turns out not to be very helpful.

  10. Functional nanomaterials and devices for electronics, sensors and energy harvesting

    CERN Document Server

    Balestra, Francis; Kilchytska, Valeriya; Flandre, Denis

    2014-01-01

    This book contains reviews of recent experimental and theoretical results related to nanomaterials. It focuses on novel functional materials and nanostructures in combination with silicon on insulator (SOI) devices, as well as on the physics of new devices and sensors, nanostructured materials and nano scaled device characterization. Special attention is paid to fabrication and properties of modern low-power, high-performance, miniaturized, portable sensors in a wide range of applications such as telecommunications, radiation control, biomedical instrumentation and chemical analysis. In this book, new approaches exploiting nanotechnologies (such as UTBB FD SOI, Fin FETs, nanowires, graphene or carbon nanotubes on dielectric) to pave a way between “More Moore” and “More than Moore” are considered, in order to create different kinds of sensors and devices which will consume less electrical power, be more portable and totally compatible with modern microelectronics products.

  11. Functional outcome in subretinal electronic implants depends on foveal eccentricity.

    Science.gov (United States)

    Stingl, Katarina; Bartz-Schmidt, Karl-Ulrich; Gekeler, Florian; Kusnyerik, Akos; Sachs, Helmut; Zrenner, Eberhart

    2013-11-19

    An active microelectronic subretinal implant, developed to replace the photoreceptive function in hereditary degenerations of the outer retina, has been applied in a pilot and clinical study in patients with end-stage retinal degeneration. The study population comprised 20 blind patients, all of whom lost vision as result of a hereditary retinal disease. An active visual implant was placed surgically within the subretinal space of each patient: subfoveal placement in eight patients (group 1) and parafoveal placement in 12 (group 2). Standardized low-vision tests, including light perception, light localization, movement detection, grating acuity, and visual acuity by Landolt C-rings, were used under masked, randomized implant-OFF and implant-ON conditions. For the chip-mediated vision functional results of both subject groups were compared. Three of 20 patients were excluded from analysis because of surgical or technical implant issues. Among patients with nonfoveal placement of the implant, 80% could perceive light, 10% recognized location, and 10% correctly distinguished stripe patterns up to a resolution of 0.33 cycles/degree. No nonfoveal placement patient passed the motion or Landolt C-ring tests. When the implant was placed subfoveally, 100% of patients could perceive light and determine light localization, 75% could resolve motion up to 35°/s, 88% correctly distinguished stripe patterns up to a resolution of 3.3 cycles/degree, and 38% passed a Landolt C-ring test with a decimal visual acuity of up to 20/546 (logMAR 1.43). Subfoveal placement of active subretinal visual implants allows superior measurable outcomes compared to para- or nonfoveal placement locations. (ClinicalTrials.gov numbers, NCT01024803, NCT00515814.).

  12. Electronic Nose Functionality for Breath Gas Analysis during Parabolic Flight

    Science.gov (United States)

    Dolch, Michael E.; Hummel, Thomas; Fetter, Viktor; Helwig, Andreas; Lenic, Joachim; Moukhamedieva, Lana; Tsarkow, Dimitrij; Chouker, Alexander; Schelling, Gustav

    2017-06-01

    The presence of humans in space represents a constant threat for their health and safety. Environmental factors such as living in a closed confinement, as well as exposure to microgravity and radiation, are associated with significant changes in bone metabolism, muscular atrophy, and altered immune response, which has impacts on human performance and possibly results in severe illness. Thus, maintaining and monitoring of crew health status has the highest priority to ensure whole mission success. With manned deep space missions to moon or mars appearing at the horizon where short-term repatriation back to earth is impossible the availability of appropriate diagnostic platforms for crew health status is urgently needed. In response to this need, the present experiment evaluated the functionality and practicability of a metal oxide based sensor system (eNose) together with a newly developed breath gas collecting device under the condition of altering acceleration. Parabolic flights were performed with an Airbus A300 ZeroG at Bordeaux, France. Ambient air and exhaled breath of five healthy volunteers was analyzed during steady state flight and parabolic flight maneuvres. All volunteers completed the study, the breath gas collecting device valves worked appropriately, and breathing through the collecting device was easy and did not induce discomfort. During breath gas measurements, significant changes in metal oxide sensors, mainly sensitive to aromatic and sulphur containing compounds, were observed with alternating conditions of acceleration. Similarly, metal oxide sensors showed significant changes in all sensors during ambient air measurements. The eNose as well as the newly developed breath gas collecting device, showed appropriate functionality and practicability during alternating conditions of acceleration which is a prerequisite for the intended use of the eNose aboard the International Space Station (ISS) for breath gas analysis and crew health status

  13. Three-dimensional electron microscopy of macromolecular assemblies: visualization of biological molecules in their native state

    National Research Council Canada - National Science Library

    Frank, J

    2006-01-01

    ... Clusters 2.8 Support Grids 33 33 3 Principle of Image Formation in the Transmission Electron Microscope 34 3.1 Introduction 34 3.2 The Weak-Phase Object Approximation 35 3.3 The Contrast Transfer...

  14. Biological versus chemical leaching of electronic waste for copper and gold recovery

    OpenAIRE

    Isildar , Arda

    2016-01-01

    The well-being of the society depends on a number of metals, including base metals, precious metals and increasingly rare earth elements (REE). The usage of these metals increased in numerous applications, including electrical and electronic equipment (EEE), and their interrupted supply is at stake. There is an increasing interest in the secondary sources of these metals, particularly waste electrical and electronic equipment (WEEE) in order to compensate their potential supply deficit. This ...

  15. Nanomaterials on flexible substrates to explore innovative functions: From energy harvesting to bio-integrated electronics

    International Nuclear Information System (INIS)

    Koo, Ja Hoon; Seo, Jungmok; Lee, Taeyoon

    2012-01-01

    Recent efforts in the semiconductor industry have focused on the realization of electronics with unusual form factors and functions which are not achievable using the current planar Si-based technology. Deposition of high-quality films or nanomaterials on low-temperature elastomeric substrates has been a technical challenge for flexible electronics. However, together with the development of new synthesis routes that enable the formation of robust thin films and nanomaterials on compliant substrates, including the dry transfer printing technique and fabrication of uniform nanogaps/nanowrinkles using the unique stretchable characteristics of elastomeric substrates, flexible electronics has emerged as a promising technology that can enrich our lives in a variety of ways. As examples, potential applications include skin-like smart prostheses, paper-like displays, disposable electronic noses, and hemispherically-shaped electronic eye cameras. Here, we review recent results demonstrating ingenious new functionalities using nanomaterials on flexible substrates, focusing on fabrication techniques, materials, operation mechanisms, and signal outputs.

  16. Alfvénic oscillations of the electron distribution function: Linear theory and experimental measurements

    International Nuclear Information System (INIS)

    Schroeder, J. W. R.; Skiff, F.; Howes, G. G.; Kletzing, C. A.; Carter, T. A.; Dorfman, S.

    2015-01-01

    Wave propagation can be an accurate method for determining material properties. High frequency whistler mode waves (0.7 < ω/|Ω ce | < 1) in an overdense plasma (ω pe > |Ω ce |) are damped primarily by Doppler-shifted electron cyclotron resonance. A kinetic description of whistler mode propagation parallel to the background magnetic field shows that damping is proportional to the parallel electron distribution function. This property enables an experimental determination of the parallel electron distribution function using a measurement of whistler mode wave absorption. The whistler mode wave absorption diagnostic uses this technique on UCLA’s Large Plasma Device (LaPD) to measure the distribution of high energy electrons (5 − 10v te ) with 0.1% precision. The accuracy is limited by systematic effects that need to be considered carefully. Ongoing research uses this diagnostic to investigate the effect of inertial Alfvén waves on the electron distribution function. Results presented here verify experimentally the linear effects of inertial Alfvén waves on the reduced electron distribution function, a necessary step before nonlinear physics can be tested. Ongoing experiments with the whistler mode wave absorption diagnostic are making progress toward the first direct detection of electrons nonlinearly accelerated by inertial Alfvén waves, a process believed to play an important role in auroral generation

  17. Automated Quantitative Assessment of Proteins' Biological Function in Protein Knowledge Bases

    Directory of Open Access Journals (Sweden)

    Gabriele Mayr

    2008-01-01

    Full Text Available Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

  18. Form and function: Perspectives on structural biology and resources for the future

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, D. (ed.)

    1990-12-01

    The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs.

  19. PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance

    Science.gov (United States)

    van Oers, Johanna M. M.; Roa, Sergio; Werling, Uwe; Liu, Yiyong; Genschel, Jochen; Sellers, Rani S.; Modrich, Paul; Scharff, Matthew D.; Edelmann, Winfried

    2010-01-01

    The DNA mismatch repair protein PMS2 was recently found to encode a novel endonuclease activity. To determine the biological functions of this activity in mammals, we generated endonuclease-deficient Pms2E702K knock-in mice. Pms2EK/EK mice displayed increased genomic mutation rates and a strong cancer predisposition. In addition, class switch recombination, but not somatic hypermutation, was impaired in Pms2EK/EK B cells, indicating a specific role in Ig diversity. In contrast to Pms2−/− mice, Pms2EK/EK male mice were fertile, indicating that this activity is dispensable in spermatogenesis. Therefore, the PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance and tumor suppression. PMID:20624957

  20. Molecular Characteristics and Biological Functions of Surface-Active and Surfactant Proteins.

    Science.gov (United States)

    Sunde, Margaret; Pham, Chi L L; Kwan, Ann H

    2017-06-20

    Many critical biological processes take place at hydrophobic:hydrophilic interfaces, and a wide range of organisms produce surface-active proteins and peptides that reduce surface and interfacial tension and mediate growth and development at these boundaries. Microorganisms produce both small lipid-associated peptides and amphipathic proteins that allow growth across water:air boundaries, attachment to surfaces, predation, and improved bioavailability of hydrophobic substrates. Higher-order organisms produce surface-active proteins with a wide variety of functions, including the provision of protective foam environments for vulnerable reproductive stages, evaporative cooling, and gas exchange across airway membranes. In general, the biological functions supported by these diverse polypeptides require them to have an amphipathic nature, and this is achieved by a diverse range of molecular structures, with some proteins undergoing significant conformational change or intermolecular association to generate the structures that are surface active.

  1. Automated quantitative assessment of proteins' biological function in protein knowledge bases.

    Science.gov (United States)

    Mayr, Gabriele; Lepperdinger, Günter; Lackner, Peter

    2008-01-01

    Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

  2. Form and function: Perspectives on structural biology and resources for the future

    International Nuclear Information System (INIS)

    Vaughan, D.

    1990-12-01

    The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs

  3. Microbialites and microbial communities: Biological diversity, biogeochemical functioning, diagenetic processes, tracers of environmental changes

    OpenAIRE

    Camoin, Gilbert; Gautret, Pascale

    2006-01-01

    Editorial; This special issue is dedicated to microbialites and microbial communities and addresses their biological diversity, their biogeochemical functioning, their roles in diagenetic processes and their environmental significance. It is the logical successor of the special issue that one of us edited after the workshop on “Microbial mediation in carbonate diagenesis” which was held in Chichilianne (France) in 1997 (Camoin, G., Ed., 1999. Microbial mediation in carbonate diagenesis. Sedim...

  4. Functionalized Nanoporous Silica for Removal of Heavy Metals from Biological Systems; Adsorption and Application

    Energy Technology Data Exchange (ETDEWEB)

    Yantasee, Wassana; Rutledge, Ryan D.; Chouyyok, Wilaiwan; Sukwarotwat, Vichaya; Orr, Galya; Warner, Cynthia L.; Warner, Marvin G.; Fryxell, Glen E.; Wiacek, Robert J.; Timchalk, Charles; Addleman, Raymond S.

    2010-10-01

    Functionalized nanoporous silica, often referred to as self-assembled monolayers on mesoporous supports (SAMMS) have previously demonstrated the ability to serve as very effective heavy metal sorbents in a range of aquatic and environmental systems suggesting they may be advantageously utilized for biomedical applications such as chelation therapy. Herein we evaluate surface chemistries for heavy metal capture from biological fluids, various facets of the materials biocompatibility and the suitability of these materials as potential therapeutics. Of the materials tested, thiol-functionalized SAMMS proved most capable of removing selected heavy metals from biological solutions (i.e. blood, urine, etc.) As a result, thiol SAMMS was further analyzed to assess the material’s performance under a number of different biologically relevant conditions (i.e. variable pH and ionic strength) as well to gauge any potentially negative cellular effects resulting from interaction with the sorbent, such as cellular toxicity or possible chelation of essential minerals. Additionally, cellular uptake studies demonstrated no cell membrane permeation by the silica-based materials generally highlighting their ability to remain cellularly inert and thus non-toxic. As a result, it has been determined that organic ligand-functionalized nanoporous silica materials could be a valuable material for detoxification therapeutics and potentially other biomedical applications as needed.

  5. Biological rhythms, higher brain function, and behavior: Gaps, opportunities, and challenges.

    Science.gov (United States)

    Benca, Ruth; Duncan, Marilyn J; Frank, Ellen; McClung, Colleen; Nelson, Randy J; Vicentic, Aleksandra

    2009-12-11

    Increasing evidence suggests that disrupted temporal organization impairs behavior, cognition, and affect; further, disruption of circadian clock genes impairs sleep-wake cycle and social rhythms which may be implicated in mental disorders. Despite this strong evidence, a gap in understanding the neural mechanisms of this interaction obscures whether biological rhythms disturbances are the underlying causes or merely symptoms of mental disorder. Here, we review current understanding, emerging concepts, gaps, and opportunities pertinent to (1) the neurobiology of the interactions between circadian oscillators and the neural circuits subserving higher brain function and behaviors of relevance to mental health, (2) the most promising approaches to determine how biological rhythms regulate brain function and behavior under normal and pathological conditions, (3) the gaps and challenges to advancing knowledge on the link between disrupted circadian rhythms/sleep and psychiatric disorders, and (4) the novel strategies for translation of basic science discoveries in circadian biology to clinical settings to define risk, prevent or delay onset of mental illnesses, design diagnostic tools, and propose new therapeutic strategies. The review is organized around five themes pertinent to (1) the impact of molecular clocks on physiology and behavior, (2) the interactions between circadian signals and cognitive functions, (3) the interface of circadian rhythms with sleep, (4) a clinical perspective on the relationship between circadian rhythm abnormalities and affective disorders, and (5) the pre-clinical models of circadian rhythm abnormalities and mood disorders.

  6. Paul Langerhans: a prilgrim "traveling" from functional histology to marine biology.

    Science.gov (United States)

    Raica, Marius; Cimpean, Anca Maria

    2017-06-01

    The nineteenth century was the time of a real revolution in science and medicine. A lot of seminal discoveries in medicine and biology were done in this time, and many of them were coincident with the introduction of the compound microscope by Hermann van Deijl and the standard histological technique by Paul Ehrlich. The main tissue types and individual cells were characterized and originally classified more than hundred years ago, although less attention was paid to their basic functions. This was mainly due to the modality of tissue specimen processing that allowed particularly detailed descriptive studies. Even so, we can notice some attempts to correlate the structure with the function. The German scientist Paul Langerhans, well-known for the discovery of Langerhans islets of the pancreas and Langerhans cells from the epidermis, tried to change the conventional fate of morphological studies introducing in his works functional hypothesis based on traditional microscopic observations even from the beginning of his scientific career. Paul Langerhans was a complex personality of the second half of the nineteenth century, not only in medicine, but also in other fields of biology. In the present review, presented is the life and research activity of Paul Langerhans, not only because of the importance of his discoveries, but also for perspectives that were opened by these findings in unexpected fields of medicine and biology.

  7. Functional soil microbial diversity across Europe estimated by EEA, MicroResp and BIOLOG

    DEFF Research Database (Denmark)

    Winding, Anne; Rutgers, Michiel; Creamer, Rachel

    Soil microorganisms are abundant and essential for the bio-geochemical processes of soil, soil quality and soil ecosystem services. All this is dependent on the actual functions the microbial communities are performing in the soil. Measuring soil respiration has for many years been the basis...... consisting of 81 soil samples covering five Biogeograhical Zones and three land-uses in order to test the sensitivity, ease and cost of performance and biological significance of the data output. The techniques vary in how close they are to in situ functions; dependency on growth during incubation......; and whether it is only bacteria or also fungi and /or extracellular enzymes. Also they vary in the functions tested and the number of functions. All three techniques were able to separate the soils according to land-use and biogeographical zone, however with different strengths. The MicroResp technique...

  8. An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology

    DEFF Research Database (Denmark)

    Nielsen, Jens; Olsson, Lisbeth

    2002-01-01

    . With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification - an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has become available...... for an increasing number of microorganisms. This has resulted in substantial research efforts in assigning function to all identified open reading frames - referred to as functional genomics. In both metabolic engineering and functional genomics there is a trend towards application of a macroscopic view on cell......Microbial physiology has traditionally played a very important role in both fundamental research and in industrial applications of microorganisms. The classical approach in microbial physiology has been to analyze the role of individual components (genes or proteins) in the overall cell function...

  9. Development of a Free-Electron Laser Center and Research in Medicine, Biology and Materials Science,

    Science.gov (United States)

    1992-05-14

    where enhanced nonproton ion movements can be observed during the photocycle ( Marinetti and Mauzerall, 1986). We do not have the possibility to measure...Biological Membranes. C.L. 17 Bolis, E.J.M. Helmreich and H. Passow, editors. Alan R. Liss Inc., NY 39-50. Marinetti , T., and D. Mauzerall 1986. Large

  10. Predicting Drug Use at Electronic Music Dance Events: Self-Reports and Biological Measurement

    Science.gov (United States)

    Johnson, Mark B.; Voas, Robert A.; Miller, Brenda A.; Holder, Harold D.

    2009-01-01

    Most information on the prevalence of drug use comes from self-report surveys. The sensitivity of such information is cause for concern about the accuracy of self-report measures. In this study, self-reported drug use in the last 48 hr is compared to results from biological assays of saliva samples from 371 young adults entering clubs. The…

  11. A Bayesian spatial model for neuroimaging data based on biologically informed basis functions.

    Science.gov (United States)

    Huertas, Ismael; Oldehinkel, Marianne; van Oort, Erik S B; Garcia-Solis, David; Mir, Pablo; Beckmann, Christian F; Marquand, Andre F

    2017-11-01

    The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data are characterised as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state. This model is estimated using a Bayesian framework which accurately quantifies uncertainty and automatically finds the most accurate and parsimonious combination of basis functions describing the data. We demonstrate the utility of this framework by predicting quantitative SPECT images of striatal dopamine function and we compare a variety of basis sets including generic isotropic functions, anatomical representations of the striatum derived from structural MRI, and two different soft functional parcellations of the striatum derived from resting-state fMRI (rfMRI). We found that a combination of ∼50 multiscale functional basis functions accurately represented the striatal dopamine activity, and that functional basis functions derived from an advanced parcellation technique known as Instantaneous Connectivity Parcellation (ICP) provided the most parsimonious models of dopamine function. Importantly, functional basis functions derived from resting fMRI were more accurate than both structural and generic basis sets in representing dopamine function in the striatum for a fixed model order. We demonstrate the translational validity of our framework by constructing classification models for discriminating parkinsonian disorders and their subtypes. Here, we show that ICP approach is the only basis set that performs well across all comparisons and performs better overall than the classical voxel-based approach

  12. All-electron density functional theory and time-dependent density functional theory with high-order finite elements

    OpenAIRE

    Lehtovaara, Lauri; Havu, Ville; Puska, Martti

    2009-01-01

    We present for static density functional theory and time-dependent density functional theory calculations an all-electron method which employs high-order hierarchical finite-element bases. Our mesh generation scheme, in which structured atomic meshes are merged to an unstructured molecular mesh, allows a highly nonuniform discretization of the space. Thus it is possible to represent the core and valence states using the same discretization scheme, i.e., no pseudopotentials or similar treatmen...

