Crystal and molecular structure of eight organic acid-base adducts from 2-methylquinoline and different acids

NASA Astrophysics Data System (ADS)

Zhang, Jing; Jin, Shouwen; Tao, Lin; Liu, Bin; Wang, Daqi

2014-08-01

Eight supramolecular complexes with 2-methylquinoline and acidic components as 4-aminobenzoic acid, 2-aminobenzoic acid, salicylic acid, 5-chlorosalicylic acid, 3,5-dinitrosalicylic acid, malic acid, sebacic acid, and 1,5-naphthalenedisulfonic acid were synthesized and characterized by X-ray crystallography, IR, mp, and elemental analysis. All of the complexes are organic salts except compound 2. All supramolecular architectures of 1-8 involve extensive classical hydrogen bonds as well as other noncovalent interactions. The results presented herein indicate that the strength and directionality of the classical hydrogen bonds (ionic or neutral) between acidic components and 2-methylquinoline are sufficient to bring about the formation of binary organic acid-base adducts. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, the complexes 1-8 displayed 2D-3D framework structure.

Dissociation kinetics of Fe(III)- and Al(III)-natural organic matter complexes at pH 6.0 and 8.0 and 25 °C

NASA Astrophysics Data System (ADS)

Jones, Adele M.; Pham, A. Ninh; Collins, Richard N.; Waite, T. David

2009-05-01

The rate at which iron- and aluminium-natural organic matter (NOM) complexes dissociate plays a critical role in the transport of these elements given the readiness with which they hydrolyse and precipitate. Despite this, there have only been a few reliable studies on the dissociation kinetics of these complexes suggesting half-times of some hours for the dissociation of Fe(III) and Al(III) from a strongly binding component of NOM. First-order dissociation rate constants are re-evaluated here at pH 6.0 and 8.0 and 25 °C using both cation exchange resin and competing ligand methods for Fe(III) and a cation exchange resin method only for Al(III) complexes. Both methods provide similar results at a particular pH with a two-ligand model accounting satisfactorily for the dissociation kinetics results obtained. For Fe(III), half-times on the order of 6-7 h were obtained for dissociation of the strong component and 4-5 min for dissociation of the weak component. For aluminium, the half-times were on the order of 1.5 h and 1-2 min for the strong and weak components, respectively. Overall, Fe(III) complexes with NOM are more stable than analogous complexes with Al(III), implying Fe(III) may be transported further from its source upon dilution and dispersion.

Primordial Evolution in the Finitary Process Soup

NASA Astrophysics Data System (ADS)

Görnerup, Olof; Crutchfield, James P.

A general and basic model of primordial evolution—a soup of reacting finitary and discrete processes—is employed to identify and analyze fundamental mechanisms that generate and maintain complex structures in prebiotic systems. The processes—ɛ-machines as defined in computational mechanics—and their interaction networks both provide well defined notions of structure. This enables us to quantitatively demonstrate hierarchical self-organization in the soup in terms of complexity. We found that replicating processes evolve the strategy of successively building higher levels of organization by autocatalysis. Moreover, this is facilitated by local components that have low structural complexity, but high generality. In effect, the finitary process soup spontaneously evolves a selection pressure that favors such components. In light of the finitary process soup's generality, these results suggest a fundamental law of hierarchical systems: global complexity requires local simplicity.

Preliminary investigation of phosphorus adsorption onto two types of iron oxide-organic matter complexes.

PubMed

Yan, Jinlong; Jiang, Tao; Yao, Ying; Lu, Song; Wang, Qilei; Wei, Shiqiang

2016-04-01

Iron oxide (FeO) coated by natural organic matter (NOM) is ubiquitous. The associations of minerals with organic matter (OM) significantly changes their surface properties and reactivity, and thus affect the environmental fate of pollutants, including nutrients (e.g., phosphorus (P)). In this study, ferrihydrite/goethite-humic acid (FH/GE-HA) complexes were prepared and their adsorption characteristics on P at various pH and ionic strength were investigated. The results indicated that the FeO-OM complexes showed a decreased P adsorption capacity in comparison with bare FeO. The maximum adsorption capacity (Qmax) decreased in the order of FH (22.17 mg/g)>FH-HA (5.43 mg/g)>GE (4.67 mg/g)>GE-HA (3.27 mg/g). After coating with HA, the amorphous FH-HA complex still showed higher P adsorption than the crystalline GE-HA complex. The decreased P adsorption observed might be attributed to changes of the FeO surface charges caused by OM association. The dependence of P adsorption on the specific surface area of adsorbents suggests that the FeO component in the complexes is still the main contributor for the adsorption surfaces. The P adsorptions on FeO-HA complexes decreased with increasing initial pH or decreasing initial ionic strength. A strong dependence of P adsorption on ionic strength and pH may demonstrate that outer-sphere complexes between the OM component on the surface and P possibly coexist with inner-sphere surface complexes between the FeO component and P. Therefore, previous over-emphasis on the contributions of original minerals to P immobilization possibly over-estimates the P loading capacity of soils, especially in humic-rich areas. Copyright © 2015. Published by Elsevier B.V.

Superresolution microscopy reveals the three-dimensional organization of meiotic chromosome axes in intact Caenorhabditis elegans tissue

PubMed Central

Köhler, Simone; Wojcik, Michal; Dernburg, Abby F.

2017-01-01

When cells enter meiosis, their chromosomes reorganize as linear arrays of chromatin loops anchored to a central axis. Meiotic chromosome axes form a platform for the assembly of the synaptonemal complex (SC) and play central roles in other meiotic processes, including homologous pairing, recombination, and chromosome segregation. However, little is known about the 3D organization of components within the axes, which include cohesin complexes and additional meiosis-specific proteins. Here, we investigate the molecular organization of meiotic chromosome axes in Caenorhabditis elegans through STORM (stochastic optical reconstruction microscopy) and PALM (photo-activated localization microscopy) superresolution imaging of intact germ-line tissue. By tagging one axis protein (HIM-3) with a photoconvertible fluorescent protein, we established a spatial reference for other components, which were localized using antibodies against epitope tags inserted by CRISPR/Cas9 genome editing. Using 3D averaging, we determined the position of all known components within synapsed chromosome axes to high spatial precision in three dimensions. We find that meiosis-specific HORMA domain proteins span a gap between cohesin complexes and the central region of the SC, consistent with their essential roles in SC assembly. Our data further suggest that the two different meiotic cohesin complexes are distinctly arranged within the axes: Although cohesin complexes containing the kleisin REC-8 protrude above and below the plane defined by the SC, complexes containing COH-3 or -4 kleisins form a central core, which may physically separate sister chromatids. This organization may help to explain the role of the chromosome axes in promoting interhomolog repair of meiotic double-strand breaks by inhibiting intersister repair. PMID:28559338

75 FR 2172 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-14

... complex order auction (COA) and book (COB) rule. The COA system facilitates the handling and execution of complex orders by allowing for complex orders to rest in the system and allowing for inbound complex... order), and the stock component of a stock-option complex order handled by the system is executed on...

Some Characteristics of One Type of High Reliability Organization.

ERIC Educational Resources Information Center

Roberts, Karlene H.

1990-01-01

Attempts to define organizational processes necessary to operate safely technologically complex organizations. Identifies nuclear powered aircraft carriers as examples of potentially hazardous organizations with histories of excellent operations. Discusses how carriers deal with components of risk and antecedents to catastrophe cited by Perrow and…

Low-Dimensional Models for Physiological Systems: Nonlinear Coupling of Gas and Liquid Flows

NASA Astrophysics Data System (ADS)

Staples, A. E.; Oran, E. S.; Boris, J. P.; Kailasanath, K.

2006-11-01

Current computational models of biological organisms focus on the details of a specific component of the organism. For example, very detailed models of the human heart, an aorta, a vein, or part of the respiratory or digestive system, are considered either independently from the rest of the body, or as interacting simply with other systems and components in the body. In actual biological organisms, these components and systems are strongly coupled and interact in complex, nonlinear ways leading to complicated global behavior. Here we describe a low-order computational model of two physiological systems, based loosely on a circulatory and respiratory system. Each system is represented as a one-dimensional fluid system with an interconnected series of mass sources, pumps, valves, and other network components, as appropriate, representing different physical organs and system components. Preliminary results from a first version of this model system are presented.

Genome complexity, robustness and genetic interactions in digital organisms

NASA Astrophysics Data System (ADS)

Lenski, Richard E.; Ofria, Charles; Collier, Travis C.; Adami, Christoph

1999-08-01

Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined `metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

Genome complexity, robustness and genetic interactions in digital organisms.

PubMed

Lenski, R E; Ofria, C; Collier, T C; Adami, C

1999-08-12

Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined 'metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

Mapping complex traits as a dynamic system

PubMed Central

Sun, Lidan; Wu, Rongling

2017-01-01

Despite increasing emphasis on the genetic study of quantitative traits, we are still far from being able to chart a clear picture of their genetic architecture, given an inherent complexity involved in trait formation. A competing theory for studying such complex traits has emerged by viewing their phenotypic formation as a “system” in which a high-dimensional group of interconnected components act and interact across different levels of biological organization from molecules through cells to whole organisms. This system is initiated by a machinery of DNA sequences that regulate a cascade of biochemical pathways to synthesize endophenotypes and further assemble these endophenotypes toward the end-point phenotype in virtue of various developmental changes. This review focuses on a conceptual framework for genetic mapping of complex traits by which to delineate the underlying components, interactions and mechanisms that govern the system according to biological principles and understand how these components function synergistically under the control of quantitative trait loci (QTLs) to comprise a unified whole. This framework is built by a system of differential equations that quantifies how alterations of different components lead to the global change of trait development and function, and provides a quantitative and testable platform for assessing the multiscale interplay between QTLs and development. The method will enable geneticists to shed light on the genetic complexity of any biological system and predict, alter or engineer its physiological and pathological states. PMID:25772476

Energy Transformations of Soil Organic Matter in a Changing World

NASA Astrophysics Data System (ADS)

Herrmann, A. M.; Coucheney, E.; Grice, S. M.; Ritz, K.; Harris, J.

2011-12-01

The role of soils in governing the terrestrial carbon balance is acknowledged as being important but remains poorly understood within the context of climate change. Soils exchange energy with their surroundings and are therefore open systems thermodynamically, but little is known how energy transformations of decomposition processes are affected by temperature. Soil organic matter and the soil biomass can be conceptualised as analogous to the 'fuel' and 'biological engine' of the earth, respectively, and are pivotal in driving the belowground carbon cycle. Thermodynamic principles of soil organic matter decomposition were evaluated by means of isothermal microcalorimetry (TAM Air, TA Instruments, Sollentuna Sweden: (i) Mineral forest soils from the Flakaliden long-term nitrogen fertilisation experiment (Sweden) were amended with a range of different substrates representing structurally simple to complex, ecologically pertinent organic matter and heat signatures were determined at temperatures between 5 and 25°C. (ii) Thermodynamic and resource-use efficiencies of the biomass were determined in arable soils which received contrasting long-term management regimes with respect to organic matter and nitrogen since 1956. The work showed that (i) structurally labile components have higher activation energy and temperature dependence than structurally more complex organic components. This is, however, in contrast to the thermodynamic argument which suggests the opposite that reactions metabolising structurally complex, aromatic components have higher temperature dependence than reactions metabolising structurally more labile components. (ii) Microbial communities exposed to long-term stress by heavy metal and low pH were less thermodynamic efficient and showed a decrease in resource-use efficiency in comparison with conventional input regimes. Differences in efficiencies were mirrored in both the phenotypic and functional profiles of the communities. We will present our findings illustrating the capacity of isothermal microcalorimetry to evaluate temperature dependencies of soil organic matter decomposition, associated energy transformations and thermodynamic principles in soil ecosystems.

Nonsomatotopic organization of the higher motor centers in octopus.

PubMed

Zullo, Letizia; Sumbre, German; Agnisola, Claudio; Flash, Tamar; Hochner, Binyamin

2009-10-13

Hyperredundant limbs with a virtually unlimited number of degrees of freedom (DOFs) pose a challenge for both biological and computational systems of motor control. In the flexible arms of the octopus, simplification strategies have evolved to reduce the number of controlled DOFs. Motor control in the octopus nervous system is hierarchically organized. A relatively small central brain integrates a huge amount of visual and tactile information from the large optic lobes and the peripheral nervous system of the arms and issues commands to lower motor centers controlling the elaborated neuromuscular system of the arms. This unique organization raises new questions on the organization of the octopus brain and whether and how it represents the rich movement repertoire. We developed a method of brain microstimulation in freely behaving animals and stimulated the higher motor centers-the basal lobes-thus inducing discrete and complex sets of movements. As stimulation strength increased, complex movements were recruited from basic components shared by different types of movement. We found no stimulation site where movements of a single arm or body part could be elicited. Discrete and complex components have no central topographical organization but are distributed over wide regions.

BIOMARKERS OF PM EXPOSURE TO COMBUSTION SOURCE EMISSIONS & ORGANIC (TOXIC) COMPONENTS

EPA Science Inventory

Fine particles (PM2.5) and associated semivolatile organic compounds (SVOC) contain a very complex mixture of both organic and inorganic chemicals that may contribute to toxicity of the particles. The health effects of PM2.5 exposures in humans result from both acute and chronic...

Escherichia coli Biofilms Have an Organized and Complex Extracellular Matrix Structure

PubMed Central

Hung, Chia; Zhou, Yizhou; Pinkner, Jerome S.; Dodson, Karen W.; Crowley, Jan R.; Heuser, John; Chapman, Matthew R.; Hadjifrangiskou, Maria; Henderson, Jeffrey P.; Hultgren, Scott J.

2013-01-01

ABSTRACT Bacterial biofilms are ubiquitous in nature, and their resilience is derived in part from a complex extracellular matrix that can be tailored to meet environmental demands. Although common developmental stages leading to biofilm formation have been described, how the extracellular components are organized to allow three-dimensional biofilm development is not well understood. Here we show that uropathogenic Escherichia coli (UPEC) strains produce a biofilm with a highly ordered and complex extracellular matrix (ECM). We used electron microscopy (EM) techniques to image floating biofilms (pellicles) formed by UPEC. EM revealed intricately constructed substructures within the ECM that encase individual, spatially segregated bacteria with a distinctive morphology. Mutational and biochemical analyses of these biofilms confirmed curli as a major matrix component and revealed important roles for cellulose, flagella, and type 1 pili in pellicle integrity and ECM infrastructure. Collectively, the findings of this study elucidated that UPEC pellicles have a highly organized ultrastructure that varies spatially across the multicellular community. PMID:24023384

Insights into the interaction between carbamazepine and natural dissolved organic matter in the Yangtze Estuary using fluorescence excitation-emission matrix spectra coupled with parallel factor analysis.

PubMed

Wang, Ying; Zhang, Manman; Fu, Jun; Li, Tingting; Wang, Jinggang; Fu, Yingyu

2016-10-01

The interaction between carbamazepine (CBZ) and dissolved organic matter (DOM) from three zones (the nearshore, the river channel, and the coastal areas) in the Yangtze Estuary was investigated using fluorescence quenching titration combined with excitation emission matrix spectra and parallel factor analysis (PARAFAC). The complexation between CBZ and DOM was demonstrated by the increase in hydrogen bonding and the disappearance of the C=O stretch obtained from the Fourier transform infrared spectroscopy analysis. The results indicated that two protein-like substances (component 2 and component3) and two humic-like substances (component 1 and 4) were identified in the DOM from the Yangtze Estuary. The fluorescence quenching curves of each component with the addition of CBZ and the Ryan and Weber model calculation results both demonstrated that the different components exhibited different complexation activities with CBZ. The protein-like components had a stronger affinity with CBZ than did the humic-like substances. On the other hand, the autochthonous tyrosine-like C2 played an important role in the complexation with DOM from the river channel and coastal areas, while C3 influenced by anthropogenic activities showed an obvious effect in the nearshore area. DOMs from the river channel have the highest binding capacity for CBZ, which may ascribe to the relatively high phenol content group in the DOM.

A REVIEW OF BIOACCUMULATION MODELING APPROACHES FOR PERSISTENT ORGANIC POLLUTANTS

EPA Science Inventory

Persistent organic pollutants and mercury are likely to bioaccumulate in biological components of the environment, including fish and wildlife. The complex and long-term dynamics involved with bioaccumulation are often represented with models. Current scientific developments in t...

Self-Organization in Coordination-Driven Self-Assembly

PubMed Central

Northrop, Brian H.; Zheng, Yao-Rong; Chi, Ki-Whan; Stang, Peter J.

2009-01-01

Conspectus Self-assembly allows for the preparation of highly complex molecular and supramolecular systems from relatively simple starting materials. Typically, self-assembled supramolecules are constructed by combining complementary pairs of two highly symmetric molecular components, thus limiting the chances of forming unwanted side products. Combining asymmetric molecular components or multiple complementary sets of molecules in one complex mixture can produce myriad different ordered and disordered supramolecular assemblies. Alternatively, spontaneous self-organization phenomena can promote the formation of specific product(s) out of a collection of multiple possibilities. Self-organization processes are common throughout much of nature and are especially common in biological systems. Recently, researchers have studied self-organized self-assembly in purely synthetic systems. This Account describes our investigations of self-organization in the coordination-driven self-assembly of platinum(II)-based metallosupramolecules. The modularity of the coordination-driven approach to self-assembly has allowed us to systematically study a wide variety of different factors that can control the extent of supramolecular self-organization. In particular, we have evaluated the effects of the symmetry and polarity of ambidentate donor subunits, differences in geometrical parameters (e.g. the size, angularity, and dimensionality) of Pt(II)-based acceptors and organic donors, the influence of temperature and solvent, and the effects of intermolecular steric interactions and hydrophobic interactions on self-organization. Our studies have shown that the extent of self-organization in the coordination-driven self-assembly of both 2D polygons and 3D polyhedra ranges from no organization (a statistical mixture of multiple products), to amplified organization (wherein a particular product or products are favored over others), and all the way to the absolute self-organization of discrete supramolecular assemblies. In many cases, inputs such as dipolar interactions, steric interactions, and differences in the geometric parameters of subunits—used either alone or as multiple factors simultaneously—can achieve absolute self-organization of discrete supramolecules. We have also observed instances where self-organization is not absolute and varies in its deviation from statistical results. Steric interactions are particularly useful control factors for driving such amplified self-organization because they can be subtly tuned through small structural variations. Having the ability to fully understand and control the self-organization of complex mixtures into specific synthetic supramolecules can provide a better understanding of analogous processes in biological systems. Furthermore, self-organization may allow for the facile synthesis of complex multifunctional, multicomponent systems from simply mixing a collection of much simpler, judiciously designed individual molecular components. PMID:19555073

Heterogeneous Oxidation of Laboratory-generated Mixed Composition and Biomass Burning Particles

NASA Astrophysics Data System (ADS)

Lim, C. Y.; Sugrue, R. A.; Hagan, D. H.; Cappa, C. D.; Kroll, J. H.; Browne, E. C.

2016-12-01

Heterogeneous oxidation of organic aerosol (OA) can significantly transform the chemical and physical properties of particulate matter in the atmosphere, leading to changes to the chemical composition of OA and potential volatilization of organic compounds. It has become increasingly apparent that the heterogeneous oxidation kinetics of OA depend on the phase and morphology of the particles. However, most laboratory experiments to date have been performed on single-component, purely organic precursors, which may exhibit fundamentally different behavior than more complex particles in the atmosphere. Here we present laboratory studies of the heterogeneous oxidation of two more complex chemical systems: thin, organic coatings on inorganic seed particles and biomass burning OA. In the first system, squalane (C30H62), a model compound for reduced OA, is coated onto dry ammonium sulfate particles at various thicknesses (10-20 nm) and exposed to hydroxyl radical (OH) in a flow tube reactor. In the second, we use a semi-batch reactor to study the heterogeneous OH-initiated oxidation of biomass burning particles as a part of the 2016 FIREX campaign in Missoula, MT. The resulting changes in chemical composition are monitored with an Aerodyne High Resolution Time-of-flight Aerosol Mass Spectrometer (AMS) and a soot-particle AMS for the non-refractory and refractory systems, respectively. We show that the heterogeneous oxidation kinetics of these multicomponent particles are substantially different than that of the single-component particles. The oxidation of organic coatings is rapid, undergoing dramatic changes to carbon oxidation state and losing a significant amount of organic mass after relatively low OH exposures (equivalent to several days of atmospheric processing). In the case of biomass burning particles, the kinetics are complex, with different components (inferred by aerosol mass spectrometry) undergoing oxidation at different rates.

Corolla Is a Novel Protein That Contributes to the Architecture of the Synaptonemal Complex of Drosophila

PubMed Central

Collins, Kimberly A.; Unruh, Jay R.; Slaughter, Brian D.; Yu, Zulin; Lake, Cathleen M.; Nielsen, Rachel J.; Box, Kimberly S.; Miller, Danny E.; Blumenstiel, Justin P.; Perera, Anoja G.; Malanowski, Kathryn E.; Hawley, R. Scott

2014-01-01

In most organisms the synaptonemal complex (SC) connects paired homologs along their entire length during much of meiotic prophase. To better understand the structure of the SC, we aim to identify its components and to determine how each of these components contributes to SC function. Here, we report the identification of a novel SC component in Drosophila melanogaster female oocytes, which we have named Corolla. Using structured illumination microscopy, we demonstrate that Corolla is a component of the central region of the SC. Consistent with its localization, we show by yeast two-hybrid analysis that Corolla strongly interacts with Cona, a central element protein, demonstrating the first direct interaction between two inner-synaptonemal complex proteins in Drosophila. These observations help provide a more complete model of SC structure and function in Drosophila females. PMID:24913682

Complement Activation in Inflammatory Skin Diseases

PubMed Central

Giang, Jenny; Seelen, Marc A. J.; van Doorn, Martijn B. A.; Rissmann, Robert; Prens, Errol P.; Damman, Jeffrey

2018-01-01

The complement system is a fundamental part of the innate immune system, playing a crucial role in host defense against various pathogens, such as bacteria, viruses, and fungi. Activation of complement results in production of several molecules mediating chemotaxis, opsonization, and mast cell degranulation, which can contribute to the elimination of pathogenic organisms and inflammation. Furthermore, the complement system also has regulating properties in inflammatory and immune responses. Complement activity in diseases is rather complex and may involve both aberrant expression of complement and genetic deficiencies of complement components or regulators. The skin represents an active immune organ with complex interactions between cellular components and various mediators. Complement involvement has been associated with several skin diseases, such as psoriasis, lupus erythematosus, cutaneous vasculitis, urticaria, and bullous dermatoses. Several triggers including auto-antibodies and micro-organisms can activate complement, while on the other hand complement deficiencies can contribute to impaired immune complex clearance, leading to disease. This review provides an overview of the role of complement in inflammatory skin diseases and discusses complement factors as potential new targets for therapeutic intervention. PMID:29713318

Limitations and potential of spectral subtractions in fourier-transform infrared (FTIR) spectroscopy of soil samples

USDA-ARS?s Scientific Manuscript database

Soil science research is increasingly applying Fourier transform infrared (FTIR) spectroscopy for analysis of soil organic matter (SOM). However, the compositional complexity of soils and the dominance of the mineral component can limit spectroscopic resolution of SOM and other minor components. The...

An Assembly Funnel Makes Biomolecular Complex Assembly Efficient

PubMed Central

Zenk, John; Schulman, Rebecca

2014-01-01

Like protein folding and crystallization, the self-assembly of complexes is a fundamental form of biomolecular organization. While the number of methods for creating synthetic complexes is growing rapidly, most require empirical tuning of assembly conditions and/or produce low yields. We use coarse-grained simulations of the assembly kinetics of complexes to identify generic limitations on yields that arise because of the many simultaneous interactions allowed between the components and intermediates of a complex. Efficient assembly occurs when nucleation is fast and growth pathways are few, i.e. when there is an assembly “funnel”. For typical complexes, an assembly funnel occurs in a narrow window of conditions whose location is highly complex specific. However, by redesigning the components this window can be drastically broadened, so that complexes can form quickly across many conditions. The generality of this approach suggests assembly funnel design as a foundational strategy for robust biomolecular complex synthesis. PMID:25360818

78 FR 33869 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Filing and Immediate Effectiveness of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-05

... systems to execute Stock/Option Orders,\\7\\ Stock/Complex Orders,\\8\\ and the option components of such... Change Amending Exchange Rule 6.91 To Remove Provisions Governing How the Complex Matching Engine Handles Electronic Complex Orders That Contain a Stock Leg May 30, 2013. Pursuant to Section 19(b)(1) \\1\\ of the...

Combining Toxicological and Chemical Characterization of Complex Mixtures to Understand the Impact of the Unknown Fraction

EPA Science Inventory

Toxicological assessment of adverse health outcomes associated with exposure to complex mixtures provides an integrated response of the organism (or in vitro test system) that accounts for additivity among the components (both dose and response) as well as any greater than or les...

The Capabilities of Chaos and Complexity

PubMed Central

Abel, David L.

2009-01-01

To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic) components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone)? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. “System” will be rigorously defined. Can a low-informational rapid succession of Prigogine’s dissipative structures self-order into bona fide organization? PMID:19333445

Possible complex organic compounds on Mars.

PubMed

Kobayashi, K; Sato, T; Kajishima, S; Kaneko, T; Ishikawa, Y; Saito, T

1997-01-01

It is suggested that primitive Mars had somehow similar environments as primitive Earth. If life was born on the primitive earth using organic compounds which were produced from the early Earth environment, the same types of organic compounds were also formed on primitive Mars. Such organic compounds might have been preserved on Mars still now. We are studying possible organic formation on primitive and present Mars. A gaseous mixture of CO2, CO, N2 and H2O with various mixing ratios were irradiated with high energy protons (major components of cosmic rays). Hydrogen cyanide and formaldehyde were detected among volatile products, and yellow-brown-colored water-soluble non-volatile substances were produced, which gave amino acids after acid-hydrolysis. Major part of "amino acid precursors" were not simple molecules like aminonitriles, but complex compounds which eluted earlier than free amino acids in cation-exchange HPLC. These organic compounds should be major targets in the future Mars mission. Strategy for the detection of the complex organics on Mars will be discussed.

Emergence of a snake-like structure in mobile distributed agents: an exploratory agent-based modeling approach.

PubMed

Niazi, Muaz A

2014-01-01

The body structure of snakes is composed of numerous natural components thereby making it resilient, flexible, adaptive, and dynamic. In contrast, current computer animations as well as physical implementations of snake-like autonomous structures are typically designed to use either a single or a relatively smaller number of components. As a result, not only these artificial structures are constrained by the dimensions of the constituent components but often also require relatively more computationally intensive algorithms to model and animate. Still, these animations often lack life-like resilience and adaptation. This paper presents a solution to the problem of modeling snake-like structures by proposing an agent-based, self-organizing algorithm resulting in an emergent and surprisingly resilient dynamic structure involving a minimal of interagent communication. Extensive simulation experiments demonstrate the effectiveness as well as resilience of the proposed approach. The ideas originating from the proposed algorithm can not only be used for developing self-organizing animations but can also have practical applications such as in the form of complex, autonomous, evolvable robots with self-organizing, mobile components with minimal individual computational capabilities. The work also demonstrates the utility of exploratory agent-based modeling (EABM) in the engineering of artificial life-like complex adaptive systems.

Emergence of a Snake-Like Structure in Mobile Distributed Agents: An Exploratory Agent-Based Modeling Approach

PubMed Central

Niazi, Muaz A.

2014-01-01

The body structure of snakes is composed of numerous natural components thereby making it resilient, flexible, adaptive, and dynamic. In contrast, current computer animations as well as physical implementations of snake-like autonomous structures are typically designed to use either a single or a relatively smaller number of components. As a result, not only these artificial structures are constrained by the dimensions of the constituent components but often also require relatively more computationally intensive algorithms to model and animate. Still, these animations often lack life-like resilience and adaptation. This paper presents a solution to the problem of modeling snake-like structures by proposing an agent-based, self-organizing algorithm resulting in an emergent and surprisingly resilient dynamic structure involving a minimal of interagent communication. Extensive simulation experiments demonstrate the effectiveness as well as resilience of the proposed approach. The ideas originating from the proposed algorithm can not only be used for developing self-organizing animations but can also have practical applications such as in the form of complex, autonomous, evolvable robots with self-organizing, mobile components with minimal individual computational capabilities. The work also demonstrates the utility of exploratory agent-based modeling (EABM) in the engineering of artificial life-like complex adaptive systems. PMID:24701135

Teamwork as an Essential Component of High-Reliability Organizations

PubMed Central

Baker, David P; Day, Rachel; Salas, Eduardo

2006-01-01

Organizations are increasingly becoming dynamic and unstable. This evolution has given rise to greater reliance on teams and increased complexity in terms of team composition, skills required, and degree of risk involved. High-reliability organizations (HROs) are those that exist in such hazardous environments where the consequences of errors are high, but the occurrence of error is extremely low. In this article, we argue that teamwork is an essential component of achieving high reliability particularly in health care organizations. We describe the fundamental characteristics of teams, review strategies in team training, demonstrate the criticality of teamwork in HROs and finally, identify specific challenges the health care community must address to improve teamwork and enhance reliability. PMID:16898980

Complex Topographic Feature Ontology Patterns

USGS Publications Warehouse

Varanka, Dalia E.; Jerris, Thomas J.

2015-01-01

Semantic ontologies are examined as effective data models for the representation of complex topographic feature types. Complex feature types are viewed as integrated relations between basic features for a basic purpose. In the context of topographic science, such component assemblages are supported by resource systems and found on the local landscape. Ontologies are organized within six thematic modules of a domain ontology called Topography that includes within its sphere basic feature types, resource systems, and landscape types. Context is constructed not only as a spatial and temporal setting, but a setting also based on environmental processes. Types of spatial relations that exist between components include location, generative processes, and description. An example is offered in a complex feature type ‘mine.’ The identification and extraction of complex feature types are an area for future research.

The component alignment model: a new approach to health care information technology strategic planning.

PubMed

Martin, J B; Wilkins, A S; Stawski, S K

1998-08-01

The evolving health care environment demands that health care organizations fully utilize information technologies (ITs). The effective deployment of IT requires the development and implementation of a comprehensive IT strategic plan. A number of approaches to health care IT strategic planning exist, but they are outdated or incomplete. The component alignment model (CAM) introduced here recognizes the complexity of today's health care environment, emphasizing continuous assessment and realignment of seven basic components: external environment, emerging ITs, organizational infrastructure, mission, IT infrastructure, business strategy, and IT strategy. The article provides a framework by which health care organizations can develop an effective IT strategic planning process.

Structural characteristics of fulvic acids from Continental Shelf sediments

USGS Publications Warehouse

Hatcher, P.G.; Breger, I.A.; Mattingly, M.A.

1980-01-01

Fulvic acids are those components of soil organic matter that remain soluble after a dilute alkaline extract of the soil is acidified to pH 2 (refs 1, 2). This extraction procedure has been applied to marine sediments, and the organic compounds so recovered have been called marine sedimentary fulvic acids. These fulvic acids are thought to form more complex humic substances in marine sediments by condensation reactions3. However, the chemical structural compositions of marine fulvic acids have not been defined sufficiently to allow this precursor relationship to be made. Here NMR spectroscopy is used to identify more clearly the chemical structural components of some marine sedimentary fulvic acids, thus enabling a more useful examination of their relationship to more complex humic substances. ?? 1980 Nature Publishing Group.

Spatially explicit risk assessment of an estuarine fish in Barataria Bay, Louisiana, following the Deepwater Horizon Oil spill: evaluating tradeoffs in model complexity and parsimony

EPA Science Inventory

As ecological risk assessments (ERA) move beyond organism-based determinations towards probabilistic population-level assessments, model complexity must be evaluated against the goals of the assessment, the information available to parameterize components with minimal dependence ...

γ-Tubulin complex in Trypanosoma brucei: molecular composition, subunit interdependence and requirement for axonemal central pair protein assembly.

PubMed

Zhou, Qing; Li, Ziyin

2015-11-01

γ-Tubulin complex constitutes a key component of the microtubule-organizing center and nucleates microtubule assembly. This complex differs in complexity in different organisms: the budding yeast contains the γ-tubulin small complex (γTuSC) composed of γ-tubulin, gamma-tubulin complex protein (GCP)2 and GCP3, whereas animals contain the γ-tubulin ring complex (γTuRC) composed of γTuSC and three additional proteins, GCP4, GCP5 and GCP6. In Trypanosoma brucei, the composition of the γ-tubulin complex remains elusive, and it is not known whether it also regulates assembly of the subpellicular microtubules and the spindle microtubules. Here we report that the γ-tubulin complex in T. brucei is composed of γ-tubulin and three GCP proteins, GCP2-GCP4, and is primarily localized in the basal body throughout the cell cycle. Depletion of GCP2 and GCP3, but not GCP4, disrupted the axonemal central pair microtubules, but not the subpellicular microtubules and the spindle microtubules. Furthermore, we showed that the γTuSC is required for assembly of two central pair proteins and that γTuSC subunits are mutually required for stability. Together, these results identified an unusual γ-tubulin complex in T. brucei, uncovered an essential role of γTuSC in central pair protein assembly, and demonstrated the interdependence of individual γTuSC components for maintaining a stable complex. © 2015 John Wiley & Sons Ltd.