  13. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth

    Science.gov (United States)

    Bromage, Timothy G.; Idaghdour, Youssef; Lacruz, Rodrigo S.; Crenshaw, Thomas D.; Ovsiy, Olexandra; Rotter, Björn; Hoffmeier, Klaus; Schrenk, Friedemann

    2016-01-01

    The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien) chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA) drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the biological bases that

  14. Correlation functions of electronic and nuclear spins in a Heisenberg antiferromagnet semi-infinite media

    International Nuclear Information System (INIS)

    Sarmento, E.F.

    1980-01-01

    Results are found for the correlation dynamic functions (or the correspondent green functions) between any combination including pairs of electronic anel nuclear spin operators in an antiferromagnet semi-infinite media., at low temperature T N . These correlation functions, are used to investigate, at the same time, the properties of surface spin waves in volume and surface. The dispersion relatons of nuclear and electronic spin waves coupled modes, in surface are found, resolving a system of linearized equatons of spin operators a system of linearized equations of spin operators. (author) [pt

  15. Challenges regarding the start-up of an anaerobic biological sulphate reactor using H2 and CO2 as electron donor and carbon sources

    CSIR Research Space (South Africa)

    Roux, SP

    2009-05-01

    Full Text Available Include neutralization and chemical precipitation as well as membrane dependent processes. Biological sulphate reduction is another, environmentally benign option but relies heavily on the availability of an economically viable electron donor...

  16. Time-dependent density functional theory for many-electron systems interacting with cavity photons.

    Science.gov (United States)

    Tokatly, I V

    2013-06-07

    Time-dependent (current) density functional theory for many-electron systems strongly coupled to quantized electromagnetic modes of a microcavity is proposed. It is shown that the electron-photon wave function is a unique functional of the electronic (current) density and the expectation values of photonic coordinates. The Kohn-Sham system is constructed, which allows us to calculate the above basic variables by solving self-consistent equations for noninteracting particles. We suggest possible approximations for the exchange-correlation potentials and discuss implications of this approach for the theory of open quantum systems. In particular we show that it naturally leads to time-dependent density functional theory for systems coupled to the Caldeira-Leggett bath.

  17. Effects of surface functionalization on the electronic and structural properties of carbon nanotubes: A computational approach

    Science.gov (United States)

    Ribeiro, M. S.; Pascoini, A. L.; Knupp, W. G.; Camps, I.

    2017-12-01

    Carbon nanotubes (CNTs) have important electronic, mechanical and optical properties. These features may be different when comparing a pristine nanotube with other presenting its surface functionalized. These changes can be explored in areas of research and application, such as construction of nanodevices that act as sensors and filters. Following this idea, in the current work, we present the results from a systematic study of CNT's surface functionalized with hydroxyl and carboxyl groups. Using the entropy as selection criterion, we filtered a library of 10k stochastically generated complexes for each functional concentration (5, 10, 15, 20 and 25%). The structurally related parameters (root-mean-square deviation, entropy, and volume/area) have a monotonic relationship with functionalization concentration. Differently, the electronic parameters (frontier molecular orbital energies, electronic gap, molecular hardness, and electrophilicity index) present and oscillatory behavior. For a set of concentrations, the nanotubes present spin polarized properties that can be used in spintronics.

  18. Communication: Near-locality of exchange and correlation density functionals for 1- and 2-electron systems

    International Nuclear Information System (INIS)

    Sun, Jianwei; Yang, Zenghui; Peng, Haowei; Perdew, John P.

    2016-01-01

    The uniform electron gas and the hydrogen atom play fundamental roles in condensed matter physics and quantum chemistry. The former has an infinite number of electrons uniformly distributed over the neutralizing positively charged background, and the latter only one electron bound to the proton. The uniform electron gas was used to derive the local spin density approximation to the exchange-correlation functional that undergirds the development of the Kohn-Sham density functional theory. We show here that the ground-state exchange-correlation energies of the hydrogen atom and many other 1- and 2-electron systems are modeled surprisingly well by a different local spin density approximation (LSDA0). LSDA0 is constructed to satisfy exact constraints but agrees surprisingly well with the exact results for a uniform two-electron density in a finite, curved three-dimensional space. We also apply LSDA0 to excited or noded 1-electron densities, where it works less well. Furthermore, we show that the localization of the exact exchange hole for a 1- or 2-electron ground state can be measured by the ratio of the exact exchange energy to its optimal lower bound.

  19. Structural and functional investigations of biological catalysts for optimization of solar-driven H II production systems

    Science.gov (United States)

    King, Paul W.; Svedruzic, Drazenka; Cohen, Jordi; Schulten, Klaus; Seibert, Michael; Ghirardi, Maria L.

    2006-08-01

    Research efforts to develop efficient systems for H II production encompass a variety of biological and chemical approaches. For solar-driven H II production we are investigating an approach that integrates biological catalysts, the [FeFe] hydrogenases, with a photoelectrochemical cell as a novel bio-hybrid system. Structurally the [FeFe] hydrogenases consist of an iron-sulfur catalytic site that in some instances is electronically wired to accessory iron-sulfur clusters proposed to function in electron transfer. The inherent structural complexity of most examples of these enzymes is compensated by characteristics desired for bio-hybrid systems (i.e., low activation energy, high catalytic activity and solubility) with the benefit of utilizing abundant, less costly non-precious metals. Redesign and modification of [FeFe] hydrogenases is being undertaken to reduce complexity and to optimize structural properties for various integration strategies. The least complex examples of [FeFe] hydrogenase are found in the species of photosynthetic green algae and are being studied as design models for investigating the effects of structural minimization on substrate transfer, catalytic activity and oxygen sensitivity. Redesigning hydrogenases for effective use in bio-hybrid systems requires a detailed understanding of the relationship between structure and catalysis. To achieve better mechanistic understanding of [FeFe] hydrogenases both structural and dynamic models are being used to identify potential substrate transfer mechanisms which are tested in an experimental system. Here we report on recent progress of our investigations in the areas of [FeFe] hydrogenase overexpression, minimization and biochemical characterization.

  20. Synthesis, characterization and functionalization of silicon nanoparticle based hybrid nanomaterials for photovoltaic and biological applications

    Science.gov (United States)

    Xu, Zejing

    Silicon nanoparticles are attractive candidates for biological, photovoltaic and energy storage applications due to their size dependent optoelectronic properties. These include tunable light emission, high brightness, and stability against photo-bleaching relative to organic dyes (see Chapter 1). The preparation and characterization of silicon nanoparticle based hybrid nanomaterials and their relevance to photovoltaic and biological applications are described. The surface-passivated silicon nanoparticles were produced in one step from the reactive high-energy ball milling (RHEBM) of silicon wafers with various organic ligands. The surface structure and optical properties of the passivated silicon nanoparticles were systematically characterized. Fast approaches for purifying and at the same time size separating the silicon nanoparticles using a gravity GPC column were developed. The hydrodynamic diameter and size distribution of these size-separated silicon nanoparticles were determined using GPC and Diffusion Ordered NMR Spectroscopy (DOSY) as fast, reliable alternative approaches to TEM. Water soluble silicon nanoparticles were synthesized by grafting PEG polymers onto functionalized silicon nanoparticles with distal alkyne or azide moieties. The surface-functionalized silicon nanoparticles were produced from the reactive high-energy ball milling (RHEBM) of silicon wafers with a mixture of either 5-chloro-1-pentyne in 1-pentyne or 1,7 octadiyne in 1-hexyne to afford air and water stable chloroalkyl or alkynyl terminated nanoparticles, respectively. Nanoparticles with the ω-chloroalkyl substituents were easily converted to ω-azidoalkyl groups through the reaction of the silicon nanoparticles with sodium azide in DMF. The azido terminated nanoparticles were then grafted with monoalkynyl-PEG polymers using a copper catalyzed alkyne-azide cycloaddition (CuAAC) reaction to afford core-shell silicon nanoparticles with a covalently attached PEG shell. Covalently

  1. Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities

    Directory of Open Access Journals (Sweden)

    Isganitis Timothy

    2006-02-01

    Full Text Available Abstract Background Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily. Results We describe a system that builds upon the complex infrastructure of the Biozon database and applies methods similar to those of Google to rank documents that match queries. We explore different prominence models and study the spectral properties of the corresponding data graphs. We evaluate the information content of principal and non-principal eigenspaces, and test various scoring functions which combine contributions from multiple eigenspaces. We also test the effect of similarity data and other variations which are unique to the biological knowledge domain on the quality of the results. Query result sets are assessed using a probabilistic approach that measures the significance of coherence between directly connected nodes in the data graph. This model allows us, for the first time, to compare different prominence models quantitatively and effectively and to observe unique trends. Conclusion Our tests show that the ranked query results outperform unsorted results with respect to our significance measure and the top ranked entities are typically linked to many other biological entities. Our study resulted in a working ranking system of biological entities that was integrated into Biozon at http://biozon.org.

  2. Electron Transfer in Chemistry and Biology – The Primary Events in ...

    Indian Academy of Sciences (India)

    The ions are embedded in an environment (ligand. Box 2. A few examples of Electron Transfer Proteins. Protein. Metal ions. Cytochromes. Fe a, a3, b, c1, c, etc. cyt. aa3. Ferridoxins. Fe. Rubredoxins. Fe. Xanthine oxidase. Fe/Mo. Aldehyde oxidase. Fe/Mo. Succinate dehydrogenase. Stellacyanin, plastocyanin and azurin.

  3. Conducting polymer based biomolecular electronic devices

    Indian Academy of Sciences (India)

    Biomolecular electronics is rapidly evolving from physics, chemistry, biology, electronics and information technology. Organic materials such as proteins, pigments and conducting polymers have been considered as alternatives for carrying out the functions that are presently being performed by semiconductor silicon.

  4. Study of the electron energy distribution function in plasma produced by a rf discharge in a mixture of inert gases

    International Nuclear Information System (INIS)

    Vagner, S.D.; Ignat'ev, B.K.

    1983-01-01

    Electron energy distribution functions (EEDF) are recorded in an rf discharge in a mixture of neon and argon. The rates of different ionization processes and the energy losses of the electrons in the bulk of the discharge are calculated. The experimentally recorded electron energy distribution functions are compared with distributions calculated using a nonlocal theory. The effect of an rf voltage in the probe circuit on the recorded electron energy distribution functions is investigated experimentally

  5. Advances in structural and functional analysis of membrane proteins by electron crystallography.

    Science.gov (United States)

    Wisedchaisri, Goragot; Reichow, Steve L; Gonen, Tamir

    2011-10-12

    Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Tuning electron transport through functionalized C20H10 molecular junctions.

    Science.gov (United States)

    Zoppi, Laura; Ferretti, Andrea; Baldridge, Kim K

    2015-10-13

    First-principles methodology based on density functional theory (DFT) is used to investigate charge transport phenomena in molecular junctions, with the central active molecular element based on corannulene, C20H10, assembled between two carbon nanotubes (CNT). A number of key factors associated with the design of the molecular nanojunction are shown to have an impact on electron transport to varying degrees, including (I) the composition of the spacer linking the leads to the active element, (II) the composition of the active molecule element, (III) the sensor capabilities of the active element, and (IV) the response of the junction to an external electric field. This study demonstrates the ability to integrate molecular electronic functionality into electronic nanocircuits and provides novel insight into the design of new types of molecular-based devices by revealing the relationship between charge transport mechanisms and the electronic structure of molecular junction components.

  7. Functional profiles reveal unique ecological roles of various biological soil crust organisms

    Science.gov (United States)

    Bowker, M.A.; Mau, R.L.; Maestre, F.T.; Escolar, C.; Castillo-Monroy, A. P.

    2011-01-01

    1. At the heart of the body of research on biodiversity effects on ecosystem function is the debate over whether different species tend to be functionally singular or redundant. When we consider ecosystem multi-function, the provision of multiple ecosystem functions simultaneously, we may find that seemingly redundant species may in fact play unique roles in ecosystems. 2. Over the last few decades, the significance of biological soil crusts (BSCs) as ecological boundaries and ecosystem engineers, and their multi-functional nature, has become increasingly well documented. We compiled 'functional profiles' of the organisms in this understudied community, to determine whether functional singularity emerges when multiple ecosystem functions are considered. 3. In two data sets, one representing multiple sites around the semi-arid regions of Spain (regional scale), and another from a single site in central Spain (local scale), we examined correlations between the abundance or frequency of BSC species in a community, and multiple surrogates of ecosystem functioning. There was a wide array of apparent effects of species on specific functions. 4. Notably, in gypsiferous soils and at regional scale, we found that indicators of carbon (C) and phosphorus cycling were apparently suppressed and promoted by the lichens Diploschistes diacapsis and Squamarina lentigera, respectively. The moss Pleurochaete squarrosa appears to promote C cycling in calcareous soils at this spatial scale. At the local scale in gypsiferous soils, D. diacapsis positively correlated with carbon cycling, but negatively with nitrogen cycling, whereas numerous lichens exhibited the opposite profile. 5. We found a high degree of functional singularity, i.e. that species were highly individualistic in their effects on multiple functions. Many functional attributes were not easily predictable from existing functional grouping systems based primarily on morphology. 6. Our results suggest that maintaining

  8. A 400KV multi-functional electron and ion radiation accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Zhou Youyi; Wang Xurong; Deng Gulin (Sichuan Univ., Chengdu, SC (China). Inst. of Nuclear Science and Technology)

    In this paper we describe a 400 kV multi-functional electron and positive ion irradiation accelerator based upon a 400 kC Cockcroft-Walton, which was successfully used to accelerate electrons and positive ions with an electron beam current of more than 5 mA. It has a scanning window of 1200 mm in width, a scanning frame of 4500 x 1400 mm. The transmitting speed of the scanning frame is between 0.1-5 m backward and forward, continuously adjustable. The conversion time from accelerating positive ions to electrons is less than twenty minutes, and vice versa. It is proved that this accelerator can meet more requirements in the fields of nuclear physics and electron irradiation applications. (author).

  9. A 400KV multi-functional electron and ion radiation accelerator

    Science.gov (United States)

    Youyi, Zhou; Xurong, Wang; Gulin, Deng

    1993-07-01

    In this paper we describe a 400kV multi-functional electron and positive ion irradiation accelerator based upon a 400kV Cockcroft-Walton, which was successfully used to accelerate electrons and positive ions with electron beam current of more than 5 mA. It has a scanning window of 1200mm in width, a scanning frame of 4500×1400mm. The transmitting speed of the scanning frame is between 0.1-5m backward and forward, continuously adjustable. The conversion time from accelerating positive ions to electrons is less than twenty minutes, and vice versa. It is proved that this accelerator can meet more requirements in the fields of nuclear physics and electron irradiation applications.

  10. A 400KV multi-functional electron and ion radiation accelerator

    International Nuclear Information System (INIS)

    Zhou Youyi; Wang Xurong; Deng Gulin

    1993-01-01

    In this paper we describe a 400 kV multi-functional electron and positive ion irradiation accelerator based upon a 400 kC Cockcroft-Walton, which was successfully used to accelerate electrons and positive ions with an electron beam current of more than 5 mA. It has a scanning window of 1200 mm in width, a scanning frame of 4500 x 1400 mm. The transmitting speed of the scanning frame is between 0.1-5 m backward and forward, continuously adjustable. The conversion time from accelerating positive ions to electrons is less than twenty minutes, and vice versa. It is proved that this accelerator can meet more requirements in the fields of nuclear physics and electron irradiation applications. (author)

  11. Simulating photoacoustic waves produced by individual biological particles with spheroidal wave functions

    Science.gov (United States)

    Li, Yong; Fang, Hui; Min, Changjun; Yuan, Xiaocong

    2015-10-01

    Under the usual approximation of treating a biological particle as a spheroidal droplet, we consider the analysis of its size and shape with the high frequency photoacoustics and develop a numerical method which can simulate its characteristic photoacoustic waves. This numerical method is based on the calculation of spheroidal wave functions, and when comparing to the finite element model (FEM) calculation, can reveal more physical information and can provide results independently at each spatial points. As the demonstration, red blood cells (RBCs) and MCF7 cell nuclei are studied, and their photoacoustic responses including field distribution, spectral amplitude, and pulse forming are calculated. We expect that integrating this numerical method with the high frequency photoacoustic measurement will form a new modality being extra to the light scattering method, for fast assessing the morphology of a biological particle.

  12. A Critical Role for Cysteine 57 in the Biological Functions of Selenium Binding Protein-1.

    Science.gov (United States)

    Ying, Qi; Ansong, Emmanuel; Diamond, Alan M; Yang, Wancai

    2015-11-18

    The concentration of selenium-binding protein1 (SBP1) is often lower in tumors than in the corresponding tissue and lower levels have been associated with poor clinical outcomes. SBP1 binds tightly selenium although what role selenium plays in its biological functions remains unknown. Previous studies indicated that cysteine 57 is the most likely candidate amino acid for selenium binding. In order to investigate the role of cysteine 57 in SBP1, this amino acid was altered to a glycine and the mutated protein was expressed in human cancer cells. The SBP1 half-life, as well as the cellular response to selenite cytotoxicity, was altered by this change. The ectopic expression of SBP1(GLY) also caused mitochondrial damage in HCT116 cells. Taken together, these results indicated that cysteine 57 is a critical determinant of SBP1 function and may play a significant role in mitochondrial function.

  13. Reconstruction of electron energy distribution function from probe characteristics at intermediate and high pressures

    International Nuclear Information System (INIS)

    Arslanbekov, R.R.; Kolokolov, N.B.; Kudryavtsev, A.A.; Khromov, N.A.

    1991-01-01

    Kinetic theory of electron current on a probe, enabling essentially broaden the area of application of a probe method for determination of electron energy distribution function (EEDF) onto the areas of intermediate and high pressures. Method of quadrature summs makes it possible to reconstruct EEDF from integral equation for arbitrary energy dependences of diffusion parameter at any given energy interval. High efficiency of the method is demonstrated by solution of model as well as experimental tasks

  14. Ambipolar field role in formation of electron distribution function in gas discharge plasma.

    Science.gov (United States)

    Yuan, Chengxun; Bogdanov, E A; Kudryavtsev, A A; Rabadanov, K M; Zhou, Zhongxiang

    2017-11-06

    It is shown that the local approximation for electron distribution function (EDF) determination at plasma periphery, where the ambipolar field is dominant, is not applicable even at high pressures when the characteristic plasma size exceeds the energy relaxation length of the electrons R > λ ε . Therefore, consistent results can be obtained only when solving the complete kinetic equation in both energy and spatial variables (i.e. it is necessary to solve nonlocal kinetic equation).

  15. Treatment of cancer of the pancreas by intraoperative electron beam therapy: physical and biological aspects

    International Nuclear Information System (INIS)

    Bagne, F.R.; Dobelbower, R.R. Jr.; Milligan, A.J.; Bronn, D.G.

    1989-01-01

    Radiation therapy has had a significant and an expanded role in the management of cancer of the pancreas during the last decade. In particular, for locally advanced disease, radiation therapy has improved the median survival of patients to 1 year. Intraoperative electron beam therapy has been applied to unresectable and resectable pancreatic cancer in an attempt to enhance local control of disease and to improve patient survival. This paper presents a survey of the role of radiation therapy in treatment of cancer of the pancreas, provides information on the radiobiological aspects of this treatment modality and details the physical and dosimetric characteristics of intraoperative radiation therapy with electrons. Presented are the design specifics of an applicator system, central axis beam data, applicator parameters, dose distribution data, shielding, treatment planning and means of verification. Emphasis is placed on the collaboration and cooperation necessary for all members of the intraoperative radiation therapy team including surgeons, radiation therapists, medical physicists, anesthesiologists, technologists, and nurses.29 references

  16. Magnetic Resonance Imaging of Biological Specimens by Electron Paramagnetic Resonance of Nitroxide Spin Labels

    Science.gov (United States)

    Berliner, Lawrence J.; Fujii, Hirotada

    1985-02-01

    Electron paramagnetic resonance imaging was demonstrated on two plant species, Apium graveolens and Coleus blumei. This was accomplished by soaking stems of these plants in the paramagnetic nitroxide imaging agent 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl. The experiments were accomplished at L-band frequency (1.4 to 1.9 gigahertz) with single-turn, flat-loop surface coils. One-dimensional imaging spectra were diagnostic of capillary structure and long-term stability.

  17. Mechanistic Basis for Biological Polymer Stability, Electron Transfer and Molecular Sensing in Extreme Environments

    Science.gov (United States)

    2015-12-02

    optimum for enolase catalysis was 80C, close to the measured thermal stability of the protein which was 15. SUBJECT TERMS thermally stable proteins...analysis of two thermophilic enzymes, electron transfer reactions in cyanobacteria, and the first description of a thermophilic microbial fuel cell...temperature optimum for enolase catalysis was 80°C, close to the measured thermal stability of the protein which was determined to be 75°C, while the pH

  18. An electron localization function study of the strain energy in carbon compounds

    Science.gov (United States)

    Chevreau, Hilaire; Sevin, Alain

    2000-05-01

    It is shown, through an electron localization function (ELF) analysis of the strain in carbon compounds, that, globally, the valence basins V(CH) and V(CC) tend to preserve a VSEPR (valence shell electron pair repulsion) geometry. This point is clearly illustrated by the valence attractors location. The properties of V(CC) basins, associated with the CC bonds, remain as constant as possible. The main effect of the strain is to modify the maximal electron localization in each V(CC) basin. This study points out once more the difficulty in relating global strain to local bond properties.

  19. Hot-electron-assisted femtochemistry at surfaces: A time-dependent density functional theory approach

    DEFF Research Database (Denmark)

    Gavnholt, Jeppe; Rubio, Angel; Olsen, Thomas

    2009-01-01

    Using time-evolution time-dependent density functional theory (TDDFT) within the adiabatic local-density approximation, we study the interactions between single electrons and molecular resonances at surfaces. Our system is a nitrogen molecule adsorbed on a ruthenium surface. The surface is modeled...... at two levels of approximation, first as a simple external potential and later as a 20-atom cluster. We perform a number of calculations on an electron hitting the adsorbed molecule from inside the surface and establish a picture, where the resonance is being probed by the hot electron. This enables us...

  20. Structure-function insights of membrane and soluble proteins revealed by electron crystallography.

    Science.gov (United States)

    Dreaden, Tina M; Devarajan, Bharanidharan; Barry, Bridgette A; Schmidt-Krey, Ingeborg

    2013-01-01

    Electron crystallography is emerging as an important method in solving protein structures. While it has found extensive applications in the understanding of membrane protein structure and function at a wide range of resolutions, from revealing oligomeric arrangements to atomic models, electron crystallography has also provided invaluable information on the soluble α/β-tubulin which could not be obtained by any other method to date. Examples of critical insights from selected structures of membrane proteins as well as α/β-tubulin are described here, demonstrating the vast potential of electron crystallography that is first beginning to unfold.

  1. Effects of the reconnection electric field on crescent electron distribution functions in asymmetric guide field reconnection

    Science.gov (United States)

    Bessho, N.; Chen, L. J.; Hesse, M.; Wang, S.

    2017-12-01

    In asymmetric reconnection with a guide field in the Earth's magnetopause, electron motion in the electron diffusion region (EDR) is largely affected by the guide field, the Hall electric field, and the reconnection electric field. The electron motion in the EDR is neither simple gyration around the guide field nor simple meandering motion across the current sheet. The combined meandering motion and gyration has essential effects on particle acceleration by the in-plane Hall electric field (existing only in the magnetospheric side) and the out-of-plane reconnection electric field. We analyze electron motion and crescent-shaped electron distribution functions in the EDR in asymmetric guide field reconnection, and perform 2-D particle-in-cell (PIC) simulations to elucidate the effect of reconnection electric field on electron distribution functions. Recently, we have analytically expressed the acceleration effect due to the reconnection electric field on electron crescent distribution functions in asymmetric reconnection without a guide field (Bessho et al., Phys. Plasmas, 24, 072903, 2017). We extend the theory to asymmetric guide field reconnection, and predict the crescent bulge in distribution functions. Assuming 1D approximation of field variations in the EDR, we derive the time period of oscillatory electron motion (meandering + gyration) in the EDR. The time period is expressed as a hybrid of the meandering period and the gyro period. Due to the guide field, electrons not only oscillate along crescent-shaped trajectories in the velocity plane perpendicular to the antiparallel magnetic fields, but also move along parabolic trajectories in the velocity plane coplanar with magnetic field. The trajectory in the velocity space gradually shifts to the acceleration direction by the reconnection electric field as multiple bounces continue. Due to the guide field, electron distributions for meandering particles are bounded by two paraboloids (or hyperboloids) in the

  2. The association between biological rhythms, depression, and functioning in bipolar disorder: a large multi-center study.

    Science.gov (United States)

    Pinho, M; Sehmbi, M; Cudney, L E; Kauer-Sant'anna, M; Magalhães, P V; Reinares, M; Bonnín, C M; Sassi, R B; Kapczinski, F; Colom, F; Vieta, E; Frey, B N; Rosa, A R

    2015-05-22

    We examined the relationship between biological rhythms and severity of depressive symptoms in subjects with bipolar disorder and the effects of biological rhythms alterations on functional impairment. Bipolar patients (n = 260) and healthy controls (n = 191) were recruited from mood disorders programs in three sites (Spain, Brazil, and Canada). Parameters of biological rhythms were measured using the Biological Rhythms Assessment in Neuropsychiatry (BRIAN), an interviewer administered questionnaire that assesses disruptions in sleep, eating patterns, social rhythms, and general activity. Multivariate analyses of covariance showed significant intergroup differences after controlling for potential confounders (Pillai's F = 49.367; df = 2, P biological rhythms disturbance, followed by patients with subsyndromal symptoms, euthymic patients, and healthy controls. Biological rhythms and HAMD scores were independent predictors of poor functioning (F = 12.841, df = 6, P biological rhythms disturbance. Biological rhythms disturbance was also an independent predictor of functional impairment. Although the directionality of this relationship remains unknown, our results suggest that stability of biological rhythms should be an important target of acute and long-term management of bipolar disorder and may aid in the improvement of functioning. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Functional characteristics of commercial ambulatory electronic prescribing systems: a field study.

    Science.gov (United States)

    Wang, C Jason; Marken, Richard S; Meili, Robin C; Straus, Julie B; Landman, Adam B; Bell, Douglas S

    2005-01-01

    To compare the functional capabilities being offered by commercial ambulatory electronic prescribing systems with a set of expert panel recommendations. A descriptive field study of ten commercially available ambulatory electronic prescribing systems, each of which had established a significant market presence. Data were collected from vendors by telephone interview and at sites where the systems were functioning through direct observation of the systems and through personal interviews with prescribers and technical staff. The capabilities of electronic prescribing systems were compared with 60 expert panel recommendations for capabilities that would improve patient safety, health outcomes, or patients' costs. Each recommended capability was judged as having been implemented fully, partially, or not at all by each system to which the recommendation applied. Vendors' claims about capabilities were compared with the capabilities found in the site visits. On average, the systems fully implemented 50% of the recommended capabilities, with individual systems ranging from 26% to 64% implementation. Only 15% of the recommended capabilities were not implemented by any system. Prescribing systems that were part of electronic health records (EHRs) tended to implement more recommendations. Vendors' claims about their systems' capabilities had a 96% sensitivity and a 72% specificity when site visit findings were considered the gold standard. The commercial electronic prescribing marketplace may not be selecting for capabilities that would most benefit patients. Electronic prescribing standards should include minimal functional capabilities, and certification of adherence to standards may need to take place where systems are installed and operating.

  4. Reconstruction of the electron energy distribution function from probe characteristics at intermediate and high pressures

    International Nuclear Information System (INIS)

    Arslanbekov, R.R.; Kolokolov, N.B.; Kudryavtsev, A.A.; Khromov, N.A.

    1991-01-01

    Gorbunov et al. have developed a kinetic theory of the electron current drawn by a probe, which substantially extends the region of applicability of the probe method for determining the electron energy distribution function, enabling probes to be used for intermediate and high pressures (up to p ≤ 0.5 atm for monatomic gases). They showed that for λ var-epsilon >> a + d (where a is the probe radius, d is the sheath thickness, and λ var-epsilon is the electron energy relaxation length) the current density j e (V) drawn by the probe is related to the unperturbed distribution function by an integral equation involving the distribution function. The kernal of the integral equation can be written as a function of the diffusion parameter. In the present paper the method of quadrature sums is employed in order to obtain the electron energy distribution function from probe characteristics at intermediate and high pressures. This technique enables them to recover the distribution function from the integral equation when the diffusion parameter has an arbitrary energy dependence ψ 0 (var-epsilon) in any given energy range. The effectiveness of the method is demonstrated by application to both model problems and experimental data

  5. Three-dimensional optical transfer functions in the aberration-corrected scanning transmission electron microscope.

    Science.gov (United States)

    Jones, L; Nellist, P D

    2014-05-01

    In the scanning transmission electron microscope, hardware aberration correctors can now correct for the positive spherical aberration of round electron lenses. These correctors make use of nonround optics such as hexapoles or octupoles, leading to the limiting aberrations often being of a nonround type. Here we explore the effect of a number of potential limiting aberrations on the imaging performance of the scanning transmission electron microscope through their resulting optical transfer functions. In particular, the response of the optical transfer function to changes in defocus are examined, given that this is the final aberration to be tuned just before image acquisition. The resulting three-dimensional optical transfer functions also allow an assessment of the performance of a system for focal-series experiments or optical sectioning applications. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

  6. Non-equilibrium Green function method: theory and application in simulation of nanometer electronic devices

    International Nuclear Information System (INIS)

    Do, Van-Nam

    2014-01-01

    We review fundamental aspects of the non-equilibrium Green function method in the simulation of nanometer electronic devices. The method is implemented into our recently developed computer package OPEDEVS to investigate transport properties of electrons in nano-scale devices and low-dimensional materials. Concretely, we present the definition of the four real-time Green functions, the retarded, advanced, lesser and greater functions. Basic relations among these functions and their equations of motion are also presented in detail as the basis for the performance of analytical and numerical calculations. In particular, we review in detail two recursive algorithms, which are implemented in OPEDEVS to solve the Green functions defined in finite-size opened systems and in the surface layer of semi-infinite homogeneous ones. Operation of the package is then illustrated through the simulation of the transport characteristics of a typical semiconductor device structure, the resonant tunneling diodes. (review)

  7. Measurement of the electron structure function F2e at LEP energies

    Directory of Open Access Journals (Sweden)

    J. Abdallah

    2014-10-01

    Full Text Available The hadronic part of the electron structure function F2e has been measured for the first time, using e+e− data collected by the DELPHI experiment at LEP, at centre-of-mass energies of s=91.2–209.5 GeV. The data analysis is simpler than that of the measurement of the photon structure function. The electron structure function F2e data are compared to predictions of phenomenological models based on the photon structure function. It is shown that the contribution of large target photon virtualities is significant. The data presented can serve as a cross-check of the photon structure function F2γ analyses and help in refining existing parameterisations.

  8. Synthesis and electronic properties of chemically functionalized graphene on metal surfaces

    International Nuclear Information System (INIS)

    Grüneis, Alexander

    2013-01-01

    A review on the electronic properties, growth and functionalization of graphene on metals is presented. Starting from the derivation of the electronic properties of an isolated graphene layer using the nearest neighbor tight-binding (TB) approximation for π and σ electrons, the TB model is then extended to third-nearest neighbors and interlayer coupling. The latter is relevant to few-layer graphene and graphite. Next, the conditions under which epitaxial graphene can be obtained by chemical vapor deposition are reviewed with a particular emphasis on the Ni(111) surface. Regarding functionalization, I first discuss the intercalation of monolayer Au into the graphene/Ni(111) interface, which renders graphene quasi-free-standing. The Au intercalated quasi-free-standing graphene is then the basis for chemical functionalization. Functionalization of graphene is classified into covalent, ionic and substitutional functionalization. As archetypical examples for these three possibilities I discuss covalent functionalization by hydrogen, ionic functionalization by alkali metals and substitutional functionalization by nitrogen heteroatoms.

  9. Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions

    Directory of Open Access Journals (Sweden)

    Werner Mark

    2008-08-01

    Full Text Available Abstract Background Variations in the influenza Hemagglutinin protein contributes to antigenic drift resulting in decreased efficiency of seasonal influenza vaccines and escape from host immune response. We performed an in silico study to determine characteristics of novel variable and conserved motifs in the Hemagglutinin protein from previously reported H3N2 strains isolated from Hong Kong from 1968–1999 to predict viral motifs involved in significant biological functions. Results 14 MEME blocks were generated and comparative analysis of the MEME blocks identified blocks 1, 2, 3 and 7 to correlate with several biological functions. Analysis of the different Hemagglutinin sequences elucidated that the single block 7 has the highest frequency of amino acid substitution and the highest number of co-mutating pairs. MEME 2 showed intermediate variability and MEME 1 was the most conserved. Interestingly, MEME blocks 2 and 7 had the highest incidence of potential post-translational modifications sites including phosphorylation sites, ASN glycosylation motifs and N-myristylation sites. Similarly, these 2 blocks overlap with previously identified antigenic sites and receptor binding sites. Conclusion Our study identifies motifs in the Hemagglutinin protein with different amino acid substitution frequencies over a 31 years period, and derives relevant functional characteristics by correlation of these motifs with potential post-translational modifications sites, antigenic and receptor binding sites.

  10. Integration of multiscale dendritic spine structure and function data into systems biology models

    Directory of Open Access Journals (Sweden)

    James J Mancuso

    2014-11-01

    Full Text Available Comprising 1011 neurons with 1014 synaptic connections the human brain is the ultimate systems biology puzzle. An increasing body of evidence highlights the observation that changes in brain function, both normal and pathological, consistently correlate with dynamic changes in neuronal anatomy. Anatomical changes occur on a full range of scales from the trafficking of individual proteins, to alterations in synaptic morphology both individually and on a systems level, to reductions in long distance connectivity and brain volume. The major sites of contact for synapsing neurons are dendritic spines, which provide an excellent metric for the number and strength of signaling connections between elements of functional neuronal circuits. A comprehensive model of anatomical changes and their functional consequences would be a holy grail for the field of systems neuroscience but its realization appears far on the horizon. Various imaging technologies have advanced to allow for multi-scale visualization of brain plasticity and pathology, but computational analysis of the massive big data sets involved forms the bottleneck toward the creation of multiscale models of brain structure and function. While a full accounting of techniques and progress toward a comprehensive model of brain anatomy and function is beyond the scope of this or any other single paper, this review serves to highlight the opportunities for analysis of neuronal spine anatomy and function provided by new imaging technologies and the high-throughput application of older technologies while surveying the strengths and weaknesses of currently available computational analytical tools and room for future improvement.

  11. A New Approach to Studying Biological and Soft Materials Using Focused Ion Beam Scanning Electron Microscopy (FIB SEM)

    International Nuclear Information System (INIS)

    Stokes, D J; Morrissey, F; Lich, B H

    2006-01-01

    Over the last decade techniques such as confocal light microscopy, in combination with fluorescent labelling, have helped biologists and life scientists to study biological architectures at tissue and cell level in great detail. Meanwhile, obtaining information at very small length scales is possible with the combination of sample preparation techniques and transmission electron microscopy (TEM) or scanning transmission electron microscopy (STEM). Scanning electron microscopy (SEM) is well known for the determination of surface characteristics and morphology. However, the desire to understand the three dimensional relationships of meso-scale hierarchies has led to the development of advanced microscopy techniques, to give a further complementary approach. A focused ion beam (FIB) can be used as a nano-scalpel and hence allows us to reveal internal microstructure in a site-specific manner. Whilst FIB instruments have been used to study and verify the three-dimensional architecture of man made materials, SEM and FIB technologies have now been brought together in a single instrument representing a powerful combination for the study of biological specimens and soft materials. We demonstrate the use of FIB SEM to study three-dimensional relationships for a range of length scales and materials, from small-scale cellular structures to the larger scale interactions between biomedical materials and tissues. FIB cutting of heterogeneous mixtures of hard and soft materials, resulting in a uniform cross-section, has proved to be of particular value since classical preparation methods tend to introduce artefacts. Furthermore, by appropriate selection, we can sequentially cross-section to create a series of 'slices' at specific intervals. 3D reconstruction software can then be used to volume-render information from the 2D slices, enabling us to immediately see the spatial relationships between microstructural components

  12. The growth and electronic structure of azobenzene-based functional molecules on layered crystals

    International Nuclear Information System (INIS)

    Iwicki, J; Ludwig, E; Buck, J; Kalläne, M; Kipp, L; Rossnagel, K; Köhler, F; Herges, R

    2012-01-01

    In situ ultraviolet photoelectron spectroscopy is used to study the growth of ultrathin films of azobenzene-based functional molecules (azobenzene, Disperse Orange 3 and a triazatriangulenium platform with an attached functional azo-group) on the layered metal TiTe 2 and on the layered semiconductor HfS 2 at liquid nitrogen temperatures. Effects of intermolecular interactions, of the substrate electronic structure, and of the thermal energy of the sublimated molecules on the growth process and on the adsorbate electronic structure are identified and discussed. A weak adsorbate-substrate interaction is particularly observed for the layered semiconducting substrate, holding the promise of efficient molecular photoswitching.