Soil Organic Matter and Soil Productivity: Searching for the Missing Link

Treesearch

Felipe G. Sanchez

1998-01-01

Soil-organic matter (SOM) is a complex array of components including soil fauna and flora at different stages of decomposition (Berg et al., 1982). Its concentration in soils can vary from 0.5% in mineral soils to almost 100% in peat soils (Brady, 1974). Organic matter (OM) in the surface mineral soil is considered a major determinant of forest ecosystem productivity...

DIESEL EXHAUST RESEARCH: WHAT HAS IT TOLD US ABOUT AMBIENT ORGANIC PM TOXICITY.

EPA Science Inventory

Diesel exhaust is a complex mixture of components which includes organic gaseous and particulate material. Sources of the exhaust are derived from both on road and off road engines. Use of diesel fuel continues to increase in the US and globally, though the development and use o...

Determining the biochemical properties of the Oxalate Biosynthetic Component (Obc)1 from Burkholderia mallei

USDA-ARS?s Scientific Manuscript database

Oxalic acid is produced by a variety of organisms ranging from simple microbes to complex animals. This acid has been proposed to fulfill various physiological and pathological functions which vary between organisms. In bacteria from the Burkholderia genus, oxalate secretion has been shown to be quo...

Genetics Home Reference: fibrochondrogenesis

MedlinePlus

... provide instructions for making components of type XI collagen, which is a complex molecule that gives structure ... the body's joints and organs. Specifically, type XI collagen is found in cartilage, a tough but flexible ...

PPI layouts: BioJS components for the display of Protein-Protein Interactions.

PubMed

Salazar, Gustavo A; Meintjes, Ayton; Mulder, Nicola

2014-01-01

We present two web-based components for the display of Protein-Protein Interaction networks using different self-organizing layout methods: force-directed and circular. These components conform to the BioJS standard and can be rendered in an HTML5-compliant browser without the need for third-party plugins. We provide examples of interaction networks and how the components can be used to visualize them, and refer to a more complex tool that uses these components. http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7753.

Modeling relations in nature and eco-informatics: a practical application of rosennean complexity.

PubMed

Kineman, John J

2007-10-01

The purpose of eco-informatics is to communicate critical information about organisms and ecosystems. To accomplish this, it must reflect the complexity of natural systems. Present information systems are designed around mechanistic concepts that do not capture complexity. Robert Rosen's relational theory offers a way of representing complexity in terms of information entailments that are part of an ontologically implicit 'modeling relation'. This relation has corresponding epistemological components that can be captured empirically, the components being structure (associated with model encoding) and function (associated with model decoding). Relational complexity, thus, provides a long-awaited theoretical underpinning for these concepts that ecology has found indispensable. Structural information pertains to the material organization of a system, which can be represented by data. Functional information specifies potential change, which can be inferred from experiment and represented as models or descriptions of state transformations. Contextual dependency (of structure or function) implies meaning. Biological functions imply internalized or system-dependent laws. Complexity can be represented epistemologically by relating structure and function in two different ways. One expresses the phenomenal relation that exists in any present or past instance, and the other draws the ontology of a system into the empirical world in terms of multiple potentials subject to natural forms of selection and optimality. These act as system attractors. Implementing these components and their theoretical relations in an informatics system will provide more-complete ecological informatics than is possible from a strictly mechanistic point of view. This approach will enable many new possibilities for supporting science and decision making.

The γ-tubulin complex in Trypanosoma brucei: molecular composition, subunit interdependence and requirement for axonemal central pair protein assembly

PubMed Central

Zhou, Qing; Li, Ziyin

2015-01-01

The γ-tubulin complex constitutes a key component of the microtubule-organizing center and nucleates microtubule assembly. This complex differs in complexity in different organisms: the budding yeast contains the γ-tubulin small complex (γTuSC) composed of γ-tubulin, GCP2 and GCP3, whereas animals contain the γ-tubulin ring complex (γTuRC) composed of γTuSC and three additional proteins, GCP4, GCP5 and GCP6. In Trypanosoma brucei, the composition of the γ-tubulin complex remains elusive, and it is not known whether it also regulates assembly of the subpellicular microtubules and the spindle microtubules. Here we report that the γ-tubulin complex in T. brucei is composed of γ-tubulin and three GCP proteins, GCP2-GCP4, and is primarily localized in the basal body throughout the cell cycle. Depletion of GCP2 and GCP3, but not GCP4, disrupted the axonemal central pair microtubules, but not the subpellicular microtubules and the spindle microtubules. Furthermore, we showed that the γTuSC is required for assembly of two central pair proteins and that γTuSC subunits are mutually required for stability. Together, these results identified an unusual γ-tubulin complex in T. brucei, uncovered an essential role of γTuSC in central pair protein assembly, and demonstrated the interdependence of individual γTuSC components for maintaining a stable complex. PMID:26224545

State-Space Estimation of Soil Organic Carbon Stock

NASA Astrophysics Data System (ADS)

Ogunwole, Joshua O.; Timm, Luis C.; Obidike-Ugwu, Evelyn O.; Gabriels, Donald M.

2014-04-01

Understanding soil spatial variability and identifying soil parameters most determinant to soil organic carbon stock is pivotal to precision in ecological modelling, prediction, estimation and management of soil within a landscape. This study investigates and describes field soil variability and its structural pattern for agricultural management decisions. The main aim was to relate variation in soil organic carbon stock to soil properties and to estimate soil organic carbon stock from the soil properties. A transect sampling of 100 points at 3 m intervals was carried out. Soils were sampled and analyzed for soil organic carbon and other selected soil properties along with determination of dry aggregate and water-stable aggregate fractions. Principal component analysis, geostatistics, and state-space analysis were conducted on the analyzed soil properties. The first three principal components explained 53.2% of the total variation; Principal Component 1 was dominated by soil exchange complex and dry sieved macroaggregates clusters. Exponential semivariogram model described the structure of soil organic carbon stock with a strong dependence indicating that soil organic carbon values were correlated up to 10.8m.Neighbouring values of soil organic carbon stock, all waterstable aggregate fractions, and dithionite and pyrophosphate iron gave reliable estimate of soil organic carbon stock by state-space.

Genetics Home Reference: otospondylomegaepiphyseal dysplasia

MedlinePlus

... instructions for making one component of type XI collagen, which is a complex molecule that gives structure ... support the body's joints and organs. Type XI collagen is found in cartilage, a tough but flexible ...

Toward self-organization and complex matter.

PubMed

Lehn, Jean-Marie

2002-03-29

Beyond molecular chemistry based on the covalent bond, supramolecular chemistry aims at developing highly complex chemical systems from components interacting through noncovalent intermolecular forces. Over the past quarter century, supramolecular chemistry has grown into a major field and has fueled numerous developments at the interfaces with biology and physics. Some of the conceptual advances and future challenges are profiled here.

Major component analysis of dynamic networks of physiologic organ interactions

NASA Astrophysics Data System (ADS)

Liu, Kang K. L.; Bartsch, Ronny P.; Ma, Qianli D. Y.; Ivanov, Plamen Ch

2015-09-01

The human organism is a complex network of interconnected organ systems, where the behavior of one system affects the dynamics of other systems. Identifying and quantifying dynamical networks of diverse physiologic systems under varied conditions is a challenge due to the complexity in the output dynamics of the individual systems and the transient and nonlinear characteristics of their coupling. We introduce a novel computational method based on the concept of time delay stability and major component analysis to investigate how organ systems interact as a network to coordinate their functions. We analyze a large database of continuously recorded multi-channel physiologic signals from healthy young subjects during night-time sleep. We identify a network of dynamic interactions between key physiologic systems in the human organism. Further, we find that each physiologic state is characterized by a distinct network structure with different relative contribution from individual organ systems to the global network dynamics. Specifically, we observe a gradual decrease in the strength of coupling of heart and respiration to the rest of the network with transition from wake to deep sleep, and in contrast, an increased relative contribution to network dynamics from chin and leg muscle tone and eye movement, demonstrating a robust association between network topology and physiologic function.

Trypanosome outer kinetochore proteins suggest conservation of chromosome segregation machinery across eukaryotes

PubMed Central

D’Archivio, Simon

2017-01-01

Kinetochores are multiprotein complexes that couple eukaryotic chromosomes to the mitotic spindle to ensure proper segregation. The model for kinetochore assembly is conserved between humans and yeast, and homologues of several components are widely distributed in eukaryotes, but key components are absent in some lineages. The recent discovery in a lineage of protozoa called kinetoplastids of unconventional kinetochores with no apparent homology to model organisms suggests that more than one system for eukaryotic chromosome segregation may exist. In this study, we report a new family of proteins distantly related to outer kinetochore proteins Ndc80 and Nuf2. The family member in kinetoplastids, KKT-interacting protein 1 (KKIP1), associates with the kinetochore, and its depletion causes severe defects in karyokinesis, loss of individual chromosomes, and gross defects in spindle assembly or stability. Immunopurification of KKIP1 from stabilized kinetochores identifies six further components, which form part of a trypanosome outer kinetochore complex. These findings suggest that kinetochores in organisms such as kinetoplastids are built from a divergent, but not ancestrally distinct, set of components and that Ndc80/Nuf2-like proteins are universal in eukaryotic division. PMID:28034897

Genetics Home Reference: Weissenbacher-Zweymüller syndrome

MedlinePlus

... instructions for making one component of type XI collagen, which is a complex molecule that gives structure ... support the body's joints and organs. Type XI collagen is found in cartilage, a tough but flexible ...

MAGGIE Component 1: Identification and Purification of Native and Recombinant Multiprotein Complexes and Modified Proteins from Pyrococcus furiosus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, Michael W.; W. W. Adams, Michael

2014-01-07

Virtualy all cellular processes are carried out by dynamic molecular assemblies or multiprotein complexes (PCs), the composition of which is largely unknown. Structural genomics efforts have demonstrated that less than 25% of the genes in a given prokaryotic genome will yield stable, soluble proteins when expressed using a one-ORF-at-a-time approach. We proposed that much of the remaining 75% of the genes encode proteins that are part of multiprotein complexes or are modified post-translationally, for example, with metals. The problem is that PCs and metalloproteins (MPs) cannot be accurately predicted on a genome-wide scale. The only solution to this dilemma ismore » to experimentally determine PCs and MPs in biomass of a model organism and to develop analytical tools that can then be applied to the biomass of any other organism. In other words, organisms themselves must be analyzed to identify their PCs and MPs: “native proteomes” must be determined. This information can then be utilized to design multiple ORF expression systems to produce recombinant forms of PCs and MPs. Moreover, the information and utility of this approach can be enhanced by using a hyperthermophile, one that grows optimally at 100°C, as a model organism. By analyzing the native proteome at close to 100 °C below the optimum growth temperature, we will trap reversible and dynamic complexes, thereby enabling their identification, purification, and subsequent characterization. The model organism for the current study is Pyrococcus furiosus, a hyperthermophilic archaeon that grows optimally at 100°C. It is grown up to 600-liter scale and kg quantities of biomass are available. In this project we identified native PCs and MPs using P. furiosus biomass (with MS/MS analyses to identify proteins by component 4). In addition, we provided samples of abundant native PCs and MPs for structural characterization (using SAXS by component 5). We also designed and evaluated generic bioinformatics and experimental protocols for PC and MP production in other prokaryotes of DOE interest. The research resulted in ten peer-reviewed publications including in Nature and Nature Methods.« less

PPI layouts: BioJS components for the display of Protein-Protein Interactions

PubMed Central

Salazar, Gustavo A.; Meintjes, Ayton; Mulder, Nicola

2014-01-01

Summary: We present two web-based components for the display of Protein-Protein Interaction networks using different self-organizing layout methods: force-directed and circular. These components conform to the BioJS standard and can be rendered in an HTML5-compliant browser without the need for third-party plugins. We provide examples of interaction networks and how the components can be used to visualize them, and refer to a more complex tool that uses these components. Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7753 PMID:25075288

[Nucleolus transformation in oocytes of mouse antral follicles. Revealing of coilin and RNA polymerase I complex components].

PubMed

Pochukalina, G N; Parfenov, V N

2008-01-01

This study is the continuation of our previous investigation of the nucleolus transformation in growing oocytes from mouse multilayer follicles (Pochukalina, Parfenov, 2006). Here in the present research we have examined the features of organization and molecular composition of nucleolus like body, or postnucleolus, in two groups of oocytes with different chromatin configuration from mouse antral follicles. Using light and electron immunocytochemistry, we have defined the dynamics of ribosomal RNA synthesis and processing molecular component distribution in postnucleolus. Considerable changes in RNA polymerase I distribution and its colocalization with coilin at the periphery of postnucleolus were revealed. Putative role of coilin in formation of complexes with ribosomal RNA synthesis/processing components is discussed.

Processing of simple and complex acoustic signals in a tonotopically organized ear

PubMed Central

Hummel, Jennifer; Wolf, Konstantin; Kössl, Manfred; Nowotny, Manuela

2014-01-01

Processing of complex signals in the hearing organ remains poorly understood. This paper aims to contribute to this topic by presenting investigations on the mechanical and neuronal response of the hearing organ of the tropical bushcricket species Mecopoda elongata to simple pure tone signals as well as to the conspecific song as a complex acoustic signal. The high-frequency hearing organ of bushcrickets, the crista acustica (CA), is tonotopically tuned to frequencies between about 4 and 70 kHz. Laser Doppler vibrometer measurements revealed a strong and dominant low-frequency-induced motion of the CA when stimulated with either pure tone or complex stimuli. Consequently, the high-frequency distal area of the CA is more strongly deflected by low-frequency-induced waves than by high-frequency-induced waves. This low-frequency dominance will have strong effects on the processing of complex signals. Therefore, we additionally studied the neuronal response of the CA to native and frequency-manipulated chirps. Again, we found a dominant influence of low-frequency components within the conspecific song, indicating that the mechanical vibration pattern highly determines the neuronal response of the sensory cells. Thus, we conclude that the encoding of communication signals is modulated by ear mechanics. PMID:25339727

Hydrolytic microbial communities in terrestrial ecosystems

NASA Astrophysics Data System (ADS)

Manucharova, Natalia; Chernov, Timofey; Kolcova, Ekaterina; Zelezova, Alena; Lukacheva, Euhenia; Zenova, Galina

2014-05-01

Hydrolytic microbial communities in terrestrial ecosystems Manucharova N.A., Chernov T.I., Kolcova E.M., Zelezova A.D., Lukacheva E.G. Lomonosov Moscow State University, Russia Vertical differentiation of terrestrial biogeocenoses is conditioned by the formation of vertical tiers that differ considerably in the composition and structure of microbial communities. All the three tiers, phylloplane, litter and soil, are united by a single flow of organic matter, and are spatially separated successional stages of decomposition of organic substances. Decomposition of organic matter is mainly due to the activity of microorganisms producing enzymes - hydrolase and lyase - which destroy complex organic compounds. Application of molecular biological techniques (FISH) in environmental studies provides a more complete information concerning the taxonomic diversity and potential hydrolytic activity of microbial complexes of terrestrial ecosystems that exist in a wide range of environmental factors (moisture, temperature, redox potential, organic matter). The combination of two molecular biological techniques (FISH and DGGE-analysis of fragments of gene 16S rRNA total amplificate) enables an informative assessment of the differences in the structure of dominant and minor components of hydrolytic complexes formed in different tiers of terrestrial ecosystems. The functional activity of hydrolytic microbial complexes of terrestrial ecosystems is determined by the activity of dominant and minor components, which also have a high gross enzymatic activity. Degradation of biopolymers in the phylloplane is mainly due to the representatives of the Proteobacteria phylogenetic group (classes alpha and beta). In mineral soil horizons, the role of hydrolytic representatives of Firmicutes and Actinobacteria increases. Among the key environmental parameters that determine the functional activity of the hydrolytic (chitinolytic) complex of soil layer (moisture, nutrient supply, successional time), the most significant one is moisture. Moisture levels providing maximum activity of a hydrolytic microbial complex depend on the soil type. Development of a hydrolytic microbial complex occurs in a very wide moisture range - from values close to field capacity to those close to the wilting moisture point. The functional role of mycelial actinobacteria in the metabolism of chitin consists, on the one hand, in active decomposition of this biopolymer, and on the other hand, in the regulation of microbial hydrolytic complex activity through the production of biologically active regulatory metabolites, which occurs in a wide range of environmental parameters (moisture, temperature, organic matter, successional time). Experimental design is applicable to identify in situ optimal values of environmental factors that considerably affect the functional parameters of hydrolytic microbial complexes.

Study of the structural organization of cyclodextrin-DNA complex loaded anionic and pH-sensitive liposomes

NASA Astrophysics Data System (ADS)

Silva, Sônia M. L.; Coelho, Letícia N.; Malachias, Ângelo; Perez, Carlos A.; Pesquero, Jorge L.; Magalhães-Paniago, Rogério; de Oliveira, Mônica C.

2011-04-01

The present study investigated the effect of the 6-monodeoxy-6-monoamine-β-cyclodextrin(Am-β-CD)/DNA (Am-β-CD/DNA) complex, as well as of culture medium components and proteins, at pH 7.4 and 5.0, on membranes of anionic and pH-sensitive liposomes comprised of DOPE-CHEMS, using energy dispersive X-ray diffraction (EDXD). At pH 7.4, the Am-β-CD/DNA complex induced the appearance of lamellar and hexagonal phases of DOPE. However, at pH 5.0, only non-lamellar phases could be observed. The presence of biological components led to a disruption of lipid order, but the pH-sensitivity of liposomes was maintained.

Ultraviolet-B radiation mobilizes uranium from uranium-dissolved organic carbon complexes in aquatic systems, demonstrated by asymmetrical flow field-flow fractionation.

PubMed

Nehete, Sachin Vilas; Christensen, Terje; Salbu, Brit; Teien, Hans-Christian

2017-05-05

Humic substances have a tendency to form complexes with metal ions in aquatic medium, impacting the metal mobility, decreasing bioavailability and toxicity. Ultraviolet-B (UV-B) radiation exposure degrades the humic substance, changes their molecular weight distribution and their metal binding capacity in aquatic medium. In this study, we experimented the effect of UV-B radiation on the uranium complexed with fulvic acids and humic acids in a soft water system at different pH, uranium concentrations and radiant exposure. The concentration and distribution of uranium in a complexed form were investigated by asymmetrical flow field-flow fractionation coupled to multi detection technique (AsFlFFF-UV-ICP-MS). The major concentration of uranium present in complexes was primarily associated with average and higher molecular weight fulvic and humic acids components. The concentration of uranium in a complexed form increased with increasing fulvic and humic acid concentrations as well as pH of the solution. The higher molecular weight fraction of uranium was degraded due to the UV-B exposure, transforming about 50% of the uranium-dissolved organic carbon complexes into low molecular weight uranium species in complex form with organic ligands and/or free form. The result also suggests AsFlFFF-UV-ICP-MS to be an important separation and detection technique for understanding the interaction of radionuclides with dissolved organic matter, tracking size distribution changes during degradation of organic complexes for understanding mobility, bioavailability and ecosystem transfer of radionuclides as well as metals. Copyright © 2017 Elsevier B.V. All rights reserved.

Drosophila as a model system to study autophagy.

PubMed

Zirin, Jonathan; Perrimon, Norbert

2010-12-01

Originally identified as a response to starvation in yeast, autophagy is now understood to fulfill a variety of roles in higher eukaryotes, from the maintenance of cellular homeostasis to the cellular response to stress, starvation, and infection. Although genetics and biochemical studies in yeast have identified many components involved in autophagy, the findings that some of the essential components of the yeast pathway are missing in higher organisms underscore the need to study autophagy in more complex systems. This review focuses on the use of the fruitfly, Drosophila melanogaster as a model system for analysis of autophagy. Drosophila is an organism well-suited for genetic analysis and represents an intermediate between yeast and mammals with respect to conservation of the autophagy machinery. Furthermore, the complex biology and physiology of Drosophila presents an opportunity to model human diseases in a tissue specific and analogous context.

Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans.

PubMed

Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C G; Benavente, Ricardo

2012-10-09

The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed no sequence homology. This discrepancy challenged the hypothesis that the SC arose only once in evolution. To pursue this matter we focused on the evolution of SYCP1 and SYCP3, the two major structural SC proteins of mammals. Remarkably, our comparative bioinformatic and expression studies revealed that SYCP1 and SYCP3 are also components of the SC in the basal metazoan Hydra. In contrast to previous assumptions, we therefore conclude that SYCP1 and SYCP3 form monophyletic groups of orthologous proteins across metazoans.

Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans

PubMed Central

Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C. G.; Benavente, Ricardo

2012-01-01

The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed no sequence homology. This discrepancy challenged the hypothesis that the SC arose only once in evolution. To pursue this matter we focused on the evolution of SYCP1 and SYCP3, the two major structural SC proteins of mammals. Remarkably, our comparative bioinformatic and expression studies revealed that SYCP1 and SYCP3 are also components of the SC in the basal metazoan Hydra. In contrast to previous assumptions, we therefore conclude that SYCP1 and SYCP3 form monophyletic groups of orthologous proteins across metazoans. PMID:23012415

Origins of cellular geometry

PubMed Central

2011-01-01

Cells are highly complex and orderly machines, with defined shapes and a startling variety of internal organizations. Complex geometry is a feature of both free-living unicellular organisms and cells inside multicellular animals. Where does the geometry of a cell come from? Many of the same questions that arise in developmental biology can also be asked of cells, but in most cases we do not know the answers. How much of cellular organization is dictated by global cell polarity cues as opposed to local interactions between cellular components? Does cellular structure persist across cell generations? What is the relationship between cell geometry and tissue organization? What ensures that intracellular structures are scaled to the overall size of the cell? Cell biology is only now beginning to come to grips with these questions. PMID:21880160

Biophysical characterization of an integrin-targeted lipopolyplex gene delivery vector.

PubMed

Mustapa, M Firouz Mohd; Bell, Paul C; Hurley, Christopher A; Nicol, Alastair; Guénin, Erwann; Sarkar, Supti; Writer, Michele J; Barker, Susie E; Wong, John B; Pilkington-Miksa, Michael A; Papahadjopoulos-Sternberg, Brigitte; Shamlou, Parviz Ayazi; Hailes, Helen C; Hart, Stephen L; Zicha, Daniel; Tabor, Alethea B

2007-11-13

Nonviral gene delivery vectors now show good therapeutic potential: however, detailed characterization of the composition and macromolecular organization of such particles remains a challenge. This paper describes experiments to elucidate the structure of a ternary, targeted, lipopolyplex synthetic vector, the LID complex. This consists of a lipid component, Lipofectin (L) (1:1 DOTMA:DOPE), plasmid DNA (D), and a dual-function, cationic peptide component (I) containing DNA condensation and integrin-targeting sequences. Fluorophore-labeled lipid, peptide, and DNA components were used to formulate the vector, and the stoichiometry of the particles was established by fluorescence correlation spectroscopy (FCS). The size of the complex was measured by FCS, and the sizes of LID, L, LD, and ID complexes were measured by dynamic light scattering (DLS). Fluorescence quenching experiments and freeze-fracture electron microscopy were then used to demonstrate the arrangement of the lipid, peptide, and DNA components within the complex. These experiments showed that the cationic portion of the peptide, I, interacts with the plasmid DNA, resulting in a tightly condensed DNA-peptide inner core; this is surrounded by a disordered lipid layer, from which the integrin-targeting sequence of the peptide partially protrudes.

Using McStas for modelling complex optics, using simple building bricks

NASA Astrophysics Data System (ADS)

Willendrup, Peter K.; Udby, Linda; Knudsen, Erik; Farhi, Emmanuel; Lefmann, Kim

2011-04-01

The McStas neutron ray-tracing simulation package is a versatile tool for producing accurate neutron simulations, extensively used for design and optimization of instruments, virtual experiments, data analysis and user training.In McStas, component organization and simulation flow is intrinsically linear: the neutron interacts with the beamline components in a sequential order, one by one. Historically, a beamline component with several parts had to be implemented with a complete, internal description of all these parts, e.g. a guide component including all four mirror plates and required logic to allow scattering between the mirrors.For quite a while, users have requested the ability to allow “components inside components” or meta-components, allowing to combine functionality of several simple components to achieve more complex behaviour, i.e. four single mirror plates together defining a guide.We will here show that it is now possible to define meta-components in McStas, and present a set of detailed, validated examples including a guide with an embedded, wedged, polarizing mirror system of the Helmholtz-Zentrum Berlin type.

[Proteins and saponins in the lipid preparation obtained by extraction of soybean flour].

PubMed

Baukova, N A; Alekseeva, S G; Sorokoumova, G M; Selishcheva, A A; Martynova, O M; Rogozhkina, E A; Shvets, V I

2002-01-01

A complex lipid preparation was obtained by extraction of soybean flour with organic solvents. This preparation was shown to include not only phospholipids (major components), but also up to 30% saponins. These compounds were identified by TLC, HPLC, and 1H-NMR spectroscopy. Minor components of the lipid extract were represented by polypeptides associated with phospholipids via electrostatic or hydrophobic forces.

Linking hygroscopicity and the surface microstructure of model inorganic salts, simple and complex carbohydrates, and authentic sea spray aerosol particles.

PubMed

Estillore, Armando D; Morris, Holly S; Or, Victor W; Lee, Hansol D; Alves, Michael R; Marciano, Meagan A; Laskina, Olga; Qin, Zhen; Tivanski, Alexei V; Grassian, Vicki H

2017-08-09

Individual airborne sea spray aerosol (SSA) particles show diversity in their morphologies and water uptake properties that are highly dependent on the biological, chemical, and physical processes within the sea subsurface and the sea surface microlayer. In this study, hygroscopicity data for model systems of organic compounds of marine origin mixed with NaCl are compared to data for authentic SSA samples collected in an ocean-atmosphere facility providing insights into the SSA particle growth, phase transitions and interactions with water vapor in the atmosphere. In particular, we combine single particle morphology analyses using atomic force microscopy (AFM) with hygroscopic growth measurements in order to provide important insights into particle hygroscopicity and the surface microstructure. For model systems, a range of simple and complex carbohydrates were studied including glucose, maltose, sucrose, laminarin, sodium alginate, and lipopolysaccharides. The measured hygroscopic growth was compared with predictions from the Extended-Aerosol Inorganics Model (E-AIM). It is shown here that the E-AIM model describes well the deliquescence transition and hygroscopic growth at low mass ratios but not as well for high ratios, most likely due to a high organic volume fraction. AFM imaging reveals that the equilibrium morphology of these single-component organic particles is amorphous. When NaCl is mixed with the organics, the particles adopt a core-shell morphology with a cubic NaCl core and the organics forming a shell similar to what is observed for the authentic SSA samples. The observation of such core-shell morphologies is found to be highly dependent on the salt to organic ratio and varies depending on the nature and solubility of the organic component. Additionally, single particle organic volume fraction AFM analysis of NaCl : glucose and NaCl : laminarin mixtures shows that the ratio of salt to organics in solution does not correspond exactly for individual particles - showing diversity within the ensemble of particles produced even for a simple two component system.

Animal models and conserved processes

PubMed Central

2012-01-01

Background The concept of conserved processes presents unique opportunities for using nonhuman animal models in biomedical research. However, the concept must be examined in the context that humans and nonhuman animals are evolved, complex, adaptive systems. Given that nonhuman animals are examples of living systems that are differently complex from humans, what does the existence of a conserved gene or process imply for inter-species extrapolation? Methods We surveyed the literature including philosophy of science, biological complexity, conserved processes, evolutionary biology, comparative medicine, anti-neoplastic agents, inhalational anesthetics, and drug development journals in order to determine the value of nonhuman animal models when studying conserved processes. Results Evolution through natural selection has employed components and processes both to produce the same outcomes among species but also to generate different functions and traits. Many genes and processes are conserved, but new combinations of these processes or different regulation of the genes involved in these processes have resulted in unique organisms. Further, there is a hierarchy of organization in complex living systems. At some levels, the components are simple systems that can be analyzed by mathematics or the physical sciences, while at other levels the system cannot be fully analyzed by reducing it to a physical system. The study of complex living systems must alternate between focusing on the parts and examining the intact whole organism while taking into account the connections between the two. Systems biology aims for this holism. We examined the actions of inhalational anesthetic agents and anti-neoplastic agents in order to address what the characteristics of complex living systems imply for inter-species extrapolation of traits and responses related to conserved processes. Conclusion We conclude that even the presence of conserved processes is insufficient for inter-species extrapolation when the trait or response being studied is located at higher levels of organization, is in a different module, or is influenced by other modules. However, when the examination of the conserved process occurs at the same level of organization or in the same module, and hence is subject to study solely by reductionism, then extrapolation is possible. PMID:22963674

A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria

PubMed Central

Hoppins, Suzanne; Collins, Sean R.; Cassidy-Stone, Ann; Hummel, Eric; DeVay, Rachel M.; Lackner, Laura L.; Westermann, Benedikt; Schuldiner, Maya

2011-01-01

To broadly explore mitochondrial structure and function as well as the communication of mitochondria with other cellular pathways, we constructed a quantitative, high-density genetic interaction map (the MITO-MAP) in Saccharomyces cerevisiae. The MITO-MAP provides a comprehensive view of mitochondrial function including insights into the activity of uncharacterized mitochondrial proteins and the functional connection between mitochondria and the ER. The MITO-MAP also reveals a large inner membrane–associated complex, which we term MitOS for mitochondrial organizing structure, comprised of Fcj1/Mitofilin, a conserved inner membrane protein, and five additional components. MitOS physically and functionally interacts with both outer and inner membrane components and localizes to extended structures that wrap around the inner membrane. We show that MitOS acts in concert with ATP synthase dimers to organize the inner membrane and promote normal mitochondrial morphology. We propose that MitOS acts as a conserved mitochondrial skeletal structure that differentiates regions of the inner membrane to establish the normal internal architecture of mitochondria. PMID:21987634

Supramolecular chemistry: from molecular information towards self-organization and complex matter

NASA Astrophysics Data System (ADS)

Lehn, Jean-Marie

2004-03-01

Molecular chemistry has developed a wide range of very powerful procedures for constructing ever more sophisticated molecules from atoms linked by covalent bonds. Beyond molecular chemistry lies supramolecular chemistry, which aims at developing highly complex chemical systems from components interacting via non-covalent intermolecular forces. By the appropriate manipulation of these interactions, supramolecular chemistry became progressively the chemistry of molecular information, involving the storage of information at the molecular level, in the structural features, and its retrieval, transfer, and processing at the supramolecular level, through molecular recognition processes operating via specific interactional algorithms. This has paved the way towards apprehending chemistry also as an information science. Numerous receptors capable of recognizing, i.e. selectively binding, specific substrates have been developed, based on the molecular information stored in the interacting species. Suitably functionalized receptors may perform supramolecular catalysis and selective transport processes. In combination with polymolecular organization, recognition opens ways towards the design of molecular and supramolecular devices based on functional (photoactive, electroactive, ionoactive, etc) components. A step beyond preorganization consists in the design of systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined supramolecular architectures by self-assembly from their components. Self-organization processes, directed by the molecular information stored in the components and read out at the supramolecular level through specific interactions, represent the operation of programmed chemical systems. They have been implemented for the generation of a variety of discrete functional architectures of either organic or inorganic nature. Self-organization processes also give access to advanced supramolecular materials, such as supramolecular polymers and liquid crystals, and provide an original approach to nanoscience and nanotechnology. In particular, the spontaneous but controlled generation of well-defined, functional supramolecular architectures of nanometric size through self-organization represents a means of performing programmed engineering and processing of nanomaterials. Supramolecular chemistry is intrinsically a dynamic chemistry, in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when a molecular entity contains covalent bonds that may form and break reversibly, so as to make possible a continuous change in constitution and structure by reorganization and exchange of building blocks. This behaviour defines a constitutional dynamic chemistry that allows self-organization by selection as well as by design at both the molecular and supramolecular levels. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization by selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation in a Darwinistic fashion. The merging of the features, information and programmability, dynamics and reversibility, constitution and structural diversity, points towards the emergence of adaptative and evolutionary chemistry. Together with the corresponding fields of physics and biology, it constitutes a science of informed matter, of organized, adaptative complex matter. This article was originally published in 2003 by the Israel Academy of Sciences and Humanities in the framework of its Albert Einstein Memorial Lectures series. Reprinted by permission of the Israel Academy of Sciences and Humanities.

Employing Geodatabases for Planetary Mapping Conduct - Requirements, Concepts and Solutions

NASA Technical Reports Server (NTRS)

vanGasselt, Stephan; Nass, A.