  13. A Survey of Biology Teachers Use of Activity-Oriented, Laboratory Practical Exercises to Promote Functional Biology Education

    Directory of Open Access Journals (Sweden)

    Abigail Mgboyibo Osuafor

    2016-08-01

    Full Text Available A major goal of science education is fostering students’ intellectual competencies such as independent learning, problem-solving, decision-making and critical thinking. This goal can only be achieved when students are actively involved in the teaching-learning process through activity-based, practical-oriented instructional methods involving the use of laboratories. This study therefore, investigated the extent to which the biology teachers employ activity-oriented, laboratory/practical instructional methods in order to improve the learning outcome of their students. The descriptive survey involved 73 Biology teachers randomly selected from all the six education zones of Anambra state, Nigeria. Four research questions were posed and four hypotheses were formulated to guide the conduct of the study. A 32-item structured questionnaire which has reliability co-efficient of 0.82 was used to collect data. Data were analyzed using mean, standard deviation and t-tests. Results show that Biology teachers adopt practical-oriented strategies in teaching biology, conduct practical activities to a high extent, and perceive practical exercises as essential to effective teaching and learning of the subject. Provision of adequate number of laboratory materials, employment of adequate number of biology teachers, making provision for well designed laboratory activities in the curriculum and training of teachers on how to effectively combine theory with practical are some of the strategies that will encourage biology teachers to conduct practical lessons. There was no significant difference between male and female biology teachers in their responses to the different aspects investigated. Based on these findings, some recommendations were made that include that curriculum designers should incorporate guides for practical activities that go with each topic in the curriculum so as to encourage the teachers to teach theory with practical as a unified whole to

  14. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

    Directory of Open Access Journals (Sweden)

    Christopher Y Park

    Full Text Available A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not already well studied. Many of these processes are well studied in some organism, but not necessarily in an investigator's organism of interest. Sequence-based search methods (e.g. BLAST have been used to transfer such annotation information between organisms. We demonstrate that functional genomics can complement traditional sequence similarity to improve the transfer of gene annotations between organisms. Our method transfers annotations only when functionally appropriate as determined by genomic data and can be used with any prediction algorithm to combine transferred gene function knowledge with organism-specific high-throughput data to enable accurate function prediction. We show that diverse state-of-art machine learning algorithms leveraging functional knowledge transfer (FKT dramatically improve their accuracy in predicting gene-pathway membership, particularly for processes with little experimental knowledge in an organism. We also show that our method compares favorably to annotation transfer by sequence similarity. Next, we deploy FKT with state-of-the-art SVM classifier to predict novel genes to 11,000 biological processes across six diverse organisms and expand the coverage of accurate function predictions to processes that are often ignored because of a dearth of annotated genes in an organism. Finally, we perform in vivo experimental investigation in Danio rerio and confirm the regulatory role of our top predicted novel gene, wnt5b, in leftward cell migration during heart development. FKT is immediately applicable to many bioinformatics

  15. Reconstruction of biological functions: novel implant concepts for cardiovascular, ophthal-mologic and otolaryngologic applications

    Directory of Open Access Journals (Sweden)

    Grabow Niels

    2017-09-01

    Full Text Available Biomedical engineering innovations towards the reconstruction of biological functions seek to improve the quality of patients’ lives. The coordinated research project “RESPONSE – Partnership for Innovation in Implant Technology” (BMBF program Twenty20 – Partnership for Innovation, 2014 - 2021 is focusing on the development of novel concepts for (i cardiovascular scaffolds, glaucoma and ENT stents, (ii transcatheter heart valves and venous valves, (iii polymeric implants and polymer/drug formulations. Current clinical paradigm shifts, fostered by the progress in implant technology and a growing global demand, frame the background for the joint research efforts of academia and industry in the RESPONSE consortium.

  16. Fast Transverse Beam Instability Caused by Electron Cloud Trapped in Combined Function Magnets

    Energy Technology Data Exchange (ETDEWEB)

    Antipov, Sergey [Univ. of Chicago, IL (United States)

    2017-03-01

    Electron cloud instabilities affect the performance of many circular high-intensity particle accelerators. They usually have a fast growth rate and might lead to an increase of the transverse emittance and beam loss. A peculiar example of such an instability is observed in the Fermilab Recycler proton storage ring. Although this instability might pose a challenge for future intensity upgrades, its nature had not been completely understood. The phenomena has been studied experimentally by comparing the dynamics of stable and unstable beam, numerically by simulating the build-up of the electron cloud and its interaction with the beam, and analytically by constructing a model of an electron cloud driven instability with the electrons trapped in combined function dipoles. Stabilization of the beam by a clearing bunch reveals that the instability is caused by the electron cloud, trapped in beam optics magnets. Measurements of microwave propagation confirm the presence of the cloud in the combined function dipoles. Numerical simulations show that up to 10$^{-2}$ of the particles can be trapped by their magnetic field. Since the process of electron cloud build-up is exponential, once trapped this amount of electrons significantly increases the density of the cloud on the next revolution. In a combined function dipole this multi-turn accumulation allows the electron cloud reaching final intensities orders of magnitude greater than in a pure dipole. The estimated fast instability growth rate of about 30 revolutions and low mode frequency of 0.4 MHz are consistent with experimental observations and agree with the simulations. The created instability model allows investigating the beam stability for the future intensity upgrades.

  17. Integrating phenotypic data from electronic patient records with molecular level systems biology

    DEFF Research Database (Denmark)

    Brunak, Søren

    2011-01-01

    Electronic patient records remain a rather unexplored, but potentially rich data source for discovering correlations between diseases. We describe a general approach for gathering phenotypic descriptions of patients from medical records in a systematic and non-cohort dependent manner. By extracting...... phenotype information from the free-text in such records we demonstrate that we can extend the information contained in the structured record data, and use it for producing fine-grained patient stratification and disease co-occurrence statistics. The approach uses a dictionary based on the International...

  18. The relative biological effectiveness (RBE) of high-energy electrons, x-rays and Co-60 gamma-rays

    International Nuclear Information System (INIS)

    Kiyono, Kunihiro

    1974-01-01

    Linac (Mitsubishi-Shimizu 15 MeV medical linear accelerator) electron beams with actual generated energies of 8, 10, 12 and 15 MeV were compared with X-ray beams having energies of 8 and 10 MV. The RBE values were calculated from 50 percent hatch-ability (LD 50 ) in silk-worm embryos, 30-days lethality (LDsub(50/30)) in ddY mice, and mean lethal dose (Do) in cultured mouse YL cells or human FL cells. To estimate the RBE in clinical experiments, LRD (leukocyte reduction dose) value was calculated for each patient irradiated on the chest or lumbar vertebrae. It was concluded that there is little difference in practical significance between 8 to 10 MV X-rays and 8 to 15 MeV electrons, and that the biological effects of Linac radiations are about 90 to 100 percent of the effect of 60 Co gamma rays. The RBE values gradually decreased, contrary to the elevation of energy between 8 and 15 MeV for electrons and between 8 and 10 MV for X-rays. These values were compared with those of earlier reviews of work in this field, and were briefly discussed. (Evans, J.)

  19. Holography and coherent diffraction with low-energy electrons: A route towards structural biology at the single molecule level.

    Science.gov (United States)

    Latychevskaia, Tatiana; Longchamp, Jean-Nicolas; Escher, Conrad; Fink, Hans-Werner

    2015-12-01

    The current state of the art in structural biology is led by NMR, X-ray crystallography and TEM investigations. These powerful tools however all rely on averaging over a large ensemble of molecules. Here, we present an alternative concept aiming at structural analysis at the single molecule level. We show that by combining electron holography and coherent diffraction imaging estimations concerning the phase of the scattered wave become needless as the phase information is extracted from the data directly and unambiguously. Performed with low-energy electrons the resolution of this lens-less microscope is just limited by the De Broglie wavelength of the electron wave and the numerical aperture, given by detector geometry. In imaging freestanding graphene, a resolution of 2Å has been achieved revealing the 660.000 unit cells of the graphene sheet from a single data set. Once applied to individual biomolecules the method shall ultimately allow for non-destructive imaging and imports the potential to distinguish between different conformations of proteins with atomic resolution. Copyright © 2015. Published by Elsevier B.V.

  20. A theoretical study for electronic and transport properties of covalent functionalized MoS2 monolayer

    Science.gov (United States)

    Gao, Lijuan; Yang, Zhao-Di; Zhang, Guiling

    2017-06-01

    The geometries, electronic and electron transport properties of a series of functionalized MoS2 monolayers were investigated using density-functional theory (DFT) and the non-equilibrium Green's function (NEGF) methods. n-Propyl, n-trisilicyl, phenyl, p-nitrophenyl and p-methoxyphenyl are chosen as electron-donating groups. The results show covalent functionalization with electron-donating groups could make a transformation from typical semiconducting to metallic properties for appearance of midgap level across the Fermi level (Ef). The calculations of transport properties for two-probe devices indicate that conductivities of functionalized systems are obviously enhanced relative to pristine MoS2 monolayer. Grafted groups contribute to the major transport path and play an important role in enhancing conductivity. The NDR effect is found. The influence of grafted density is also studied. Larger grafted density leads to wider bandwidth of midgap level, larger current response of I-V curves and larger current difference between peak and valley.

  1. Visualizing rotational wave functions of electronically excited nitric oxide molecules by using an ion imaging technique.

    Science.gov (United States)

    Mizuse, Kenta; Chizuwa, Nao; Ikeda, Dai; Imajo, Takashi; Ohshima, Yasuhiro

    2018-01-31

    Here we report the dissociative ionization imaging of electronically excited nitric oxide (NO) molecules to visualize rotational wave functions in the electronic excited state (A 2 Σ + ). The NO molecules were excited to a single rotational energy eigenstate in the first electronic excited state by a resonant nanosecond ultraviolet pulse. The molecules were then irradiated by a strong, circularly polarized femtosecond imaging pulse. Spatial distribution of the ejected N + and O + fragment ions from the dissociative NO 2+ was recorded as a direct measure of the molecular axis distribution using a high-resolution slice ion imaging apparatus. The circularly polarized probe pulse realizes the isotropic ionization and thus undistorted shapes of the functions can be visualized. Due to the higher ionization efficiency of the excited molecules relative to the ground state ones, signals from the excited NO were enhanced. We can, therefore, extract shapes of the square of rotational wave functions in the electronic excited state although the unexcited ground state molecules are the majority in an ensemble. The observed images show s-function-like and p-function-like shapes depending on the excitation wavelengths. These shapes well reflect the rotational (angular momentum) character of the prepared states. The present approach directly leads to the evaluation method of the molecular axis alignment in photo-excited ensembles, and it could also lead to a visualization method for excited state molecular dynamics.

  2. The origin of neutron biological effectiveness as a function of energy

    Science.gov (United States)

    Baiocco, G.; Barbieri, S.; Babini, G.; Morini, J.; Alloni, D.; Friedland, W.; Kundrát, P.; Schmitt, E.; Puchalska, M.; Sihver, L.; Ottolenghi, A.

    2016-01-01

    The understanding of the impact of radiation quality in early and late responses of biological targets to ionizing radiation exposure necessarily grounds on the results of mechanistic studies starting from physical interactions. This is particularly true when, already at the physical stage, the radiation field is mixed, as it is the case for neutron exposure. Neutron Relative Biological Effectiveness (RBE) is energy dependent, maximal for energies ~1 MeV, varying significantly among different experiments. The aim of this work is to shed light on neutron biological effectiveness as a function of field characteristics, with a comprehensive modeling approach: this brings together transport calculations of neutrons through matter (with the code PHITS) and the predictive power of the biophysical track structure code PARTRAC in terms of DNA damage evaluation. Two different energy dependent neutron RBE models are proposed: the first is phenomenological and based only on the characterization of linear energy transfer on a microscopic scale; the second is purely ab-initio and based on the induction of complex DNA damage. Results for the two models are compared and found in good qualitative agreement with current standards for radiation protection factors, which are agreed upon on the basis of RBE data. PMID:27654349

  3. The origin of neutron biological effectiveness as a function of energy

    Science.gov (United States)

    Baiocco, G.; Barbieri, S.; Babini, G.; Morini, J.; Alloni, D.; Friedland, W.; Kundrát, P.; Schmitt, E.; Puchalska, M.; Sihver, L.; Ottolenghi, A.

    2016-09-01

    The understanding of the impact of radiation quality in early and late responses of biological targets to ionizing radiation exposure necessarily grounds on the results of mechanistic studies starting from physical interactions. This is particularly true when, already at the physical stage, the radiation field is mixed, as it is the case for neutron exposure. Neutron Relative Biological Effectiveness (RBE) is energy dependent, maximal for energies ~1 MeV, varying significantly among different experiments. The aim of this work is to shed light on neutron biological effectiveness as a function of field characteristics, with a comprehensive modeling approach: this brings together transport calculations of neutrons through matter (with the code PHITS) and the predictive power of the biophysical track structure code PARTRAC in terms of DNA damage evaluation. Two different energy dependent neutron RBE models are proposed: the first is phenomenological and based only on the characterization of linear energy transfer on a microscopic scale; the second is purely ab-initio and based on the induction of complex DNA damage. Results for the two models are compared and found in good qualitative agreement with current standards for radiation protection factors, which are agreed upon on the basis of RBE data.

  4. Electron beam induced dis-infection of biologically treated waste water effluent

    International Nuclear Information System (INIS)

    Rawat, K.P.; Khader, S.A.; Sarma, K.S.S.

    2012-01-01

    The conservation of water is need of the hour as there is vast gap between demand and supply. The waste water generated in conventional waste water treatment plant can be recycled for irrigation. The presence of pathogenic micro-organism makes it unsafe for this purpose. EB is very effective in killing all forms of pathogens. The biologically treated waste water effluent was used for this purpose. The pathogen count reduced to undetectable level with the EB dose of 0.45 kGy. The BOD and COD values were within the permissible limit. The other physico-chemical parameters remained unaltered. The ability of EB to deliver higher dose rates makes it ideal for handling large volumes of effluent generated in megacities. (author)

  5. Carcinogenesis: alterations in reciprocal interactions of normal functional structure of biologic systems.

    Science.gov (United States)

    Davydyan, Garri

    2015-12-01

    The evolution of biologic systems (BS) includes functional mechanisms that in some conditions may lead to the development of cancer. Using mathematical group theory and matrix analysis, previously, it was shown that normally functioning BS are steady functional structures regulated by three basis regulatory components: reciprocal links (RL), negative feedback (NFB) and positive feedback (PFB). Together, they form an integrative unit maintaining system's autonomy and functional stability. It is proposed that phylogenetic development of different species is implemented by the splitting of "rudimentary" characters into two relatively independent functional parts that become encoded in chromosomes. The functional correlate of splitting mechanisms is RL. Inversion of phylogenetic mechanisms during ontogenetic development leads cell differentiation until cells reach mature states. Deterioration of reciprocal structure in the genome during ontogenesis gives rise of pathological conditions characterized by unsteadiness of the system. Uncontrollable cell proliferation and invasive cell growth are the leading features of the functional outcomes of malfunctioning systems. The regulatory element responsible for these changes is RL. In matrix language, pathological regulation is represented by matrices having positive values of diagonal elements ( TrA  > 0) and also positive values of matrix determinant ( detA  > 0). Regulatory structures of that kind can be obtained if the negative entry of the matrix corresponding to RL is replaced with the positive one. To describe not only normal but also pathological states of BS, a unit matrix should be added to the basis matrices representing RL, NFB and PFB. A mathematical structure corresponding to the set of these four basis functional patterns (matrices) is a split quaternion (coquaternion). The structure and specific role of basis elements comprising four-dimensional linear space of split quaternions help to understand what

  6. X-ray holographic microscopy with zone plates applied to biological samples in the water window using 3rd harmonic radiation from the free-electron laser FLASH.

    Science.gov (United States)

    Gorniak, T; Heine, R; Mancuso, A P; Staier, F; Christophis, C; Pettitt, M E; Sakdinawat, A; Treusch, R; Guerassimova, N; Feldhaus, J; Gutt, C; Grübel, G; Eisebitt, S; Beyer, A; Gölzhäuser, A; Weckert, E; Grunze, M; Vartanyants, I A; Rosenhahn, A

    2011-06-06

    The imaging of hydrated biological samples - especially in the energy window of 284-540 eV, where water does not obscure the signal of soft organic matter and biologically relevant elements - is of tremendous interest for life sciences. Free-electron lasers can provide highly intense and coherent pulses, which allow single pulse imaging to overcome resolution limits set by radiation damage. One current challenge is to match both the desired energy and the intensity of the light source. We present the first images of dehydrated biological material acquired with 3rd harmonic radiation from FLASH by digital in-line zone plate holography as one step towards the vision of imaging hydrated biological material with photons in the water window. We also demonstrate the first application of ultrathin molecular sheets as suitable substrates for future free-electron laser experiments with biological samples in the form of a rat fibroblast cell and marine biofouling bacteria Cobetia marina.

  7. Determining the impacts of trawling on benthic function in European waters : a biological traits approach

    DEFF Research Database (Denmark)

    Bolam, Stefan; Kenny, Andrew; Garcia, Clement

    trait composition and environmental variables (depth, sediment granulometry); ii) determine the relationship between traits and habitat type (EUNIS level 4); and iii) assess the relationships between trawling pressure (using data derived under BENTHIS; see Eigaard et al., this volume) and traits...... characteristics, have allowed us to better understand the interactions between the benthic fauna and their environment at a functional level. We present the initial findings of work conducted under the auspices of the EU-funded project ‘BENTHIS’ which aims to improve our understanding of the impacts of trawling...... on benthic ecosystem functioning over much larger spatial scales than previously undertaken. Biological traits information from 887 stations across European waters (Norwegian, UK, Belgian, Dutch, Danish waters, the Mediterranean and Black Sea) were analysed to: i) quantify the relationships between infaunal...

  8. Functionalization and microfluidic integration of silicon nanowire biologically gated field effect transistors

    DEFF Research Database (Denmark)

    Pfreundt, Andrea; Svendsen, Winnie Edith; Dimaki, Maria

    2016-01-01

    This thesis deals with the development of a novel biosensor for the detection of biomolecules based on a silicon nanowire biologically gated field-effect transistor and its integration into a point-of-care device. The sensor and electrical on-chip integration was developed in a different project....... The presented research is based on this sensor structure and investigates its potential as a versatile biomarker detection platform by evaluating different functionalization approaches. The functionalization of the silicon sensor surface with organic molecules was investigated in detail to determine...... the suitability of different methods for the preparation of organic interfaces for protein attachment. Oxide-free silicon surfaces offer unique possibilities to create highly sensitive sensor surfaces for charge detection due to the lack of an insulating oxide layer, but the highly reactive surface presents...

  9. Functionalization and microfluidic integration of silicon nanowire biologically gated field effect transistors

    DEFF Research Database (Denmark)

    Pfreundt, Andrea

    This thesis deals with the development of a novel biosensor for the detection of biomolecules based on a silicon nanowire biologically gated field-effect transistor and its integration into a point-of-care device. The sensor and electrical on-chip integration was developed in a different project....... The presented research is based on this sensor structure and investigates its potential as a versatile biomarker detection platform by evaluating different functionalization approaches. The functionalization of the silicon sensor surface with organic molecules was investigated in detail to determine...... the suitability of different methods for the preparation of organic interfaces for protein attachment. Oxide-free silicon surfaces offer unique possibilities to create highly sensitive sensor surfaces for charge detection due to the lack of an insulating oxide layer, but the highly reactive surface presents...

  10. Structural and Conformational Chemistry from Electrochemical Molecular Machines. Replicating Biological Functions. A Review.

    Science.gov (United States)

    Otero, Toribio F

    2017-12-14

    Each constitutive chain of a conducting polymer electrode acts as a reversible multi-step electrochemical molecular motor: reversible reactions drive reversible conformational movements of the chain. The reaction-driven cooperative actuation of those molecular machines generates, or destroys, inside the film the free volume required to lodge/expel balancing counterions and solvent: reactions drive reversible film volume variations, which basic structural components are here identified and quantified from electrochemical responses. The content of the reactive dense gel (chemical molecular machines, ions and water) mimics that of the intracellular matrix in living functional cells. Reaction-driven properties (composition-dependent properties) and devices replicate biological functions and organs. An emerging technological world of soft, wet, reaction-driven, multifunctional and biomimetic devices and the concomitant zoomorphic or anthropomorphic robots is presented. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Enzymes for ecdysteroid biosynthesis: their biological functions in insects and beyond.

    Science.gov (United States)

    Niwa, Ryusuke; Niwa, Yuko S

    2014-01-01

    Steroid hormones are responsible for the coordinated regulation of many aspects of biological processes in multicellular organisms. Since the last century, many studies have identified and characterized steroidogenic enzymes in vertebrates, including mammals. However, much less is known about invertebrate steroidogenic enzymes. In the last 15 years, a number of steroidogenic enzymes and their functions have been characterized in ecdysozoan animals, especially in the fruit fly Drosophila melanogaster. In this review, we summarize the latest knowledge of enzymes crucial for synthesizing ecdysteroids, the principal insect steroid hormones. We also discuss the functional conservation and diversity of ecdysteroidogenic enzymes in other insects and even non-insect species, such as nematodes, vertebrates, and lower eukaryotes.

  12. The RNAi Universe in Fungi: A Varied Landscape of Small RNAs and Biological Functions.

    Science.gov (United States)

    Torres-Martínez, Santiago; Ruiz-Vázquez, Rosa M

    2017-09-08

    RNA interference (RNAi) is a conserved eukaryotic mechanism that uses small RNA molecules to suppress gene expression through sequence-specific messenger RNA degradation, translational repression, or transcriptional inhibition. In filamentous fungi, the protective function of RNAi in the maintenance of genome integrity is well known. However, knowledge of the regulatory role of RNAi in fungi has had to wait until the recent identification of different endogenous small RNA classes, which are generated by distinct RNAi pathways. In addition, RNAi research on new fungal models has uncovered the role of small RNAs and RNAi pathways in the regulation of diverse biological functions. In this review, we give an up-to-date overview of the different classes of small RNAs and RNAi pathways in fungi and their roles in the defense of genome integrity and regulation of fungal physiology and development, as well as in the interaction of fungi with biotic and abiotic environments.

  13. Synthesis and Biological Evaluation of Polar Functionalities Containing Nitrodihydroimidazooxazoles as Anti-TB Agents.

    Science.gov (United States)

    Yempalla, Kushalava Reddy; Munagala, Gurunadham; Singh, Samsher; Kour, Gurleen; Sharma, Shweta; Chib, Reena; Kumar, Sunil; Wazir, Priya; Singh, G D; Raina, Sushil; Bharate, Sonali S; Khan, Inshad Ali; Vishwakarma, Ram A; Singh, Parvinder Pal

    2015-10-08

    Novel polar functionalities containing 6-nitro-2,3-dihydroimidazooxazole (NHIO) analogues were synthesized to produce a compound with enhanced solubility. Polar functionalities including sulfonyl, uridyl, and thiouridyl-bearing NHIO analogues were synthesized and evaluated against Mycobacterium tuberculosis (MTB) H37Rv. The aqueous solubility of compounds with MIC values ≤0.5 μg/mL were tested, and six compounds showed enhanced aqueous solubility. The best six compounds were further tested against resistant (Rif(R) and MDR) and dormant strains of MTB and tested for cytotoxicity in HepG2 cell line. Based on its overall in vitro characteristics and solubility profile, compound 6d was further shown to possess high microsomal stability, solubility under all tested biological conditions (PBS, SGF and SIF), and favorable oral in vivo pharmacokinetics and in vivo efficacy.

  14. Large work function difference driven electron transfer from electrides to single-walled carbon nanotubes

    KAUST Repository

    Menamparambath, Mini Mol

    2014-06-23

    A difference in work function plays a key role in charge transfer between two materials. Inorganic electrides provide a unique opportunity for electron transfer since interstitial anionic electrons result in a very low work function of 2.4-2.6 eV. Here we investigated charge transfer between two different types of electrides, [Ca2N]+·e- and [Ca 24Al28O64]4+·4e-, and single-walled carbon nanotubes (SWNTs) with a work function of 4.73-5.05 eV. [Ca2N]+·e- with open 2-dimensional electron layers was more effective in donating electrons to SWNTs than closed cage structured [Ca24Al28O64] 4+·4e- due to the higher electron concentration (1.3 × 1022 cm-3) and mobility (∼200 cm 2 V-1 s-1 at RT). A non-covalent conjugation enhanced near-infrared fluorescence of SWNTs as high as 52%. The field emission current density of electride-SWNT-silver paste dramatically increased by a factor of 46000 (14.8 mA cm-2) at 2 V μm-1 (3.5 wt% [Ca2N]+·e-) with a turn-on voltage of 0.85 V μm-1. This journal is © the Partner Organisations 2014.

  15. Differential Function of Lip Residues in the Mechanism and Biology of an Anthrax Hemophore

    Energy Technology Data Exchange (ETDEWEB)

    Ekworomadu, MarCia T.; Poor, Catherine B.; Owens, Cedric P.; Balderas, Miriam A.; Fabian, Marian; Olson, John S.; Murphy, Frank; Balkabasi, Erol; Honsa, Erin S.; He, Chuan; Goulding, Celia W.; Maresso, Anthony W. (Baylor); (UCI); (Cornell); (Rice); (UC)

    2014-10-02

    To replicate in mammalian hosts, bacterial pathogens must acquire iron. The majority of iron is coordinated to the protoporphyrin ring of heme, which is further bound to hemoglobin. Pathogenic bacteria utilize secreted hemophores to acquire heme from heme sources such as hemoglobin. Bacillus anthracis, the causative agent of anthrax disease, secretes two hemophores, IsdX1 and IsdX2, to acquire heme from host hemoglobin and enhance bacterial replication in iron-starved environments. Both proteins contain NEAr-iron Transporter (NEAT) domains, a conserved protein module that functions in heme acquisition in Gram-positive pathogens. Here, we report the structure of IsdX1, the first of a Gram-positive hemophore, with and without bound heme. Overall, IsdX1 forms an immunoglobin-like fold that contains, similar to other NEAT proteins, a 3{sub 10}-helix near the heme-binding site. Because the mechanistic function of this helix in NEAT proteins is not yet defined, we focused on the contribution of this region to hemophore and NEAT protein activity, both biochemically and biologically in cultured cells. Site-directed mutagenesis of amino acids in and adjacent to the helix identified residues important for heme and hemoglobin association, with some mutations affecting both properties and other mutations affecting only heme stabilization. IsdX1 with mutations that reduced the ability to associate with hemoglobin and bind heme failed to restore the growth of a hemophore-deficient strain of B. anthracis on hemoglobin as the sole iron source. These data indicate that not only is the 3{sub 10}-helix important for NEAT protein biology, but also that the processes of hemoglobin and heme binding can be both separate as well as coupled, the latter function being necessary for maximal heme-scavenging activity. These studies enhance our understanding of NEAT domain and hemophore function and set the stage for structure-based inhibitor design to block NEAT domain interaction with

  16. Structure of the channeling electrons wave functions under dynamical chaos conditions

    International Nuclear Information System (INIS)

    Shul’ga, N.F.; Syshchenko, V.V.; Tarnovsky, A.I.; Isupov, A.Yu.

    2016-01-01

    The stationary wave functions of fast electrons axially channeling in the silicon crystal near [1 1 0] direction have been found numerically for integrable and non-integrable cases, for which the classical motion is regular and chaotic, respectively. The nodal structure of the wave functions in the quasi-classical region, where the energy levels density is high, is agreed with quantum chaos theory predictions.

  17. Electron binding energies of organic azides: Green’s function and density functional theory versus Hartree Fock calculations

    Science.gov (United States)

    Mateus, Margarida P. S.; Cabral, Benedito J. C.

    2007-11-01

    Theoretical calculations for the electron binding energies (EBEs) of several organic azides including hydrazoic acid, methyl azide, ethyl azide, 2-chloroethyl azide, 2-azidoethanol, azidoacetone, 2-azidoacetic acid, 3-azido-2-butanone, and 2-azidoethyl acetate are reported. EBEs were calculated with ab initio Green's function (GF) and density functional theory (DFT). Complete basis-set extrapolated coupled cluster calculations with single, double, and perturbative triple excitations [CCSD(T)] for the first ionization energy of azides are also reported. It is shown that EBEs from GF and DFT calculations are in better agreement with experiment than Hartree-Fock predictions.

  18. Benchmarks for electronically excited states: Time-dependent density functional theory and density functional theory based multireference configuration interaction

    DEFF Research Database (Denmark)

    Silva-Junior, Mario R.; Schreiber, Marko; Sauer, Stephan P. A.

    2008-01-01

    Time-dependent density functional theory (TD-DFT) and DFT-based multireference configuration interaction (DFT/MRCI) calculations are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies, oscillator strengths, and excited-state dipole...... moments are computed using the same geometries (MP2/6-31G*) and basis set (TZVP) as in our previous ab initio benchmark study on electronically excited states. The results from TD-DFT (with the functionals BP86, B3LYP, and BHLYP) and from DFT/MRCI are compared against the previous high-level ab initio...

  19. Characterization and biological function of milk-derived miRNAs.

    Science.gov (United States)

    Golan-Gerstl, Regina; Elbaum Shiff, Yaffa; Moshayoff, Vardit; Schecter, Daniel; Leshkowitz, Dena; Reif, Shimon

    2017-10-01

    Breastfeeding is associated with reduced risk of infection, immune-mediated disorders, obesity, and even cancer. Recently it was found that breast milk contains a variety of microRNAs (miRNAs) in the skim and fat layer that can be transferred to infants, and appear to play important roles in those biological functions. This study applied next generation sequencing and quantitative real-time PCR analysis to determine the miRNA expression profile of the skim and fat fraction of human, goat, and bovine milk as well as infant formulas. Human and mammalian milk were found to contain known advantageous miRNAs in exosomes and also in the fat layer. These miRNAs are highly conserved in human, bovine and goat milk. However, they were not detected in several infant formulas. Further, miRNAs present in milk were able to enter normal and tumor cells and affect their biological functions. Following incubation of milk derived human miRNA with normal and cancer cells, the expression of miRNA-148a was upregulated and the expression of the DNA methyltransferase1 target gene of miRNA-148a was down regulated. These results reinforce previous findings on the importance of miRNA in breast milk. Future studies should concentrate on the addition of miRNA to infant formulas. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. What will result from the interaction between functional and evolutionary biology?

    Science.gov (United States)

    Morange, Michel

    2011-03-01

    The modern synthesis has been considered to be wrongly called a "synthesis", since it had completely excluded embryology, and many other disciplines. The recent developments of Evo-Devo have been seen as a step in the right direction, as complementing the modern synthesis, and probably leading to a "new synthesis". My argument is that the absence of embryology from the modern synthesis was the visible sign of a more profound lack: the absence of functional biology in the evolutionary synthesis. I will consider the reasons for this absence, as well as the recent transformations which favoured a closer interaction between these two branches of biology. Then I will describe two examples of recent work in which functional and evolutionary questioning were tightly linked. The most significant part of the paper will be devoted to the transformation of evolutionary theory that can be expected from this encounter: a deep transformation, or simply an experimental confirmation of this theory? I will not choose between these two different possibilities, but will discuss some of the difficulties which make the choice problematic. Copyright © 2010 Elsevier Ltd. All rights reserved.

  1. Functional and molecular characterization of the role of CTCF in human embryonic stem cell biology.

    Science.gov (United States)

    Balakrishnan, Sri Kripa; Witcher, Michael; Berggren, Travis W; Emerson, Beverly M

    2012-01-01

    The CCCTC-binding factor CTCF is the only known vertebrate insulator protein and has been shown to regulate important developmental processes such as imprinting, X-chromosome inactivation and genomic architecture. In this study, we examined the role of CTCF in human embryonic stem cell (hESC) biology. We demonstrate that CTCF associates with several important pluripotency genes, including NANOG, SOX2, cMYC and LIN28 and is critical for hESC proliferation. CTCF depletion impacts expression of pluripotency genes and accelerates loss of pluripotency upon BMP4 induced differentiation, but does not result in spontaneous differentiation. We find that CTCF associates with the distal ends and internal sites of the co-regulated 160 kb NANOG-DPPA3-GDF3 locus. Each of these sites can function as a CTCF-dependent enhancer-blocking insulator in heterologous assays. In hESCs, CTCF exists in multisubunit protein complexes and can be poly(ADP)ribosylated. Known CTCF cofactors, such as Cohesin, differentially co-localize in the vicinity of specific CTCF binding sites within the NANOG locus. Importantly, the association of some cofactors and protein PARlation selectively changes upon differentiation although CTCF binding remains constant. Understanding how unique cofactors may impart specialized functions to CTCF at specific genomic locations will further illuminate its role in stem cell biology.

  2. Functional and molecular characterization of the role of CTCF in human embryonic stem cell biology.

    Directory of Open Access Journals (Sweden)

    Sri Kripa Balakrishnan

    Full Text Available The CCCTC-binding factor CTCF is the only known vertebrate insulator protein and has been shown to regulate important developmental processes such as imprinting, X-chromosome inactivation and genomic architecture. In this study, we examined the role of CTCF in human embryonic stem cell (hESC biology. We demonstrate that CTCF associates with several important pluripotency genes, including NANOG, SOX2, cMYC and LIN28 and is critical for hESC proliferation. CTCF depletion impacts expression of pluripotency genes and accelerates loss of pluripotency upon BMP4 induced differentiation, but does not result in spontaneous differentiation. We find that CTCF associates with the distal ends and internal sites of the co-regulated 160 kb NANOG-DPPA3-GDF3 locus. Each of these sites can function as a CTCF-dependent enhancer-blocking insulator in heterologous assays. In hESCs, CTCF exists in multisubunit protein complexes and can be poly(ADPribosylated. Known CTCF cofactors, such as Cohesin, differentially co-localize in the vicinity of specific CTCF binding sites within the NANOG locus. Importantly, the association of some cofactors and protein PARlation selectively changes upon differentiation although CTCF binding remains constant. Understanding how unique cofactors may impart specialized functions to CTCF at specific genomic locations will further illuminate its role in stem cell biology.

  3. Biology of bone and how it orchestrates the form and function of the skeleton

    Science.gov (United States)

    Sommerfeldt, D. W.; Rubin, C. T.

    2001-01-01

    The principal role of the skeleton is to provide structural support for the body. While the skeleton also serves as the body's mineral reservoir, the mineralized structure is the very basis of posture, opposes muscular contraction resulting in motion, withstands functional load bearing, and protects internal organs. Although the mass and morphology of the skeleton is defined, to some extent, by genetic determinants, it is the tissue's ability to remodel--the local resorption and formation of bone--which is responsible for achieving this intricate balance between competing responsibilities. The aim of this review is to address bone's form-function relationship, beginning with extensive research in the musculoskeletal disciplines, and focusing on several recent cellular and molecular discoveries which help understand the complex interdependence of bone cells, growth factors, physical stimuli, metabolic demands, and structural responsibilities. With a clinical and spine-oriented audience in mind, the principles of bone cell and molecular biology and physiology are presented, and an attempt has been made to incorporate epidemiologic data and therapeutic implications. Bone research remains interdisciplinary by nature, and a deeper understanding of bone biology will ultimately lead to advances in the treatment of diseases and injuries to bone itself.

  4. A Multi-Functional Power Electronic Converter in Distributed Generation Power Systems

    DEFF Research Database (Denmark)

    Chen, Zhe; Blaabjerg, Frede; Pedersen, John Kim

    2005-01-01

    This paper presents a power electronic converter which is used as an interface for a distributed generation unit/energy storage device, and also functioned as an active power compensator in a hybrid compensation system. The operation and control of the converter have been described. An example...... and passive filters connected to each distorting load or distributed generation (DG) unit. The passive filters are distributely located to remove major harmonics and provide reactive power compensation. The active power electronic filter corrects the system unbalance, removes the remaining harmonic components...... of the converter interfacing a wind power generation unit is also given. The power electronic interface performs the optimal operation in the wind turbine system to extract the maximum wind power, while it also plays a key role in a hybrid compensation system that consists of the active power electronic converter...

  5. Modification Of The Electron Energy Distribution Function During Lithium Experiments On The National Spherical Torus Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Jaworski, M A; Gray, T K; Kaita, R; Kallman, J; Kugel, H; LeBlanc, B; McLean, A; Sabbagh, S A; Soukanovskii, V; Stotler, D P

    2011-06-03

    The National Spherical Torus Experiment (NSTX) has recently studied the use of a liquid lithium divertor (LLD). Divertor Langmuir probes have also been installed for making measurements of the local plasma conditions. A non-local probe interpretation method is used to supplement the classical probe interpretation and obtain measurements of the electron energy distribution function (EEDF) which show the occurrence of a hot-electron component. Analysis is made of two discharges within a sequence that exhibited changes in plasma fueling efficiency. It is found that the local electron temperature increases and that this increase is most strongly correlated with the energy contained within the hot-electron population. Preliminary interpretative modeling indicates that kinetic effects are likely in the NSTX.

  6. Conceptual density functional theory for electron transfer and transport in mesoscopic systems.

    Science.gov (United States)

    Bueno, Paulo R; Miranda, David A

    2017-02-22

    Molecular and supramolecular systems are essentially mesoscopic in character. The electron self-exchange, in the case of energy fluctuations, or electron transfer/transport, in the case of the presence of an externally driven electrochemical potential, between mesoscopic sites is energetically driven in such a manner where the electrochemical capacitance (C [small mu, Greek, macron] ) is fundamental. Thus, the electron transfer/transport through channels connecting two distinct energetic (ΔE [small mu, Greek, macron] ) and spatially separated mesoscopic sites is capacitively modulated. Remarkably, the relationship between the quantum conductance (G) and the standard electrochemical rate constant (k r ), which is indispensable to understanding the physical and chemical characteristics governing electron exchange in molecular scale systems, was revealed to be related to C [small mu, Greek, macron] , that is, C [small mu, Greek, macron] = G/k r . Accordingly, C [small mu, Greek, macron] is the proportional missing term that controls the electron transfer/transport in mesoscopic systems in a wide-range, and equally it can be understood from first principles density functional quantum mechanical approaches. Indeed the differences in energy between states is calculated (or experimentally accessed) throughout the electrochemical capacitance as ΔE [small mu, Greek, macron] = β/C [small mu, Greek, macron] , and thus constitutes the driving force for G and/or k r , where β is only a proportional constant that includes the square of the unit electron charge times the square of the number of electron particles interchanged.