2010-01-01

Planetary geologic mapping has become complex in terms of merging and co-registering a variety of different datasets for analysis and mapping. But it has also become more convenient when it comes to conducting actual (geoscientific) mapping with the help of desktop Geographic Information Systems (GIS). The complexity and variety of data, however, are major issues that need to be taken care of in order to provide mappers with a consistent and easy-to-use mapping basis. Furthermore, a high degree of functionality and interoperability of various commercial and open-source GIS and remote sensing applications allow mappers to organize map data, map components and attribute data in a more sophisticated and intuitional way when compared to workflows 15 years ago. Integration of mapping results of different groups becomes an awkward task as each mapper follows his/her own style, especially if mapping conduct is not coordinated and organized programmatically. Problems of data homogenization start with various interpretations and implementations of planetary map projections and reference systems which form the core component of any mapping and analysis work. If the data basis is inconsistent, mapping results in terms of objects georeference become hard to integrate. Apart from data organization and referencing issues, which are important on the mapping as well as the data-processing side of every project, the organization of planetary geologic map units and attributes, as well as their representation within a common GIS environment, are key components that need to be taken care of in a consistent and persistent way.

Pseudo-enantiomeric chiral components and formation of the helical micro- and nanostructures in charge-transfer complexes

NASA Astrophysics Data System (ADS)

Langer, Jerzy J.; Hreczycho, Grzegorz

2018-03-01

Helical organic micro- and nanostructures are formed by a charge-transfer complex, cinchonidine-TCNQ. These unusual forms result from the chirality, the steric structure and specific interactions of cinchonidine molecules. These materials are semiconductors (10-4 S cm-1), with the typical absorption spectra in IR and UV-vis, but also have a characteristic of CD spectrum. Surprisingly, conductive micro and nano helices are not formed in pseudo-enantiomeric cinchonine, i.e. the complex of cinchonine and TCNQ.

Switching industrial production processes from complex to defined media: method development and case study using the example of Penicillium chrysogenum.

PubMed

Posch, Andreas E; Spadiut, Oliver; Herwig, Christoph

2012-06-22

Filamentous fungi are versatile cell factories and widely used for the production of antibiotics, organic acids, enzymes and other industrially relevant compounds at large scale. As a fact, industrial production processes employing filamentous fungi are commonly based on complex raw materials. However, considerable lot-to-lot variability of complex media ingredients not only demands for exhaustive incoming components inspection and quality control, but unavoidably affects process stability and performance. Thus, switching bioprocesses from complex to defined media is highly desirable. This study presents a strategy for strain characterization of filamentous fungi on partly complex media using redundant mass balancing techniques. Applying the suggested method, interdependencies between specific biomass and side-product formation rates, production of fructooligosaccharides, specific complex media component uptake rates and fungal strains were revealed. A 2-fold increase of the overall penicillin space time yield and a 3-fold increase in the maximum specific penicillin formation rate were reached in defined media compared to complex media. The newly developed methodology enabled fast characterization of two different industrial Penicillium chrysogenum candidate strains on complex media based on specific complex media component uptake kinetics and identification of the most promising strain for switching the process from complex to defined conditions. Characterization at different complex/defined media ratios using only a limited number of analytical methods allowed maximizing the overall industrial objectives of increasing both, method throughput and the generation of scientific process understanding.

Switching industrial production processes from complex to defined media: method development and case study using the example of Penicillium chrysogenum

PubMed Central

2012-01-01

Background Filamentous fungi are versatile cell factories and widely used for the production of antibiotics, organic acids, enzymes and other industrially relevant compounds at large scale. As a fact, industrial production processes employing filamentous fungi are commonly based on complex raw materials. However, considerable lot-to-lot variability of complex media ingredients not only demands for exhaustive incoming components inspection and quality control, but unavoidably affects process stability and performance. Thus, switching bioprocesses from complex to defined media is highly desirable. Results This study presents a strategy for strain characterization of filamentous fungi on partly complex media using redundant mass balancing techniques. Applying the suggested method, interdependencies between specific biomass and side-product formation rates, production of fructooligosaccharides, specific complex media component uptake rates and fungal strains were revealed. A 2-fold increase of the overall penicillin space time yield and a 3-fold increase in the maximum specific penicillin formation rate were reached in defined media compared to complex media. Conclusions The newly developed methodology enabled fast characterization of two different industrial Penicillium chrysogenum candidate strains on complex media based on specific complex media component uptake kinetics and identification of the most promising strain for switching the process from complex to defined conditions. Characterization at different complex/defined media ratios using only a limited number of analytical methods allowed maximizing the overall industrial objectives of increasing both, method throughput and the generation of scientific process understanding. PMID:22727013

Synaptonemal Complex Components Persist at Centromeres and Are Required for Homologous Centromere Pairing in Mouse Spermatocytes

PubMed Central

Kouznetsova, Anna; Scherthan, Harry; Höög, Christer; Dawson, Dean S.; Pezza, Roberto J.

2012-01-01

Recent studies in simple model organisms have shown that centromere pairing is important for ensuring high-fidelity meiotic chromosome segregation. However, this process and the mechanisms regulating it in higher eukaryotes are unknown. Here we present the first detailed study of meiotic centromere pairing in mouse spermatogenesis and link it with key events of the G2/metaphase I transition. In mouse we observed no evidence of the persistent coupling of centromeres that has been observed in several model organisms. We do however find that telomeres associate in non-homologous pairs or small groups in B type spermatogonia and pre-leptotene spermatocytes, and this association is disrupted by deletion of the synaptonemal complex component SYCP3. Intriguingly, we found that, in mid prophase, chromosome synapsis is not initiated at centromeres, and centromeric regions are the last to pair in the zygotene-pachytene transition. In late prophase, we first identified the proteins that reside at paired centromeres. We found that components of the central and lateral element and transverse filaments of the synaptonemal complex are retained at paired centromeres after disassembly of the synaptonemal complex along diplotene chromosome arms. The absence of SYCP1 prevents centromere pairing in knockout mouse spermatocytes. The localization dynamics of SYCP1 and SYCP3 suggest that they play different roles in promoting homologous centromere pairing. SYCP1 remains only at paired centromeres coincident with the time at which some kinetochore proteins begin loading at centromeres, consistent with a role in assembly of meiosis-specific kinetochores. After removal of SYCP1 from centromeres, SYCP3 then accumulates at paired centromeres where it may promote bi-orientation of homologous centromeres. We propose that, in addition to their roles as synaptonemal complex components, SYCP1 and SYCP3 act at the centromeres to promote the establishment and/or maintenance of centromere pairing and, by doing so, improve the segregation fidelity of mammalian meiotic chromosomes. PMID:22761579

Analysis of volatile metabolites in biological fluids as indicators of prodromal disease condition

NASA Technical Reports Server (NTRS)

Zlatkis, A.

1982-01-01

The volatile profile cannot be defined as a single class of substances, rather it is a broad spectrum of materials of different polarities characterized by having a boiling-point in the low to medium range (up to approximately 300 C) and the fact that the compounds are suitable for gas chromatography without derivatization. The organic volatile profiles are very complex mixtures of metabolic byproducts, intermediates, and terminal products of enzymatic degradations composed mainly of alcohols, ketones, aldehydes, pyrazines, sulfides, isothiocyanates, pyrroles, and furans. The concentration of organic volatiles in biological fluids covers a wide range with many important components present at trace levels. The complexity of the organic volatile fraction requires the use of capillary columns for their separation.

Music video shot segmentation using independent component analysis and keyframe extraction based on image complexity

NASA Astrophysics Data System (ADS)

Li, Wei; Chen, Ting; Zhang, Wenjun; Shi, Yunyu; Li, Jun

2012-04-01

In recent years, Music video data is increasing at an astonishing speed. Shot segmentation and keyframe extraction constitute a fundamental unit in organizing, indexing, retrieving video content. In this paper a unified framework is proposed to detect the shot boundaries and extract the keyframe of a shot. Music video is first segmented to shots by illumination-invariant chromaticity histogram in independent component (IC) analysis feature space .Then we presents a new metric, image complexity, to extract keyframe in a shot which is computed by ICs. Experimental results show the framework is effective and has a good performance.

New concepts on functional chronic pelvic and perineal pain: pathophysiology and multidisciplinary management.

PubMed

Ploteau, Stéphane; Labat, Jean Jacques; Riant, Thibault; Levesque, Amélie; Robert, Roger; Nizard, Julien

2015-03-01

The management of chronic pelvic and perineal pain has been improved by a better understanding of the mechanisms of this pain and an optimized integrated multidisciplinary approach to the patient. The concept of organic lesions responsible for a persistent nociceptive factor has gradually been replaced by that of dysregulation of nociceptive messages derived from the pelvis and perineum. In this setting, painful diseases identified by organ specialists are usually also involved and share several common denominators (triggering factors, predisposing clinical context). These diseases include painful bladder syndrome, irritable bowel syndrome, vulvodynia, and chronic pelvic pain syndrome. The painful symptoms vary from one individual to another and according to his or her capacity to activate pain inhibition/control processes. Although the patient often attributes chronic pain to a particular organ (with the corollary that pain will persist until the organ has been treated), this pain is generally no longer derived from the organ but is expressed via this organ. Several types of clinical presentation of complex pelvic pain have therefore been pragmatically identified to facilitate the management of treatment failures resulting from a purely organ-based approach, which can also reinforce the patient's impression of incurability. These subtypes correspond to neuropathic pain, central sensitization (fibromyalgia), complex regional pain syndrome, and emotional components similar to those observed in post-traumatic stress disorder. These various components are also often associated and self-perpetuating. Consequently, when pelvic pain cannot be explained by an organ disease, this model, using each of these four components associated with their specific mechanisms, can be used to propose personalized treatment options and also to identify patients at high risk of postoperative pelvic pain (multi-operated patients, central sensitization, post-traumatic stress disorder, etc.), which constitutes a major challenge for prevention of these types of pain that have major implications for patients and society.

The influence of organic-mineral complexes on micro-elements dynamic in ecological systems of vegetables cultivation

NASA Astrophysics Data System (ADS)

Bulgariu, D.; Buzgar, N.; Bulgariu, L.; Rusu, C.; Munteanu, N.

2009-04-01

In ecological systems of vegetable cultivation (hortic antrosols; soils from greenhouses), exists an ensemble of equilibriums between organic-mineral combinations, very sensitive even to relatively small variations of physical-chemical conditions in soils. As such, these can manifest a strong influence on organic matter, clay minerals and microelements from soil, which in turn impacts on the productivity of these soils and the quality of obtained products (vegetables, fruit). Although many studies consider these organic-mineral combinations are meta-stable combinations, our work has shown that the stability of organic-mineral combinations in hortic antrosols (especially for clay-humic, clay-ironhumic combinations and chelates) is higher. We believe that this is due to the higher flexibility of these combinations' structures with the variation of chemical-mineralogical composition and physical-chemical conditions in soil. This paper highlights the results of our research on the differentiation possibility of organic-mineral complexes, depending on their structure and composition (using Raman and FT-IR spectrometry) and the influences manifested by the organic-mineral complexes on the micro-elements dynamic from ecological systems of fresh vegetable cultivation. The non-destructive separation of organic-mineral compounds from soil samples was carried out through iso-dynamic magnetic separation and extraction in aqueous two-phase systems (PEG-based). The Raman and FT-IR spectrometry analyses on raw soil samples, extracts obtained from soil samples and separated mineral fractions have been supplemented by the results obtained through chemical, microscopic and thermal analyses and by UV-VIS absorption spectrometry. Ours experimental studies have been done on representative samples of hortic antrosol from Copou glasshouse (Iasi, Romania), and was studied five micro-elements: Zn, Ni, Cu, Mn, Cr and P. The total contents of the five microelements and their fractions differential bonded on mineral and organic components of hortic antrosols, have been determined by atomic absorption spectrometry after combined sequential extraction in solid phase extraction - aqueous biphasic (PEG based) systems. The specific mechanisms of the microelements interaction with organic components have been estimated on the basis of studies realized on fractions obtained after each extraction step by Raman and FTIR spectrometry. These data have been correlated with those obtained by chemical analysis and UV-VIS spectrometry. In conditions of hortic antrosol, from total contents of Zn, Ni, Cu, Mn and Cr, more than 65 % are binding on organic components. A specific phenomenon of hortic antrosols is the microelements complexation exclusively with the functional groups of organic macromolecules. This phenomenon has two important consequences: (i) the strong fixation of microelements (these can be extracted only in very extremely conditions, which implied the organic part destroying) and (ii) their presence determined major modifications in the structure, conformation and stability of organic macromolecules. Under these conditions, the type and structure of organic-mineral compounds represent determinant factors for the dynamic of micro-elements and organic compounds in ecological systems of vegetables cultivation. Acknowledgments The authors would like to acknowledge the financial support from Romanian Ministry of Education and Research (Project PNCDI 2-D5 no. 51045/07 an Project PNCDI 2-D5 no. 52141 / 08).

Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus

NASA Astrophysics Data System (ADS)

Jiang, Wen; Chang, Juan; Jakana, Joanita; Weigele, Peter; King, Jonathan; Chiu, Wah

2006-02-01

The critical viral components for packaging DNA, recognizing and binding to host cells, and injecting the condensed DNA into the host are organized at a single vertex of many icosahedral viruses. These component structures do not share icosahedral symmetry and cannot be resolved using a conventional icosahedral averaging method. Here we report the structure of the entire infectious Salmonella bacteriophage epsilon15 (ref. 1) determined from single-particle cryo-electron microscopy, without icosahedral averaging. This structure displays not only the icosahedral shell of 60 hexamers and 11 pentamers, but also the non-icosahedral components at one pentameric vertex. The densities at this vertex can be identified as the 12-subunit portal complex sandwiched between an internal cylindrical core and an external tail hub connecting to six projecting trimeric tailspikes. The viral genome is packed as coaxial coils in at least three outer layers with ~90 terminal nucleotides extending through the protein core and the portal complex and poised for injection. The shell protein from icosahedral reconstruction at higher resolution exhibits a similar fold to that of other double-stranded DNA viruses including herpesvirus, suggesting a common ancestor among these diverse viruses. The image reconstruction approach should be applicable to studying other biological nanomachines with components of mixed symmetries.

Comparative Chemistry and Toxicity of Diesel and Biomass Combustion Emissions

EPA Science Inventory

Air pollution includes a complex mixture of carbonaceous gases and particles emitted from multiple anthropogenic, biogenic, and biomass burning sources, and also includes secondary organic components that form during atmospheric aging of these emissions. Exposure to these mixture...

EXPERIMENTS AT THE INTERFACE OF CARBON PARTICLE CHEMISTRY AND TOXCIOLOGY

EPA Science Inventory

Air pollution includes a complex mixture of carbonaceous gases and particles emitted from multiple anthropogenic, biogenic, and biomass burning sources, and also includes secondary organic components that form during atmospheric aging of these emissions. Exposure to these mixture...

Guayule resin detection and influence on guayule rubber

USDA-ARS?s Scientific Manuscript database

Guayule (Parthenium argentatum) is a natural rubber (cis-1,4-polyisoprene) producing crop, native to North America. Guayule also produces organic resins, complex mixtures of terpenes, triglycerides, guayulins, triterpenoids and other components. During natural rubber extraction, guayule resins can b...

A view at the interface between particle chemistry and toxicology

EPA Science Inventory

Air pollution includes a complex mixture of carbonaceous gases and particles emitted from multiple anthropogenic, biogenic, and biomass burning sources, and also includes secondary organic components that form during atmospheric aging of these emissions. Exposure to these mixture...

Bottom-up construction of a superstructure in a porous uranium-organic crystal

NASA Astrophysics Data System (ADS)

Li, Peng; Vermeulen, Nicolaas A.; Malliakas, Christos D.; Gómez-Gualdrón, Diego A.; Howarth, Ashlee J.; Mehdi, B. Layla; Dohnalkova, Alice; Browning, Nigel D.; O'Keeffe, Michael; Farha, Omar K.

2017-05-01

Bottom-up construction of highly intricate structures from simple building blocks remains one of the most difficult challenges in chemistry. We report a structurally complex, mesoporous uranium-based metal-organic framework (MOF) made from simple starting components. The structure comprises 10 uranium nodes and seven tricarboxylate ligands (both crystallographically nonequivalent), resulting in a 173.3-angstrom cubic unit cell enclosing 816 uranium nodes and 816 organic linkers—the largest unit cell found to date for any nonbiological material. The cuboctahedra organize into pentagonal and hexagonal prismatic secondary structures, which then form tetrahedral and diamond quaternary topologies with unprecedented complexity. This packing results in the formation of colossal icosidodecahedral and rectified hexakaidecahedral cavities with internal diameters of 5.0 nanometers and 6.2 nanometers, respectively—ultimately giving rise to the lowest-density MOF reported to date.

Spectroscopic and thermal properties of short wavelength metal (II) complexes containing α-isoxazolylazo-β-diketones as co-ligands

NASA Astrophysics Data System (ADS)

Huang, Fuxin; Wu, Yiqun; Gu, Donghong; Gan, Fuxi

2005-10-01

Two new azo dyes of α-isoxazolylazo-β-diketones and their Ni(II) and Cu(II) complexes with blue-violet light wavelength were synthesized using a coupling component, different diazo components and metal (II) ions (Ni 2+ and Cu 2+). Based on the elemental analysis, MS spectra and FT-IR spectral analyses, azo dyes were unequivocally shown to exist as hydrazoketo and azoenol forms which were respectively obtained from the solution forms and from the solid forms. The action of sodium methoxide (NaOMe) on azo dyes in solutions converts hydrazoketo form into azoenol form, so azo dyes are coordinated with metal (II) ions as co-ligands in the azoenol forms. The solubility of all the compounds in common organic solvents such as 2,2,3,3-tetrafluoro-1-propanol (TFP) or chloroform (CHCl 3) and absorption properties of spin-coating thin films were measured. The difference of absorption maxima from the complexes to their ligands was discussed. In addition, the TG analysis of the complexes was also determined, and their thermal stability was evaluated. It is found that these new metal (II) complexes had potential application for high-density digital versatile disc-recordable (HD-DVD-R) system due to their good solubility in organic solvents, reasonable and controllable absorption spectra in blue-violet light region and high thermal stability.

Three-component entanglements consisting of three crescent-shaped bidentate ligands coordinated to an octahedral metal centre.

PubMed

Durola, Fabien; Russo, Luca; Sauvage, Jean-Pierre; Rissanen, Kari; Wenger, Oliver S

2007-01-01

3,3'-biisoquinoline ligands (biiq) L, bearing aromatic substituents on their 8 and 8' positions, have been used to generate interwoven systems consisting of three crescent-shaped ligands disposed around an octahedral metal centre. Mono-ligand complexes of the type [ReL(CO)3py]+ (py: pyridine) have also been prepared, leading to sterically non-hindering complexes in spite of the endotopic nature of the chelate used. The three-component entanglements have been prepared by using either FeII or RuII as gathering metal centre. The synthetic procedure is simple and efficient, affording fully characterised complexes as their PF6 or SbCl6 salts. X-ray crystallography clearly shows that the crescent-shaped ligands do not repel each other in the tris-chelate complexes. In an analogous way, the ReI complexes show open structures with no steric repulsion between the L ligand and the ancillary CO or py groups. The FeL3 or RuL3 compounds are very unusual in the sense that, contrary to all the other tris-bidentate chelate complexes made till now, the three organic components are tangled up, in a situation which will be very favourable to the formation of new non trivial topologies of the catenane type.

The effect of organic contaminants on the spectral induced polarization response of porous media - mechanistic approach

NASA Astrophysics Data System (ADS)

Schwartz, N.; Huisman, J. A.; Furman, A.

2012-12-01

In recent years, there is a growing interest in using geophysical methods in general and spectral induced polarization (SIP) in particular as a tool to detect and monitor organic contaminants within the subsurface. The general idea of the SIP method is to inject alternating current through a soil volume and to measure the resultant potential in order to obtain the relevant soil electrical properties (e.g. complex impedance, complex conductivity/resistivity). Currently, a complete mechanistic understanding of the effect of organic contaminants on the SIP response of soil is still absent. In this work, we combine laboratory experiments with modeling to reveal the main processes affecting the SIP signature of soil contaminated with organic pollutant. In a first set of experiments, we investigate the effect of non-aqueous phase liquids (NAPL) on the complex conductivity of unsaturated porous media. Our results show that addition of NAPL to the porous media increases the real component of the soil electrical conductivity and decreases the polarization of the soil (imaginary component of the complex conductivity). Furthermore, addition of NAPL to the soil resulted in an increase of the electrical conductivity of the soil solution. Based on these results, we suggest that adsorption of NAPL to the soil surface, and exchange process between polar organic compounds in the NAPL and inorganic ions in the soil are the main processes affecting the SIP signature of the contaminated soil. To further support our hypothesis, the temporal change of the SIP signature of a soil as function of a single organic cation concentration was measured. In addition to the measurements of the soil electrical properties, we also measured the effect of the organic cation on the chemical composition of both the bulk and the surface of the soil. The results of those experiments again showed that the electrical conductivity of the soil increased with increasing contaminant concentration. In addition, direct evidence showed that the organic cation was adsorbed on the soil surface and exchanged with inorganic ions that usually exist in soil. This experiment confirmed that adsorption to the soil surface and the associated release of inorganic ions is the main mechanism affecting the complex conductivity of the contaminated porous media. Furthermore, our results show that adsorption of organic ions to the soil surface resulted in a decrease of the soil polarization. Using a chemical complexation model of the soil surface and a model for the polarization of the Stern layer, we were able to show that the decrease in the polarization of the soil can be related to the decrease in the surface site density of inorganic ions, and that the contribution of the soil-organic complexes to the polarization of the soil is negligible. We attribute this to the strong interaction between polar organic compounds and soil which results in a significant decrease in the mobility of the organic compounds in the Stern layer. The results of this work are essential to better interpret SIP signatures of soil contaminated with organic contaminants.

Emerging players in the initiation of eukaryotic DNA replication

PubMed Central

2012-01-01

Faithful duplication of the genome in eukaryotes requires ordered assembly of a multi-protein complex called the pre-replicative complex (pre-RC) prior to S phase; transition to the pre-initiation complex (pre-IC) at the beginning of DNA replication; coordinated progression of the replisome during S phase; and well-controlled regulation of replication licensing to prevent re-replication. These events are achieved by the formation of distinct protein complexes that form in a cell cycle-dependent manner. Several components of the pre-RC and pre-IC are highly conserved across all examined eukaryotic species. Many of these proteins, in addition to their bona fide roles in DNA replication are also required for other cell cycle events including heterochromatin organization, chromosome segregation and centrosome biology. As the complexity of the genome increases dramatically from yeast to human, additional proteins have been identified in higher eukaryotes that dictate replication initiation, progression and licensing. In this review, we discuss the newly discovered components and their roles in cell cycle progression. PMID:23075259

Lessons from Jurassic Park: patients as complex adaptive systems.

PubMed

Katerndahl, David A

2009-08-01

With realization that non-linearity is generally the rule rather than the exception in nature, viewing patients and families as complex adaptive systems may lead to a better understanding of health and illness. Doctors who successfully practise the 'art' of medicine may recognize non-linear principles at work without having the jargon needed to label them. Complex adaptive systems are systems composed of multiple components that display complexity and adaptation to input. These systems consist of self-organized components, which display complex dynamics, ranging from simple periodicity to chaotic and random patterns showing trends over time. Understanding the non-linear dynamics of phenomena both internal and external to our patients can (1) improve our definition of 'health'; (2) improve our understanding of patients, disease and the systems in which they converge; (3) be applied to future monitoring systems; and (4) be used to possibly engineer change. Such a non-linear view of the world is quite congruent with the generalist perspective.

Design of Bioactive Organic-inorganic Hybrid Materials with Self-setting Ability

NASA Astrophysics Data System (ADS)

Miyazaki, T.; Machida, S.; Morita, Y.; Ishida, E.

2011-10-01

Paste-like materials with ability of self-setting are attractive for bone substitutes, since they can be injected from the small hole with minimized invasion to the patient. Although bone cements which set as apatite are clinically used, there is limitation on clinical applications due to their mechanical properties such as high brittleness and low fracture toughness. To overcome this problem, organic-inorganic hybrids based on a flexible polymer are attractive. We have obtained an idea for design of self-setting hybrids using polyion complex fabricated by ionic interaction of anionic and cationic polymers. We aimed at preparation of organic-inorganic hybrids exhibiting self-setting ability and bioactivity. The liquid component was prepared from cationic chitosan aqueous solution. The powder component was prepared by mixing various carrageenans with α-tricalcium phosphate (α-TCP). The obtained cements set within 1 day. Compressive strength showed tendency to increase with increase in α-TCP content in the powder component. The prepared cements formed the apatite in simulated body fluid within 3 days. Novel self-setting materials based on organic-inorganic hybrid can be designed utilizing ionic interaction of polysaccharide.

HPLC-Orbitrap analysis for identification of organic molecules in complex material

NASA Astrophysics Data System (ADS)

Gautier, T.; Schmitz-Afonso, I.; Carrasco, N.; Touboul, D.; Szopa, C.; Buch, A.; Pernot, P.

2015-10-01

We performed High Performance Liquid Chromatography (HPLC) coupled to Orbitrap High Resolution Mass Spectrometry (OHR MS) analysis of Titan's tholins. This analysis allowed us to determine the exact composition and structure of some of the major components of tholins.

Cellular Organization and Cytoskeletal Regulation of the Hippo Signaling Network

PubMed Central

Sun, Shuguo; Irvine, Kenneth D.

2016-01-01

The Hippo signaling network integrates diverse upstream signals to control cell fate decisions and regulate organ growth. Recent studies have provided new insights into the cellular organization of Hippo signaling, its relationship to cell-cell junctions, and how the cytoskeleton modulates Hippo signaling. Cell-cell junctions serve as platforms for Hippo signaling by localizing scaffolding proteins that interact with core components of the pathway. Interactions of Hippo pathway components with cell-cell junctions and the cytoskeleton also suggest potential mechanisms for the regulation of the pathway by cell contact and cell polarity. As our understanding of the complexity of Hippo signaling increases, a future challenge will be to understand how the diverse inputs into the pathway are integrated, and to define their respective contributions in vivo. PMID:27268910

Underestimation of phosphorus fraction change in the supernatant after phosphorus adsorption onto iron oxides and iron oxide-natural organic matter complexes.

PubMed

Yan, Jinlong; Jiang, Tao; Yao, Ying; Wang, Jun; Cai, Yuanli; Green, Nelson W; Wei, Shiqiang

2017-05-01

The phosphorus (P) fraction distribution and formation mechanism in the supernatant after P adsorption onto iron oxides and iron oxide-humic acid (HA) complexes were analyzed using the ultrafiltration method in this study. With an initial P concentration of 20mg/L (I=0.01mol/L and pH=7), it was shown that the colloid (1kDa-0.45μm) component of P accounted for 10.6%, 11.6%, 6.5%, and 4.0% of remaining total P concentration in the supernatant after P adsorption onto ferrihydrite (FH), goethite (GE), ferrihydrite-humic acid complex (FH-HA), goethite-humic acid complex (GE-HA), respectively. The <1kDa component of P was still the predominant fraction in the supernatant, and underestimated colloidal P accounted for 2.2%, 55.1%, 45.5%, and 38.7% of P adsorption onto the solid surface of FH, FH-HA, GE and GE-HA, respectively. Thus, the colloid P could not be neglected. Notably, it could be interpreted that Fe 3+ hydrolysis from the adsorbents followed by the formation of colloidal hydrous ferric oxide aggregates was the main mechanism for the formation of the colloid P in the supernatant. And colloidal adsorbent particles co-existing in the supernatant were another important reason for it. Additionally, dissolve organic matter dissolved from iron oxide-HA complexes could occupy large adsorption sites of colloidal iron causing less colloid P in the supernatant. Ultimately, we believe that the findings can provide a new way to deeply interpret the geochemical cycling of P, even when considering other contaminants such as organic pollutants, heavy metal ions, and arsenate at the sediment/soil-water interface in the real environment. Copyright © 2016. Published by Elsevier B.V.

Utilization of forest slash to sequester carbon in loblolly pine plantations in the lower coastal plain

Treesearch

F. Sanchez; E.A. Carter; W. Edwards

2002-01-01

Soil-organic matter (SOM) is a complex array of components including soil fauna and flora at different stages of decomposition (Berg et al., 1982). Its concentration in soils can vary from 0.5% in mineral soils to almost 100% in peat soils (Brady, 1974). Organic matter (OM) in the surface mineral soil is considered a major determinant of forest ecosystem productivity...

STRIP1, a core component of STRIPAK complexes, is essential for normal mesoderm migration in the mouse embryo.

PubMed

Bazzi, Hisham; Soroka, Ekaterina; Alcorn, Heather L; Anderson, Kathryn V

2017-12-19

Regulated mesoderm migration is necessary for the proper morphogenesis and organ formation during embryonic development. Cell migration and its dependence on the cytoskeleton and signaling machines have been studied extensively in cultured cells; in contrast, remarkably little is known about the mechanisms that regulate mesoderm cell migration in vivo. Here, we report the identification and characterization of a mouse mutation in striatin-interacting protein 1 ( Strip1 ) that disrupts migration of the mesoderm after the gastrulation epithelial-to-mesenchymal transition (EMT). STRIP1 is a core component of the biochemically defined mammalian striatin-interacting phosphatases and kinase (STRIPAK) complexes that appear to act through regulation of protein phosphatase 2A (PP2A), but their functions in mammals in vivo have not been examined. Strip1 -null mutants arrest development at midgestation with profound disruptions in the organization of the mesoderm and its derivatives, including a complete failure of the anterior extension of axial mesoderm. Analysis of cultured mesoderm explants and mouse embryonic fibroblasts from null mutants shows that the mesoderm migration defect is correlated with decreased cell spreading, abnormal focal adhesions, changes in the organization of the actin cytoskeleton, and decreased velocity of cell migration. The results show that STRIPAK complexes are essential for cell migration and tissue morphogenesis in vivo. Copyright © 2017 the Author(s). Published by PNAS.

Escherichia coli biofilms have an organized and complex extracellular matrix structure.

PubMed

Hung, Chia; Zhou, Yizhou; Pinkner, Jerome S; Dodson, Karen W; Crowley, Jan R; Heuser, John; Chapman, Matthew R; Hadjifrangiskou, Maria; Henderson, Jeffrey P; Hultgren, Scott J

2013-09-10

Bacterial biofilms are ubiquitous in nature, and their resilience is derived in part from a complex extracellular matrix that can be tailored to meet environmental demands. Although common developmental stages leading to biofilm formation have been described, how the extracellular components are organized to allow three-dimensional biofilm development is not well understood. Here we show that uropathogenic Escherichia coli (UPEC) strains produce a biofilm with a highly ordered and complex extracellular matrix (ECM). We used electron microscopy (EM) techniques to image floating biofilms (pellicles) formed by UPEC. EM revealed intricately constructed substructures within the ECM that encase individual, spatially segregated bacteria with a distinctive morphology. Mutational and biochemical analyses of these biofilms confirmed curli as a major matrix component and revealed important roles for cellulose, flagella, and type 1 pili in pellicle integrity and ECM infrastructure. Collectively, the findings of this study elucidated that UPEC pellicles have a highly organized ultrastructure that varies spatially across the multicellular community. Bacteria can form biofilms in diverse niches, including abiotic surfaces, living cells, and at the air-liquid interface of liquid media. Encasing these cellular communities is a self-produced extracellular matrix (ECM) that can be composed of proteins, polysaccharides, and nucleic acids. The ECM protects biofilm bacteria from environmental insults and also makes the dissolution of biofilms very challenging. As a result, formation of biofilms within humans (during infection) or on industrial material (such as water pipes) has detrimental and costly effects. In order to combat bacterial biofilms, a better understanding of components required for biofilm formation and the ECM is required. This study defined the ECM composition and architecture of floating pellicle biofilms formed by Escherichia coli.

Stability of nickel(II) glycylglycinate complexes in aqueous solutions of dimethylsulfoxide at 298.15 K

NASA Astrophysics Data System (ADS)

Naumov, V. V.; Isaeva, V. A.; Kovaleva, Yu. A.; Sharnin, V. A.

2013-07-01

Stability constants of nickel(II) glycylglycinate complexes in aqueous solutions of dimethylsulfoxide of variable composition (from 0.00 to 0.60 mole fractions DMSO) are determined according to potentiometry at 298.15 K and an ionic strength of 0.1 M (NaClO4). It is determined that with a rise in the concentration of an organic cosolvent in solution, the stability of nickel(II) complexes with glycylglycinate ion on the whole increases, but the log K stability = f( X DMSO) dependences are of a critical character with a maximum of 0.3 mole fractions DMSO. It is demonstrated that the rise in the stability of complexes is related to the destabilization of ligands in the low concentration range of the organic component, while the presence of a maximum is due to the different dynamics of the solvation contributions from reagents during changes in the Gibbs energy of reaction.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Becker, C.D.; Woodfield, W.G.; Strand, J.A.