  7. Electronic and structural properties of ultrathin tungsten nanowires and nanotubes by density functional theory calculation

    International Nuclear Information System (INIS)

    Sun, Shih-Jye; Lin, Ken-Huang; Li, Jia-Yun; Ju, Shin-Pon

    2014-01-01

    The simulated annealing basin-hopping method incorporating the penalty function was used to predict the lowest-energy structures for ultrathin tungsten nanowires and nanotubes of different sizes. These predicted structures indicate that tungsten one-dimensional structures at this small scale do not possess B.C.C. configuration as in bulk tungsten material. In order to analyze the relationship between multi-shell geometries and electronic transfer, the electronic and structural properties of tungsten wires and tubes including partial density of state and band structures which were determined and analyzed by quantum chemistry calculations. In addition, in order to understand the application feasibility of these nanowires and tubes on nano-devices such as field emitters or chemical catalysts, the electronic stability of these ultrathin tungsten nanowires was also investigated by density functional theory calculations.

  8. Density-functional theory based on the electron distribution on the energy coordinate

    Science.gov (United States)

    Takahashi, Hideaki

    2018-03-01

    We developed an electronic density functional theory utilizing a novel electron distribution n(ɛ) as a basic variable to compute ground state energy of a system. n(ɛ) is obtained by projecting the electron density n({\\boldsymbol{r}}) defined on the space coordinate {\\boldsymbol{r}} onto the energy coordinate ɛ specified with the external potential {\\upsilon }ext}({\\boldsymbol{r}}) of interest. It was demonstrated that the Kohn–Sham equation can also be formulated with the exchange-correlation functional E xc[n(ɛ)] that employs the density n(ɛ) as an argument. It turned out an exchange functional proposed in our preliminary development suffices to describe properly the potential energies of several types of chemical bonds with comparable accuracies to the corresponding functional based on local density approximation. As a remarkable feature of the distribution n(ɛ) it inherently involves the spatially non-local information of the exchange hole at the bond dissociation limit in contrast to conventional approximate functionals. By taking advantage of this property we also developed a prototype of the static correlation functional E sc including no empirical parameters, which showed marked improvements in describing the dissociations of covalent bonds in {{{H}}}2,{{{C}}}2{{{H}}}4 and {CH}}4 molecules.

  9. Path integrals for electronic densities, reactivity indices, and localization functions in quantum systems.

    Science.gov (United States)

    Putz, Mihai V

    2009-11-10

    The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI) development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr's quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions - all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving) many-electronic systems.

  10. Path Integrals for Electronic Densities, Reactivity Indices, and Localization Functions in Quantum Systems

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz

    2009-11-01

    Full Text Available The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr’s quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions – all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving many-electronic systems.

  11. Density functional study of AgScO 2: Electronic and optical properties

    Indian Academy of Sciences (India)

    2017-06-20

    Jun 20, 2017 ... The density functional theory (DFT) in the framework of full potential linearized augmented plane wave (FP-LAPW) scheme has been used for the present calculations with local densityapproximation (LDA) and generalized gradient approximation (GGA). Electronic properties deal with energy bands and ...

  12. Density functional theory for strongly-interacting electrons: Perspectives for Physics and Chemistry

    NARCIS (Netherlands)

    Gori Giorgi, P.; Seidl, M.

    2010-01-01

    Improving the accuracy and thus broadening the applicability of electronic density functional theory (DFT) is crucial to many research areas, from material science, to theoretical chemistry, biophysics and biochemistry. In the last three years, the mathematical structure of the strong-interaction

  13. Transmission Electron Microscopy Specimen Preparation Method for Multiphase Porous Functional Ceramics

    DEFF Research Database (Denmark)

    Zhang, Wei; Kuhn, Luise Theil; Jørgensen, Peter Stanley

    2013-01-01

    An optimum method is proposed to prepare thin foil transmission electron microscopy (TEM) lamellae of multiphase porous functional ceramics: prefilling the pore space of these materials with an epoxy resin prior to focused ion beam milling. Several advantages of epoxy impregnation are demonstrate...

  14. Method of calculation of electron states in large molecules using one-center functions of fragments

    Science.gov (United States)

    Gribov, L. A.

    2016-12-01

    A method of calculation of electron states in large molecules is proposed on the basis of the linear combinations of one-center functions of fragments with their interactions subsequently taken into account. It is shown that the computing procedure can be implemented similarly to the conventional one using LCAO.

  15. Construction of New Electronic Density Functionals with Error Estimation Through Fitting

    DEFF Research Database (Denmark)

    Petzold, V.; Bligaard, T.; Jacobsen, K. W.

    2012-01-01

    We investigate the possibilities and limitations for the development of new electronic density functionals through large-scale fitting to databases of binding energies obtained experimentally or through high-quality calculations. We show that databases with up to a few hundred entries allow for up...

  16. Orbital energies and negative electron affinities from density functional theory: Insight from the integer discontinuity

    Science.gov (United States)

    Teale, Andrew M.; de Proft, Frank; Tozer, David J.

    2008-07-01

    Orbital energies in Kohn-Sham density functional theory (DFT) are investigated, paying attention to the role of the integer discontinuity in the exact exchange-correlation potential. A series of closed-shell molecules are considered, comprising some that vertically bind an excess electron and others that do not. High-level ab initio electron densities are used to calculate accurate orbital energy differences, Δɛ, between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO), using the same potential for both. They are combined with accurate vertical ionization potentials, I0, and electron affinities, A0, to determine accurate ``average'' orbital energies. These are the orbital energies associated with an exchange-correlation potential that averages over a constant jump in the accurate potential, of magnitude ΔXC=(I0-A0)-Δɛ, as given by the discontinuity analysis. Local functional HOMO energies are shown to be almost an order of magnitude closer to these average values than to -I0, with typical discrepancies of just 0.02 a.u. For systems that do not bind an excess electron, this level of agreement is only achieved when A0 is set equal to the negative experimental affinity from electron transmission spectroscopy (ETS); it degrades notably when the zero ground state affinity is instead used. Analogous observations are made for the local functional LUMO energies, although the need to use the ETS affinities is less pronounced for systems where the ETS values are very negative. The application of an asymptotic correction recovers the preference, leading to positive LUMO energies (but bound orbitals) for these systems, consistent with the behavior of the average energies. The asymptotically corrected LUMO energies typically agree with the average values to within 0.02 a.u., comparable to that observed with the HOMOs. The study provides numerical support for the view that local functionals exhibit a near-average behavior

  17. Novel Aspects of Materials Processing by Ultrafast Lasers: From Electronic to Biological and Cultural Heritage Applications

    International Nuclear Information System (INIS)

    Fotakis, C; Zorba, V; Stratakis, E; Athanassiou, A; Tzanetakis, P; Zergioti, I; Papagoglou, D G; Sambani, K; Filippidis, G; Farsari, M; Pouli, V; Bounos, G; Georgiou, S

    2007-01-01

    Materials processing by ultrafast lasers offers several distinct possibilities for micro/nano scale applications. This is due to the unique characteristics of the laser-matter interactions involved, when sub-picosecond pulses are employed. Prospects arising will be discussed in the context of surface and in bulk laser induced modifications. In particular, examples of diverse applications including the development and functionalization of laser engineered surfaces, the laser transfer of biomolecules and the functionalization of 3D structures constructed by three-photon stereolithography will be presented. Furthermore, the removal of molecular substrates by ultrafast laser ablation will be discussed with emphasis placed on assessing the photochemical changes induced in the remaining bulk material. The results indicate that in femtosecond laser processing of organic materials, besides the well acknowledged morphological advantages, a second fundamental factor responsible for its success pertains to the selective chemical effects. This is crucial for the laser cleaning of sensitive painted artworks

  18. Tuning electronic properties in graphene quantum dots by chemical functionalization: Density functional theory calculations

    Science.gov (United States)

    Abdelsalam, Hazem; Elhaes, Hanan; Ibrahim, Medhat A.

    2018-03-01

    The energy gap and dipole moment of chemically functionalized graphene quantum dots are investigated by density functional theory. The energy gap can be tuned through edge passivation by different elements or groups. Edge passivation by oxygen considerably decreases the energy gap in hexagonal nanodots. Edge states in triangular quantum dots can also be manipulated by passivation with fluorine. The dipole moment depends on: (a) shape and edge termination of the quantum dot, (b) attached group, and (c) position to which the groups are attached. Depending on the position of attached groups, the total dipole can be increased, decreased, or eliminated.

  19. Role of soil biology and soil functions in relation to land use intensity.

    Science.gov (United States)

    Bondi, Giulia; Wall, David; Bacher, Matthias; Emmet-Booth, Jeremy; Graça, Jessica; Marongiu, Irene; Creamer, Rachel

    2017-04-01

    The delivery of the ecosystem's functions is predominantly controlled by soil biology. The biology found in a gram of soil contains more than ten thousand individual species of bacteria and fungi (Torsvik et al., 1990). Understanding the role and the requirements of these organisms is essential for the protection and the sustainable use of soils. Soil biology represents the engine of all the processes occurring in the soil and it supports the ecosystem services such as: 1) nutrient mineralisation 2) plant production 3) water purification and regulation and 4) carbon cycling and storage. During the last years land management type and intensity have been identified as major drivers for microbial performance in soil. For this reason land management needs to be appropriately studied to understand the role of soil biology within this complex interplay of functions. We aimed to study whether and how land management drives soil biological processes and related functions. To reach this objective we built a land use intensity index (LUI) able to quantify the impact of the common farming practices carried out in Irish grassland soils. The LUI is derived from a detailed farmer questionnaire on grassland management practices at 38 farms distributed in the five major agro-climatic regions of Ireland defined by Holden and Brereton (2004). Soils were classified based on their drainage status according to the Irish Soil Information System by Creamer et al. (2014). This detailed questionnaire is then summarised into 3 management intensity components: (i) intensity of Fertilisation (Fi), (ii) frequency of Mowing (Mi) and (iii) intensity of Livestock Grazing (Gi). Sites were sampled to assess the impact of land management intensity on microbial community structure and enzyme behaviour in relation to nitrogen, phosphorus and carbon cycling. Preliminary results for enzymes linked to C and N cycles showed higher activity in relation to low grazing pressure (low Gi). Enzymes linked to P

  20. Unsupervised Learning and Pattern Recognition of Biological Data Structures with Density Functional Theory and Machine Learning.

    Science.gov (United States)

    Chen, Chien-Chang; Juan, Hung-Hui; Tsai, Meng-Yuan; Lu, Henry Horng-Shing

    2018-01-11

    By introducing the methods of machine learning into the density functional theory, we made a detour for the construction of the most probable density function, which can be estimated by learning relevant features from the system of interest. Using the properties of universal functional, the vital core of density functional theory, the most probable cluster numbers and the corresponding cluster boundaries in a studying system can be simultaneously and automatically determined and the plausibility is erected on the Hohenberg-Kohn theorems. For the method validation and pragmatic applications, interdisciplinary problems from physical to biological systems were enumerated. The amalgamation of uncharged atomic clusters validated the unsupervised searching process of the cluster numbers and the corresponding cluster boundaries were exhibited likewise. High accurate clustering results of the Fisher's iris dataset showed the feasibility and the flexibility of the proposed scheme. Brain tumor detections from low-dimensional magnetic resonance imaging datasets and segmentations of high-dimensional neural network imageries in the Brainbow system were also used to inspect the method practicality. The experimental results exhibit the successful connection between the physical theory and the machine learning methods and will benefit the clinical diagnoses.

  1. How biological soil crusts became recognized as a functional unit: a selective history

    Science.gov (United States)

    Lange, Otto L.; Belnap, Jayne

    2016-01-01

    It is surprising that despite the world-wide distribution and general importance of biological soil crusts (biocrusts), scientific recognition and functional analysis of these communities is a relatively young field of science. In this chapter, we sketch the historical lines that led to the recognition of biocrusts as a community with important ecosystem functions. The idea of biocrusts as a functional ecological community has come from two main scientific branches: botany and soil science. For centuries, botanists have long recognized that multiple organisms colonize the soil surface in the open and often dry areas occurring between vascular plants. Much later, after the initial taxonomic and phyto-sociological descriptions were made, soil scientists and agronomists observed that these surface organisms interacted with soils in ways that changed the soil structure. In the 1970’s, research on these communities as ecological units that played an important functional role in drylands began in earnest, and these studies have continued to this day. Here, we trace the history of these studies from the distant past until 1990, when biocrusts became well-known to scientists and the public.

  2. Self-Consistent Hybrid Functional Calculations: Implications for Structural, Electronic, and Optical Properties of Oxide Semiconductors

    Science.gov (United States)

    Fritsch, Daniel; Morgan, Benjamin J.; Walsh, Aron

    2017-01-01

    The development of new exchange-correlation functionals within density functional theory means that increasingly accurate information is accessible at moderate computational cost. Recently, a newly developed self-consistent hybrid functional has been proposed (Skone et al., Phys. Rev. B 89:195112, 2014), which allows for a reliable and accurate calculation of material properties using a fully ab initio procedure. Here, we apply this new functional to wurtzite ZnO, rutile SnO2, and rocksalt MgO. We present calculated structural, electronic, and optical properties, which we compare to results obtained with the PBE and PBE0 functionals. For all semiconductors considered here, the self-consistent hybrid approach gives improved agreement with experimental structural data relative to the PBE0 hybrid functional for a moderate increase in computational cost, while avoiding the empiricism common to conventional hybrid functionals. The electronic properties are improved for ZnO and MgO, whereas for SnO2 the PBE0 hybrid functional gives the best agreement with experimental data.

  3. Two-electron Rabi oscillations in real-time time-dependent density-functional theory.

    Science.gov (United States)

    Habenicht, Bradley F; Tani, Noriyuki P; Provorse, Makenzie R; Isborn, Christine M

    2014-11-14

    We investigate the Rabi oscillations of electrons excited by an applied electric field in several simple molecular systems using time-dependent configuration interaction (TDCI) and real-time time-dependent density-functional theory (RT-TDDFT) dynamics. While the TDCI simulations exhibit the expected single-electron Rabi oscillations at a single resonant electric field frequency, Rabi oscillations in the RT-TDDFT simulations are a two-electron process. The existence of two-electron Rabi oscillations is determined both by full population inversion between field-free molecular orbitals and the behavior of the instantaneous dipole moment during the simulations. Furthermore, the Rabi oscillations in RT-TDDFT are subject to an intensity threshold of the electric field, below which Rabi oscillations do not occur and above which the two-electron Rabi oscillations occur at a broad range of frequencies. It is also shown that at field intensities near the threshold intensity, the field frequency predicted to induce Rabi oscillations by linear response TDDFT only produces detuned Rabi oscillations. Instead, the field frequency that yields the full two-electron population inversion and Rabi oscillation behavior is shown to be the average of single-electron transition frequencies from the ground S0 state and the doubly-excited S2 state. The behavior of the two-electron Rabi oscillations is rationalized via two possible models. The first model is a multi-photon process that results from the electric field interacting with the three level system such that three level Rabi oscillations may occur. The second model suggests that the mean-field nature of RT-TDDFT induces paired electron propagation.

  4. Two-electron Rabi oscillations in real-time time-dependent density-functional theory

    International Nuclear Information System (INIS)

    Habenicht, Bradley F.; Tani, Noriyuki P.; Provorse, Makenzie R.; Isborn, Christine M.

    2014-01-01

    We investigate the Rabi oscillations of electrons excited by an applied electric field in several simple molecular systems using time-dependent configuration interaction (TDCI) and real-time time-dependent density-functional theory (RT-TDDFT) dynamics. While the TDCI simulations exhibit the expected single-electron Rabi oscillations at a single resonant electric field frequency, Rabi oscillations in the RT-TDDFT simulations are a two-electron process. The existence of two-electron Rabi oscillations is determined both by full population inversion between field-free molecular orbitals and the behavior of the instantaneous dipole moment during the simulations. Furthermore, the Rabi oscillations in RT-TDDFT are subject to an intensity threshold of the electric field, below which Rabi oscillations do not occur and above which the two-electron Rabi oscillations occur at a broad range of frequencies. It is also shown that at field intensities near the threshold intensity, the field frequency predicted to induce Rabi oscillations by linear response TDDFT only produces detuned Rabi oscillations. Instead, the field frequency that yields the full two-electron population inversion and Rabi oscillation behavior is shown to be the average of single-electron transition frequencies from the ground S 0 state and the doubly-excited S 2 state. The behavior of the two-electron Rabi oscillations is rationalized via two possible models. The first model is a multi-photon process that results from the electric field interacting with the three level system such that three level Rabi oscillations may occur. The second model suggests that the mean-field nature of RT-TDDFT induces paired electron propagation

  5. The electron beam deposition of titanium on polyetheretherketone (PEEK) and the resulting enhanced biological properties.

    Science.gov (United States)

    Han, Cheol-Min; Lee, Eun-Jung; Kim, Hyoun-Ee; Koh, Young-Hag; Kim, Keung N; Ha, Yoon; Kuh, Sung-Uk

    2010-05-01

    The surface of polyetheretherketone (PEEK) was coated with a pure titanium (Ti) layer using an electron beam (e-beam) deposition method in order to enhance its biocompatibility and adhesion to bone tissue. The e-beam deposition method was a low-temperature coating process that formed a dense, uniform and well crystallized Ti layer without deteriorating the characteristics of the PEEK implant. The Ti coating layer strongly adhered to the substrate and remarkably enhanced its wettability. The Ti-coated samples were evaluated in terms of their in vitro cellular behaviors and in vivo osteointegration, and the results were compared to a pure PEEK substrate. The level of proliferation of the cells (MC3T3-E1) was measured using a methoxyphenyl tetrazolium salt (MTS) assay and more than doubled after the Ti coating. The differentiation level of cells was measured using the alkaline phosphatase (ALP) assay and also doubled. Furthermore, the in vivo animal tests showed that the Ti-coated PEEK implants had a much higher bone-in-contact (BIC) ratio than the pure PEEK implants. These in vitro and in vivo results suggested that the e-beam deposited Ti coating significantly improved the potential of PEEK for hard tissue applications. Copyright 2009 Elsevier Ltd. All rights reserved.

  6. Excitation energies with linear response density matrix functional theory along the dissociation coordinate of an electron-pair bond in N-electron systems

    International Nuclear Information System (INIS)

    Meer, R. van; Gritsenko, O. V.; Baerends, E. J.