The Freshwater Sciences Section of PNL has initiated biologically oriented studies at the P and M solvent refined coal (SRC) pilot plant on the Fort Lewis Reservation in western Washington. Essentially, the study objectives are to identify residual components in the treated SRC process and assess potential for adverse impact on water quality and aquatic biota. Since inception of research in mid-1976, six static toxicity tests with treated SRC process effluent have been conducted. Toxic components, not yet specifically identified, sometimes occur in the effluent. It is believed these components involve organic hydrocarbons of the phenol and cresol groups. Analysesmore » have been obtained on inorganic and organic constituents in partially-treated and treated process effluent. Concentrations of inorganics identified in the effluent did not differ greatly from their concentrations in Lake Sequalitchew or SRC plant tap water, but the low concentrations may be due primarily to dilution with freshwater before discharge. Organics identified in the effluent are similar to those found in samples contaminated with petroleum, and involve many complex hydrocarbons.« less

Molecular basis of cell integrity and morphogenesis in Saccharomyces cerevisiae.

PubMed Central

Cid, V J; Durán, A; del Rey, F; Snyder, M P; Nombela, C; Sánchez, M

1995-01-01

In fungi and many other organisms, a thick outer cell wall is responsible for determining the shape of the cell and for maintaining its integrity. The budding yeast Saccharomyces cerevisiae has been a useful model organism for the study of cell wall synthesis, and over the past few decades, many aspects of the composition, structure, and enzymology of the cell wall have been elucidated. The cell wall of budding yeasts is a complex and dynamic structure; its arrangement alters as the cell grows, and its composition changes in response to different environmental conditions and at different times during the yeast life cycle. In the past few years, we have witnessed a profilic genetic and molecular characterization of some key aspects of cell wall polymer synthesis and hydrolysis in the budding yeast. Furthermore, this organism has been the target of numerous recent studies on the topic of morphogenesis, which have had an enormous impact on our understanding of the intracellular events that participate in directed cell wall synthesis. A number of components that direct polarized secretion, including those involved in assembly and organization of the actin cytoskeleton, secretory pathways, and a series of novel signal transduction systems and regulatory components have been identified. Analysis of these different components has suggested pathways by which polarized secretion is directed and controlled. Our aim is to offer an overall view of the current understanding of cell wall dynamics and of the complex network that controls polarized growth at particular stages of the budding yeast cell cycle and life cycle. PMID:7565410

Novel use of UV broad-band excitation and stretched exponential function in the analysis of fluorescent dissolved organic matter: study of interaction between protein and humic-like components

NASA Astrophysics Data System (ADS)

Panigrahi, Suraj Kumar; Mishra, Ashok Kumar

2017-09-01

A combination of broad-band UV radiation (UV A and UV B; 250-400 nm) and a stretched exponential function (StrEF) has been utilised in efforts towards convenient and sensitive detection of fluorescent dissolved organic matter (FDOM). This approach enables accessing the gross fluorescence spectral signature of both protein-like and humic-like components in a single measurement. Commercial FDOM components are excited with the broad-band UV excitation; the variation of spectral profile as a function of varying component ratio is analysed. The underlying fluorescence dynamics and non-linear quenching of amino acid moieties are studied with the StrEF (exp(-V[Q] β )). The complex quenching pattern reflects the inner filter effect (IFE) as well as inter-component interactions. The inter-component interactions are essentially captured through the ‘sphere of action’ and ‘dark complex’ models. The broad-band UV excitation ascertains increased excitation energy, resulting in increased population density in the excited state and thereby resulting in enhanced sensitivity.

Origins and identities of key manure odor components

USDA-ARS?s Scientific Manuscript database

Odor is just one of many environmental issues associated with animal manures. Odor arises from a number of different locations in animal production systems, but the chemistry and biochemical origin is similar across sites. A complex mixture of volatile organic compounds (VOC) and inorganic compoun...

UNDERSTANDING PLANT-SOIL RELATIONSHIPS USING CONTROLLED ENVIRONMENT FACILITIES

EPA Science Inventory

Although soil is a component of terrestrial ecosystems, it is comprised of a complex web of interacting organisms, and therefore, can be considered itself as an ecosystem. Soil microflora and fauna derive energy from plants and plant residues and serve important functions in mai...

Enabling the identification, quantification, and characterization of organics in complex mixtures to understand atmospheric aerosols

NASA Astrophysics Data System (ADS)

Isaacman, Gabriel Avram

Particles in the atmosphere are known to have negative health effects and important but highly uncertain impacts on global and regional climate. A majority of this particulate matter is formed through atmospheric oxidation of naturally and anthropogenically emitted gases to yield highly oxygenated secondary organic aerosol (SOA), an amalgamation of thousands of individual chemical compounds. However, comprehensive analysis of SOA composition has been stymied by its complexity and lack of available measurement techniques. In this work, novel instrumentation, analysis methods, and conceptual frameworks are introduced for chemically characterizing atmospherically relevant mixtures and ambient aerosols, providing a fundamentally new level of detailed knowledge on their structures, chemical properties, and identification of their components. This chemical information is used to gain insights into the formation, transformation and oxidation of organic aerosols. Biogenic and anthropogenic mixtures are observed in this work to yield incredible complexity upon oxidation, producing over 100 separable compounds from a single precursor. As a first step toward unraveling this complexity, a method was developed for measuring the polarity and volatility of individual compounds in a complex mixture using two-dimensional gas chromatography, which is demonstrated in Chapter 2 for describing the oxidation of SOA formed from a biogenic compound (longifolene: C15H24). Several major products and tens of substantial minor products were produced, but none could be identified by traditional methods or have ever been isolated and studied in the laboratory. A major realization of this work was that soft ionization mass spectrometry could be used to identify the molecular mass and formula of these unidentified compounds, a major step toward a comprehensive description of complex mixtures. This was achieved by coupling gas chromatography to high resolution time-of-flight mass spectrometry with vacuum ultraviolet (VUV) photo-ionization. Chapters 3 and 4 describe this new analytical technique and its initial application to determine the structures of unknown compounds and formerly unresolvable mixtures, including a complete description of the chemical composition of two common petroleum products related to anthropogenic emissions: diesel fuel and motor oil. The distribution of hydrocarbon isomers in these mixtures - found to be mostly of branched, cyclic, and saturated -- is described with unprecedented detail. Instead of measuring average bulk aerosol properties, the methods developed and applied in this work directly measure the polarity, volatility, and structure of individual components to allow a mechanistic understanding of oxidation processes. Novel characterizations of these complex mixtures are used to elucidate the role of structure and functionality in particle-phase oxidation, including in Chapter 4 the first measurements of relative reaction rates in a complex hydrocarbon particle. Molecular structure is observed to influence particle-phase oxidation in unexpected and important ways, with cyclization decreasing reaction rates by ~30% and branching increasing reaction rates by ~20-50%. The observed structural dependence is proposed to result in compositional changes in anthropogenic organic aerosol downwind of urban areas, which has been confirmed in subsequent work by applying the techniques described here. Measurement of organic aerosol components is extended to ambient environments through the development of instrumentation with the unprecedented capability to measure hourly concentrations and gas/particle partitioning of individual highly oxygenated organic compounds in the atmosphere. Chapters 5 and 6 describe development of new procedures and hardware for the calibration and analysis of oxygenates using the Semi-Volatile Thermal desorption Aerosol Gas chromatograph (SV-TAG), a custom instrument for in situ quantification of gas- and particle-phase organic compounds in the atmosphere. High time resolution measurement of oxygenated compounds is achieved through a reproducible and quantitative methodology for in situ "derivatization" -- replacing highly polar functional groups that cannot be analyzed by traditional gas chromatography with less polar groups. Implementation of a two-channel sampling system for the simultaneous collection of particle-phase and total gas-plus-particle phase samples allows for the first direct measurements of gas/particle partitioning in the atmosphere, significantly advancing the study of atmospheric composition and variability, as well as the processes governing condensation and re-volatilization. This work presents the first in situ measurements of a large suite of highly oxygenated biogenic oxidation products in both the gas- and particle-phase. Isoprene, the most ubiquitous biogenic emission, oxidizes to form 2-methyltetrols and C5 alkene triols, while α-pinene, the most common monoterpene, forms pinic, pinonic, hydroxyglutaric, and other acids. These compounds are reported in Chapter 7 with unprecedented time resolution and are shown for the first time to have a large gas-phase component, contrary to typical assumptions. Hourly comparisons of these products with anthropogenic aerosol components elucidate the interaction of human and natural emissions at two rural sites: the southeastern, U.S. and Amazonia, Brazil. Anthropogenic influence on SOA formation is proposed to occur through the increase in liquid water caused by anthropogenic sulfate. Furthermore, these unparalleled observations of gas/particle partitioning of biogenic oxidation products demonstrate that partitioning of oxygenates is unexpectedly independent of volatility: many volatile, highly oxygenated compounds have a large particle-phase component that is poorly described by traditional models. These novel conclusions are reached in part by applying the new frameworks developed in previous chapters to understand the properties of unidentified compounds, demonstrating the importance of detailed characterization of atmospheric organic mixtures. Comprehensive analysis of anthropogenic and biogenic emissions and oxidation product mixtures is coupled in this work with high time-resolution measurement of individual organic components to yield significant insights into the transformations of organic aerosols. Oxidation chemistry is observed in both laboratory and field settings to depend on molecular properties, volatility, and atmospheric composition. However, this work demonstrates that these complex processes can be understood through the quantification of individual known and unidentified compounds, combined with their classification into descriptive frameworks.

Network representations of immune system complexity

PubMed Central

Subramanian, Naeha; Torabi-Parizi, Parizad; Gottschalk, Rachel A.; Germain, Ronald N.; Dutta, Bhaskar

2015-01-01

The mammalian immune system is a dynamic multi-scale system composed of a hierarchically organized set of molecular, cellular and organismal networks that act in concert to promote effective host defense. These networks range from those involving gene regulatory and protein-protein interactions underlying intracellular signaling pathways and single cell responses to increasingly complex networks of in vivo cellular interaction, positioning and migration that determine the overall immune response of an organism. Immunity is thus not the product of simple signaling events but rather non-linear behaviors arising from dynamic, feedback-regulated interactions among many components. One of the major goals of systems immunology is to quantitatively measure these complex multi-scale spatial and temporal interactions, permitting development of computational models that can be used to predict responses to perturbation. Recent technological advances permit collection of comprehensive datasets at multiple molecular and cellular levels while advances in network biology support representation of the relationships of components at each level as physical or functional interaction networks. The latter facilitate effective visualization of patterns and recognition of emergent properties arising from the many interactions of genes, molecules, and cells of the immune system. We illustrate the power of integrating ‘omics’ and network modeling approaches for unbiased reconstruction of signaling and transcriptional networks with a focus on applications involving the innate immune system. We further discuss future possibilities for reconstruction of increasingly complex cellular and organism-level networks and development of sophisticated computational tools for prediction of emergent immune behavior arising from the concerted action of these networks. PMID:25625853

Preparation and properties of chrome-free colored Ti/Zr based conversion coating on aluminum alloy

NASA Astrophysics Data System (ADS)

Yi, AiHua; Li, WenFang; Du, Jun; Mu, SongLin

2012-06-01

A golden conversion coating on the surface of aluminum alloy was prepared by adding tannic acid and coating-forming accelerator in the treatment solution containing titanium and zirconium ions. The growth process, main component and corrosion resistance of the conversion coating were characterized by EDS, SEM, XRD, XPS, FIIR and electrochemical workstation. The results showed that the main components of the conversion coating were Na3AlF6 and the conversion coating owns a double-layer structure. The outer layer consists of metal-organic complex and the inner layer is mainly made up of Na3AlF6. The mechanism of the formation of the golden conversion coating can be deemed as nucleation, growth of Na3AlF6 crystal and formation of metal-organic complex. In potentiodynamic polarization test, the corrosion current density decreases to 0.283 μA cm-2 from 5.894 μA cm-2, which indicates an obvious improvement of corrosion resistance.

Tissue-Specific Regulation of Chromatin Insulator Function

PubMed Central

Matzat, Leah H.; Dale, Ryan K.; Moshkovich, Nellie; Lei, Elissa P.

2012-01-01

Chromatin insulators organize the genome into distinct transcriptional domains and contribute to cell type–specific chromatin organization. However, factors regulating tissue-specific insulator function have not yet been discovered. Here we identify the RNA recognition motif-containing protein Shep as a direct interactor of two individual components of the gypsy insulator complex in Drosophila. Mutation of shep improves gypsy-dependent enhancer blocking, indicating a role as a negative regulator of insulator activity. Unlike ubiquitously expressed core gypsy insulator proteins, Shep is highly expressed in the central nervous system (CNS) with lower expression in other tissues. We developed a novel, quantitative tissue-specific barrier assay to demonstrate that Shep functions as a negative regulator of insulator activity in the CNS but not in muscle tissue. Additionally, mutation of shep alters insulator complex nuclear localization in the CNS but has no effect in other tissues. Consistent with negative regulatory activity, ChIP–seq analysis of Shep in a CNS-derived cell line indicates substantial genome-wide colocalization with a single gypsy insulator component but limited overlap with intact insulator complexes. Taken together, these data reveal a novel, tissue-specific mode of regulation of a chromatin insulator. PMID:23209434

Proteins and saccharides of the sea urchin organic matrix of mineralization: characterization and localization in the spine skeleton.

PubMed

Ameye, L; De Becker, G; Killian, C; Wilt, F; Kemps, R; Kuypers, S; Dubois, P

2001-04-01

Properties of the echinoderm skeleton are under biological control, which is exerted in part by the organic matrix embedded in the mineralized part of the skeleton. This organic matrix consists of proteins and glycoproteins whose carbohydrate component is specifically involved in the control mechanisms. The saccharide moiety of the organic matrix of the spines of the echinoid Paracentrotus lividus was characterized using enzyme-linked lectin assays (ELLAs). O-glycoproteins, different types of complex N-glycoproteins, and terminal sialic acids were detected. Sialic acids are known to interact with Ca ions and could play an important role in the mineralization process. Some of the carbohydrate components detected by ELLAs as well as two organic matrix proteins (SM30 and SM50) were localized within different subregions of the spine skeleton using field-emission scanning electron microscopy. The mappings show that some of these components are not homogeneously distributed in the different skeletal subregions. For example, some N-glycoproteins were preferentially located in the putative amorphous subregion of the skeleton, whereas some O-glycoproteins were localized in the subregion where skeletal growth is inhibited. These results suggest that the biological control exerted on the skeletal properties can be partly modulated by local differences in the organic matrix composition. Copyright 2001 Academic Press.

Bottom-up construction of a superstructure in a porous uranium-organic crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Peng; Vermeulen, Nicolaas A.; Malliakas, Christos D.

Bottom-up construction of highly intricate structures from simple building blocks remains one of the most difficult challenges in chemistry. We report a structurally complex, mesoporous uranium-based metal-organic framework (MOF) made from simple starting components. The structure comprises 10 uranium nodes and seven tricarboxylate ligands (both crystallographically nonequivalent), resulting in a 173.3-angstrom cubic unit cell enclosing 816 uranium nodes and 816 organic linkers—the largest unit cell found to date for any nonbiological material. The cuboctahedra organize into pentagonal and hexagonal prismatic secondary structures, which then form tetrahedral and diamond quaternary topologies with unprecedented complexity. This packing results in the formation ofmore » colossal icosidodecahedral and rectified hexakaidecahedral cavities with internal diameters of 5.0 nanometers and 6.2 nanometers, respectively—ultimately giving rise to the lowest-density MOF reported to date.« less

Environmental characteristics and changes of sediment pore water dissolved organic matter in four Chinese lakes.

PubMed

Mostofa, Khan M G; Li, Wen; Wu, Fengchang; Liu, Cong-Qiang; Liao, Haiqing; Zeng, Li; Xiao, Min

2018-01-01

Sediment pore waters were examined in four Chinese lakes (Bosten, Qinghai, Chenghai and Dianchi) to characterise the sources of dissolved organic matter (DOM) and their microbial changes in the sediment depth profiles. Parallel factor (PARAFAC) modelling on the sample fluorescence spectra confirmed that the pore water DOM was mostly composed of two components with a mixture of both allochthonous and autochthonous fulvic acid-like substances in three lakes, except Lake Dianchi, and protein-like components in Lake Bosten. However, DOM in Lake Dianchi was composed of three components, including a fulvic acid-like, and two unidentified components, which could originate from mixed sources of either sewerage-impacted allochthonous or autochthonous organic matter (OM). Dissolved organic carbon (DOC) concentrations were typically high (583-7410 μM C) and fluctuated and increased vertically in the depth profile. The fluorescence intensity of the fulvic acid-like substance and absorbance at 254 nm increased vertically in the sediment pore waters of three lakes. A significant relationship between DOC and the fluorescence intensity of the fulvic acid-like component in the sediment pore waters of three lakes, except Lake Dianchi, suggested that the fulvic acid-like component could significantly contribute to total DOM and could originate via complex microbial processes in early diagenesis on OM (ca. phytoplankton, terrestrial plant material) in these lakes. Pore water DOM components could therefore be a useful indicator to assess the DOM sources of the lake sediment during sedimentation over the past several decades, which have been heavily affected by ambient terrestrial vegetation and human activities.

Electronic structure and charge transfer excited states of endohedral fullerene containing electron donoracceptor complexes utilized in organic photovoltaics

NASA Astrophysics Data System (ADS)

Amerikheirabadi, Fatemeh

Organic Donor-Acceptor complexes form the main component of the organic photovoltaic devices (OPVs). The open circuit voltage of OPVs is directly related to the charge transfer excited state energies of these complexes. Currently a large number of different molecular complexes are being tested for their efficiency in photovoltaic devices. In this work, density functional theory as implemented in the NRLMOL code is used to investigate the electronic structure and related properties of these donor-acceptor complexes. The charge transfer excitation energies are calculated using the perturbative delta self-consistent field method recently developed in our group as the standard time dependent density functional approaches fail to accurately provide them. The model photovoltaics systems analyzed are as follows: Sc3N C 80--ZnTPP, Y3 N C80-- ZnTPP and Sc3 N C80-- ZnPc. In addition, a thorough analysis of the isolated donor and acceptor molecules is also provided. The studied acceptors are chosen from a class of fullerenes named trimetallic nitride endohedral fullerenes. These molecules have shown to possess advantages as acceptors such as long lifetimes of the charge-separated states.

Sample preparation for SFM imaging of DNA, proteins, and DNA-protein complexes.

PubMed

Ristic, Dejan; Sanchez, Humberto; Wyman, Claire

2011-01-01

Direct imaging is invaluable for understanding the mechanism of complex genome transactions where proteins work together to organize, transcribe, replicate, and repair DNA. Scanning (or atomic) force microscopy is an ideal tool for this, providing 3D information on molecular structure at nanometer resolution from defined components. This is a convenient and practical addition to in vitro studies as readily obtainable amounts of purified proteins and DNA are required. The images reveal structural details on the size and location of DNA-bound proteins as well as protein-induced arrangement of the DNA, which are directly correlated in the same complexes. In addition, even from static images, the different forms observed and their relative distributions can be used to deduce the variety and stability of different complexes that are necessarily involved in dynamic processes. Recently available instruments that combine fluorescence with topographic imaging allow the identification of specific molecular components in complex assemblies, which broadens the applications and increases the information obtained from direct imaging of molecular complexes. We describe here basic methods for preparing samples of proteins, DNA, and complexes of the two for topographic imaging and quantitative analysis. We also describe special considerations for combined fluorescence and topographic imaging of molecular complexes.

Supercritical fluid extraction of the non-polar organic compounds in meteorites

NASA Astrophysics Data System (ADS)

Sephton, M. A.; Pillinger, C. T.; Gilmour, I.

2001-01-01

The carbonaceous chondrite meteorites contain a variety of extraterrestrial organic molecules. These organic components provide a valuable insight into the formation and evolution of the solar system. Attempts at obtaining and interpreting this information source are hampered by the small sample sizes available for study and the interferences from terrestrial contamination. Supercritical fluid extraction represents an efficient and contamination-free means of isolating extraterrestrial molecules. Gas chromatography-mass spectrometry analyses of extracts from Orgueil and Cold Bokkeveld reveal a complex mixture of free non-polar organic molecules which include normal alkanes, isoprenoid alkanes, tetrahydronaphthalenes and aromatic hydrocarbons. These organic assemblages imply contributions from both terrestrial and extraterrestrial sources.

MODIFICATION OF METAL PARTITIONING BY SUPPLEMENTING ACID VOLATILE SULFIDE IN FRESHWATER SEDIMENTS

EPA Science Inventory

Acid volatile sulfide is a component of sediments which complexes some cationic metals and thereby influences the toxicity of these metals to benthic organisms. EPA has proposed AVS as a key normalization phase for the development of sediment quality criteria for metals. Experime...

Nature versus design: synthetic biology or how to build a biological non-machine.

PubMed

Porcar, M; Peretó, J

2016-04-18

The engineering ideal of synthetic biology presupposes that organisms are composed of standard, interchangeable parts with a predictive behaviour. In one word, organisms are literally recognized as machines. Yet living objects are the result of evolutionary processes without any purposiveness, not of a design by external agents. Biological components show massive overlapping and functional degeneracy, standard-free complexity, intrinsic variation and context dependent performances. However, although organisms are not full-fledged machines, synthetic biologists may still be eager for machine-like behaviours from artificially modified biosystems.

The medical practice as business organization.

PubMed

Bender, A D; Aaronson, W E; Krasnick, C J; Bender, J G

1996-03-01

Medical practices historically have not been examined in terms of their organizational structures and of the appropriateness of their structures for survival as business entities. In this paper, we propose a model for the typical medical practice and discuss its fit with current organizational theory. It is apparent that the medical practice organization does not fit with the demands of a rapidly changing and complex environment. To survive and grow, the medical practice organization must align itself with others that have an interest and stake in the health care system, develop teamwork among physicians, bridge the gap between physicians and others in the organization, and recognize that the work done in the organization depends on other components of the organization.

Self-Assembling Amphiphilic Molecules: A Possible Relationship Between Interstellar Chemistry and Meteoritic Organics

NASA Technical Reports Server (NTRS)

Sandford, Scott A.; Dworkin, Jason P.; Deamer, David W.; Allamandola, Louis J.; DeVincenzi, Donald (Technical Monitor)

2001-01-01

Interstellar gas and dust comprise the primary material from which the solar system formed. Evidence that some of this material was organic in nature and survived incorporation into the protosolar nebula is provided by the presence of deuterium-enriched organics in meteorites and interplanetary dust particles. Once the inner planets had sufficiently cooled, late accretionary infall of meteoroids and cosmic dust must have seeded them with some of these complex organic compounds. Delivery of such extraterrestrial compounds may have contributed to the organic inventory necessary for the origin of life. Interstellar ices, the building blocks of comets, tie up a large fraction of the biogenic elements available in molecular clouds. In our efforts to understand their synthesis, chemical composition, and physical properties, we report here that a complex mixture of molecules is produced by ultraviolet (UV) photolysis of realistic, interstellar ice analogs, and that some of the components have properties relevant to the origin of life, including the ability to self-assemble into vesicular structures.

Peculiarities of organizing the construction of nuclear medicine facilities and the transportation of radionuclide

NASA Astrophysics Data System (ADS)

Telichenko, Valeriy; Malykha, Galina; Dorogan, Igor

2017-10-01

The article is devoted to the organization of construction of nuclear medicine facilities in Russia. The article describes the main methods of nuclear medical diagnostics, as well as the peculiarities of nuclear medicine facilities that determine the need for application of specific methods for organizing and managing the construction, methods of requirements management in the organization of construction of nuclear medicine facilities. Sustainable development of the transport of radioactive isotopes from the place of production to places of consumption is very important for the safety of the population. The requirements management system is an important and necessary component in organizing the construction of complex facilities, such as nuclear medicine facilities. The author developed and proposed a requirements management system for the design, construction and operation of a nuclear medicine facility, which provides for a cyclic sequence of actions. This system allows reducing the consumption of resources including material and energy during construction and operation of complex objects.

Cellular Organization and Cytoskeletal Regulation of the Hippo Signaling Network.

PubMed

Sun, Shuguo; Irvine, Kenneth D

2016-09-01

The Hippo signaling network integrates diverse upstream signals to control cell fate decisions and regulate organ growth. Recent studies have provided new insights into the cellular organization of Hippo signaling, its relationship to cell-cell junctions, and how the cytoskeleton modulates Hippo signaling. Cell-cell junctions serve as platforms for Hippo signaling by localizing scaffolding proteins that interact with core components of the pathway. Interactions of Hippo pathway components with cell-cell junctions and the cytoskeleton also suggest potential mechanisms for the regulation of the pathway by cell contact and cell polarity. As our understanding of the complexity of Hippo signaling increases, a future challenge will be to understand how the diverse inputs into the pathway are integrated and to define their respective contributions in vivo. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.

PubMed

Bernecky, Carrie; Grob, Patricia; Ebmeier, Christopher C; Nogales, Eva; Taatjes, Dylan J

2011-03-01

The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly.

Molecular Architecture of the Human Mediator–RNA Polymerase II–TFIIF Assembly

PubMed Central

Bernecky, Carrie; Grob, Patricia; Ebmeier, Christopher C.; Nogales, Eva; Taatjes, Dylan J.

2011-01-01

The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator–pol II interface is not well-characterized, whereas attempts to structurally define the Mediator–pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator–pol II–TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator–pol II–TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator–pol II–TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator–CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator–pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly. PMID:21468301

Characterization of atrazine binding to dissolved organic matter of soil under different types of land use.

PubMed

Zhu, Long-Ji; Zhao, Yue; Chen, Yan-Ni; Cui, Hong-Yang; Wei, Yu-Quan; Liu, Hai-Long; Chen, Xiao-Meng; Wei, Zi-Min

2018-01-01

Atrazine is widely used in agriculture. In this study, dissolved organic matter (DOM) from soils under four types of land use (forest (F), meadow (M), cropland (C) and wetland (W)) was used to investigate the binding characteristics of atrazine. Fluorescence excitation-emission matrix-parallel factor (EEM-PARAFAC) analysis, two-dimensional correlation spectroscopy (2D-COS) and Stern-Volmer model were combined to explore the complexation between DOM and atrazine. The EEM-PARAFAC indicated that DOM from different sources had different structures, and humic-like components had more obvious quenching effects than protein-like components. The Stern-Volmer model combined with correlation analysis showed that log K values of PARAFAC components had a significant correlation with the humification of DOM, especially for C3 component, and they were all in the same order as follows: meadow soil (5.68)>wetland soil (5.44)>cropland soil (5.35)>forest soil (5.04). The 2D-COS further confirmed that humic-like components firstly combined with atrazine followed by protein-like components. These findings suggest that DOM components can significantly influence the bioavailability, mobility and migration of atrazine in different land uses. Copyright © 2016 Elsevier Inc. All rights reserved.

Simulating evolution of protein complexes through gene duplication and co-option.

PubMed

Haarsma, Loren; Nelesen, Serita; VanAndel, Ethan; Lamine, James; VandeHaar, Peter

2016-06-21

We present a model of the evolution of protein complexes with novel functions through gene duplication, mutation, and co-option. Under a wide variety of input parameters, digital organisms evolve complexes of 2-5 bound proteins which have novel functions but whose component proteins are not independently functional. Evolution of complexes with novel functions happens more quickly as gene duplication rates increase, point mutation rates increase, protein complex functional probability increases, protein complex functional strength increases, and protein family size decreases. Evolution of complexity is inhibited when the metabolic costs of making proteins exceeds the fitness gain of having functional proteins, or when point mutation rates get so large the functional proteins undergo deleterious mutations faster than new functional complexes can evolve. Copyright © 2016 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ortiz, Rosario, E-mail: r_oh@ciencias.unam.mx; Kouznetsova, Anna, E-mail: Anna.Kouznetsova@ki.se; Echeverría-Martínez, Olga M., E-mail: omem@ciencias.unam.mx

The synaptonemal complex (SC) is a proteinaceous structure that holds the homologous chromosomes in close proximity while they exchange genetic material in a process known as meiotic recombination. This meiotic recombination leads to genetic variability in sexually reproducing organisms. The ultrastructure of the SC is studied by electron microscopy and it is observed as a tripartite structure. Two lateral elements (LE) separated by a central region (CR) confer its classical tripartite organization. The LEs are the anchoring platform for the replicated homologous chromosomes to properly exchange genetic material with one another. An accurate assembly of the LE is indispensable formore » the proper completion of meiosis. Ultrastructural studies suggested that the LE is organized as a multilayered unit. However, no validation of this model has been previously provided. In this ultrastructural study, by using mice with different genetic backgrounds that affect the LE width, we provide further evidence that support a multilayered organization of the LE. Additionally, we provide data suggesting additional roles of the different cohesin complex components in the structure of the LEs of the SC. - Highlights: • The lateral element of the synaptonemal complex is a multilayered structure. • The width of the lateral element in synaptonemal complex-null mice is different. • Two cohesin complex cores plus one axial element form a wild-type lateral element. • The layers of the lateral element can be analyzed in different null mice models.« less

Estimation of atmospheric columnar organic matter (OM) mass concentration from remote sensing measurements of aerosol spectral refractive indices

NASA Astrophysics Data System (ADS)

Zhang, Ying; Li, Zhengqiang; Sun, Yele; Lv, Yang; Xie, Yisong

2018-04-01

Aerosols have adverse effects on human health and air quality, changing Earth's energy balance and lead to climate change. The components of aerosol are important because of the different spectral characteristics. Based on the low hygroscopic and high scattering properties of organic matter (OM) in fine modal atmospheric aerosols, we develop an inversion algorithm using remote sensing to obtain aerosol components including black carbon (BC), organic matter (OM), ammonium nitrate-like (AN), dust-like (DU) components and aerosol water content (AW). In the algorithm, the microphysical characteristics (i.e. volume distribution and complex refractive index) of particulates are preliminarily separated to fine and coarse modes, and then aerosol components are retrieved using bimodal parameters. We execute the algorithm using remote sensing measurements of sun-sky radiometer at AERONET site (Beijing RADI) in a period from October of 2014 to January of 2015. The results show a reasonable distribution of aerosol components and a good fit for spectral feature calculations. The mean OM mass concentration in atmospheric column is account for 14.93% of the total and 56.34% of dry and fine-mode aerosol, being a fairly good correlation (R = 0.56) with the in situ observations near the surface layer.

Photophysical properties of [Ru(2,2‧-bipyridine)3]2+ encapsulated within the Uio-66 zirconium based metal organic framework

NASA Astrophysics Data System (ADS)

Larsen, Randy W.; Wojtas, Lukasz

2017-03-01

The ability to encapsulate photo-active guest molecules within the pores of metal organic frameworks (MOFs) affords the opportunity to develop robust photocatalysts as well as solar energy conversion systems. An important criteria for such systems is stability of the new materials towards moisture, high temperatures, etc which preclude the use of many MOF frameworks. Here, the ability to encapsulate [Ru(II)(2,2‧-bipyridine)3]2+([Ru(bpy)3]2+) into the cavities of the zirconium based MOF Uio-66 as well as the photophysical properties of the complex are reported. The X-ray powder diffraction data of the orange Uio-66 powder are consistent with the formation of Uio-66 in the presence of [Ru(bpy)3]2+. The steady state emission exhibits a significant bathochromic shift from 603 nm in ethanol to 610 nm in Uio-66. The corresponding emission decay of the encapsulated [Ru(bpy)3]2+ complex is biexponential with a fast component of 128 ns and a slower component of 1176 ns (20 deg C). The slow component is consistent with encapsulation of [Ru(bpy)3]2+ into cavities with restricted volume that prevents the population of a triplet ligand field transition that is anti-bonding with respect to the Ru-N bonds. The origin of the fast component is unclear but may involve interactions of the [Ru(bpy)3]2+ encapsulated within large cavities formed through missing ligand defect sites within the Uio-66 materials. Co-encapsulated quenchers contained within these larger cavities gives rise to the reduced lifetimes of the [Ru(bpy)3]2+ complexes.

Imaging of DNA and Protein by SFM and Combined SFM-TIRF Microscopy.

PubMed

Grosbart, Małgorzata; Ristić, Dejan; Sánchez, Humberto; Wyman, Claire

2018-01-01

Direct imaging is invaluable for understanding the mechanism of complex genome transactions where proteins work together to organize, transcribe, replicate and repair DNA. Scanning (or atomic) force microscopy is an ideal tool for this, providing 3D information on molecular structure at nm resolution from defined components. This is a convenient and practical addition to in vitro studies as readily obtainable amounts of purified proteins and DNA are required. The images reveal structural details on the size and location of DNA bound proteins as well as protein-induced arrangement of the DNA, which are directly correlated in the same complexes. In addition, even from static images, the different forms observed and their relative distributions can be used to deduce the variety and stability of different complexes that are necessarily involved in dynamic processes. Recently available instruments that combine fluorescence with topographic imaging allow the identification of specific molecular components in complex assemblies, which broadens the applications and increases the information obtained from direct imaging of molecular complexes. We describe here basic methods for preparing samples of proteins, DNA and complexes of the two for topographic imaging and quantitative analysis. We also describe special considerations for combined fluorescence and topographic imaging of molecular complexes.

A divergent heritage for complex organics in Isheyevo lithic clasts

NASA Astrophysics Data System (ADS)

van Kooten, Elishevah M. M. E.; Nagashima, Kazuhide; Kasama, Takeshi; Wampfler, Susanne F.; Ramsey, Jon P.; Frimann, Søren; Balogh, Zoltan I.; Schiller, Martin; Wielandt, Daniel P.; Franchi, Ian A.; Jørgensen, Jes K.; Krot, Alexander N.; Bizzarro, Martin

2017-05-01

Primitive meteorites are samples of asteroidal bodies that contain a high proportion of chemically complex organic matter (COM) including prebiotic molecules such as amino acids, which are thought to have been delivered to Earth via impacts during the early history of the Solar System. Thus, understanding the origin of COM, including their formation pathway(s) and environment(s), is critical to elucidate the origin of life on Earth as well as assessing the potential habitability of exoplanetary systems. The Isheyevo CH/CBb carbonaceous chondrite contains chondritic lithic clasts with variable enrichments in 15N believed to be of outer Solar System origin. Using transmission electron microscopy (TEM-EELS) and in situ isotope analyses (SIMS and NanoSIMS), we report on the structure of the organic matter as well as the bulk H and N isotope composition of Isheyevo lithic clasts. These data are complemented by electron microprobe analyses of the clast mineral chemistry and bulk Mg and Cr isotopes obtained by inductively coupled plasma and thermal ionization mass spectrometry, respectively (MC-ICPMS and TIMS). Weakly hydrated (A) clasts largely consist of Mg-rich anhydrous silicates with local hydrated veins composed of phyllosilicates, magnetite and globular and diffuse organic matter. Extensively hydrated clasts (H) are thoroughly hydrated and contain Fe-sulfides, sometimes clustered with organic matter, as well as magnetite and carbonates embedded in a phyllosilicate matrix. The A-clasts are characterized by a more 15N-rich bulk nitrogen isotope composition (δ15N = 200-650‰) relative to H-clasts (δ15N = 50-180‰) and contain extremely 15N-rich domains with δ15N < 5000‰. The D/H ratios of the clasts are correlated with the degree of clast hydration and define two distinct populations, which we interpret as reflecting mixing between D-poor fluid(s) and distinct organic endmember components that are variably D-rich. High-resolution N isotope data of 15N-rich domains show that the lithic clast diffuse organic matter is typically more 15N-rich than globular organic matter. The correlated δ15N values and C/N ratios of nanoglobules require the existence of multiple organic components, in agreement with the H isotope data. The combined H and N isotope data suggest that the organic precursors of the lithic clasts are defined by an extremely 15N-poor (similar to solar) and D-rich component for H-clasts, and a moderately 15N-rich and D-rich component for A-clasts. In contrast, the composition of the putative fluids is inferred to include D-poor but moderately to extremely 15N-rich H- and N-bearing components. The variable 15N enrichments in H- and A-clasts are associated with structural differences in the N bonding environments of their diffuse organic matter, which are dominated by amine groups in H-clasts and nitrile functional groups in A-clasts. We suggest that the isotopically divergent organic precursors in Isheyevo clasts may be similar to organic moieties in carbonaceous chondrites (CI, CM, CR) and thermally recalcitrant organic compounds in ordinary chondrites, respectively. The altering fluids, which are inferred to cause the 15N enrichments observed in the clasts, may be the result of accretion of variable abundances of NH3 and HCN ices. Finally, using bulk Mg and Cr isotope composition of clasts, we speculate on the accretion regions of the various primitive chondrites and components and the origin of the Solar System's N and H isotope variability.

Anion-π interaction in metal-organic networks formed by metal halides and tetracyanopyrazine

NASA Astrophysics Data System (ADS)

Rosokha, Sergiy V.; Kumar, Amar

2017-06-01

Co-crystallization of tetracyanopyrazine, TCP, with the tetraalkylammonium salts of linear [CuBr2]-, planar [PtCl4]2- or [Pt2Br6]2-, or octahedral [PtBr6]2- complexes resulted in formation of the alternating [MlXn]m-/TCP stacks separated by the Alk4N+ cations. These hybrid stacks showed multiple short contacts between halide ligands of the [MlXn]m- complexes and carbon atoms of the TCP acceptor indicating strong anion-π bonding between these species. It confirmed that the anion-π interaction is sufficiently strong to bring together such disparate components as ionic metal complexes and neutral aromatic molecules regardless of the geometry of the coordination compound. Structural features of the solid-state stacks and [MlXn]m-·TCP dyads resulted from the quantum-mechanical computations suggests that the molecular-orbital (weakly-covalent) component play an important role in association of the [MlXn]m- complexes with the TCP acceptor.

Functional Specialization and Flexibility in Human Association Cortex

PubMed Central

Yeo, B. T. Thomas; Krienen, Fenna M.; Eickhoff, Simon B.; Yaakub, Siti N.; Fox, Peter T.; Buckner, Randy L.; Asplund, Christopher L.; Chee, Michael W.L.

2015-01-01

The association cortex supports cognitive functions enabling flexible behavior. Here, we explored the organization of human association cortex by mathematically formalizing the notion that a behavioral task engages multiple cognitive components, which are in turn supported by multiple overlapping brain regions. Application of the model to a large data set of neuroimaging experiments (N = 10 449) identified complex zones of frontal and parietal regions that ranged from being highly specialized to highly flexible. The network organization of the specialized and flexible regions was explored with an independent resting-state fMRI data set (N = 1000). Cortical regions specialized for the same components were strongly coupled, suggesting that components function as partially isolated networks. Functionally flexible regions participated in multiple components to different degrees. This heterogeneous selectivity was predicted by the connectivity between flexible and specialized regions. Functionally flexible regions might support binding or integrating specialized brain networks that, in turn, contribute to the ability to execute multiple and varied tasks. PMID:25249407

Ambient Air Pollution and Increases in Blood Pressure: Role for biological constituents of particulate matter

EPA Science Inventory

Particulate matter (PM) is a complex mixture of extremely small particles and liquid droplets made up of a number of components including elemental carbon, organic chemicals, metals, acids (such as nitrates and sulfates), and soil and dust particles. Epidemiological studies con...

BEND3 mediates transcriptional repression and heterochromatin organization

PubMed Central

Khan, Abid; Prasanth, Supriya G

2015-01-01

Transcription repression plays a central role in gene regulation. Transcription repressors utilize diverse strategies to mediate transcriptional repression. We have recently demonstrated that BEND3 (BANP, E5R and Nac1 domain) protein represses rDNA transcription by stabilizing a NoRC component. We discuss the role of BEND3 as a global regulator of gene expression and propose a model whereby BEND3 associates with chromatin remodeling complexes to modulate gene expression and heterochromatin organization. PMID:26507581

BEND3 mediates transcriptional repression and heterochromatin organization.

PubMed

Khan, Abid; Prasanth, Supriya G

2015-01-01

Transcription repression plays a central role in gene regulation. Transcription repressors utilize diverse strategies to mediate transcriptional repression. We have recently demonstrated that BEND3 (BANP, E5R and Nac1 domain) protein represses rDNA transcription by stabilizing a NoRC component. We discuss the role of BEND3 as a global regulator of gene expression and propose a model whereby BEND3 associates with chromatin remodeling complexes to modulate gene expression and heterochromatin organization.

Role of Alcohols in Growth, Lipid Composition, and Membrane Fluidity of Yeasts, Bacteria, and Archaea ▿

PubMed Central

Huffer, Sarah; Clark, Melinda E.; Ning, Jonathan C.; Blanch, Harvey W.; Clark, Douglas S.

2011-01-01

Increased membrane fluidity, which causes cofactor leakage and loss of membrane potential, has long been documented as a cause for decreased cell growth during exposure to ethanol, butanol, and other alcohols. Reinforcement of the membrane with more complex lipid components is thus thought to be beneficial for the generation of more tolerant organisms. In this study, organisms with more complex membranes, namely, archaea, did not maintain high growth rates upon exposure to alcohols, indicating that more complex lipids do not necessarily fortify the membrane against the fluidizing effects of alcohols. In the presence of alcohols, shifts in lipid composition to more saturated and unbranched lipids were observed in most of the organisms tested, including archaea, yeasts, and bacteria. However, these shifts did not always result in a decrease in membrane fluidity or in greater tolerance of the organism to alcohol exposure. In general, organisms tolerating the highest concentrations of alcohols maintained membrane fluidity after alcohol exposure, whereas organisms that increased membrane rigidity were less tolerant. Altered lipid composition was a common response to alcohol exposure, with the most tolerant organisms maintaining a modestly fluid membrane. Our results demonstrate that increased membrane fluidity is not the sole cause of growth inhibition and that alcohols may also denature proteins within the membrane and cytosol, adversely affecting metabolism and decreasing cell growth. PMID:21784917

Clinical review: Extracorporeal blood purification in severe sepsis

PubMed Central

Venkataraman, Ramesh; Subramanian, Sanjay; Kellum, John A

2003-01-01

Sepsis and septic shock are the leading causes of acute renal failure, multiple organ system dysfunction, and death in the intensive care unit. The pathogenesis of sepsis is complex and comprises a mosaic of interconnected pathways. Several attempts to improve patient outcomes by targeting specific components of this network have been unsuccessful. For these reasons, the ideal immunomodulating strategy would be one that restores immunologic stability rather than blindly inhibiting or stimulating one or another component of this complex network. Hence, the recent focus of immunomodulatory therapy in sepsis has shifted to nonspecific methods of influencing the entire inflammatory response without suppressing it. Here, we discuss the various modalities of extracorporeal blood purification, the existing evidence, and future prospects. PMID:12720560

Carrier generation and electronic properties of a single-component pure organic metal

NASA Astrophysics Data System (ADS)

Kobayashi, Yuka; Terauchi, Takeshi; Sumi, Satoshi; Matsushita, Yoshitaka

2017-01-01

Metallic conduction generally requires high carrier concentration and wide bandwidth derived from strong orbital interaction between atoms or molecules. These requisites are especially important in organic compounds because a molecule is fundamentally an insulator; only multi-component salts with strong intermolecular interaction--namely, only charge transfer complexes and conducting polymers--have demonstrated intrinsic metallic behaviour. Herein we report a single-component electroactive molecule, zwitterionic tetrathiafulvalene(TTF)-extended dicarboxylate radical (TED), exhibiting metallic conduction even at low temperatures. TED exhibits d.c. conductivities of 530 S cm-1 at 300 K and 1,000 S cm-1 at 50 K with copper-like electronic properties. Spectroscopic and theoretical investigations of the carrier-generation mechanism and the electronic states of this single molecular species reveal a unique electronic structure with a spin-density gradient in the extended TTF moieties that becomes, in itself, a metallic state.

Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

NASA Astrophysics Data System (ADS)

Walter, Jean-Charles; Walliser, Nils-Ole; David, Gabriel; Dorignac, Jérôme; Geniet, Frédéric; Palmeri, John; Parmeggiani, Andrea; Wingreen, Ned S.; Broedersz, Chase P.

2018-03-01

The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the ‘tightness’ of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site.

Rhabdoid and Undifferentiated Phenotype in Renal Cell Carcinoma: Analysis of 32 Cases Indicating a Distinctive Common Pathway of Dedifferentiation Frequently Associated With SWI/SNF Complex Deficiency.

PubMed

Agaimy, Abbas; Cheng, Liang; Egevad, Lars; Feyerabend, Bernd; Hes, Ondřej; Keck, Bastian; Pizzolitto, Stefano; Sioletic, Stefano; Wullich, Bernd; Hartmann, Arndt

2017-02-01

Undifferentiated (anaplastic) and rhabdoid cell features are increasingly recognized as adverse prognostic findings in renal cell carcinoma (RCC), but their molecular pathogenesis has not been studied sufficiently. Recent studies identified alterations in the Switch Sucrose nonfermentable (SWI/SNF) chromatin remodeling complex as molecular mechanisms underlying dedifferentiation and rhabdoid features in carcinomas of different organs. We herein have analyzed 32 undifferentiated RCCs having in common an undifferentiated (anaplastic) phenotype, prominent rhabdoid features, or both, irrespective of the presence or absence of conventional RCC component. Cases were stained with 6 SWI/SNF pathway members (SMARCB1, SMARCA2, SMARCA4, ARID1A, SMARCC1, and SMARCC2) in addition to conventional RCC markers. Patients were 20 males and 12 females aged 32 to 85 years (mean, 59). A total of 22/27 patients with known stage presented with ≥pT3. A differentiated component varying from microscopic to major component was detected in 20/32 cases (16 clear cell and 2 cases each chromophobe and papillary RCC). The undifferentiated component varied from rhabdoid dyscohesive cells to large epithelioid to small monotonous anaplastic cells. Variable loss of at least 1 SWI/SNF complex subunit was noted in the undifferentiated/rhabdoid component of 21/32 cases (65%) compared with intact or reduced expression in the differentiated component. A total of 15/17 patients (88%) with follow-up died of metastatic disease (mostly within 1 y). Only 2 patients were disease free at last follow-up (1 and 6 y). No difference in survival, age distribution, or sex was observed between the SWI/SNF-deficient and the SWI/SNF-intact group. This is the first study exploring the role of SWI/SNF deficiency as a potential mechanism underlying undifferentiated and rhabdoid phenotype in RCC. Our results highlight the association between the aggressive rhabdoid phenotype and the SWI/SNF complex deficiency, consistent with studies on similar neoplasms in other organs. Thorough sampling of such tumors that are usually huge and locally advanced is necessary for recognizing the clone of origin and hence for proper subtyping and also for differentiating them from undifferentiated urothelial carcinoma.

Numerical simulation of stress distribution in Inconel 718 components realized by metal injection molding during supercritical debinding

NASA Astrophysics Data System (ADS)

Agne, Aboubakry; Barrière, Thierry

2018-05-01

Metal injection molding (MIM) is a process combining advantages of thermoplastic injection molding and powder metallurgy process in order to manufacture components with complex and near net-shape geometries. The debinding of a green component can be performed in two steps, first by using solvent debinding in order to extract the organic part of the binder and then by thermal degradation of the rest of the binder. A shorter and innovative method for extracting an organic binder involves the use of supercritical fluid instead of a regular solvent. The debinding via a supercritical fluid was recently investigated to extract organic binders contained in components obtained by Metal Injection Molding. It consists to put the component in an enclosure subjected to high pressure and temperature. The supercritical fluid has various properties depending on these two conditions, e.g., density and viscosity. The high-pressure combined with the high temperature during the process affect the component structure. Three mechanisms contributing to the deformation of the component can been differentiated: thermal expansion, binder extraction and supercritical fluid effect on the outer surfaces of the component. If one supposes that, the deformation due to binder extraction is negligible, thermal expansion and the fluid effect are probably the main mechanisms that can produce several stress. A finite-element model, which couples fluid-structures interaction and structural mechanics, has been developed and performed on the Comsol Multiphysics® finite-element software platform allowed to estimate the stress distribution during the supercritical debinding of MIM component composed of Inconel 718 powders, polypropylene, polyethylene glycol and stearic acid as binder. The proposed numerical simulations allow the estimation of the stress distribution with respect to the processing parameters for MIM components during the supercritical debinding process using a stationary solver.

Production of haemolysins by strains of the Actinobacillus minor/"porcitonsillarum" complex.

PubMed

Arya, Gitanjali; Niven, Donald F

2010-03-24

Actinobacillus minor and "Actinobacillus porcitonsillarum" are distinguished by their haemolytic activities, the latter organism being haemolytic and the former, non-haemolytic. Analysis of a whole genome shotgun sequence, however, revealed that A. minor strain 202, like "A. porcitonsillarum", possesses a haemolysin-encoding apxII operon. The purpose of this study was therefore to investigate haemolysin production by this organism and also by three additional members of the A. minor/"porcitonsillarum" complex, strains 33PN and 7ATS and A. minor strain NM305(T). Primers based on sequences within the apxII genes of strain 202 allowed the amplification of appropriately sized fragments from DNA from strain 33PN suggesting that this organism also possesses an apxII operon. Analysis of a whole genome shotgun sequence failed to reveal any trace of an apxII operon in strain NM305(T) and attempts to amplify apxII genes from DNA from strain 7ATS also failed. Strains 202 and 33PN, and surprisingly, the type strain of A. minor and strain 7ATS, were all found to be haemolysin-positive as growth media from cultures of these organisms could promote the lysis of erythrocytes in suspension. The erythrocyte specificities of the haemolysins produced by strains 202 and 33PN indicated that the haemolytic activities exhibited by these organisms were due to ApxII. In keeping with the apparent lack of apxII genes in strains NM305(T) and 7ATS, the haemolysins produced by these organisms were not erythrocyte-specific and with both organisms, haemolytic activity appeared to be due to a combination of heat-stable and heat-labile components. The identities of these components, however, remain unknown. Copyright 2009 Elsevier B.V. All rights reserved.

Structural determinants for membrane association and dynamic organization of the hepatitis C virus NS3-4A complex

PubMed Central

Brass, Volker; Berke, Jan Martin; Montserret, Roland; Blum, Hubert E.; Penin, François; Moradpour, Darius

2008-01-01

Hepatitis C virus (HCV) NS3-4A is a membrane-associated multifunctional protein harboring serine protease and RNA helicase activities. It is an essential component of the HCV replication complex and a prime target for antiviral intervention. Here, we show that membrane association and structural organization of HCV NS3-4A are ensured in a cooperative manner by two membrane-binding determinants. We demonstrate that the N-terminal 21 amino acids of NS4A form a transmembrane α-helix that may be involved in intramembrane protein–protein interactions important for the assembly of a functional replication complex. In addition, we demonstrate that amphipathic helix α0, formed by NS3 residues 12–23, serves as a second essential determinant for membrane association of NS3-4A, allowing proper positioning of the serine protease active site on the membrane. These results allowed us to propose a dynamic model for the membrane association, processing, and structural organization of NS3-4A on the membrane. This model has implications for the functional architecture of the HCV replication complex, proteolytic targeting of host factors, and drug design. PMID:18799730

Pigment organization in the photosynthetic apparatus of Roseiflexus castenholzii.

PubMed

Collins, Aaron M; Xin, Yueyong; Blankenship, Robert E

2009-08-01

The light-harvesting-reaction center (LHRC) complex from the chlorosome-lacking filamentous anoxygenic phototroph (FAP), Roseiflexus castenholzii (R. castenholzii) was purified and characterized for overall pigment organization. The LHRC is a single complex that is comprised of light harvesting (LH) and reaction center (RC) polypeptides as well as an attached c-type cytochrome. The dominant carotenoid found in the LHRC is keto-gamma-carotene, which transfers excitation to the long wavelength antenna band with 35% efficiency. Linear dichroism and fluorescence polarization measurements indicate that the long wavelength antenna pigments absorbing around 880 nm are perpendicular to the membrane plane, with the corresponding Q(y) transition dipoles in the plane of the membrane. The antenna pigments absorbing around 800 nm, as well as the bound carotenoid, are oriented at a large angle with respect to the membrane. The antenna pigments spectroscopically resemble the well-studied LH2 complex from purple bacteria, however the close association with the RC makes the light harvesting component of this complex functionally more like LH1.

Biomimicry Promotes the Efficiency of a 10-Step Sequential Enzymatic Reaction on Nanoparticles, Converting Glucose to Lactate.

PubMed

Mukai, Chinatsu; Gao, Lizeng; Nelson, Jacquelyn L; Lata, James P; Cohen, Roy; Wu, Lauren; Hinchman, Meleana M; Bergkvist, Magnus; Sherwood, Robert W; Zhang, Sheng; Travis, Alexander J

2017-01-02

For nanobiotechnology to achieve its potential, complex organic-inorganic systems must grow to utilize the sequential functions of multiple biological components. Critical challenges exist: immobilizing enzymes can block substrate-binding sites or prohibit conformational changes, substrate composition can interfere with activity, and multistep reactions risk diffusion of intermediates. As a result, the most complex tethered reaction reported involves only 3 enzymes. Inspired by the oriented immobilization of glycolytic enzymes on the fibrous sheath of mammalian sperm, here we show a complex reaction of 10 enzymes tethered to nanoparticles. Although individual enzyme efficiency was higher in solution, the efficacy of the 10-step pathway measured by conversion of glucose to lactate was significantly higher when tethered. To our knowledge, this is the most complex organic-inorganic system described, and it shows that tethered, multi-step biological pathways can be reconstituted in hybrid systems to carry out functions such as energy production or delivery of molecular cargo. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biomimicry promotes the efficiency of a 10-step sequential enzymatic reaction on nanoparticles, converting glucose to lactate

PubMed Central

Mukai, Chinatsu; Gao, Lizeng; Nelson, Jacquelyn L.; Lata, James P.; Cohen, Roy; Wu, Lauren; Hinchman, Meleana M.; Bergkvist, Magnus; Sherwood, Robert W.; Zhang, Sheng; Travis, Alexander J.

2016-01-01

For nanobiotechnology to achieve its potential, complex organic-inorganic systems must grow to utilize the sequential functions of multiple biological components. Critical challenges exist: immobilizing enzymes can block substrate-binding sites or prohibit conformational changes, substrate composition can interfere with activity, and multistep reactions risk diffusion of intermediates. As a result, the most complex tethered reaction reported involves only 3 enzymes. Inspired by the oriented immobilization of glycolytic enzymes on the fibrous sheath of mammalian sperm, here we show a complex reaction of 10 enzymes tethered to nanoparticles. Although individual enzyme efficiency was higher in solution, the efficacy of the 10-step pathway measured by conversion of glucose to lactate was significantly higher when tethered. To our knowledge, this is the most complex organic-inorganic system described, and it shows that tethered, multi-step biological pathways can be reconstituted in hybrid systems to carry out functions such as energy production or delivery of molecular cargo. PMID:27901298

Health effects of carbon-containing particulate matter: focus on sources and recent research program results.

PubMed

Rohr, Annette; McDonald, Jacob

2016-02-01

Air pollution is a complex mixture of gas-, vapor-, and particulate-phase materials comprised of inorganic and organic species. Many of these components have been associated with adverse health effects in epidemiological and toxicological studies, including a broad spectrum of carbonaceous atmospheric components. This paper reviews recent literature on the health impacts of organic aerosols, with a focus on specific sources of organic material; it is not intended to be a comprehensive review of all the available literature. Specific emission sources reviewed include engine emissions, wood/biomass combustion emissions, biogenic emissions and secondary organic aerosol (SOA), resuspended road dust, tire and brake wear, and cooking emissions. In addition, recent findings from large toxicological and epidemiological research programs are reviewed in the context of organic PM, including SPHERES, NPACT, NERC, ACES, and TERESA. A review of the extant literature suggests that there are clear health impacts from emissions containing carbon-containing PM, but difficulty remains in apportioning responses to certain groupings of carbonaceous materials, such as organic and elemental carbon, condensed and gas phases, and primary and secondary material. More focused epidemiological and toxicological studies, including increased characterization of organic materials, would increase understanding of this issue.

Application of Smart Infrastructure Systems approach to precision medicine.

PubMed

Govindaraju, Diddahally R; Annaswamy, Anuradha M

2015-12-01

All biological variation is hierarchically organized dynamic network system of genomic components, organelles, cells, tissues, organs, individuals, families, populations and metapopulations. Individuals are axial in this hierarchy, as they represent antecedent, attendant and anticipated aspects of health, disease, evolution and medical care. Humans show individual specific genetic and clinical features such as complexity, cooperation, resilience, robustness, vulnerability, self-organization, latent and emergent behavior during their development, growth and senescence. Accurate collection, measurement, organization and analyses of individual specific data, embedded at all stratified levels of biological, demographic and cultural diversity - the big data - is necessary to make informed decisions on health, disease and longevity; which is a central theme of precision medicine initiative (PMI). This initiative also calls for the development of novel analytical approaches to handle complex multidimensional data. Here we suggest the application of Smart Infrastructure Systems (SIS) approach to accomplish some of the goals set forth by the PMI on the premise that biological systems and the SIS share many common features. The latter has been successfully employed in managing complex networks of non-linear adaptive controls, commonly encountered in smart engineering systems. We highlight their concordance and discuss the utility of the SIS approach in precision medicine programs.

Development studies of a novel wet oxidation process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rogers, T.W.; Dhooge, P.M.

1995-10-01

Many DOE waste streams and remediates contain complex and variable mixtures of organic compounds, toxic metals, and radionuclides. These materials are often dispersed in organic or inorganic matrices, such as personal protective equipment, various sludges, soils, and water. Incineration and similar combustive processes do not appear to be viable options for treatment of these waste streams due to various considerations. The objective of this project is to develop a novel catalytic wet oxidation process for the treatment of multi-component wastes. The DETOX process uses a unique combination of metal catalysts to increase the rate of oxidation of organic materials.

Nurses in corporate America: embracing power through influence.

PubMed

Weaver, Charlotte A

2002-06-01

Executive positions in corporate America offer nurse leaders the opportunity to influence product development and services delivered to ensure that the best possible solutions are provided to health care organizations, providers, and patients. This opportunity to "make a difference" is a critical component for nurses' attraction to migrating to the business side of the health care industry. However, making the transition from leadership positions in health care delivery organizations to corporate businesses carries big challenges. A major demand is for nurse leaders to adjust from direct span of control organizational models to matrix management structures used in complex business organizations.

Creating biomaterials with spatially organized functionality.

PubMed

Chow, Lesley W; Fischer, Jacob F

2016-05-01

Biomaterials for tissue engineering provide scaffolds to support cells and guide tissue regeneration. Despite significant advances in biomaterials design and fabrication techniques, engineered tissue constructs remain functionally inferior to native tissues. This is largely due to the inability to recreate the complex and dynamic hierarchical organization of the extracellular matrix components, which is intimately linked to a tissue's biological function. This review discusses current state-of-the-art strategies to control the spatial presentation of physical and biochemical cues within a biomaterial to recapitulate native tissue organization and function. © 2016 by the Society for Experimental Biology and Medicine.

Systematic approaches to comprehensive analyses of natural organic matter

USGS Publications Warehouse

Leenheer, Jerry A.

2009-01-01

The more that is learned of the chemistry of aquatic natural organic matter (NOM) the greater is the scientific appreciation of the vast complexity of this subject. This complexity is due not only to a multiplicity of precursor molecules in any environment but to their associations with each other and with other components of local environments such as clays, mineral acids and dissolved metals. In addition, this complex system is subject to constant change owing to environmental variables and microbial action. Thus, there is a good argument that no two NOM samples are exactly the same even from the same source at nearly the same time. When ubiquity of occurrence, reaction with water treatment chemicals, and subsequent human exposure are added to the list of NOM issues, one can understand the appeal that this subject holds for a wide variety of environmental scientists.

Are maternal mitochondria the selfish entities that are masters of the cells of eukaryotic multicellular organisms?

PubMed Central

Barlow, Peter W; Baldelli, E; Baluška, Frantisek

2009-01-01

The Energide concept, as well as the endosymbiotic theory of eukaryotic cell organization and evolution, proposes that present-day cells of eukaryotic organisms are mosaics of specialized and cooperating units, or organelles. Some of these units were originally free-living prokaryotes, which were engulfed during evolutionary time. Mitochondria represent one of these types of previously independent organisms, the Energide, is another type. This new perspective on the organization of the cell has been further expanded to reveal the concept of a public milieu, the cytosol, in which Energides and mitochondria live, each with their own private internal milieu. The present paper discusses how the endosymbiotic theory implicates a new hypothesis about the hierarchical and communicational organization of the integrated prokaryotic components of the eukaryotic cell and provides a new angle from which to consider the theory of evolution and its bearing upon cellular complexity. Thus, it is proposed that the “selfish gene” hypothesis of Dawkins1 is not the only possible perspective for comprehending genomic and cellular evolution. Our proposal is that maternal mitochondria are the selfish “master” entities of the eukaryotic cell with respect not only to their propagation from cell-to-cell and from generation-to-generation but also to their regulation of all other cellular functions. However, it should be recognized that the concept of “master” and “servant” cell components is a metaphor; in present-day living organisms their organellar components are considered to be interdependent and inseparable. PMID:19513277

Heat detection and compositions and devices therefor

NASA Technical Reports Server (NTRS)

Rembaum, A. (Inventor)

1975-01-01

Temperature change of a substrate such as a microelectronic component is sensed and detected by means of a mixture of a weak molecular complex of an electron donor compound such as an organic amine and an electron acceptor compound such as nitroaromatic compound. The mixture is encapsulated in a clear binder such as a vinyl resin.

A Model for School Board Operation.

ERIC Educational Resources Information Center

Hickcox, Edward S.; And Others

A school board must operate in such a way that it can cope with the increasingly larger size, complex organization, and sophisticated programs of schools. The relationships among the community, board, and school can be viewed as component parts of a system. Formal and informal lines of communication exist among these parts--between the community…

A Qualitative Examination of the Implementation of a Community-Academic Coalition

ERIC Educational Resources Information Center

Boydell, Katherine M.; Volpe, Tiziana

2004-01-01

Many recent grant initiatives have mandated coalition building as a key component of their health promotion efforts. Health service leaders are increasingly representing their organizations on coalitions and need to better understand the complexities involved in their creation and management. In this paper we focus on the implementation of a…

Conceptual Frameworks in Undergraduate Nursing Curricula: Report of a National Survey.

ERIC Educational Resources Information Center

McEwen, Melanie; Brown, Sandra C.

2002-01-01

Responses from 300 accredited nursing schools indicated that they used eclectic conceptual frameworks for curriculum; the most common component was the nursing process. Associate degree programs were more likely to use simple-to-complex organization. Diploma programs were more likely to use the medical model than baccalaureate programs. Frameworks…

The Role of Molecular Motors in the Mechanics of Active Gels and the Effects of Inertia, Hydrodynamic Interaction and Compressibility in Passive Microrheology

DTIC Science & Technology

2014-07-01

to use the two-point microrheology technique 88 to measure the complex compressibility of biopolymers and cell components such as F-actin and...loads [23, 115]. Several works have used a continuum-mechanics level of description to model self- organization [64, 2] and rheology [79, 12, 33] of...morphogenesis [94]. Several works have used a continuum-mechanics level of description to model self- organization [64, 2] and rheology [79, 12, 33] of

Raman Spectroscopy Reveals New Insights into the Zonal Organization of Native and Tissue-Engineered Articular Cartilage

PubMed Central

2016-01-01

Tissue architecture is intimately linked with its functions, and loss of tissue organization is often associated with pathologies. The intricate depth-dependent extracellular matrix (ECM) arrangement in articular cartilage is critical to its biomechanical functions. In this study, we developed a Raman spectroscopic imaging approach to gain new insight into the depth-dependent arrangement of native and tissue-engineered articular cartilage using bovine tissues and cells. Our results revealed previously unreported tissue complexity into at least six zones above the tidemark based on a principal component analysis and k-means clustering analysis of the distribution and orientation of the main ECM components. Correlation of nanoindentation and Raman spectroscopic data suggested that the biomechanics across the tissue depth are influenced by ECM microstructure rather than composition. Further, Raman spectroscopy together with multivariate analysis revealed changes in the collagen, glycosaminoglycan, and water distributions in tissue-engineered constructs over time. These changes were assessed using simple metrics that promise to instruct efforts toward the regeneration of a broad range of tissues with native zonal complexity and functional performance. PMID:28058277

Irradiated Benzene Ice Provides Clues to Meteoritic Organic Chemistry

NASA Technical Reports Server (NTRS)

Callahan, Michael Patrick; Gerakines, Perry Alexander; Martin, Mildred G.; Hudson, Reggie L.; Peeters, Zan

2013-01-01

Aromatic hydrocarbons account for a significant portion of the organic matter in carbonaceous chondrite meteorites, as a component of both the low molecular weight, solvent-extractable compounds and the insoluble organic macromolecular material. Previous work has suggested that the aromatic compounds in carbonaceous chondrites may have originated in the radiation-processed icy mantles of interstellar dust grains. Here we report new studies of the organic residue made from benzene irradiated at 19 K by 0.8 MeV protons. Polyphenyls with up to four rings were unambiguously identified in the residue by gas chromatography-mass spectrometry. Atmospheric pressure photoionization Fourier transform mass spectrometry was used to determine molecular composition, and accurate mass measurements suggested the presence of polyphenyls, partially hydrogenated polyphenyls, and other complex aromatic compounds. The profile of low molecular weight compounds in the residue compared well with extracts from the Murchison and Orgueil meteorites. These results are consistent with the possibility that solid phase radiation chemistry of benzene produced some of the complex aromatics found in meteorites.

Three-Dimensional Bioprinting: Toward the Era of Manufacturing Human Organs as Spare Parts for Healthcare and Medicine^.

PubMed

Mir, Tanveer Ahmad; Nakamura, Makoto

2017-06-01

Three-dimensional (3D) printing technology has been used in industrial worlds for decades. Three-dimensional bioprinting has recently received an increasing attention across the globe among researchers, academicians, students, and even the ordinary people. This emerging technique has a great potential to engineer highly organized functional bioconstructs with complex geometries and tailored components for engineering bioartificial tissues/organs for widespread applications, including transplantation, therapeutic investigation, drug development, bioassay, and disease modeling. Although many specialized 3D printers have been developed and applied to print various types of 3D tissue constructs, bioprinting technologies still have several technical challenges, including high resolution distribution of cells, controlled deposition of bioinks, suitable bioink materials, maturation of cells, and effective vascularization and innervation within engineered complex structures. In this brief review, we discuss about bioprinting approach, current limitations, and possibility of future advancements for producing engineered bioconstructs and bioartificial organs with desired functionalities.