    2014-01-01

    Time dependent density matrix functional theory in its adiabatic linear response formulation delivers exact excitation energies ω α and oscillator strengths f α for two-electron systems if extended to the so-called phase including natural orbital (PINO) theory. The Löwdin-Shull expression for the energy of two-electron systems in terms of the natural orbitals and their phases affords in this case an exact phase-including natural orbital functional (PILS), which is non-primitive (contains other than just J and K integrals). In this paper, the extension of the PILS functional to N-electron systems is investigated. With the example of an elementary primitive NO functional (BBC1) it is shown that current density matrix functional theory ground state functionals, which were designed to produce decent approximations to the total energy, fail to deliver a qualitatively correct structure of the (inverse) response function, due to essential deficiencies in the reconstruction of the two-body reduced density matrix (2RDM). We now deduce essential features of an N-electron functional from a wavefunction Ansatz: The extension of the two-electron Löwdin-Shull wavefunction to the N-electron case informs about the phase information. In this paper, applications of this extended Löwdin-Shull (ELS) functional are considered for the simplest case, ELS(1): one (dissociating) two-electron bond in the field of occupied (including core) orbitals. ELS(1) produces high quality ω α (R) curves along the bond dissociation coordinate R for the molecules LiH, Li 2 , and BH with the two outer valence electrons correlated. All of these results indicate that response properties are much more sensitive to deficiencies in the reconstruction of the 2RDM than the ground state energy, since derivatives of the functional with respect to both the NOs and the occupation numbers need to be accurate

  7. Towards double-functionalized small diamondoids: selective electronic band-gap tuning

    International Nuclear Information System (INIS)

    Adhikari, Bibek; Fyta, Maria

    2015-01-01

    Diamondoids are nanoscale diamond-like cage structures with hydrogen terminations, which can occur in various sizes and with a diverse type of modifications. In this work, we focus on the structural alterations and the effect of doping and functionalization on the electronic properties of diamondoids, from the smallest adamantane to heptamantane. The results are based on quantum mechanical calculations. We perform a self-consistent study, starting with doping the smallest diamondoid, adamantane. Boron, nitrogen, silicon, oxygen, and phosphorus are chosen as dopants at sites which have been previously optimized and are also consistent with the literature. At a next step, an amine- and a thiol- group are separately used to functionalize the adamantane molecule. We mainly focus on a double functionalization of diamondoids up to heptamantane using both these atomic groups. The effect of isomeration in the case of tetramantane is also studied. We discuss the higher efficiency of a double-functionalization compared to doping or a single-functionalization of diamondoids in tuning the electronic properties, such as the electronic band-gap, of modified small diamondoids in view of their novel nanotechnological applications. (paper)

  8. The relation between the electron energy loss spectra of hafnia and its dielectric function

    Science.gov (United States)

    Vos, Maarten; Grande, Pedro Luis

    2014-12-01

    Recently two papers have been published deriving the dielectric function from hafnia from electron energy loss data (Jin et al. Applied Physics Letters 100 083713 (2006), Behar et al. Phys. Rev A. 80 062901 (2009)). The obtained dielectric functions are compared in their optical limit and differ considerably. Here we try to clarify the situation by presenting new experimental data and review the analysis procedure used in the earlier work. We conclude that the discrepancy is most likely caused by a shortcoming in the way that the momentum-dependence of the dielectric function is modelled.

  9. Electronic structures of 1-ML C84/Ag(111): Energy level alignment and work function variation

    Science.gov (United States)

    Wang, Peng; Zhao, Li-Li; Zhang, Jin-Juan; Li, Wen-Jie; Liu, Wei-Hui; Chen, Da; Sheng, Chun-Qi; Wang, Jia-Ou; Qian, Hai-Jie; Ibrahim, Kurash; Li, Hong-Nian

    2017-12-01

    The electronic structures of fullerene/metal interface are critical to the performance of devices based on fullerene in molecular electronics and organic electronics. Herein, we investigate the electronic structures at the interface between C84 and Ag(111) by photoelectron spectroscopy and soft X-ray absorption spectroscopy techniques. It is observed that C84 monolayer on Ag(111) surface (1-ML C84/Ag(111)) has metallic nature. A charge transfer from substrate to the unoccupied states of C84 is determined to be 1.3 electrons per molecule. However, the work function of 1-ML C84 (4.72 eV) is observed slightly larger than that of the clean Ag(111) substrate (4.50 eV). A bidirectional charge transfer model is introduced to understand the work function variation of the fullerene/metal system. In addition to the charge transfer from substrate to the adsorbate's unoccupied states, there exists non-negligible back charge transfer from fullerene occupied molecular orbital to the metal substrate through interfacial hybridization. The Fermi level will be pinned at ∼4.72 eV for C84 monolayer on coinage metal substrate.

  10. International Workshop on Electronic Density Functional Theory : Recent Progress and New Directions

    CERN Document Server

    Vignale, Giovanni; Das, Mukunda

    1998-01-01

    This book is an outcome of the International Workshop on Electronic Density Functional Theory, held at Griffith University in Brisbane, Australia, in July 1996. Density functional theory, standing as it does at the boundary between the disciplines of physics, chemistry, and materials science, is a great mixer. Invited experts from North America, Europe, and Australia mingled with students from several disciplines, rapidly taking up the informal style for which Australia is famous. A list of participants is given at the end of the book. Density functional theory (DFT) is a subtle approach to the very difficult problem of predicting the behavior of many interacting particles. A major application is the study of many-electron systems. This was the workshop theme, embracing inter alia computational chemistry and condensed matter physics. DFT circumvents the more conceptually straightforward (but more computationally intensive) approach in which one solves the many-body Schrodinger equation. It relies instead on r...

  11. Investigation of Multiconfigurational Short-Range Density Functional Theory for Electronic Excitations in Organic Molecules

    DEFF Research Database (Denmark)

    Hubert, Mickaël; Hedegård, Erik D.; Jensen, Hans Jørgen Aa

    2016-01-01

    inadequate when the molecule has near-degeneracies and/or low-lying double-excited states. To address these issues we have recently proposed multiconfiguration short-range density-functional theory-MC-srDFT-as a new tool in the toolbox. While initial applications for systems with multireference character......Computational methods that can accurately and effectively predict all types of electronic excitations for any molecular system are missing in the toolbox of the computational chemist. Although various Kohn-Sham density-functional methods (KS-DFT) fulfill this aim in some cases, they become......-srDFT for a selected benchmark set of electronic excitations of organic molecules, covering the most common types of organic chromophores. This investigation confirms the expectation that the MC-srDFT method is accurate for a broad range of excitations and comparable to accurate wave function methods such as CASPT2...

  12. Hybrid functionals and electronic structure of high-pressure phase of CdO

    Energy Technology Data Exchange (ETDEWEB)

    Joshi, K.B.; Paliwal, U. [Department of Physics, M. L. Sukhadia University, Udaipur 313001 (India); Sharma, B.K. [Department of Physics, University of Rajasthan, Jaipur 302004 (India)

    2011-05-15

    The electronic band structure and density of states (DOS) of B2-phase cadmium oxide (CdO) are computed following the first-principles linear combination of atomic orbitals method applying the CRYSTAL code. The PBE correlation functional coupled with Becke's ansatz for exchange is considered for calculations. The electronic band structure and DOS are examined considering HF, B3LYP and hybrid schemes. Hybrid functionals are used with 25, 15, 10 and 5% mixing of Fock exchange with PBE-GGA. Depending on the correlation functionals, and different mixings in the hybrid schemes, B2-phase CdO may have an indirect positive band gap, a negative band gap or a zero gap. The effect of pd repulsion originating from pd hybridisation is visible in the calculated band structures. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. Quantitating morphological changes in biological samples during scanning electron microscopy sample preparation with correlative super-resolution microscopy.

    Science.gov (United States)

    Zhang, Ying; Huang, Tao; Jorgens, Danielle M; Nickerson, Andrew; Lin, Li-Jung; Pelz, Joshua; Gray, Joe W; López, Claudia S; Nan, Xiaolin

    2017-01-01

    Sample preparation is critical to biological electron microscopy (EM), and there have been continuous efforts on optimizing the procedures to best preserve structures of interest in the sample. However, a quantitative characterization of the morphological changes associated with each step in EM sample preparation is currently lacking. Using correlative EM and superresolution microscopy (SRM), we have examined the effects of different drying methods as well as osmium tetroxide (OsO4) post-fixation on cell morphology during scanning electron microscopy (SEM) sample preparation. Here, SRM images of the sample acquired under hydrated conditions were used as a baseline for evaluating morphological changes as the sample went through SEM sample processing. We found that both chemical drying and critical point drying lead to a mild cellular boundary retraction of ~60 nm. Post-fixation by OsO4 causes at least 40 nm additional boundary retraction. We also found that coating coverslips with adhesion molecules such as fibronectin prior to cell plating helps reduce cell distortion from OsO4 post-fixation. These quantitative measurements offer useful information for identifying causes of cell distortions in SEM sample preparation and improving current procedures.

  14. Quantum electrodynamical time-dependent density functional theory for many-electron systems on a lattice

    Science.gov (United States)

    Farzanehpour, Mehdi; Tokatly, Ilya; Nano-Bio Spectroscopy Group; ETSF Scientific Development Centre Team

    2015-03-01

    We present a rigorous formulation of the time-dependent density functional theory for interacting lattice electrons strongly coupled to cavity photons. We start with an example of one particle on a Hubbard dimer coupled to a single photonic mode, which is equivalent to the single mode spin-boson model or the quantum Rabi model. For this system we prove that the electron-photon wave function is a unique functional of the electronic density and the expectation value of the photonic coordinate, provided the initial state and the density satisfy a set of well defined conditions. Then we generalize the formalism to many interacting electrons on a lattice coupled to multiple photonic modes and prove the general mapping theorem. We also show that for a system evolving from the ground state of a lattice Hamiltonian any density with a continuous second time derivative is locally v-representable. Spanish Ministry of Economy and Competitiveness (Grant No. FIS2013-46159-C3-1-P), Grupos Consolidados UPV/EHU del Gobierno Vasco (Grant No. IT578-13), COST Actions CM1204 (XLIC) and MP1306 (EUSpec).

  15. A Concept for Measuring Electron Distribution Functions Using Collective Thomson Scattering

    Science.gov (United States)

    Milder, A. L.; Froula, D. H.

    2017-10-01

    A.B. Langdon proposed that stable non-Maxwellian distribution functions are realized in coronal inertial confinement fusion plasmas via inverse bremsstrahlung heating. For Zvosc2 Zvosc2 vth2 > 1 , vth2 > 1 , the inverse bremsstrahlung heating rate is sufficiently fast to compete with electron-electron collisions. This process preferentially heats the subthermal electrons leading to super-Gaussian distribution functions. A method to identify the super-Gaussian order of the distribution functions in these plasmas using collective Thomson scattering will be proposed. By measuring the collective Thomson spectra over a range of angles the density, temperature and super-Gaussian order can be determined. This is accomplished by fitting non-Maxwellian distribution data with a super-Gaussian model; in order to match the density and electron temperature to within 10%, the super-Gaussian order must be varied. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

  16. Low-order tensor approximations for electronic wave functions: Hartree-Fock method with guaranteed precision.

    Science.gov (United States)

    Bischoff, Florian A; Valeev, Edward F

    2011-03-14

    Here we report a formulation of the Hartree-Fock method in an adaptive multiresolution basis set of spectral element type. A key feature of our approach is the use of low-order tensor approximations for operators and wave functions to reduce the steep rise of storage and computational costs with the number of degrees of freedom that plague finite element computations. As a proof of principle we implemented Hartree-Fock method without explicit storage of the full-dimensional wave function and with guaranteed precision (microhartree precision for up to 14 electron systems is demonstrated). Even for the one-electron method the use of low-order tensor approximation reduces storage relative to the full representation, albeit with modest increase in cost. Preliminary tests for explicitly-correlated two-electron (six-dimensional) wave function suggest a factor of 50 savings in storage. At least correlated two-electron methods should be feasible with our approach on modern workstations with guaranteed precision.

  17. Counterintuitive electron localisation from density-functional theory with polarisable solvent models

    International Nuclear Information System (INIS)

    Dale, Stephen G.; Johnson, Erin R.

    2015-01-01

    Exploration of the solvated electron phenomena using density-functional theory (DFT) generally results in prediction of a localised electron within an induced solvent cavity. However, it is well known that DFT favours highly delocalised charges, rendering the localisation of a solvated electron unexpected. We explore the origins of this counterintuitive behaviour using a model Kevan-structure system. When a polarisable-continuum solvent model is included, it forces electron localisation by introducing a strong energetic bias that favours integer charges. This results in the formation of a large energetic barrier for charge-hopping and can cause the self-consistent field to become trapped in local minima thus converging to stable solutions that are higher in energy than the ground electronic state. Finally, since the bias towards integer charges is caused by the polarisable continuum, these findings will also apply to other classical polarisation corrections, as in combined quantum mechanics and molecular mechanics (QM/MM) methods. The implications for systems beyond the solvated electron, including cationic DNA bases, are discussed

  18. Counterintuitive electron localisation from density-functional theory with polarisable solvent models

    Energy Technology Data Exchange (ETDEWEB)

    Dale, Stephen G., E-mail: sdale@ucmerced.edu [Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343 (United States); Johnson, Erin R., E-mail: erin.johnson@dal.ca [Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2 (Canada)

    2015-11-14

    Exploration of the solvated electron phenomena using density-functional theory (DFT) generally results in prediction of a localised electron within an induced solvent cavity. However, it is well known that DFT favours highly delocalised charges, rendering the localisation of a solvated electron unexpected. We explore the origins of this counterintuitive behaviour using a model Kevan-structure system. When a polarisable-continuum solvent model is included, it forces electron localisation by introducing a strong energetic bias that favours integer charges. This results in the formation of a large energetic barrier for charge-hopping and can cause the self-consistent field to become trapped in local minima thus converging to stable solutions that are higher in energy than the ground electronic state. Finally, since the bias towards integer charges is caused by the polarisable continuum, these findings will also apply to other classical polarisation corrections, as in combined quantum mechanics and molecular mechanics (QM/MM) methods. The implications for systems beyond the solvated electron, including cationic DNA bases, are discussed.

  19. Electron velocity distribution function in a plasma with temperature gradient and in the presence of suprathermal electrons: application to incoherent-scatter plasma lines

    Directory of Open Access Journals (Sweden)

    P. Guio

    1998-10-01

    Full Text Available The plasma dispersion function and the reduced velocity distribution function are calculated numerically for any arbitrary velocity distribution function with cylindrical symmetry along the magnetic field. The electron velocity distribution is separated into two distributions representing the distribution of the ambient electrons and the suprathermal electrons. The velocity distribution function of the ambient electrons is modelled by a near-Maxwellian distribution function in presence of a temperature gradient and a potential electric field. The velocity distribution function of the suprathermal electrons is derived from a numerical model of the angular energy flux spectrum obtained by solving the transport equation of electrons. The numerical method used to calculate the plasma dispersion function and the reduced velocity distribution is described. The numerical code is used with simulated data to evaluate the Doppler frequency asymmetry between the up- and downshifted plasma lines of the incoherent-scatter plasma lines at different wave vectors. It is shown that the observed Doppler asymmetry is more dependent on deviation from the Maxwellian through the thermal part for high-frequency radars, while for low-frequency radars the Doppler asymmetry depends more on the presence of a suprathermal population. It is also seen that the full evaluation of the plasma dispersion function gives larger Doppler asymmetry than the heat flow approximation for Langmuir waves with phase velocity about three to six times the mean thermal velocity. For such waves the moment expansion of the dispersion function is not fully valid and the full calculation of the dispersion function is needed.Key words. Non-Maxwellian electron velocity distribution · Incoherent scatter plasma lines · EISCAT · Dielectric response function

  20. Electron velocity distribution function in a plasma with temperature gradient and in the presence of suprathermal electrons: application to incoherent-scatter plasma lines

    Directory of Open Access Journals (Sweden)

    P. Guio

    Full Text Available The plasma dispersion function and the reduced velocity distribution function are calculated numerically for any arbitrary velocity distribution function with cylindrical symmetry along the magnetic field. The electron velocity distribution is separated into two distributions representing the distribution of the ambient electrons and the suprathermal electrons. The velocity distribution function of the ambient electrons is modelled by a near-Maxwellian distribution function in presence of a temperature gradient and a potential electric field. The velocity distribution function of the suprathermal electrons is derived from a numerical model of the angular energy flux spectrum obtained by solving the transport equation of electrons. The numerical method used to calculate the plasma dispersion function and the reduced velocity distribution is described. The numerical code is used with simulated data to evaluate the Doppler frequency asymmetry between the up- and downshifted plasma lines of the incoherent-scatter plasma lines at different wave vectors. It is shown that the observed Doppler asymmetry is more dependent on deviation from the Maxwellian through the thermal part for high-frequency radars, while for low-frequency radars the Doppler asymmetry depends more on the presence of a suprathermal population. It is also seen that the full evaluation of the plasma dispersion function gives larger Doppler asymmetry than the heat flow approximation for Langmuir waves with phase velocity about three to six times the mean thermal velocity. For such waves the moment expansion of the dispersion function is not fully valid and the full calculation of the dispersion function is needed.

    Key words. Non-Maxwellian electron velocity distribution · Incoherent scatter plasma lines · EISCAT · Dielectric response function

  1. Difficulties in applying pure Kohn-Sham density functional theory electronic structure methods to protein molecules

    Science.gov (United States)

    Rudberg, Elias

    2012-02-01

    Self-consistency-based Kohn-Sham density functional theory (KS-DFT) electronic structure calculations with Gaussian basis sets are reported for a set of 17 protein-like molecules with geometries obtained from the Protein Data Bank. It is found that in many cases such calculations do not converge due to vanishing HOMO-LUMO gaps. A sequence of polyproline I helix molecules is also studied and it is found that self-consistency calculations using pure functionals fail to converge for helices longer than six proline units. Since the computed gap is strongly correlated to the fraction of Hartree-Fock exchange, test calculations using both pure and hybrid density functionals are reported. The tested methods include the pure functionals BLYP, PBE and LDA, as well as Hartree-Fock and the hybrid functionals BHandHLYP, B3LYP and PBE0. The effect of including solvent molecules in the calculations is studied, and it is found that the inclusion of explicit solvent molecules around the protein fragment in many cases gives a larger gap, but that convergence problems due to vanishing gaps still occur in calculations with pure functionals. In order to achieve converged results, some modeling of the charge distribution of solvent water molecules outside the electronic structure calculation is needed. Representing solvent water molecules by a simple point charge distribution is found to give non-vanishing HOMO-LUMO gaps for the tested protein-like systems also for pure functionals.

  2. Electronic transport properties of fullerene functionalized carbon nanotubes: Ab initio and tight-binding calculations

    DEFF Research Database (Denmark)

    Fürst, Joachim Alexander; Hashemi, J.; Markussen, Troels

    2009-01-01

    techniques and tight-binding calculations to illustrate these materials' transmission properties and give physical arguments to interpret the numerical results. Specifically, above the Fermi energy we find a strong reduction in electron transmission due to localized states in certain regions of the structure......Fullerene functionalized carbon nanotubes-NanoBuds-form a novel class of hybrid carbon materials, which possesses many advantageous properties as compared to the pristine components. Here, we report a theoretical study of the electronic transport properties of these compounds. We use both ab initio...