Preparation and self-sterilizing properties of Ag@TiO2-styrene-acrylic complex coatings.

PubMed

Zhou, Xiang-dong; Chen, Feng; Yang, Jin-tao; Yan, Xiao-hui; Zhong, Ming-qiang

2013-04-01

In this study, we report a simple and cost-effective method for self-sterilized complex coatings obtained by Ag@TiO2 particle incorporation into styrene-acrylic latex. The Ag@TiO2 particles were prepared via a coupling agent modification process. The composite latices characterized by transmission electron microscopy (TEM) study were highly homogeneous at the nanometric scale, and the Ag@TiO2 particles were well dispersed and exhibited an intimate contact between both the organic and inorganic components. The Ag@TiO2 nanoparticles significantly enhanced the absorption in the visible region and engendered a good heat-insulating effect of the complex coatings. Moreover, the Ag@TiO2 nanoparticle incorporation into this polymer matrix renders self-sterilized nanocomposite materials upon light excitation, which are tested against Escherichia coli and Staphylococcus aureus. The complex coatings display an impressive performance in the killing of all micro-organisms with a maximum for a Ag@TiO2 loading concentration of 2-5 wt.%. The weathering endurance of the complex coating was also measured. Copyright © 2012 Elsevier B.V. All rights reserved.

Analysis of Alternative Pre-RNA Splicing in the Mouse Retina Using a Fluorescent Reporter.

PubMed

Murphy, Daniel; Kolandaivelu, Saravanan; Ramamurthy, Visvanathan; Stoilov, Peter

2016-01-01

In vivo alternative splicing is controlled in a tissue and cell type specific manner. Often individual cellular components of complex tissues will express different splicing programs. Thus, when studying splicing in multicellular organisms it is critical to determine the exon inclusion levels in individual cells positioned in the context of their native tissue or organ. Here we describe how a fluorescent splicing reporter in combination with in vivo electroporation can be used to visualize alternative splicing in individual cells within mature tissues. In a test case we show how the splicing of a photoreceptor specific exon can be visualized within the mouse retina. The retina was chosen as an example of a complex tissue that is fragile and whose cells cannot be studied in culture. With minor modifications to the injection and electroporation procedure, the protocol we outline can be applied to other tissues and organs.

Occupational safety and health as an element of a complex compensation system evaluation within an organization.

PubMed

Beck-Krala, Ewa; Klimkiewicz, Katarzyna

2016-12-01

Occupational safety and health (OSH) plays a significant role in today's organizations, because it helps in attracting and retaining employees as well as molding their attitudes and behaviors at work. This is why the issue of OSH is stressed in a comprehensive approach to employee rewards: the total reward concept. This article explains how OSH may be included in a complex evaluation process of the compensation system. Although the literature on the effectiveness of employee compensation refers mainly to financial and non-financial components, there is a need for inclusion of working conditions in such analyses. An evaluation of the compensation system that incorporates OSH can drive many benefits for both the organization and employees. Obtaining such benefits, however, requires systematic evaluation of the reward system, including OSH. Incorporation of OSH issue within the comprehensive analysis of compensation systems promotes responsible behavior of all stakeholders.

Technical Efficiency and Organ Transplant Performance: A Mixed-Method Approach

PubMed Central

de-Pablos-Heredero, Carmen; Fernández-Renedo, Carlos; Medina-Merodio, Jose-Amelio

2015-01-01

Mixed methods research is interesting to understand complex processes. Organ transplants are complex processes in need of improved final performance in times of budgetary restrictions. As the main objective a mixed method approach is used in this article to quantify the technical efficiency and the excellence achieved in organ transplant systems and to prove the influence of organizational structures and internal processes in the observed technical efficiency. The results show that it is possible to implement mechanisms for the measurement of the different components by making use of quantitative and qualitative methodologies. The analysis show a positive relationship between the levels related to the Baldrige indicators and the observed technical efficiency in the donation and transplant units of the 11 analyzed hospitals. Therefore it is possible to conclude that high levels in the Baldrige indexes are a necessary condition to reach an increased level of the service offered. PMID:25950653

STRIPAK complexes: structure, biological function, and involvement in human diseases.

PubMed

Hwang, Juyeon; Pallas, David C

2014-02-01

The mammalian striatin family consists of three proteins, striatin, S/G2 nuclear autoantigen, and zinedin. Striatin family members have no intrinsic catalytic activity, but rather function as scaffolding proteins. Remarkably, they organize multiple diverse, large signaling complexes that participate in a variety of cellular processes. Moreover, they appear to be regulatory/targeting subunits for the major eukaryotic serine/threonine protein phosphatase 2A. In addition, striatin family members associate with germinal center kinase III kinases as well as other novel components, earning these assemblies the name striatin-interacting phosphatase and kinase (STRIPAK) complexes. Recently, there has been a great increase in functional and mechanistic studies aimed at identifying and understanding the roles of STRIPAK and STRIPAK-like complexes in cellular processes of multiple organisms. These studies have identified novel STRIPAK and STRIPAK-like complexes and have explored their roles in specific signaling pathways. Together, the results of these studies have sparked increased interest in striatin family complexes because they have revealed roles in signaling, cell cycle control, apoptosis, vesicular trafficking, Golgi assembly, cell polarity, cell migration, neural and vascular development, and cardiac function. Moreover, STRIPAK complexes have been connected to clinical conditions, including cardiac disease, diabetes, autism, and cerebral cavernous malformation. In this review, we discuss the expression, localization, and protein domain structure of striatin family members. Then we consider the diverse complexes these proteins and their homologs form in various organisms, emphasizing what is known regarding function and regulation. Finally, we explore possible roles of striatin family complexes in disease, especially cerebral cavernous malformation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Constitutional dynamic chemistry: bridge from supramolecular chemistry to adaptive chemistry.

PubMed

Lehn, Jean-Marie

2012-01-01

Supramolecular chemistry aims at implementing highly complex chemical systems from molecular components held together by non-covalent intermolecular forces and effecting molecular recognition, catalysis and transport processes. A further step consists in the investigation of chemical systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, thus behaving as programmed chemical systems. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. These features define a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels.CDC introduces a paradigm shift with respect to constitutionally static chemistry. The latter relies on design for the generation of a target entity, whereas CDC takes advantage of dynamic diversity to allow variation and selection. The implementation of selection in chemistry introduces a fundamental change in outlook. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization with selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation.The merging of the features: -information and programmability, -dynamics and reversibility, -constitution and structural diversity, points to the emergence of adaptive and evolutive chemistry, towards a chemistry of complex matter.

An original data treatment for infrared spectra of organic matter, application to extracted soil organic matter

NASA Astrophysics Data System (ADS)

Gomes Rossin, Bruna; Redon, Roland; Raynaud, Michel; Nascimento, Nadia Regina; Mounier, Stéphane

2017-04-01

Infrared spectra of extracted organic matter are easy and rapid to do, but generally hard to interpreted over the presence or not of certain organic functions. Indeed, the organic matter is a complex mixture of molecules often having absorption overlapping and it is also difficult to have a well calibrated or normalised spectra due to the difficulty to have a well known solid content or homogeneity for a sample (Monakhova et al. 2015, Tadini et al. 2015, Bardy et al. 2008). In this work, the IRTF (InfraRed Fourier Transform) spectra were treated by an original algorithm developed to obtain the principal components of the IRTF spectra and their contributions for each sample. This bilinear decomposition used a PCA initialisation and the principal components were estimated from vectors calculated by PCA and linearly combined to provide non-negative signals minimizing a criterion based on cross-correlation. Hence, using this decomposition, it is possible to define IRTF signal of organic matter fractions like humic acid or fulvic acid depending on their origin like surface of depth of soil profiles. The method was used on a set of sample from Upper Negro River Basin (Amazon, Brazil) (Bueno,2009), where three soils sequences from surface to two meter depth containing 10 slices each. The sequences were sampled on a podzol well drain, a hydromorphic podzol and a cryptopodzol. From the IRTF data five representative component spectra were defined for all the extracted organic matter , and using other chemical composition information, a mechanism of organic matter fate is proposed to explain the observed results. Bardy, M., E. Fritsch, S. Derenne, T. Allard, N. R. do Nascimento, and G. T. Bueno. 2008. "Micromorphology and Spectroscopic Characteristics of Organic Matter in Waterlogged Podzols of the Upper Amazon Basin." Geoderma 145 (3-4): 222-30. Bueno, G.T. Appauvrissement et podzolisation des latérites du baissin du Rio Negro et gênese dês Podzols dans le haut bassin amazonien. [PHD] .Universidade Estadual Paulista "Júlio de Mesquita Filho";2009. Monakhova, Yulia B., Alexey M. Tsikin, Svetlana P. Mushtakova, and Mauro Mecozzi. 2015. "Independent Component Analysis and Multivariate Curve Resolution to Improve Spectral Interpretation of Complex Spectroscopic Data Sets: Application to Infrared Spectra of Marine Organic Matter Aggregates." Microchemical Journal, Devoted to the Application of Microtechniques in All Branches of Science 118 (January): 211-22. Tadini, Amanda Maria, Gustavo Nicolodelli, Stephane Mounier, Célia Regina Montes, and Débora Marcondes Bastos Pereira Milori. 2015. "The Importance of Humin in Soil Characterisation: A Study on Amazonian Soils Using Different Fluorescence Techniques." The Science of the Total Environment 537 (December): 152-58.

Dependency visualization for complex system understanding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smart, J. Allison Cory

1994-09-01

With the volume of software in production use dramatically increasing, the importance of software maintenance has become strikingly apparent. Techniques now sought and developed for reverse engineering and design extraction and recovery. At present, numerous commercial products and research tools exist which are capable of visualizing a variety of programming languages and software constructs. The list of new tools and services continues to grow rapidly. Although the scope of the existing commercial and academic product set is quite broad, these tools still share a common underlying problem. The ability of each tool to visually organize object representations is increasingly impairedmore » as the number of components and component dependencies within systems increases. Regardless of how objects are defined, complex ``spaghetti`` networks result in nearly all large system cases. While this problem is immediately apparent in modem systems analysis involving large software implementations, it is not new. As will be discussed in Chapter 2, related problems involving the theory of graphs were identified long ago. This important theoretical foundation provides a useful vehicle for representing and analyzing complex system structures. While the utility of directed graph based concepts in software tool design has been demonstrated in literature, these tools still lack the capabilities necessary for large system comprehension. This foundation must therefore be expanded with new organizational and visualization constructs necessary to meet this challenge. This dissertation addresses this need by constructing a conceptual model and a set of methods for interactively exploring, organizing, and understanding the structure of complex software systems.« less

Insight into magnesium coordination environments in benzoate and salicylate complexes through 25Mg solid-state NMR spectroscopy.

PubMed

Burgess, Kevin M N; Xu, Yang; Leclerc, Matthew C; Bryce, David L

2013-08-01

We report on the (25)Mg solid-state nuclear magnetic resonance (NMR) characterization of a series of magnesium complexes featuring Mg(2+) ions in organic coordination environments. Six compounds have been synthesized with benzoate and salicylate ligands, which are typically used as linkers in metal organic frameworks (MOFs). The use of ultrahigh-field solid-state NMR has revealed a relatively large range of values for the (25)Mg quadrupolar coupling constant, CQ((25)Mg), in these compounds. In contrast to some previously studied inorganic Mg(2+) complexes, the values of CQ((25)Mg) in organic Mg(2+) complexes are well rationalized by the degree of octahedral strain of the "MgO6" coordination polyhedra. (13)C and (25)Mg isotropic chemical shifts were also found to be sensitive to the binding mode of the carboxylate ligands. The experimental findings are corroborated by gauge-including projector-augmented-wave (GIPAW) density functional theory (DFT) computations, and these have allowed for an interpretation of the experimentally observed trend in the CQ((25)Mg) values and for the visualization of the EFG tensor principal components with respect to the molecular structure. These new insights may prove to be valuable for the understanding and interpretation of (25)Mg NMR data for Mg(2+) ions in organic binding environments such as those found in MOFs and protein-divalent metal binding sites.

Double channel emission from a redox active single component quantum dot complex.

PubMed

Bhandari, Satyapriya; Roy, Shilaj; Pramanik, Sabyasachi; Chattopadhyay, Arun

2015-01-13

Herein we report the generation and control of double channel emission from a single component system following a facile complexation reaction between a Mn(2+) doped ZnS colloidal quantum dot (Qdot) and an organic ligand (8-hydroxy quinoline; HQ). The double channel emission of the complexed quantum dot-called the quantum dot complex (QDC)-originates from two independent pathways: one from the complex (ZnQ2) formed on the surface of the Qdot and the other from the dopant Mn(2+) ions of the Qdot. Importantly, reaction of ZnQ2·2H2O with the Qdot resulted in the same QDC formation. The emission at 500 nm with an excitation maximum at 364 nm is assigned to the surface complex involving ZnQ2 and a dangling sulfide bond. On the other hand, the emission at 588 nm-with an excitation maximum at 330 nm-which is redox tunable, is ascribed to Mn(2+) dopant. The ZnQ2 complex while present in QDC has superior thermal stability in comparison to the bare complex. Interestingly, while the emission of Mn(2+) was quenched by an electron quencher (benzoquinone), that due to the surface complex remained unaffected. Further, excitation wavelength dependent tunability in chromaticity color coordinates makes the QDC a potential candidate for fabricating a light emitting device of desired color output.

Development of the GC-MS organic aerosol monitor (GC-MS OAM) for in-field detection of particulate organic compounds

NASA Astrophysics Data System (ADS)

Cropper, Paul M.; Overson, Devon K.; Cary, Robert A.; Eatough, Delbert J.; Chow, Judith C.; Hansen, Jaron C.

2017-11-01

Particulate matter (PM) is among the most harmful air pollutants to human health, but due to its complex chemical composition is poorly characterized. A large fraction of PM is composed of organic compounds, but these compounds are not regularly monitored due to limitations in current sampling and analysis techniques. The Organic Aerosol Monitor (GC-MS OAM) combines a collection device with thermal desorption, gas chromatography and mass spectrometry to quantitatively measure the carbonaceous components of PM on an hourly averaged basis. The GC-MS OAM is fully automated and has been successfully deployed in the field. It uses a chemically deactivated filter for collection followed by thermal desorption and GC-MS analysis. Laboratory tests show that detection limits range from 0.2 to 3 ng for 16 atmospherically relevant compounds, with the possibility for hundreds more. The GC-MS OAM was deployed in the field for semi-continuous measurement of the organic markers, levoglucosan, dehydroabietic acid, and polycyclic aromatic hydrocarbons (PAHs) from January to March 2015. Results illustrate the significance of this monitoring technique to characterize the organic components of PM and identify sources of pollution.

Morphological Dependence of Element Stoichiometry in the H. americanus Exoskeleton

NASA Astrophysics Data System (ADS)

Mergelsberg, S. T.; Ulrich, R. N.; Dove, P. M.

2016-02-01

The crustacean exoskeleton is a complex biocomposite of inorganic mineral and organic macromolecules that expresses highly divergent morphologies across different taxa. While the structures and compositions of the organic framework show complex links to environmental and developmental pressures, little is known about the mineral chemistry. Previous studies of the cuticle have assumed that magnesium, phosphorous, and other trace metals are largely contained in the inorganic mineral fraction. Due to analytical limitations of structural analyses and in situ spectroscopic methods, the stoichiometry of the organic and inorganic portions could not be resolved. For example, previous Raman and XRD studies conclude the higher concentrations of trace elements, such as P and Mg measured in reinforced structures, e.g. the claw and abdomen, are primarily determined by the mineral fraction. Using the American Lobster (Homarus americanus) as a model organism to establish relationships between body part function and cuticle composition, this study quantified the distributions of Mg and P in the mineral and organic fractions. The experiments were designed to dissolve the exoskeleton of 10 body parts using three types of solutions that were specific to extracting 1) the mineral phase, 2) protein, and 3) polysaccharide. Analysis of the solutions by ICP-OES shows the mineral phase contains magnesium and phosphorous at concentrations sufficient to support the formation of calcium-magnesium and phosphate minerals. The protein fraction of the body parts contains significantly more Mg and P than previously hypothesized, while the levels of P contained in the organic portion are fairly constant. The findings demonstrate the lobster cuticle contains a significant amount of non-mineralized P and Mg that is readily water-soluble in the protein component. However, for those body parts used for defense and food acquisition, such as the claw, the mineral component determines the overall composition of the exoskeleton.

Carbohydrates in Supramolecular Chemistry.

PubMed

Delbianco, Martina; Bharate, Priya; Varela-Aramburu, Silvia; Seeberger, Peter H

2016-02-24

Carbohydrates are involved in a variety of biological processes. The ability of sugars to form a large number of hydrogen bonds has made them important components for supramolecular chemistry. We discuss recent advances in the use of carbohydrates in supramolecular chemistry and reveal that carbohydrates are useful building blocks for the stabilization of complex architectures. Systems are presented according to the scaffold that supports the glyco-conjugate: organic macrocycles, dendrimers, nanomaterials, and polymers are considered. Glyco-conjugates can form host-guest complexes, and can self-assemble by using carbohydrate-carbohydrate interactions and other weak interactions such as π-π interactions. Finally, complex supramolecular architectures based on carbohydrate-protein interactions are discussed.

Internet-based data warehousing

NASA Astrophysics Data System (ADS)

Boreisha, Yurii

2001-10-01

In this paper, we consider the process of the data warehouse creation and population using the latest Internet and database access technologies. The logical three-tier model is applied. This approach allows developing of an enterprise schema by analyzing the various processes in the organization, and extracting the relevant entities and relationships from them. Integration with local schemas and population of the data warehouse is done through the corresponding user, business, and data services components. The hierarchy of these components is used to hide from the data warehouse users the entire complex online analytical processing functionality.

Recent advances in pericentriolar material organization: ordered layers and scaffolding gels.

PubMed

Fry, Andrew M; Sampson, Josephina; Shak, Caroline; Shackleton, Sue

2017-01-01

The centrosome is an unusual organelle that lacks a surrounding membrane, raising the question of what limits its size and shape. Moreover, while electron microscopy (EM) has provided a detailed view of centriole architecture, there has been limited understanding of how the second major component of centrosomes, the pericentriolar material (PCM), is organized. Here, we summarize exciting recent findings from super-resolution fluorescence imaging, structural biology, and biochemical reconstitution that together reveal the presence of ordered layers and complex gel-like scaffolds in the PCM. Moreover, we discuss how this is leading to a better understanding of the process of microtubule nucleation, how alterations in PCM size are regulated in cycling and differentiated cells, and why mutations in PCM components lead to specific human pathologies.

Recent advances in pericentriolar material organization: ordered layers and scaffolding gels

PubMed Central

Fry, Andrew M.; Sampson, Josephina; Shak, Caroline; Shackleton, Sue

2017-01-01

The centrosome is an unusual organelle that lacks a surrounding membrane, raising the question of what limits its size and shape. Moreover, while electron microscopy (EM) has provided a detailed view of centriole architecture, there has been limited understanding of how the second major component of centrosomes, the pericentriolar material (PCM), is organized. Here, we summarize exciting recent findings from super-resolution fluorescence imaging, structural biology, and biochemical reconstitution that together reveal the presence of ordered layers and complex gel-like scaffolds in the PCM. Moreover, we discuss how this is leading to a better understanding of the process of microtubule nucleation, how alterations in PCM size are regulated in cycling and differentiated cells, and why mutations in PCM components lead to specific human pathologies. PMID:29026530

[Market-based medicine or patient-based medicine?].

PubMed

Justich, Pablo R

2015-04-01

The health care has evolved over the centuries from a theocentric model to a model centered on man, environment and society. The process of neoliberal globalization has changed the relationship between the components of the health system and population. The active participation of organizations such as the World Trade Organization, the International Monetary Fund and the World Bank by the techno-medical industrial complex tends to make the health care in a model focused on economy. This, impacts negatively on all components in the process of health care and have an adverse effect on the humanized care. The analysis of each sector in particular and their interactions shows the effects of this change. Alternatives are proposed for each sector to contribute to a model of care focused on the patient, their family and the social environment.

An integrated overview of spatiotemporal organization and regulation in mitosis in terms of the proteins in the functional supercomplexes.

PubMed

Zheng, Yueyuan; Guo, Junjie; Li, Xu; Xie, Yubin; Hou, Mingming; Fu, Xuyang; Dai, Shengkun; Diao, Rucheng; Miao, Yanyan; Ren, Jian

2014-01-01

Eukaryotic cells may divide via the critical cellular process of cell division/mitosis, resulting in two daughter cells with the same genetic information. A large number of dedicated proteins are involved in this process and spatiotemporally assembled into three distinct super-complex structures/organelles, including the centrosome/spindle pole body, kinetochore/centromere and cleavage furrow/midbody/bud neck, so as to precisely modulate the cell division/mitosis events of chromosome alignment, chromosome segregation and cytokinesis in an orderly fashion. In recent years, many efforts have been made to identify the protein components and architecture of these subcellular organelles, aiming to uncover the organelle assembly pathways, determine the molecular mechanisms underlying the organelle functions, and thereby provide new therapeutic strategies for a variety of diseases. However, the organelles are highly dynamic structures, making it difficult to identify the entire components. Here, we review the current knowledge of the identified protein components governing the organization and functioning of organelles, especially in human and yeast cells, and discuss the multi-localized protein components mediating the communication between organelles during cell division.

Branchial Cilia and Sperm Flagella Recruit Distinct Axonemal Components

PubMed Central

Konno, Alu; Shiba, Kogiku; Cai, Chunhua; Inaba, Kazuo

2015-01-01

Eukaryotic cilia and flagella have highly conserved 9 + 2 structures. They are functionally diverged to play cell-type-specific roles even in a multicellular organism. Although their structural components are therefore believed to be common, few studies have investigated the molecular diversity of the protein components of the cilia and flagella in a single organism. Here we carried out a proteomic analysis and compared protein components between branchial cilia and sperm flagella in a marine invertebrate chordate, Ciona intestinalis. Distinct feature of protein recruitment in branchial cilia and sperm flagella has been clarified; (1) Isoforms of α- and β-tubulins as well as those of actins are distinctly used in branchial cilia or sperm flagella. (2) Structural components, such as dynein docking complex, tektins and an outer dense fiber protein, are used differently by the cilia and flagella. (3) Sperm flagella are specialized for the cAMP- and Ca2+-dependent regulation of outer arm dynein and for energy metabolism by glycolytic enzymes. Our present study clearly demonstrates that flagellar or ciliary proteins are properly recruited according to their function and stability, despite their apparent structural resemblance and conservation. PMID:25962172

Molecular Mechanism of Active Zone Organization at Vertebrate Neuromuscular Junctions

PubMed Central

Nishimune, Hiroshi

2013-01-01

Organization of presynaptic active zones is essential for development, plasticity, and pathology of the nervous system. Recent studies indicate a trans-synaptic molecular mechanism that organizes the active zones by connecting the pre- and the postsynaptic specialization. The presynaptic component of this trans-synaptic mechanism is comprised of cytosolic active zone proteins bound to the cytosolic domains of voltage-dependent calcium channels (P/Q-, N-, and L-type) on the presynaptic membrane. The postsynaptic component of this mechanism is the synapse organizer (laminin β2) that is expressed by the postsynaptic cell and accumulates specifically on top of the postsynaptic specialization. The pre- and the postsynaptic components interact directly between the extracellular domains of calcium channels and laminin β2 to anchor the presynaptic protein complex in front of the postsynaptic specialization. Hence, the presynaptic calcium channel functions as a scaffolding protein for active zone organization and as an ion-conducting channel for synaptic transmission. In contrast to the requirement of calcium influx for synaptic transmission, the formation of the active zone does not require the calcium influx through the calcium channels. Importantly, the active zones of adult synapses are not stable structures and require maintenance for their integrity. Furthermore, aging or diseases of the central and peripheral nervous system impair the active zones. This review will focus on the molecular mechanisms that organize the presynaptic active zones and summarize recent findings at the neuromuscular junctions and other synapses. PMID:22135013

Multiple biological complex of alkaline extract of the leaves of Sasa senanensis Rehder.

PubMed

Sakagami, Hiroshi; Zhou, Li; Kawano, Michiyo; Thet, May Maw; Tanaka, Shoji; Machino, Mamoru; Amano, Shigeru; Kuroshita, Reina; Watanabe, Shigeru; Chu, Qing; Wang, Qin-Tao; Kanamoto, Taisei; Terakubo, Shigemi; Nakashima, Hideki; Sekine, Keisuke; Shirataki, Yoshiaki; Zhang, Chang-Hao; Uesawa, Yoshihiro; Mohri, Kiminori; Kitajima, Madoka; Oizumi, Hiroshi; Oizumi, Takaaki

2010-01-01

Previous studies have shown anti-inflammatory potential of alkaline extract of the leaves of Sasa senanensis Rehder (SE). The aim of the present study was to clarity the molecular entity of SE, using various fractionation methods. SE inhibited the production of nitric oxide (NO), but not tumour necrosis factor-α by lipopolysaccharide (LPS)-stimulated mouse macrophage-like cells. Lignin carbohydrate complex prepared from SE inhibited the NO production to a comparable extent with SE, whereas chlorophyllin was more active. On successive extraction with organic solvents, nearly 90% of SE components, including chlorophyllin, were recovered from the aqueous layer. Anti-HIV activity of SE was comparable with that of lignin-carbohydrate complex, and much higher than that of chlorophyllin and n-butanol extract fractions. The CYP3A inhibitory activity of SE was significantly lower than that of grapefruit juice and chlorophyllin. Oral administration of SE slightly reduced the number of oral bacteria. When SE was applied to HPLC, nearly 70% of SE components were eluted as a single peak. These data suggest that multiple components of SE may be associated with each other in the native state or after extraction with alkaline solution.

Carotenoids, versatile components of oxygenic photosynthesis.

PubMed

Domonkos, Ildikó; Kis, Mihály; Gombos, Zoltán; Ughy, Bettina

2013-10-01

Carotenoids (CARs) are a group of pigments that perform several important physiological functions in all kingdoms of living organisms. CARs serve as protective agents, which are essential structural components of photosynthetic complexes and membranes, and they play an important role in the light harvesting mechanism of photosynthesizing plants and cyanobacteria. The protection against reactive oxygen species, realized by quenching of singlet oxygen and the excited states of photosensitizing molecules, as well as by the scavenging of free radicals, is one of the main biological functions of CARs. X-ray crystallographic localization of CARs revealed that they are present at functionally and structurally important sites of both the PSI and PSII reaction centers. Characterization of a CAR-less cyanobacterial mutant revealed that while the absence of CARs prevents the formation of PSII complexes, it does not abolish the assembly and function of PSI. CAR molecules assist in the formation of protein subunits of the photosynthetic complexes by gluing together their protein components. In addition to their aforementioned indispensable functions, CARs have a substantial role in the formation and maintenance of proper cellular architecture, and potentially also in the protection of the translational machinery under stress conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

A Project Management Perspective on Student's Declarative Commitments to Goals Established within Asynchronous Communication

ERIC Educational Resources Information Center

Chiocchio, F.; Lafreniere, A.

2009-01-01

Teamwork and technology, even as people are seeing their increased use in organizations, are becoming important components of problem-based learning in academic settings. Yet, fostering computer-assisted teamwork is complex and time consuming. Knowing how and when to intervene would prove useful. This study draws from the field of project…

Engineering Bacteria to Catabolize the Carbonaceous Component of Sarin: Teaching E. coli to Eat Isopropanol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Margaret E.; Mukhopadhyay, Aindrila; Keasling, Jay D.

In this paper, we report an engineered strain of Escherichia coli that catabolizes the carbonaceous component of the extremely toxic chemical warfare agent sarin. Enzymatic decomposition of sarin generates isopropanol waste that, with this engineered strain, is then transformed into acetyl-CoA by enzymatic conversion with a key reaction performed by the acetone carboxylase complex (ACX). We engineered the heterologous expression of the ACX complex from Xanthobacter autotrophicus PY2 to match the naturally occurring subunit stoichiometry and purified the recombinant complex from E. coli for biochemical analysis. Incorporating this ACX complex and enzymes from diverse organisms, we introduced an isopropanol degradationmore » pathway in E. coli, optimized induction conditions, and decoupled enzyme expression to probe pathway bottlenecks. Our engineered E. coli consumed 65% of isopropanol compared to no-cell controls and was able to grow on isopropanol as a sole carbon source. Finally, in the process, reconstitution of this large ACX complex (370 kDa) in a system naïve to its structural and mechanistic requirements allowed us to study this otherwise cryptic enzyme in more detail than would have been possible in the less genetically tractable native Xanthobacter system.« less

Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains.

PubMed

Bücherl, Christoph A; Jarsch, Iris K; Schudoma, Christian; Segonzac, Cécile; Mbengue, Malick; Robatzek, Silke; MacLean, Daniel; Ott, Thomas; Zipfel, Cyril

2017-03-06

Cell surface receptors govern a multitude of signalling pathways in multicellular organisms. In plants, prominent examples are the receptor kinases FLS2 and BRI1, which activate immunity and steroid-mediated growth, respectively. Intriguingly, despite inducing distinct signalling outputs, both receptors employ common downstream signalling components, which exist in plasma membrane (PM)-localised protein complexes. An important question is thus how these receptor complexes maintain signalling specificity. Live-cell imaging revealed that FLS2 and BRI1 form PM nanoclusters. Using single-particle tracking we could discriminate both cluster populations and we observed spatiotemporal separation between immune and growth signalling platforms. This finding was confirmed by visualising FLS2 and BRI1 within distinct PM nanodomains marked by specific remorin proteins and differential co-localisation with the cytoskeleton. Our results thus suggest that signalling specificity between these pathways may be explained by the spatial separation of FLS2 and BRI1 with their associated signalling components within dedicated PM nanodomains.

Photophysical properties of [Ru(2,2′-bipyridine){sub 3}]{sup 2+} encapsulated within the Uio-66 zirconium based metal organic framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larsen, Randy W., E-mail: rwlarsen@usf.edu; Wojtas, Lukasz

2017-03-15

The ability to encapsulate photo-active guest molecules within the pores of metal organic frameworks (MOFs) affords the opportunity to develop robust photocatalysts as well as solar energy conversion systems. An important criteria for such systems is stability of the new materials towards moisture, high temperatures, etc which preclude the use of many MOF frameworks. Here, the ability to encapsulate [Ru(II)(2,2′-bipyridine){sub 3}]{sup 2+}([Ru(bpy){sub 3}]{sup 2+}) into the cavities of the zirconium based MOF Uio-66 as well as the photophysical properties of the complex are reported. The X-ray powder diffraction data of the orange Uio-66 powder are consistent with the formation ofmore » Uio-66 in the presence of [Ru(bpy){sub 3}]{sup 2+}. The steady state emission exhibits a significant bathochromic shift from 603 nm in ethanol to 610 nm in Uio-66. The corresponding emission decay of the encapsulated [Ru(bpy){sub 3}]{sup 2+} complex is biexponential with a fast component of 128 ns and a slower component of 1176 ns (20 deg C). The slow component is consistent with encapsulation of [Ru(bpy){sub 3}]{sup 2+} into cavities with restricted volume that prevents the population of a triplet ligand field transition that is anti-bonding with respect to the Ru-N bonds. The origin of the fast component is unclear but may involve interactions of the [Ru(bpy){sub 3}]{sup 2+} encapsulated within large cavities formed through missing ligand defect sites within the Uio-66 materials. Co-encapsulated quenchers contained within these larger cavities gives rise to the reduced lifetimes of the [Ru(bpy){sub 3}]{sup 2+} complexes. - Graphical abstract: One-pot synthesis of Ru(II)tris(2,2-bipyridine)@Uio-66 (left) and the effects of encapsulation on the excited state energy levels and decay pathways of the Ru(II)tris(2,2-bipyridine) complex (right).« less

[Regulation of the expression of coenzyme Q-synthesis complex during ageing].

PubMed

Campos-Silva, Carmen; Reyes-Torres, Iván; Rivera, Maximiliano; Meza-Torres, Catherine; Hernández-Camacho, Juan Diego; Rodríguez-Bies, Elisabet; Navas, Plácido; López-Lluch, Guillermo

Coenzyme Q is an essential component in the activity of the mitochondrial electron transport chain. Its synthesis involves, at least, a complex of ten different proteins. In this study, an attempt is made to determine the evolution of the expression of the genes involved in coenzyme Q synthesis during mouse ageing. The messenger RNA (mRNA) of different organs, such as brain, liver, kidney and skeletal muscle from young (8 months), mature (18 months), and old (24 months) mice was extracted by using Trizol and was then analysed by real time PCR (qPCR) using specific primers for all the known components of the coenzyme Q-synthesis complex (COQ genes). Liver showed the highest age-dependent changes in mRNA levels of the different components of Q-synthesis complex, affecting the extent of the variation as well as the significance of the change. In most of the cases, mRNA levels of the different components were higher in mature animals compared to young and old animals. When mRNAs of young and old animals were compared, only minor reductions of mRNA levels were found. Kidney showed a pattern similar to that found in liver as regards the changes in expression, although with lower increases in mature animals than those observed in the liver. Brain and skeletal muscle showed low variations, with muscle being the tissue with less changes, although a pattern similar to that found in liver and kidney was found, with slight increases in mature animals. The results of this study indicate that ageing is an important factor affecting COQ gene expression, but its effect depends on the organ, and that mature animals show higher levels of mRNA than young and old animals. Taken into consideration the importance of coenzyme Q in cell metabolism and ageing, a more detailed study is needed to understand the gene regulation of the coenzyme Q-synthesis mechanisms during ageing. Copyright © 2017 SEGG. Publicado por Elsevier España, S.L.U. All rights reserved.