  3. 6-Electron exchange function as a simple estimator of aromaticity in large polyaromatic hydrocarbons

    Science.gov (United States)

    Mandado, Marcos; Mosquera, Ricardo A.

    2009-02-01

    The 6-electron exchange function (6-EEF) is defined and calculated for a series of large polyaromatic hydrocarbons (PAHs). It is shown that the 6-EEF, computed at selected points in space, is able to reproduce in PAHs the same relative values as the multicenter electron delocalization indices with an affordable computational cost and without using any definition of the atom in the molecule. Calculations for a series of D 6h PAHs ranging from C 6H 6 to C 216H 36 are performed. The results can be extrapolated to even larger PAHs and allow predicting the behaviour of a benzene ring in an infinite sheet of graphite.

  4. Locally self-consistent Green’s function approach to the electronic structure problem

    DEFF Research Database (Denmark)

    Abrikosov, I.A.; Simak, S.I.; Johansson, B.

    1997-01-01

    The locally self-consistent Green's function (LSGF) method is an order-N method for calculation of the electronic structure of systems with an arbitrary distribution of atoms of different kinds on an underlying crystal lattice. For each atom Dyson's equation is used to solve the electronic multiple...... scattering problem in a local interaction zone (LIZ) embedded in an effective medium judiciously chosen to minimize the size of the, LIZ. The excellent real-space convergence of the LSGF calculations and the reliability of its results are demonstrated for a broad spectrum of metallic alloys with different...

  5. Electron and Nucleon Localization Functions of Oganesson: Approaching the Thomas-Fermi Limit

    Science.gov (United States)

    Jerabek, Paul; Schuetrumpf, Bastian; Schwerdtfeger, Peter; Nazarewicz, Witold

    2018-02-01

    Fermion localization functions are used to discuss electronic and nucleonic shell structure effects in the superheavy element oganesson, the heaviest element discovered to date. Spin-orbit splitting in the 7 p electronic shell becomes so large (˜10 eV ) that Og is expected to show uniform-gas-like behavior in the valence region with a rather large dipole polarizability compared to the lighter rare gas elements. The nucleon localization in Og is also predicted to undergo a transition to the Thomas-Fermi gas behavior in the valence region. This effect, particularly strong for neutrons, is due to the high density of single-particle orbitals.

  6. Monte Carlo study of the effective Sherman function for electron polarimetry

    International Nuclear Information System (INIS)

    Drągowski, M.; Włodarczyk, M.; Weber, G.; Ciborowski, J.; Enders, J.; Fritzsche, Y.; Poliszczuk, A.

    2016-01-01

    The PEBSI Monte Carlo simulation was upgraded towards usefulness for electron Mott polarimetry. The description of Mott scattering was improved and polarisation transfer in Møller scattering was included in the code. An improved agreement was achieved between the simulation and available experimental data for a 100 keV polarised electron beam scattering off gold foils of various thicknesses. The dependence of the effective Sherman function on scattering angle and target thickness, as well as the method of finding optimal conditions for Mott polarimetry measurements were analysed.

  7. Monte Carlo study of the effective Sherman function for electron polarimetry

    Energy Technology Data Exchange (ETDEWEB)

    Drągowski, M., E-mail: mdragowski@fuw.edu.pl [University of Warsaw, Faculty of Physics, Pasteura 5, 02093 Warsaw (Poland); Włodarczyk, M. [University of Warsaw, Faculty of Physics, Pasteura 5, 02093 Warsaw (Poland); Weber, G. [Helmholtz Institut Jena, Fröbelstieg 3, 07743 Jena (Germany); Ciborowski, J. [University of Warsaw, Faculty of Physics, Pasteura 5, 02093 Warsaw (Poland); Enders, J.; Fritzsche, Y. [Technische Universität Darmstadt, Institut für Kernphysik, Schlossgartenstraße 9, 64289 Darmstadt (Germany); Poliszczuk, A. [University of Warsaw, Faculty of Physics, Pasteura 5, 02093 Warsaw (Poland)

    2016-12-15

    The PEBSI Monte Carlo simulation was upgraded towards usefulness for electron Mott polarimetry. The description of Mott scattering was improved and polarisation transfer in Møller scattering was included in the code. An improved agreement was achieved between the simulation and available experimental data for a 100 keV polarised electron beam scattering off gold foils of various thicknesses. The dependence of the effective Sherman function on scattering angle and target thickness, as well as the method of finding optimal conditions for Mott polarimetry measurements were analysed.

  8. Quantitative electron tomography: the effect of the three-dimensional point spread function.

    Science.gov (United States)

    Heidari, Hamed; Van den Broek, Wouter; Bals, Sara

    2013-12-01

    The intensity levels in a three-dimensional (3D) reconstruction, obtained by electron tomography, can be influenced by several experimental imperfections. Such artifacts will hamper a quantitative interpretation of the results. In this paper, we will correct for artificial intensity variations by determining the 3D point spread function (PSF) of a tomographic reconstruction based on high angle annular dark field scanning transmission electron microscopy. The large tails of the PSF cause an underestimation of the intensity of smaller particles, which in turn hampers an accurate radius estimate. Here, the error introduced by the PSF is quantified and corrected a posteriori. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. [The biological reaction of inflammation, methylglyoxal of blood plasma, functional and structural alterations in elastic type arteries at the early stage of hypertension disease].

    Science.gov (United States)

    Titov, V N; Dmitriev, V A; Oshchepkov, E V; Balakhonova, T V; Tripoten', M I; Shiriaeva, Iu K

    2012-08-01

    The article deals with studying of the relationship between biologic reaction of inflammation with glycosylation reaction and content of methylglyoxal in blood serum. The positive correlation between pulse wave velocity and content of methylglyoxal, C-reactive protein in intercellular medium and malleolar brachial index value was established. This data matches the experimental results concerning involvement of biological reaction of inflammation into structural changes of elastic type arteries under hypertension disease, formation of arteries' rigidity and increase of pulse wave velocity. The arterial blood pressure is a biological reaction of hydrodynamic pressure which is used in vivo by several biological functions: biological function of homeostasis, function of endoecology, biological function of adaptation and function of locomotion. The biological reaction of hydrodynamic (hydraulic) pressure is a mode of compensation of derangement of several biological functions which results in the very high rate of hypertension disease in population. As a matter of fact, hypertension disease is a syndrome of lingering pathological compensation by higher arterial blood pressure of the biological functions derangements occurring in the distal section at the level of paracrine cenoses of cells. The arterial blood pressure is a kind of in vivo integral indicator of deranged metabolism. The essential hypertension disease pathogenically is a result of the derangement of three biological functions: biological function of homeostasis, biological function of trophology - nutrition (biological reaction of external feeding - exotrophia) and biological function of endoecology. In case of "littering" of intercellular medium in vivo with nonspecific endogenic flogogens a phylogenetically earlier activation of biological reactions of excretion, inflammation and hydrodynamic arterial blood pressure occur. In case of derangement of biological function of homeostasis, decreasing of

  10. Biological roles of Cytochrome c: mitochondrial electron transport, programmed cell death and gain of peroxidatic activity

    Directory of Open Access Journals (Sweden)

    Victoria Colman

    2015-11-01

    Full Text Available El citocromo c (cyt c es una pequeña proteína monomérica de 13,0 kDa, que posee carga neta positiva a pH fisiológico. En su estructura se destaca un grupo hemo hexa-coordinado siendo la His18 y la Met80 la quinta y sexta posición de coordinación, respectivamente. Es una molécula soluble que se asocia mediante interacciones electrostáticas a la parte externa de la membrana mitocondrial interna, donde cumple una importante función como transportador de electrones entre los complejos III y IV de la cadena respiratoria mitocondrial, formando parte de una de las rutas catabólicas principales que llevan a la generación de ATP. Además, el cyt c participa en otras dos funciones esenciales para la célula: la apoptosis y la peroxidación de la cardiolipina de membrana. La actividad peroxidasa del cyt c es esencial para el inicio de la apoptosis, debido a que provoca la oxigenación específica de la cardiolipina para producir hidroperóxidos de cardiolipina, necesarios para la liberación de otros factores pro-apoptóticos. Durante la apoptosis, el cyt c se libera desde el espacio intermembrana de la mitocondria hacia el citosol, formando un complejo con APAF-1 y ATP, modulando las vías dependientes de caspasas. Esta función del cyt c también es muy importante ya que la muerte celular programada es un proceso celular fundamental para la correcta eliminación de células dañadas, evitando la diseminación de los restos celulares. La presente monografía pretende reunir información sobre estas tres principales funciones del cyt c, que dejan en manifiesto su importancia para la vida celular.

  11. Enhanced surface functionality via plasma modification and plasma deposition techniques to create more biologically relevant materials

    Science.gov (United States)

    Shearer, Jeffrey C.

    Functionalizing nanoparticles and other unusually shaped substrates to create more biologically relevant materials has become central to a wide range of research programs. One of the primary challenges in this field is creating highly functionalized surfaces without modifying the underlying bulk material. Traditional wet chemistry techniques utilize thin film depositions to functionalize nanomaterials with oxygen and nitrogen containing functional groups, such as --OH and --NHx. These functional groups can serve to create surfaces that are amenable to cell adhesion or can act as reactive groups for further attachment of larger structures, such as macromolecules or antiviral agents. Additional layers, such as SiO2, are often added between the nanomaterial and the functionalized coating to act as a barrier films, adhesion layers, and to increase overall hydrophilicity. However, some wet chemistry techniques can damage the bulk material during processing. This dissertation examines the use of plasma processing as an alternative method for producing these highly functionalized surfaces on nanoparticles and polymeric scaffolds through the use of plasma modification and plasma enhanced chemical vapor deposition techniques. Specifically, this dissertation will focus on (1) plasma deposition of SiO2 barrier films on nanoparticle substrates; (2) surface functionalization of amine and alcohol groups through (a) plasma co-polymerization and (b) plasma modification; and (3) the design and construction of plasma hardware to facilitate plasma processing of nanoparticles and polymeric scaffolds. The body of work presented herein first examines the fabrication of composite nanoparticles by plasma processing. SiOxC y and hexylamine films were coated onto TiO2 nanoparticles to demonstrate enhanced water dispersion properties. Continuous wave and pulsed allyl alcohol plasmas were used to produce highly functionalized Fe2 O3 supported nanoparticles. Specifically, film composition was

  12. Biological Function and Medicinal Research Significance of G-Quadruplex Interactive Proteins.

    Science.gov (United States)

    Qiu, Jun; Wang, Mingxue; Zhang, Yan; Zeng, Ping; Ou, Tian-Miao; Tan, Jia-Heng; Huang, Shi-Liang; An, Lin-Kun; Wang, Honggen; Gu, Lian-Quan; Huang, Zhi-Shu; Li, Ding

    2015-01-01

    G-quadruplexes are four-stranded DNA structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Accumulating studies have revealed that G-quadruplex structures are formed in vivo and play important roles in biological processes such as DNA replication, transcription, recombination, epigenetic regulation, meiosis, antigenic variation, and maintenance of telomeres stability. Mounting evidence indicates that a variety of proteins are capable of binding selectively and tightly to G-quadruplex and play essential roles in G-quadruplex-mediated regulation processes. Some of these proteins promote the formation or/and stabilization of G-quadruplex, while some other proteins act to unwind G-quadruplex preferentially. From a drug discovery perspective, many of these G-quadruplex binding proteins and/or their complexes with G-quadruplexes are potential drug targets. Here, we present a general summary of reported G-quadruplex binding proteins and their biological functions, with focus on those of medicinal research significance. We elaborated the possibility for some of these G-quadruplex binding proteins and their complexes with G-quadruplexes as potential drug targets.

  13. Green leaf volatiles: biosynthesis, biological functions and their applications in biotechnology.

    Science.gov (United States)

    ul Hassan, Muhammad Naeem; Zainal, Zamri; Ismail, Ismanizan

    2015-08-01

    Plants have evolved numerous constitutive and inducible defence mechanisms to cope with biotic and abiotic stresses. These stresses induce the expression of various genes to activate defence-related pathways that result in the release of defence chemicals. One of these defence mechanisms is the oxylipin pathway, which produces jasmonates, divinylethers and green leaf volatiles (GLVs) through the peroxidation of polyunsaturated fatty acids (PUFAs). GLVs have recently emerged as key players in plant defence, plant-plant interactions and plant-insect interactions. Some GLVs inhibit the growth and propagation of plant pathogens, including bacteria, viruses and fungi. In certain cases, GLVs released from plants under herbivore attack can serve as aerial messengers to neighbouring plants and to attract parasitic or parasitoid enemies of the herbivores. The plants that perceive these volatile signals are primed and can then adapt in preparation for the upcoming challenges. Due to their 'green note' odour, GLVs impart aromas and flavours to many natural foods, such as vegetables and fruits, and therefore, they can be exploited in industrial biotechnology. The aim of this study was to review the progress and recent developments in research on the oxylipin pathway, with a specific focus on the biosynthesis and biological functions of GLVs and their applications in industrial biotechnology. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  14. The role of ontologies in biological and biomedical research: a functional perspective

    KAUST Repository

    Hoehndorf, Robert

    2015-04-10

    Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

  15. FUSE: a profit maximization approach for functional summarization of biological networks.

    Science.gov (United States)

    Seah, Boon-Siew; Bhowmick, Sourav S; Dewey, C Forbes; Yu, Hanry

    2012-03-21

    The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI) using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator) that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL) principle to maximize information gain of the summary graph while satisfying the level of detail constraint. We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI. By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.

  16. FUSE: a profit maximization approach for functional summarization of biological networks

    Directory of Open Access Journals (Sweden)

    Seah Boon-Siew

    2012-03-01

    Full Text Available Abstract Background The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL principle to maximize information gain of the summary graph while satisfying the level of detail constraint. Results We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI. Conclusion By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.

  17. Biological conservation law as an emerging functionality in dynamical neuronal networks.

    Science.gov (United States)

    Podobnik, Boris; Jusup, Marko; Tiganj, Zoran; Wang, Wen-Xu; Buldú, Javier M; Stanley, H Eugene

    2017-11-07

    Scientists strive to understand how functionalities, such as conservation laws, emerge in complex systems. Living complex systems in particular create high-ordered functionalities by pairing up low-ordered complementary processes, e.g., one process to build and the other to correct. We propose a network mechanism that demonstrates how collective statistical laws can emerge at a macro (i.e., whole-network) level even when they do not exist at a unit (i.e., network-node) level. Drawing inspiration from neuroscience, we model a highly stylized dynamical neuronal network in which neurons fire either randomly or in response to the firing of neighboring neurons. A synapse connecting two neighboring neurons strengthens when both of these neurons are excited and weakens otherwise. We demonstrate that during this interplay between the synaptic and neuronal dynamics, when the network is near a critical point, both recurrent spontaneous and stimulated phase transitions enable the phase-dependent processes to replace each other and spontaneously generate a statistical conservation law-the conservation of synaptic strength. This conservation law is an emerging functionality selected by evolution and is thus a form of biological self-organized criticality in which the key dynamical modes are collective.

  18. Investigating molecular recognition and biological function at interfaces using piscidins, antimicrobial peptides from fish.

    Science.gov (United States)

    Chekmenev, Eduard Y; Vollmar, Breanna S; Forseth, Kristen T; Manion, McKenna N; Jones, Shiela M; Wagner, Tim J; Endicott, RaeLynn M; Kyriss, Brandon P; Homem, Lorraine M; Pate, Michelle; He, Jing; Raines, Joshua; Gor'kov, Peter L; Brey, William W; Mitchell, Dan J; Auman, Ann J; Ellard-Ivey, Mary J; Blazyk, Jack; Cotten, Myriam

    2006-09-01

    We studied amidated and non-amidated piscidins 1 and 3, amphipathic cationic antimicrobial peptides from fish, to characterize functional and structural similarities and differences between these peptides and better understand the structural motifs involved in biological activity and functional diversity among amidated and non-amidated isoforms. Antimicrobial and hemolytic assays were carried out to assess their potency and toxicity, respectively. Site-specific high-resolution solid-state NMR orientational restraints were obtained from (15)N-labeled amidated and non-amidated piscidins 1 and 3 in the presence of hydrated oriented lipid bilayers. Solid-state NMR and circular dichroism results indicate that the peptides are alpha-helical and oriented parallel to the membrane surface. This orientation was expected since peptide-lipid interactions are enhanced at the water-bilayer interface for amphipathic cationic antimicrobial peptides. (15)N solid-state NMR performed on oriented samples demonstrate that piscidin experiences fast, large amplitude backbone motions around an axis parallel to the bilayer normal. Under the conditions tested here, piscidin 1 was confirmed to be more antimicrobially potent than piscidin 3 and antimicrobial activity was not affected by amidation. In light of functional and structural similarities between piscidins 1 and 3, we propose that their topology and fast dynamics are related to their mechanism of action.

  19. Restoration of voice function by using biological feedback in laryngeal and hypopharyngeal carcinoma patients

    Science.gov (United States)

    Choinzonov, E. L.; Balatskaya, L. N.; Chizhevskaya, S. Yu.; Meshcheryakov, R. V.; Kostyuchenko, E. Yu.; Ivanova, T. A.

    2016-08-01

    The aim of the research is to develop and introduce a new technique of post-laryngectomy voice rehabilitation of laryngeal and hypopharyngeal carcinoma patients. The study involves comparing and analyzing 82 cases of voice function restoration by using biological feedback based on mathematical modeling of voice production. The advantage of the modern technology-based method in comparison with the conventional one is proved. Restoration of voice function using biofeedback allows taking into account patient's abilities, adjusting parameters of voice trainings, and controlling their efficiency in real-time mode. The data obtained indicate that the new method contributes to the rapid inclusion of self-regulation mechanisms of the body and results in the overall success rate of voice rehabilitation in totally laryngectomized patients reaching 92%, which reduces the rehabilitation period to 18 days, compared to 86% and 38 days in the control group, respectively. Restoration of disturbed functions after successful treatment is an important task of rehabilitation and is crucial in terms of the quality of cancer patients' lives. To assess life quality of laryngeal cancer patients, the EORTC Quality of Life Core Questionnaire (QLQ-C30), and head and neck module (QLQ-H&N35) were used. The analyzed results proved that the technique of biofeedback voice restoration significantly improves the quality of life of laryngectomized patients. It allows reducing the number of disabled people, restoring patients' ability to work-related activities, and significantly improving social adaptation of these patients.

  20. Late-stage functionalization of biologically active heterocycles through photoredox catalysis.

    Science.gov (United States)

    Dirocco, Daniel A; Dykstra, Kevin; Krska, Shane; Vachal, Petr; Conway, Donald V; Tudge, Matthew

    2014-05-05

    The direct CH functionalization of heterocycles has become an increasingly valuable tool in modern drug discovery. However, the introduction of small alkyl groups, such as methyl, by this method has not been realized in the context of complex molecule synthesis since existing methods rely on the use of strong oxidants and elevated temperatures to generate the requisite radical species. Herein, we report the use of stable organic peroxides activated by visible-light photoredox catalysis to achieve the direct methyl-, ethyl-, and cyclopropylation of a variety of biologically active heterocycles. The simple protocol, mild reaction conditions, and unique tolerability of this method make it an important tool for drug discovery. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.