Heterogeneous Monolithic Integration of Single-Crystal Organic Materials.

PubMed

Park, Kyung Sun; Baek, Jangmi; Park, Yoonkyung; Lee, Lynn; Hyon, Jinho; Koo Lee, Yong-Eun; Shrestha, Nabeen K; Kang, Youngjong; Sung, Myung Mo

2017-02-01

Manufacturing high-performance organic electronic circuits requires the effective heterogeneous integration of different nanoscale organic materials with uniform morphology and high crystallinity in a desired arrangement. In particular, the development of high-performance organic electronic and optoelectronic devices relies on high-quality single crystals that show optimal intrinsic charge-transport properties and electrical performance. Moreover, the heterogeneous integration of organic materials on a single substrate in a monolithic way is highly demanded for the production of fundamental organic electronic components as well as complex integrated circuits. Many of the various methods that have been designed to pattern multiple heterogeneous organic materials on a substrate and the heterogeneous integration of organic single crystals with their crystal growth are described here. Critical issues that have been encountered in the development of high-performance organic integrated electronics are also addressed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cardiolipin synthesizing enzymes form a complex that interacts with cardiolipin-dependent membrane organizing proteins.

PubMed

Serricchio, Mauro; Vissa, Adriano; Kim, Peter K; Yip, Christopher M; McQuibban, G Angus

2018-04-01

The mitochondrial glycerophospholipid cardiolipin plays important roles in mitochondrial biology. Most notably, cardiolipin directly binds to mitochondrial proteins and helps assemble and stabilize mitochondrial multi-protein complexes. Despite their importance for mitochondrial health, how the proteins involved in cardiolipin biosynthesis are organized and embedded in mitochondrial membranes has not been investigated in detail. Here we show that human PGS1 and CLS1 are constituents of large protein complexes. We show that PGS1 forms oligomers and associates with CLS1 and PTPMT1. Using super-resolution microscopy, we observed well-organized nanoscale structures formed by PGS1. Together with the observation that cardiolipin and CLS1 are not required for PGS1 to assemble in the complex we predict the presence of a PGS1-centered cardiolipin-synthesizing scaffold within the mitochondrial inner membrane. Using an unbiased proteomic approach we found that PGS1 and CLS1 interact with multiple cardiolipin-binding mitochondrial membrane proteins, including prohibitins, stomatin-like protein 2 and the MICOS components MIC60 and MIC19. We further mapped the protein-protein interaction sites between PGS1 and itself, CLS1, MIC60 and PHB. Overall, this study provides evidence for the presence of a cardiolipin synthesis structure that transiently interacts with cardiolipin-dependent protein complexes. Copyright © 2018 Elsevier B.V. All rights reserved.

In situ localization of nucleolin in the plant nucleolar matrix.

PubMed

Minguez, A; Moreno Diaz de la Espina, S

1996-01-10

The analysis of isolated nucleolar matrices from onion cells by light and electron microscopy, 2-D separation of proteins, and confocal microscopy has confirmed the existence of an organized nucleolar matrix with a complex protein composition to which are attached the insoluble processing complexes. In the present work, we present evidence from immunoblotting, immunofluorescence, immunogold labeling, and preferential cytochemical staining with bismuth salts that an insoluble fraction of the multifunctional protein nucleolin, is a component of the onion nucleolar matrix, and analyse its ultrastructural distribution in the described domains of the matrix.

Structural biological composites: An overview

NASA Astrophysics Data System (ADS)

Meyers, Marc A.; Lin, Albert Y. M.; Seki, Yasuaki; Chen, Po-Yu; Kad, Bimal K.; Bodde, Sara

2006-07-01

Biological materials are complex composites that are hierarchically structured and multifunctional. Their mechanical properties are often outstanding, considering the weak constituents from which they are assembled. They are for the most part composed of brittle (often, mineral) and ductile (organic) components. These complex structures, which have risen from millions of years of evolution, are inspiring materials scientists in the design of novel materials. This paper discusses the overall design principles in biological structural composites and illustrates them for five examples; sea spicules, the abalone shell, the conch shell, the toucan and hornbill beaks, and the sheep crab exoskeleton.

The role of the proline-rich domain of Ssdp1 in the modular architecture of the vertebrate head organizer

PubMed Central

Enkhmandakh, Badam; Makeyev, Alexandr V.; Bayarsaihan, Dashzeveg

2006-01-01

Lim1, Ssdp1, and Ldb1 proteins are components of the Ldb1-associated transcriptional complex, which is important in the head-organizing activity during early mouse development. Depletion of each individual protein alone causes a headless phenotype. To explore in more detail the modular architecture of the complex, we have generated two different gene-trapped mouse lines that express truncated forms of Ssdp1. Embryos derived from the gene-trapped line that encodes a truncated Ssdp1 lacking the proline-rich sequence exhibit a lethal abnormal head-development phenotype, resembling mouse embryos deficient for Lim1, Ssdp1, or Otx2 genes. Embryos derived from the second gene-trapped line, in which most of the proline-rich domain of Ssdp1 is retained, did not show abnormalities in head development. Our data demonstrate that components of the Ldb1-dependent module can be subdivided further into discrete functional domains and that the proline-rich stretch of Ssdp1 is critical for embryonic head development. Furthermore, phylogenetic comparisons revealed that in Caenorhabditis elegans, a similar proline-rich sequence is absent in Ssdp but present in Ldb1. We conclude that although the overall architecture of the Ldb1-dependent module has been preserved, the genetic specification of its individual components has diversified during evolution, without compromising the function of the module. PMID:16864769

The role of the proline-rich domain of Ssdp1 in the modular architecture of the vertebrate head organizer.

PubMed

Enkhmandakh, Badam; Makeyev, Alexandr V; Bayarsaihan, Dashzeveg

2006-08-01

Lim1, Ssdp1, and Ldb1 proteins are components of the Ldb1-associated transcriptional complex, which is important in the head-organizing activity during early mouse development. Depletion of each individual protein alone causes a headless phenotype. To explore in more detail the modular architecture of the complex, we have generated two different gene-trapped mouse lines that express truncated forms of Ssdp1. Embryos derived from the gene-trapped line that encodes a truncated Ssdp1 lacking the proline-rich sequence exhibit a lethal abnormal head-development phenotype, resembling mouse embryos deficient for Lim1, Ssdp1, or Otx2 genes. Embryos derived from the second gene-trapped line, in which most of the proline-rich domain of Ssdp1 is retained, did not show abnormalities in head development. Our data demonstrate that components of the Ldb1-dependent module can be subdivided further into discrete functional domains and that the proline-rich stretch of Ssdp1 is critical for embryonic head development. Furthermore, phylogenetic comparisons revealed that in Caenorhabditis elegans, a similar proline-rich sequence is absent in Ssdp but present in Ldb1. We conclude that although the overall architecture of the Ldb1-dependent module has been preserved, the genetic specification of its individual components has diversified during evolution, without compromising the function of the module.

Kibra functions as a tumor suppressor protein that regulates Hippo signaling in conjunction with Merlin and Expanded

PubMed Central

Yu, Jianzhong; Zheng, Yonggang; Dong, Jixin; Klusza, Stephen; Deng, Wu-Min; Pan, Duojia

2010-01-01

Summary The Hippo signaling pathway regulates organ size and tissue homeostasis from Drosophila to mammals. Central to this pathway is a kinase cascade wherein Hippo (Hpo), in complex with Salvador (Sav), phosphorylates and activates Warts (Wts), which in turn phosphorylates and inactivates the Yorkie (Yki) oncoprotein, known as the YAP coactivator in mammalian cells. The FERM domain proteins Merlin (Mer) and Expanded (Ex) are upstream components that regulate Hpo activity through unknown mechanisms. Here we identify Kibra (Kbr) as another upstream component of the Hippo signaling pathway. We show that Kbr functions together with Mer and Ex in a protein complex localized to the apical domain of epithelial cells, and that this protein complex regulates the Hippo kinase cascade via direct binding to Hpo and Sav. These results shed light on the mechanism of Ex and Mer function, and implicate Kbr as a potential tumor suppressor with relevance to neurofibromatosis. PMID:20159598

Origins of chemoreceptor curvature sorting in Escherichia coli

PubMed Central

Draper, Will; Liphardt, Jan

2017-01-01

Bacterial chemoreceptors organize into large clusters at the cell poles. Despite a wealth of structural and biochemical information on the system's components, it is not clear how chemoreceptor clusters are reliably targeted to the cell pole. Here, we quantify the curvature-dependent localization of chemoreceptors in live cells by artificially deforming growing cells of Escherichia coli in curved agar microchambers, and find that chemoreceptor cluster localization is highly sensitive to membrane curvature. Through analysis of multiple mutants, we conclude that curvature sensitivity is intrinsic to chemoreceptor trimers-of-dimers, and results from conformational entropy within the trimer-of-dimers geometry. We use the principles of the conformational entropy model to engineer curvature sensitivity into a series of multi-component synthetic protein complexes. When expressed in E. coli, the synthetic complexes form large polar clusters, and a complex with inverted geometry avoids the cell poles. This demonstrates the successful rational design of both polar and anti-polar clustering, and provides a synthetic platform on which to build new systems. PMID:28322223

Learning the organization: a model for health system analysis for new nurse administrators.

PubMed

Clark, Mary Jo

2004-01-01

Health systems are large and complex organizations in which multiple components and processes influence system outcomes. In order to effectively position themselves in such organizations, nurse administrators new to a system must gain a rapid understanding of overall system operation. Such understanding is facilitated by use of a model for system analysis. The model presented here examines the dynamic interrelationships between and among internal and external elements as they affect system performance. External elements to be analyzed include environmental factors and characteristics of system clientele. Internal elements flow from the mission and goals of the system and include system culture, services, resources, and outcomes.

Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.

PubMed

Sankar, Punnaivanam; Aghila, Gnanasekaran

2007-01-01

The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

Gene Fusion: A Genome Wide Survey

NASA Technical Reports Server (NTRS)

Liang, Ping; Riley, Monica

2001-01-01

As a well known fact, organisms form larger and complex multimodular (composite or chimeric) and mostly multi-functional proteins through gene fusion of two or more individual genes which have independent evolution histories and functions. We call each of these components a module. The existence of multimodular proteins may improves the efficiency in gene regulation and in cellular functions, and thus may give the host organism advantages in adaptation to environments. Analysis of all gene fusions in present-day organisms should allow us to examine the patterns of gene fusion in context with cellular functions, to trace back the evolution processes from the ancient smaller and uni-functional proteins to the present-day larger and complex multi-functional proteins, and to estimate the minimal number of ancestor proteins that existed in the last common ancestor for all life on earth. Although many multimodular proteins have been experimentally known, identification of gene fusion events systematically at genome scale had not been possible until recently when large number of completed genome sequences have been becoming available. In addition, technical difficulties for such analysis also exist due to the complexity of this biological and evolutionary process. We report from this study a new strategy to computationally identify multimodular proteins using completed genome sequences and the results surveyed from 22 organisms with the data from over 40 organisms to be presented during the meeting. Additional information is contained in the original extended abstract.

A gatekeeper chaperone complex directs translocator secretion during Type Three Secretion

DOE PAGES

Archuleta, Tara L.; Spiller, Benjamin W.; Kubori, Tomoko

2014-11-06

Many Gram-negative bacteria use Type Three Secretion Systems (T3SS) to deliver effector proteins into host cells. These protein delivery machines are composed of cytosolic components that recognize substrates and generate the force needed for translocation, the secretion conduit, formed by a needle complex and associated membrane spanning basal body, and translocators that form the pore in the target cell. A defined order of secretion in which needle component proteins are secreted first, followed by translocators, and finally effectors, is necessary for this system to be effective. While the secreted effectors vary significantly between organisms, the ~20 individual protein components thatmore » form the T3SS are conserved in many pathogenic bacteria. One such conserved protein, referred to as either a plug or gatekeeper, is necessary to prevent unregulated effector release and to allow efficient translocator secretion. The mechanism by which translocator secretion is promoted while effector release is inhibited by gatekeepers is unknown. We present the structure of the Chlamydial gatekeeper, CopN, bound to a translocator-specific chaperone. The structure identifies a previously unknown interface between gatekeepers and translocator chaperones and reveals that in the gatekeeper-chaperone complex the canonical translocator-binding groove is free to bind translocators. Thus, structure-based mutagenesis of the homologous complex in Shigella reveals that the gatekeeper-chaperone-translocator complex is essential for translocator secretion and for the ordered secretion of translocators prior to effectors.« less

Thermodynamics of complex structures formed between single-stranded DNA oligomers and the KH domains of the far upstream element binding protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chakraborty, Kaushik; Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in

The noncovalent interaction between protein and DNA is responsible for regulating the genetic activities in living organisms. The most critical issue in this problem is to understand the underlying driving force for the formation and stability of the complex. To address this issue, we have performed atomistic molecular dynamics simulations of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein (FBP) complexed with two single-stranded DNA (ss-DNA) oligomers in aqueous media. Attempts have been made to calculate the individual components of the net entropy change for the complexation process by adopting suitablemore » statistical mechanical approaches. Our calculations reveal that translational, rotational, and configurational entropy changes of the protein and the DNA components have unfavourable contributions for this protein-DNA association process and such entropy lost is compensated by the entropy gained due to the release of hydration layer water molecules. The free energy change corresponding to the association process has also been calculated using the Free Energy Perturbation (FEP) method. The free energy gain associated with the KH4–DNA complex formation has been found to be noticeably higher than that involving the formation of the KH3–DNA complex.« less

Surface complexation modeling of Cd(II) sorption to montmorillonite, bacteria, and their composite

NASA Astrophysics Data System (ADS)

Wang, Ning; Du, Huihui; Huang, Qiaoyun; Cai, Peng; Rong, Xingmin; Feng, Xionghan; Chen, Wenli

2016-10-01

Surface complexation modeling (SCM) has emerged as a powerful tool for simulating heavy metal adsorption processes on the surface of soil solid components under different geochemical conditions. The component additivity (CA) approach is one of the strategies that have been widely used in multicomponent systems. In this study, potentiometric titration, isothermal adsorption, zeta potential measurement, and extended X-ray absorption fine-structure (EXAFS) spectra analysis were conducted to investigate Cd adsorption on 2 : 1 clay mineral montmorillonite, on Gram-positive bacteria Bacillus subtilis, and their mineral-organic composite. We developed constant capacitance models of Cd adsorption on montmorillonite, bacterial cells, and mineral-organic composite. The adsorption behavior of Cd on the surface of the composite was well explained by CA-SCM. Some deviations were observed from the model simulations at pH < 5, where the values predicted by the model were lower than the experimental results. The Cd complexes of X2Cd, SOCd+, R-COOCd+, and R-POCd+ were the predominant species on the composite surface over the pH range of 3 to 8. The distribution ratio of the adsorbed Cd between montmorillonite and bacterial fractions in the composite as predicted by CA-SCM closely coincided with the estimated value of EXAFS at pH 6. The model could be useful for the prediction of heavy metal distribution at the interface of multicomponents and their risk evaluation in soils and associated environments.

Precerebellar and vestibular nuclei of the short-beaked echidna (Tachyglossus aculeatus).

PubMed

Ashwell, K W S; Paxinos, G; Watson, C R R

2007-09-01

The monotremes are a unique group of living mammals, which diverged from the line leading to placental mammals at least 125 million years ago. We have examined the organization of pontine, inferior olivary, lateral reticular and vestibular nuclei in the brainstem of the short-beaked echidna (Tachyglossus aculeatus) to determine if the cyto- and chemoarchitecture of these nuclei are similar to that in placental mammals and marsupials. We have used Nissl staining in conjunction with enzyme-histochemistry for acetylcholinesterase, cytochrome oxidase and NADPH diaphorase as well as immunohistochemistry for non-phosphorylated neurofilament protein (SMI-32 antibody) and calcium binding proteins (parvalbumin, calbindin, calretinin). Homologies could be established between the arch shaped inferior olivary complex of the echidna and the principal, dorsal and medial accessory subdivisions of the therian inferior olivary complex. The pontine nuclei of the echidna included basilar and reticulotegmental components with similar cyto- and chemarchitectural features to therians and there were magnocellular and subtrigeminal components of the lateral reticular nucleus, also as seen in therians. Subdivisions and chemoarchitecture of the vestibular complex of the echidna were both similar to that region in rodents. In all three precerebellar nuclear groups studied and in the vestibular nucleus organization, the cyto- and chemoarchitecture of the echidna was very similar to that seen in therian mammals and no "primitive" or "reptilian" features were evident.

Fabrication of micromechanical and microoptical systems by two-photon polymerization

NASA Astrophysics Data System (ADS)

Reinhardt, Carsten; Ovsianikov, A.; Passinger, Sven; Chichkov, Boris N.

2007-01-01

The recently developed two-photon polymerisation technique is used for the fabrication of two- and three-dimensional structures in photosensitive inorganic-organic hybrid material (ORMOCER), in SU8 , and in positive tone resist with resolutions down to 100nm. In this contribution we present applications of this powerful technology for the realization of micromechanical systems and microoptical components. We will demonstrate results on the fabrication of complex movable three-dimensional micromechanical systems and microfluidic components which cannot be realized by other technologies. This approach of structuring photosensitive materials also provides unique possibilities for the fabrication of different microoptical components such as arbitrary shaped microlenses, microprisms, and 3D-photonic crystals with high optical quality.

Spatial Associations and Chemical Composition of Organic Carbon Sequestered in Fe, Ca, and Organic Carbon Ternary Systems.

PubMed

Sowers, Tyler D; Adhikari, Dinesh; Wang, Jian; Yang, Yu; Sparks, Donald L

2018-05-25

Organo-mineral associations of organic carbon (OC) with iron (Fe) oxides play a major role in environmental OC sequestration, a process crucial to mitigating climate change. Calcium has been found to have high coassociation with OC in soils containing high Fe content, increase OC sorption extent to poorly crystalline Fe oxides, and has long been suspected to form bridging complexes with Fe and OC. Due to the growing realization that Ca may be an important component of C cycling, we launched a scanning transmission X-ray microscopy (STXM) investigation, paired with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, in order to spatially resolve Fe, Ca, and OC relationships and probe the effect of Ca on sorbed OC speciation. We performed STXM-NEXAFS analysis on 2-line ferrihydrite reacted with leaf litter-extractable dissolved OC and citric acid in the absence and presence of Ca. Organic carbon was found to highly associate with Ca ( R 2 = 0.91). Carboxylic acid moieties were dominantly sequestered; however, Ca facilitated the additional sequestration of aromatic and phenolic moieties. Also, C NEXAFS revealed polyvalent metal ion complexation. Our results provide evidence for the presence of Fe-Ca-OC ternary complexation, which has the potential to significantly impact how organo-mineral associations are modeled.

Molecular Analyzer for Complex Refractory Organic-Rich Surfaces (MACROS)

NASA Technical Reports Server (NTRS)

Getty, Stephanie A.; Cook, Jamie E.; Balvin, Manuel; Brinckerhoff, William B.; Li, Xiang; Grubisic, Andrej; Cornish, Timothy; Ferrance, Jerome; Southard, Adrian

2017-01-01

The Molecular Analyzer for Complex Refractory Organic-rich Surfaces, MACROS, is a novel instrument package being developed at NASA Goddard Space Flight Center. MACROS enables the in situ characterization of a sample's composition by coupling two powerful techniques into one compact instrument package: (1) laser desorption/ionization time-of-flight mass spectrometry (LDMS) for broad detection of inorganic mineral composition and non-volatile organics, and (2) liquid-phase extraction methods to gently isolate the soluble organic and inorganic fraction of a planetary powder for enrichment and detailed analysis by liquid chromatographic separation coupled to LDMS. The LDMS is capable of positive and negative ion detection, precision mass selection, and fragment analysis. Two modes are included for LDMS: single laser LDMS as the broad survey mode and two step laser mass spectrometry (L2MS). The liquid-phase extraction will be done in a newly designed extraction module (EM) prototype, providing selectivity in the analysis of a complex sample. For the sample collection, a diamond drill front end will be used to collect rock/icy powder. With all these components and capabilities together, MACROS offers a versatile analytical instrument for a mission targeting an icy moon, carbonaceous asteroid, or comet, to fully characterize the surface composition and advance our understanding of the chemical inventory present on that body.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simoneit, B.R.T.; Radzi bin Abas, M.; Cass, G.R.

Biomass combustion is an important primary source of carbonaceous particles in the global atmosphere. Various molecular markers have been proposed for this process but additional specific tracers are needed. The injection of natural product organic compounds into smoke occurs primarily by direct volatilization/steam stripping and by pyrolysis. Although the composition of organic matter in smoke particles is highly variable, the molecular structures of the tracers are generally source specific. Homologous compounds and biomarkers present in smoke are derived directly from plant wax, gum and resin by volatilization and secondarily from pyrolysis of biopolymers (e.g., lignin, cutin, suberin), wax, gum andmore » resin. The component complexity is illustrated with examples from controlled bums of temperate and tropical biomass fuels. Conifer smoke contains characteristic tracers from diterpenoids as well as phenolics and other oxygenated species. These are recognizable in urban airsheds. The major organic components of smoke from tropical biomass are straight-chain, aliphatic and oxygenated compounds and triterpenoids. Several compounds are potential key indicators for combustion of such biomass. The precursor to product approach of organic geochemistry can be applied successfully to provide molecular tracers for studying smoke plume chemistry and dispersion.« less

Regulation of flower development in Arabidopsis by SCF complexes.

PubMed

Ni, Weimin; Xie, Daoxin; Hobbie, Lawrence; Feng, Baomin; Zhao, Dazhong; Akkara, Joseph; Ma, Hong

2004-04-01

SCF complexes are the largest and best studied family of E3 ubiquitin protein ligases that facilitate the ubiquitylation of proteins targeted for degradation. The SCF core components Skp1, Cul1, and Rbx1 serve in multiple SCF complexes involving different substrate-specific F-box proteins that are involved in diverse processes including cell cycle and development. In Arabidopsis, mutations in the F-box gene UNUSUAL FLORAL ORGANS (UFO) result in a number of defects in flower development. However, functions of the core components Cul1 and Rbx1 in flower development are poorly understood. In this study we analyzed floral phenotypes caused by altering function of Cul1 or Rbx1, as well as the effects of mutations in ASK1 and ASK2. Plants homozygous for a point mutation in the AtCUL1 gene showed reduced floral organ number and several defects in each of the four whorls. Similarly, plants with reduced AtRbx1 expression due to RNA interference also exhibited floral morphological defects. In addition, compared to the ask1 mutant, plants homozygous for ask1 and heterozygous for ask2 displayed enhanced reduction of B function, as well as other novel defects of flower development, including carpelloid sepals and an inhibition of petal development. Genetic analyses demonstrate that AGAMOUS (AG) is required for the novel phenotypes observed in the first and second whorls. Furthermore, the genetic interaction between UFO and AtCUL1 supports the idea that UFO regulates multiple aspects of flower development as a part of SCF complexes. These results suggest that SCF complexes regulate several aspects of floral development in Arabidopsis.

Decision support systems and the healthcare strategic planning process: a case study.

PubMed

Lundquist, D L; Norris, R M

1991-01-01

The repertoire of applications that comprises health-care decision support systems (DSS) includes analyses of clinical, financial, and operational activities. As a whole, these applications facilitate developing comprehensive and interrelated business and medical models that support the complex decisions required to successfully manage today's health-care organizations. Kennestone Regional Health Care System's use of DSS to facilitate strategic planning has precipitated marked changes in the organization's method of determining capital allocations. This case study discusses Kennestone's use of DSS in the strategic planning process, including profiles of key DSS modeling components.

Molecular Studies of Complex Soil Organic Matter Interactions with Metal Ions and Mineral Surfaces using Classical Molecular Dynamics and Quantum Chemistry Methods

NASA Astrophysics Data System (ADS)

Andersen, A.; Govind, N.; Laskin, A.

2017-12-01

Mineral surfaces have been implicated as potential protectors of soil organic matter (SOM) against decomposition and ultimate mineralization to small molecules which can provide nutrients for plants and soil microbes and can also contribute to the Earth's elemental cycles. SOM is a complex mixture of organic molecules of biological origin at varying degrees of decomposition and can, itself, self-assemble in such a way as to expose some biomolecule types to biotic and abiotic attack while protecting other biomolecule types. The organization of SOM and SOM with mineral surfaces and solvated metal ions is driven by an interplay of van der Waals and electrostatic interactions leading to partitioning of hydrophilic (e.g. sugars) and hydrophobic (e.g., lipids) SOM components that can be bridged with amphiphilic molecules (e.g., proteins). Classical molecular dynamics simulations can shed light on assemblies of organic molecules alone or complexation with mineral surfaces. The role of chemical reactions is also an important consideration in potential chemical changes of the organic species such as oxidation/reduction, degradation, chemisorption to mineral surfaces, and complexation with solvated metal ions to form organometallic systems. For the study of chemical reactivity, quantum chemistry methods can be employed and combined with structural insight provided by classical MD simulations. Moreover, quantum chemistry can also simulate spectroscopic signatures based on chemical structure and is a valuable tool in interpreting spectra from, notably, x-ray absorption spectroscopy (XAS). In this presentation, we will discuss our classical MD and quantum chemistry findings on a model SOM system interacting with mineral surfaces and solvated metal ions.

Similarities between GCS and human motor cortex: complex movement coordination

NASA Astrophysics Data System (ADS)

Rodríguez, Jose A.; Macias, Rosa; Molgo, Jordi; Guerra, Dailos

2014-07-01

The "Gran Telescopio de Canarias" (GTC1) is an optical-infrared 10-meter segmented mirror telescope at the ORM observatory in Canary Islands (Spain). The GTC control system (GCS), the brain of the telescope, is is a distributed object & component oriented system based on RT-CORBA and it is responsible for the management and operation of the telescope, including its instrumentation. On the other hand, the Human motor cortex (HMC) is a region of the cerebrum responsible for the coordination of planning, control, and executing voluntary movements. If we analyze both systems, as far as the movement control of their mechanisms and body parts is concerned, we can find extraordinary similarities in their architectures. Both are structured in layers, and their functionalities are comparable from the movement conception until the movement action itself: In the GCS we can enumerate the Sequencer high level components, the Coordination libraries, the Control Kit library and the Device Driver library as the subsystems involved in the telescope movement control. If we look at the motor cortex, we can also enumerate the primary motor cortex, the secondary motor cortices, which include the posterior parietal cortex, the premotor cortex, and the supplementary motor area (SMA), the motor units, the sensory organs and the basal ganglia. From all these components/areas we will analyze in depth the several subcortical regions, of the the motor cortex, that are involved in organizing motor programs for complex movements and the GCS coordination framework, which is composed by a set of classes that allow to the high level components to transparently control a group of mechanisms simultaneously.

Molecular Analysis of Core Kinetochore Composition and Assembly in Drosophila melanogaster

PubMed Central

Przewloka, Marcin R.; Archambault, Vincent; D'Avino, Pier Paolo; Lilley, Kathryn S.; Laue, Ernest D.; McAinsh, Andrew D.; Glover, David M.

2007-01-01

Background Kinetochores are large multiprotein complexes indispensable for proper chromosome segregation. Although Drosophila is a classical model organism for studies of chromosome segregation, little is known about the organization of its kinetochores. Methodology/Principal Findings We employed bioinformatics, proteomics and cell biology methods to identify and analyze the interaction network of Drosophila kinetochore proteins. We have shown that three Drosophila proteins highly diverged from human and yeast Ndc80, Nuf2 and Mis12 are indeed their orthologues. Affinity purification of these proteins from cultured Drosophila cells identified a further five interacting proteins with weak similarity to subunits of the SPC105/KNL-1, MIND/MIS12 and NDC80 kinetochore complexes together with known kinetochore associated proteins such as dynein/dynactin, spindle assembly checkpoint components and heterochromatin proteins. All eight kinetochore complex proteins were present at the kinetochore during mitosis and MIND/MIS12 complex proteins were also centromeric during interphase. Their down-regulation led to dramatic defects in chromosome congression/segregation frequently accompanied by mitotic spindle elongation. The systematic depletion of each individual protein allowed us to establish dependency relationships for their recruitment onto the kinetochore. This revealed the sequential recruitment of individual members of first, the MIND/MIS12 and then, NDC80 complex. Conclusions/Significance The Drosophila MIND/MIS12 and NDC80 complexes and the Spc105 protein, like their counterparts from other eukaryotic species, are essential for chromosome congression and segregation, but are highly diverged in sequence. Hierarchical dependence relationships of individual proteins regulate the assembly of Drosophila kinetochore complexes in a manner similar, but not identical, to other organisms. PMID:17534428

Carbon in the Universe

NASA Technical Reports Server (NTRS)

Allamandola, Louis J.

2013-01-01

Over the past few decades, NASA missions have revealed that we live in a Universe that is not a hydrogen-dominated, physicist's paradise, but in a molecular Universe with complex molecules directly interwoven into its fabric. These missions have shown that molecules are an abundant and important component of astronomical objects at all stages of their evolution and that they play a key role in many processes that dominate the structure and evolution of galaxies. Closer to home in our galaxy, the Milky Way, they have revealed a unique and complex organic inventory of regions of star and planet formation that may well represent some of the prebiotic roots to life. Astrobiology emerges from the great interest in understanding astrochemical evolution from simple to complex molecules, especially those with biogenic potential and the roles they may play as primordial seeds in the origin of life on habitable worlds. The first part of this talk will highlight how infrared spectroscopic studies of interstellar space, combined with dedicated laboratory simulations, have revealed the widespread presence of complex organics across deep space. The remainder of the presentation will focus on the evolution of these materials and astrobiology.

Yeast silencing factor Sir4 and a subset of nucleoporins form a complex distinct from nuclear pore complexes

PubMed Central

Ptak, Christopher; Roesner, Ulyss K.

2017-01-01

Interactions occurring at the nuclear envelope (NE)–chromatin interface influence both NE structure and chromatin organization. Insights into the functions of NE–chromatin interactions have come from the study of yeast subtelomeric chromatin and its association with the NE, including the identification of various proteins necessary for tethering subtelomeric chromatin to the NE and the silencing of resident genes. Here we show that four of these proteins—the silencing factor Sir4, NE-associated Esc1, the SUMO E3 ligase Siz2, and the nuclear pore complex (NPC) protein Nup170—physically and functionally interact with one another and a subset of NPC components (nucleoporins or Nups). Importantly, this group of Nups is largely restricted to members of the inner and outer NPC rings, but it lacks numerous others including cytoplasmically and nucleoplasmically positioned Nups. We propose that this Sir4-associated Nup complex is distinct from holo-NPCs and that it plays a role in subtelomeric chromatin organization and NE tethering. PMID:28883038

Yeast silencing factor Sir4 and a subset of nucleoporins form a complex distinct from nuclear pore complexes.

PubMed

Lapetina, Diego L; Ptak, Christopher; Roesner, Ulyss K; Wozniak, Richard W

2017-10-02

Interactions occurring at the nuclear envelope (NE)-chromatin interface influence both NE structure and chromatin organization. Insights into the functions of NE-chromatin interactions have come from the study of yeast subtelomeric chromatin and its association with the NE, including the identification of various proteins necessary for tethering subtelomeric chromatin to the NE and the silencing of resident genes. Here we show that four of these proteins-the silencing factor Sir4, NE-associated Esc1, the SUMO E3 ligase Siz2, and the nuclear pore complex (NPC) protein Nup170-physically and functionally interact with one another and a subset of NPC components (nucleoporins or Nups). Importantly, this group of Nups is largely restricted to members of the inner and outer NPC rings, but it lacks numerous others including cytoplasmically and nucleoplasmically positioned Nups. We propose that this Sir4-associated Nup complex is distinct from holo-NPCs and that it plays a role in subtelomeric chromatin organization and NE tethering. © 2017 Lapetina et al.

Parents' perspectives on caring for children after solid organ transplant.

PubMed

Lerret, Stacee M; Johnson, Norah L; Haglund, Kristin A

2017-07-01

To explore parents' experiences of the transition from hospital to home and complex chronic illness management following their children's solid organ transplant (SOT). Qualitative component of a larger mixed methods longitudinal study. Parents of SOT recipients were interviewed three times following hospital discharge from five major pediatric transplant hospitals in the United States. Analysis of parent interviews (N = 48) resulted in three themes that characterized the phases of transition to home and complex chronic illness care. Three themes, corresponding to the three time periods of data collection, included "getting back to normal" at 3 weeks, "becoming routine" at 3 months, and "facing a future" at 6 months. Challenges families experienced over the course of their transition are also described. The transition from hospital to home and complex chronic condition care is challenging and changes over time. Nurses are called upon to prepare parents to become knowledgeable and confident to care for the child after hospital discharge. Nurses can best support families in transition after SOT by anticipating and understanding their dynamic challenging complex care needs. © 2017 Wiley Periodicals, Inc.

Evaluation of rapid methods for in-situ characterization of organic contaminant load and biodegradation rates in winery wastewater.

PubMed

Carvallo, M J; Vargas, I; Vega, A; Pizarro, G; Pizarr, G; Pastén, P

2007-01-01

Rapid methods for the in-situ evaluation of the organic load have recently been developed and successfully implemented in municipal wastewater treatment systems. Their direct application to winery wastewater treatment is questionable due to substantial differences between municipal and winery wastewater. We critically evaluate the use of UV-VIS spectrometry, buffer capacity testing (BCT), and respirometry as rapid methods to determine organic load and biodegradation rates of winery wastewater. We tested three types of samples: actual and treated winery wastewater, synthetic winery wastewater, and samples from a biological batch reactor. Not surprisingly, respirometry gave a good estimation of biodegradation rates for substrate of different complexities, whereas UV-VIS and BCT did not provide a quantitative measure of the easily degradable sugars and ethanol, typically the main components of the COD in the influent. However, our results strongly suggest that UV-VIS and BCT can be used to identify and estimate the concentration of complex substrates in the influent and soluble microbial products (SMP) in biological reactors and their effluent. Furthermore, the integration of UV-VIS spectrometry, BCT, and mathematical modeling was able to differentiate between the two components of SMPs: substrate utilization associated products (UAP) and biomass associated products (BAP). Since the effluent COD in biologically treated wastewaters is composed primarily by SMPs, the quantitative information given by these techniques may be used for plant control and optimization.

Evaluation of PEMFC System Contaminants on the Performance of Pt Catalyst via Cyclic Voltammetry: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, H.; Macomber, C.; Dinh, H. N.

2012-07-01

Using electrochemical cyclic voltammetry as a quick ex-situ screening tool, the impact of the extracted solution and the individual leachable constituents from prospective BOP component materials on the performance and recoverability of the platinum catalyst were evaluated. Taking an extract from Zytel{trademark} HTN51G35HSLR (PPA) as an example, the major leachable organic components are caprolactam and 1,6 hexanediol. While these organic compounds by themselves do poison the Pt catalyst to some extent, such influence is mostly recoverable by means of potential holding and potential cycling. The extracted solution, however, shows a more drastic poisoning effect and it was not recoverable. Thereforemore » the non-recoverable poisoning effect observed for the extracted solution is not from the two organic species studied. This demonstrates the complexity of such a contaminant study. Inorganic compounds that are known poisons like sulfur even in very low concentrations, may have a more dominant effect on the Pt catalyst and the recoverability.« less

Methods of analysis for complex organic aerosol mixtures from urban emission sources of particulate carbon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mazurek, M.A.; Hildemann, L.M.; Cass, G.R.

1990-04-01

Extractable organic compounds having between 6 to 40 carbon atoms comprise an important mass fraction of the fine particulate matter samples from major urban emission sources. Depending on the emission source type, this solvent-soluble fraction accounts for <20% to 100% of the total organic aerosol mass, as measured by quantitative high-resolution has chromatography (HRGC) with flame ionization detection. In addition to total extract quantitation, HRGC can be applied to further analyses of the mass distributions of elutable organics present in the complex aerosol extract mixtures, thus generating profiles that serve as fingerprints'' for the sources of interest. This HRGC analyticalmore » method is applied to emission source samples that contain between 7 to 12,000 {mu}g/filter organic carbon. It is shown to be a sensitive technique for analysis of carbonaceous aerosol extract mixtures having diverse mass loadings and species distributions. This study describes the analytical chemical methods that have been applied to: the construction of chemical mass balances based on the mass of fine organic aerosol emitted for major urban sources of particulate carbon; and the generation of discrete emission source chemical profiles derived from chromatographic characteristics of the organic aerosol components. 21 refs., 1 fig., 2 tabs.« less

Split Tolerance in a Murine Model of Heterotopic En Bloc Chest Wall Transplantation

PubMed Central

Oh, Byoungchol; Furtmüller, Georg J.; Malek, Veronika; Fryer, Madeline L.; Brayton, Cory; Walczak, Piotr; Janowski, Miroslaw

2017-01-01

Background: Congenital and acquired chest wall deformities represent a significant challenge to functional reconstruction and may impact feasibility of heart transplantation for patients with end-stage organ failure. In the recent past, the concept of replacing like-with-like tissue by using vascularized composite allografts (VCA) has been enthusiastically employed for reconstruction of complex tissue defects. Methods: In this study, we introduce a novel murine model for en bloc chest wall, heart, and thymus transplantation and thereby the use of complex tissue allografts for reconstruction of both chest wall defects and also end-stage organ failure. Additionally, this model allows us to study the features of combined vascularized bone marrow (VBM), thymus, and heart transplantation on allograft survival and function. Heterotopic chest wall, thymus, and heart transplants were performed in untreated syngeneic and allogeneic combinations and in allogeneic combinations treated with costimulation blockade (CTLA4-Ig and MR-1). Results: Indefinite (ie, 150 d, N = 3) graft survival was observed in syngeneic controls. In untreated recipients of allogeneic grafts, the skin component was rejected after 10 (±1) days, whereas rejection of the heart occurred after 13 (± 1) days (N = 3). Costimulation blockade treatment prolonged survival of the heart and chest wall component (130 d, N = 3) as well as the VBM niche as evidenced by donor-specific chimerism (average: 2.35 ± 1.44%), whereas interestingly, the skin component was rejected after 13 (±1) days. Conclusion: Thus, this novel microsurgical model of VCA combined with solid organ transplantation is technically feasible and results in split tolerance when treated with costimulatory blockade. PMID:29632774

76 FR 9067 - Self-Regulatory Organizations; Notice of Filing and Immediate Effectiveness of Proposed Rule...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-16

... pay a rebate solely for Customer complex orders that add liquidity in order to continue to attract... because this Customer rebate would attract Customer order flow to the Exchange for the benefit of all..., priced at a net debit or credit based on the relative prices of the individual components, for the same...

Nurse manager orientation.

PubMed

Hawkins, Anne; Carter, Kelly; Nugent, Mary

2009-01-01

On the basis of the principles of management and leadership, our organization has worked over the years to formalize the orientation program for new nurse managers. This program meets the needs of new nurse managers and responds to today's complex health care system needs. This article describes the components of a nurse manager orientation program for the novice nurse manager and methods for evaluating nurse manager effectiveness.

Multi-agent-based bio-network for systems biology: protein-protein interaction network as an example.

PubMed

Ren, Li-Hong; Ding, Yong-Sheng; Shen, Yi-Zhen; Zhang, Xiang-Feng

2008-10-01

Recently, a collective effort from multiple research areas has been made to understand biological systems at the system level. This research requires the ability to simulate particular biological systems as cells, organs, organisms, and communities. In this paper, a novel bio-network simulation platform is proposed for system biology studies by combining agent approaches. We consider a biological system as a set of active computational components interacting with each other and with an external environment. Then, we propose a bio-network platform for simulating the behaviors of biological systems and modelling them in terms of bio-entities and society-entities. As a demonstration, we discuss how a protein-protein interaction (PPI) network can be seen as a society of autonomous interactive components. From interactions among small PPI networks, a large PPI network can emerge that has a remarkable ability to accomplish a complex function or task. We also simulate the evolution of the PPI networks by using the bio-operators of the bio-entities. Based on the proposed approach, various simulators with different functions can be embedded in the simulation platform, and further research can be done from design to development, including complexity validation of the biological system.

Acoustic backscatter models of fish: Gradual or punctuated evolution

NASA Astrophysics Data System (ADS)

Horne, John K.

2004-05-01

Sound-scattering characteristics of aquatic organisms are routinely investigated using theoretical and numerical models. Development of the inverse approach by van Holliday and colleagues in the 1970s catalyzed the development and validation of backscatter models for fish and zooplankton. As the understanding of biological scattering properties increased, so did the number and computational sophistication of backscatter models. The complexity of data used to represent modeled organisms has also evolved in parallel to model development. Simple geometric shapes representing body components or the whole organism have been replaced by anatomically accurate representations derived from imaging sensors such as computer-aided tomography (CAT) scans. In contrast, Medwin and Clay (1998) recommend that fish and zooplankton should be described by simple theories and models, without acoustically superfluous extensions. Since van Holliday's early work, how has data and computational complexity influenced accuracy and precision of model predictions? How has the understanding of aquatic organism scattering properties increased? Significant steps in the history of model development will be identified and changes in model results will be characterized and compared. [Work supported by ONR and the Alaska Fisheries Science Center.

Speciation of Cu and Zn in drainage water from agricultural soils.

PubMed

Aldrich, Annette P; Kistler, David; Sigg, Laura

2002-11-15

Inputs of copper and zinc from agricultural soils into the aquatic system were investigated in this study, because of their heavy agricultural usage as feed additives and components of fertilizers and fungicides. As the mobility and bioavailability of these metals are affected by their speciation, the lipophilic, colloidal and organic fractions were determined in drainage water from a loamy and a humic soil treated with fungicides or manure. This study therefore investigates the impact of agricultural activity on a natural environment and furthers our understanding of the mobility of metals in agricultural soils and aquatic pollution in rural areas. Marked increases in the total dissolved metal concentrations were observed in the drainage water during rain events with up to 0.3 microM Cu and 0.26 microM Zn depending on the intensity of the rainfall and soil type. The mobile metal fractions were of a small molecular size (<10 kD) and mainly hydrophilic. Lipophilic complexes originating from a dithiocarbamate (DTC) fungicide could not be observed in the drainage water; however, small amounts of lipophilic metal complexes may be of natural origin. Cu was organically complexed to > 99.9% by abundant organic ligands (log K 10.5-11.0). About 50% of dissolved Zn were electrochemically labile, and the other 50% were complexed by strong organic ligands (log K 8.2-8.6). Therefore very little free metal species were found suggesting a low bioavailability of these metals in the drainage water even at elevated metal concentrations.

METHODS FOR THE DETERMINATION OF TOTAL ORGANIC ...

EPA Pesticide Factsheets

Organic matter in soils and sediments is widely distributed over the earth's surface occurring in almost all terrestrial and aquatic environments (Schnitzer, 1978). Soils and sediments contain a large variety of organic materials ranging from simple sugars and carbohydrates to the more complex proteins, fats, waxes, and organic acids. Important characteristics of the organic matter include their ability to: form water-soluble and water- insoluble complexes with metal ions and hydrous oxides; interact with clay minerals and bind particles together; sorb and desorb both naturally-occurring and anthropogenically-introduced organic compounds; absorb and release plant nutrients; and hold water in the soil environment. As a result of these characteristics, the determination of total organic carbon (a measure of one of the chemical components of organic matter that is often used as an indicator of its presence in a soil or sediment) is an essential part of any site characterization since its presence or absence can markedly influence how chemicals will react in the soil or sediment. Soil and sediment total organic carbon (TOC) determinations are typically requested with contaminant analyses as part of an ecological risk assessment data package. TOC contents may be used qualitatively to assess the nature of the sampling location (e.g., was it a depositional area) or may be used to normalize portions of the analytical chemistry data set (e.g., equilibrium partitioning).

Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis

DOE PAGES

Zhang, Chunhua; Brown, Michelle Q.; van de Ven, Wilhelmina; ...

2015-11-25

The exocyst complex regulates the last steps of exocytosis, which is essential to organisms across kingdoms. In humans, its dysfunction is correlated with several significant diseases, such as diabetes and cancer progression. Investigation of the dynamic regulation of the evolutionarily conserved exocyst-related processes using mutants in genetically tractable organisms such as Arabidopsis thaliana is limited by the lethality or the severity of phenotypes. We discovered that the small molecule Endosidin2 (ES2) binds to the EXO70 (exocyst component of 70 kDa) subunit of the exocyst complex, resulting in inhibition of exocytosis and endosomal recycling in both plant and human cells andmore » enhancement of plant vacuolar trafficking. An EXO70 protein with a C-terminal truncation results in dominant ES2 resistance, uncovering possible distinct regulatory roles for the N terminus of the protein. Ultimately, this study not only provides a valuable tool in studying exocytosis regulation but also offers a potentially new target for drugs aimed at addressing human disease.« less

3D bioprinting of tissues and organs.

PubMed

Murphy, Sean V; Atala, Anthony

2014-08-01

Additive manufacturing, otherwise known as three-dimensional (3D) printing, is driving major innovations in many areas, such as engineering, manufacturing, art, education and medicine. Recent advances have enabled 3D printing of biocompatible materials, cells and supporting components into complex 3D functional living tissues. 3D bioprinting is being applied to regenerative medicine to address the need for tissues and organs suitable for transplantation. Compared with non-biological printing, 3D bioprinting involves additional complexities, such as the choice of materials, cell types, growth and differentiation factors, and technical challenges related to the sensitivities of living cells and the construction of tissues. Addressing these complexities requires the integration of technologies from the fields of engineering, biomaterials science, cell biology, physics and medicine. 3D bioprinting has already been used for the generation and transplantation of several tissues, including multilayered skin, bone, vascular grafts, tracheal splints, heart tissue and cartilaginous structures. Other applications include developing high-throughput 3D-bioprinted tissue models for research, drug discovery and toxicology.

Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Chunhua; Brown, Michelle Q.; van de Ven, Wilhelmina

The exocyst complex regulates the last steps of exocytosis, which is essential to organisms across kingdoms. In humans, its dysfunction is correlated with several significant diseases, such as diabetes and cancer progression. Investigation of the dynamic regulation of the evolutionarily conserved exocyst-related processes using mutants in genetically tractable organisms such as Arabidopsis thaliana is limited by the lethality or the severity of phenotypes. We discovered that the small molecule Endosidin2 (ES2) binds to the EXO70 (exocyst component of 70 kDa) subunit of the exocyst complex, resulting in inhibition of exocytosis and endosomal recycling in both plant and human cells andmore » enhancement of plant vacuolar trafficking. An EXO70 protein with a C-terminal truncation results in dominant ES2 resistance, uncovering possible distinct regulatory roles for the N terminus of the protein. Ultimately, this study not only provides a valuable tool in studying exocytosis regulation but also offers a potentially new target for drugs aimed at addressing human disease.« less

Nanoscale Spatial Organization of Prokaryotic Cells Studied by Super-Resolution Optical Microscopy

NASA Astrophysics Data System (ADS)

McEvoy, Andrea Lynn

All cells spatially organize their interiors, and this arrangement is necessary for cell viability. Until recently, it was believed that only eukaryotic cells spatially segregate their components. However, it is becoming increasingly clear that bacteria also assemble their proteins into complex patterns. In eukaryotic cells, spatial organization arises from membrane bound organelles as well as motor transport proteins which can move cargos within the cell. To date, there are no known motor transport proteins in bacteria and most microbes lack membrane bound organelles, so it remains a mystery how bacterial spatial organization emerges. In hind-sight it is not surprising that bacteria also exhibit complex spatial organization considering much of what we have learned about the basic processes that take place in all cells, such as transcription and translation was first discovered in prokaryotic cells. Perhaps the fundamental principles that govern spatial organization in prokaryotic cells may be applicable in eukaryotic cells as well. In addition, bacteria are attractive model organism for spatial organization studies because they are genetically tractable, grow quickly and much biochemical and structural data is known about them. A powerful tool for observing spatial organization in cells is the fluorescence microscope. By specifically tagging a protein of interest with a fluorescent probe, it is possible to examine how proteins organize and dynamically assemble inside cells. A significant disadvantage of this technology is its spatial resolution (approximately 250 nm laterally and 500 nm axially). This limitation on resolution causes closely spaced proteins to look blurred making it difficult to observe the fine structure within the complexes. This resolution limit is especially problematic within small cells such as bacteria. With the recent invention of new optical microscopies, we now can surpass the existing limits of fluorescence imaging. In some cases, we can now see individual proteins inside of large complexes or observe structures with ten times the resolution of conventional imaging. These techniques are known as super-resolution microscopes. In this dissertation, I use super-resolution microscopes to understand how a model microbe, Escherichia coli, assembles complex protein structures. I focus on two spatially organized systems, the chemotaxis network and the cell division machinery. These assembly mechanisms could be general mechanisms for protein assembly in all organisms. I also characterize new fluorescent probes for use in multiple super-resolution imaging modalities and discuss the practicalities of using different super-resolution microscopes. The chemotaxis network in E. coli is the best understood signal transduction network in biology. Chemotaxis receptors cluster into complexes of thousands of proteins located at the cell poles and are used to move bacteria towards favorable stimuli in the environment. In these dense clusters, the receptors can bind each other and communicate to filter out noise and amplify weak signals. It is surprising that chemotaxis receptors are spatially segregated and the mechanism for polar localization of these complexes remains unclear. Using data from PALM images, we develop a model to understand how bacteria organize their receptors into large clusters. The model, stochastic cluster nucleation, is surprising in that is generates micron-scale periodic patterns without the need for accessory proteins to provide scaffolding or active transport. This model may be a general mechanism that cells utilize to organize small and large complexes of proteins. During cell division, E. coli must elongate, replicate its DNA and position its components properly prior to binary fission. Prior to septum formation, a ubiquitous protein called FtsZ, assembles into a ring at mid-cell (Z-ring) which constricts during cell division and recruits the remaining proteins necessary for cytokinesis. Though many details have been revealed about FtsZ, the detailed in vivo structure of the Z-ring is not well understood, and many questions remain about how ring constriction occurs. Using multiple super-resolution imaging modalities, in combination with conventional time-lapse fluorescence imaging, we show that the Z-ring does not form a long uniform filament around the circumference of the bacterium. We detail how this structure changes during division and how removal of proteins that help to position FtsZ affects the Z-ring as it proceeds through cytokinesis. Ultimately we present a simple model for Z-ring constriction during division.

Aggregate nanostructures of organic molecular materials.

PubMed

Liu, Huibiao; Xu, Jialiang; Li, Yongjun; Li, Yuliang

2010-12-21

Conjugated organic molecules are interesting materials because of their structures and their electronic, electrical, magnetic, optical, biological, and chemical properties. However, researchers continue to face great challenges in the construction of well-defined organic compounds that aggregate into larger molecular materials such as nanowires, tubes, rods, particles, walls, films, and other structural arrays. Such nanoscale materials could serve as direct device components. In this Account, we describe our recent progress in the construction of nanostructures formed through the aggregation of organic conjugated molecules and in the investigation of the optical, electrical, and electronic properties that depend on the size or morphology of these nanostructures. We have designed and synthesized functional conjugated organic molecules with structural features that favor assembly into aggregate nanostructures via weak intermolecular interactions. These large-area ordered molecular aggregate nanostructures are based on a variety of simpler structures such as fullerenes, perylenes, anthracenes, porphyrins, polydiacetylenes, and their derivatives. We have developed new methods to construct these larger structures including organic vapor-solid phase reaction, natural growth, association via self-polymerization and self-organization, and a combination of self-assembly and electrochemical growth. These methods are both facile and reliable, allowing us to produce ordered and aligned aggregate nanostructures, such as large-area arrays of nanowires, nanorods, and nanotubes. In addition, we can synthesize nanoscale materials with controlled properties. Large-area ordered aggregate nanostructures exhibit interesting electrical, optical, and optoelectronic properties. We also describe the preparation of large-area aggregate nanostructures of charge transfer (CT) complexes using an organic solid-phase reaction technique. By this process, we can finely control the morphologies and sizes of the organic nanostructures on wires, tubes, and rods. Through field emission studies, we demonstrate that the films made from arrays of CT complexes are a new kind of cathode materials, and we systematically investigate the effects of size and morphology on electrical properties. Low-dimension organic/inorganic hybrid nanostructures can be used to produce new classes of organic/inorganic solid materials with properties that are not observed in either the individual nanosize components or the larger bulk materials. We developed the combined self-assembly and templating technique to construct various nanostructured arrays of organic and inorganic semiconductors. The combination of hybrid aggregate nanostructures displays distinct optical and electrical properties compared with their individual components. Such hybrid structures show promise for applications in electronics, optics, photovoltaic cells, and biology. In this Account, we aim to provide an intuition for understanding the structure-function relationships in organic molecular materials. Such principles could lead to new design concepts for the development of new nonhazardous, high-performance molecular materials on aggregate nanostructures.

On the Complex Coupling Between the Production of Ozone and Secondary Organic Aerosol in Polluted Urban Regions

NASA Astrophysics Data System (ADS)

Stewart, D. R.; Stockwell, W. R.; Morris, V. R.; Fitzgerald, R. M.

2016-12-01

The major photochemical processes that produce ozone and aerosols are coupled together strongly in the polluted urban atmosphere. Aerosols are either directly emitted or formed through the same kind of chemistry that leads to the production of ozone. The aerosols produced through atmospheric chemistry are known as secondary aerosols and they may be composed of inorganic (nitrates, sulfates) or organic compounds. Wind blown dust and soot are two examples of primary aerosols. The component of secondary inorganic aerosols includes compounds such as ammonium nitrate, ammonium bisulfate and ammonium sulfate. Secondary organic aerosols are a very important component of PM with strong implications for health. The formation of secondary organic aerosol is linked with ozone photochemistry through the reactions of volatile organic compounds (VOC). The oxidation of VOC produces radicals that convert nitric oxide to nitrogen dioxide that photolyze to produce ozone. Larger VOC (those with more carbon atoms) undergo a number of oxidation cycles that add oxygen atoms to large organic molecules. The vapor pressure of many of these highly oxidized compounds is sufficiently low that they condense to produce secondary organic aerosols. The Community Multi-scale Air Quality model (CMAQ) and other chemical simulations have been made to quantify the relationship between varying emissions of VOC and NOx and the production of inorganic and secondary organic aerosols. The results from this analysis will be presented.

Nanospace-Mediated Self-Organization of Nanoparticles in Flexible Porous Polymer Templates.

PubMed

Kuroda, Yoshiyuki; Muto, Itaru; Shimojima, Atsushi; Wada, Hiroaki; Kuroda, Kazuyuki

2017-09-12

Self-organization is a fundamental process for the construction of complex hierarchically ordered nanostructures, which are widespread in biological systems. However, precise control of size, shape, and surface properties is required for self-organization of nanoparticles. Here, we demonstrate a novel self-organization phenomenon mediated by flexible nanospaces in templates. Inorganic nanoparticles (e.g., silica, zirconia, and titania) are deposited in porous polymer thin films with randomly distributed pores on the surface, leaving a partially filled nanospace in each pore. Heating at temperatures beyond the glass transition temperature of the template leads to self-organization of the inorganic nanoparticles into one-dimensional chainlike networks. The self-organization is mediated by the deformation and fusion of the residual nanospaces, and it can be rationally controlled by sequential heat treatments. These results show that a nanospace, defined by the nonexistence of matter, interacts indirectly with matter and can be used as a component of self-organization systems.

Storage and Bioavailability of Molybdenum in Soils Increased by Organic Matter Complexation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wichard, T.; Mishra, B; Myneni, S

2009-01-01

The micronutrient molybdenum is a necessary component of the nitrogen-fixing enzyme nitrogenase1, 2. Molybdenum is very rare in soils, and is usually present in a highly soluble form, making it susceptible to leaching3, 4. However, it is generally thought that molybdenum attaches to mineral surfaces in acidic soils; this would prevent its escape into the groundwater, but would also impede uptake by microbes3. Here we use X-ray spectroscopy to examine the chemical speciation of molybdenum in soil samples from forests in Arizona and New Jersey. We show that in the leaf litter layer, most of the molybdenum forms strong complexesmore » with plant-derived tannins and tannin-like compounds; molybdenum binds to these organic ligands across a wide pH range. In deeper soils, molybdenum binds to both iron oxides and natural organic matter. We suggest that the molybdenum bound to organic matter can be captured by small complexing agents that are released by nitrogen-fixing bacteria; the molybdenum can then be incorporated into nitrogenase. We conclude that the binding of molybdenum to natural organic matter helps prevent leaching of molybdenum, and is thus a critical step in securing new nitrogen in terrestrial ecosystems.« less

Segmentation of deformable organs from medical images using particle swarm optimization and nonlinear shape priors

NASA Astrophysics Data System (ADS)

Afifi, Ahmed; Nakaguchi, Toshiya; Tsumura, Norimichi

2010-03-01

In many medical applications, the automatic segmentation of deformable organs from medical images is indispensable and its accuracy is of a special interest. However, the automatic segmentation of these organs is a challenging task according to its complex shape. Moreover, the medical images usually have noise, clutter, or occlusion and considering the image information only often leads to meager image segmentation. In this paper, we propose a fully automated technique for the segmentation of deformable organs from medical images. In this technique, the segmentation is performed by fitting a nonlinear shape model with pre-segmented images. The kernel principle component analysis (KPCA) is utilized to capture the complex organs deformation and to construct the nonlinear shape model. The presegmentation is carried out by labeling each pixel according to its high level texture features extracted using the overcomplete wavelet packet decomposition. Furthermore, to guarantee an accurate fitting between the nonlinear model and the pre-segmented images, the particle swarm optimization (PSO) algorithm is employed to adapt the model parameters for the novel images. In this paper, we demonstrate the competence of proposed technique by implementing it to the liver segmentation from computed tomography (CT) scans of different patients.

Differential effects of citric acid on cadmium uptake and accumulation between tall fescue and Kentucky bluegrass.

PubMed

Wang, ShuTing; Dong, Qin; Wang, ZhaoLong

2017-11-01

Organic acids play an important role in cadmium availability, uptake, translocation, and detoxification. A sand culture experiment was designed to investigate the effects of citric acid on Cd uptake, translocation, and accumulation in tall fescue and Kentucky bluegrass. The results showed that two grass species presented different Cd chemical forms, organic acid components and amount in roots. The dormant Cd accumulated in roots of tall fescue was the pectate- and protein- integrated form, which contributed by 84.85%. However, in Kentucky bluegrass, the pectate- and protein- integrated Cd was only contributed by 35.78%, and the higher proportion of Cd form was the water soluble Cd-organic acid complexes. In tall fescue, citric acid dramatically enhanced 2.8 fold of Cd uptake, 3 fold of root Cd accumulation, and 2.3 fold of shoot Cd accumulation. In Kentucky bluegrass, citric acid promoted Cd accumulation in roots, but significantly decreased Cd accumulation in shoots. These results suggested that the enhancements of citric acid on Cd uptake, translocation, and accumulation in tall fescue was associated with its promotion of organic acids and the water soluble Cd-organic acid complexes in roots. Copyright © 2017 Elsevier Inc. All rights reserved.

Shade avoidance components and pathways in adult plants revealed by phenotypic profiling.

PubMed

Nozue, Kazunari; Tat, An V; Kumar Devisetty, Upendra; Robinson, Matthew; Mumbach, Maxwell R; Ichihashi, Yasunori; Lekkala, Saradadevi; Maloof, Julin N

2015-04-01

Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.

Quantification of Degeneracy in Biological Systems for Characterization of Functional Interactions Between Modules

PubMed Central

Li, Yao; Dwivedi, Gaurav; Huang, Wen; Yi, Yingfei

2012-01-01

There is an evolutionary advantage in having multiple components with overlapping functionality (i.e degeneracy) in organisms. While theoretical considerations of degeneracy have been well established in neural networks using information theory, the same concepts have not been developed for differential systems, which form the basis of many biochemical reaction network descriptions in systems biology. Here we establish mathematical definitions of degeneracy, complexity and robustness that allow for the quantification of these properties in a system. By exciting a dynamical system with noise, the mutual information associated with a selected observable output and the interacting subspaces of input components can be used to define both complexity and degeneracy. The calculation of degeneracy in a biological network is a useful metric for evaluating features such as the sensitivity of a biological network to environmental evolutionary pressure. Using a two-receptor signal transduction network, we find that redundant components will not yield high degeneracy whereas compensatory mechanisms established by pathway crosstalk will. This form of analysis permits interrogation of large-scale differential systems for non-identical, functionally equivalent features that have evolved to maintain homeostasis during disruption of individual components. PMID:22619750

Synergizing Noncovalent Bonding Interactions in the Self-Assembly of Organic Charge-Transfer Ferroelectrics and Metal-Organic Frameworks

NASA Astrophysics Data System (ADS)

Cao, Dennis

Contemporary supramolecular chemistry---chemistry beyond the molecule---seeks to leverage noncovalent bonding interactions to generate emergent properties and complexity. These aims extend beyond the solution phase and into the solid state, where crystalline organic materials have attracted much attention for their ability to imitate the physical properties of inorganic crystals. This Thesis outlines my efforts to understand the properties of the solid-state materials that are self-assembled with noncovalent bonding motifs which I have helped to realize. In the first five Chapters, I chronicle the development of the lock-arm supramolecular ordering (LASO) paradigm, which is a general molecular design strategy for amplifying the crystallization of charge transfer complexes that revolves around the synergistic action of hydrogen bonding and charge transfer interactions. In an effort to expand upon the LASO paradigm, I identify a two-point halogen-bonding motif which appears to operate orthogonally from the hydrogen bonding and charge transfer interactions. Since some of these single crystalline materials are ferroelectric at room temperature, I discuss the implications of these experimental observations and reconcile them with the centrosymmetric space groups assigned after X-ray crystallographic refinements. I conclude in the final two Chapters by recording my endeavors to control the assembly of metal-organic frameworks (MOFs) with noncovalent bonding interactions between [2]catenane-bearing struts. First of all, I describe the formation of syndiotactic pi-stacked 2D MOF layers before highlighting a two-component MOF that assembles with a magic number ratio of components that is independent of the molar proportions present in the crystallization medium.

In-situ molecular-level elucidation of organofluorine binding sites in a whole peat soil.

PubMed

Longstaffe, James G; Courtier-Murias, Denis; Soong, Ronald; Simpson, Myrna J; Maas, Werner E; Fey, Michael; Hutchins, Howard; Krishnamurthy, Sridevi; Struppe, Jochem; Alaee, Mehran; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Simpson, André J

2012-10-02

The chemical nature of xenobiotic binding sites in soils is of vital importance to environmental biogeochemistry. Interactions between xenobiotics and the naturally occurring organic constituents of soils are strongly correlated to environmental persistence, bioaccessibility, and ecotoxicity. Nevertheless, because of the complex structural and chemical heterogeneity of soils, studies of these interactions are most commonly performed indirectly, using correlative methods, fractionation, or chemical modification. Here we identify the organic components of an unmodified peat soil where some organofluorine xenobiotic compounds interact using direct molecular-level methods. Using (19)F→(1)H cross-polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) spectroscopy, the (19)F nuclei of organofluorine compounds are used to induce observable transverse magnetization in the (1)H nuclei of organic components of the soil with which they interact after sorption. The observed (19)F→(1)H CP-MAS spectra and dynamics are compared to those produced using model soil organic compounds, lignin and albumin. It is found that lignin-like components can account for the interactions observed in this soil for heptafluoronaphthol (HFNap) while protein structures can account for the interactions observed for perfluorooctanoic acid (PFOA). This study employs novel comprehensive multi-phase (CMP) NMR technology that permits the application of solution-, gel-, and solid-state NMR experiments on intact soil samples in their swollen state.

Mixture effects in samples of multiple contaminants - An inter-laboratory study with manifold bioassays.

PubMed

Altenburger, Rolf; Scholze, Martin; Busch, Wibke; Escher, Beate I; Jakobs, Gianina; Krauss, Martin; Krüger, Janet; Neale, Peta A; Ait-Aissa, Selim; Almeida, Ana Catarina; Seiler, Thomas-Benjamin; Brion, François; Hilscherová, Klára; Hollert, Henner; Novák, Jiří; Schlichting, Rita; Serra, Hélène; Shao, Ying; Tindall, Andrew; Tolefsen, Knut-Erik; Umbuzeiro, Gisela; Williams, Tim D; Kortenkamp, Andreas

2018-05-01

Chemicals in the environment occur in mixtures rather than as individual entities. Environmental quality monitoring thus faces the challenge to comprehensively assess a multitude of contaminants and potential adverse effects. Effect-based methods have been suggested as complements to chemical analytical characterisation of complex pollution patterns. The regularly observed discrepancy between chemical and biological assessments of adverse effects due to contaminants in the field may be either due to unidentified contaminants or result from interactions of compounds in mixtures. Here, we present an interlaboratory study where individual compounds and their mixtures were investigated by extensive concentration-effect analysis using 19 different bioassays. The assay panel consisted of 5 whole organism assays measuring apical effects and 14 cell- and organism-based bioassays with more specific effect observations. Twelve organic water pollutants of diverse structure and unique known modes of action were studied individually and as mixtures mirroring exposure scenarios in freshwaters. We compared the observed mixture effects against component-based mixture effect predictions derived from additivity expectations (assumption of non-interaction). Most of the assays detected the mixture response of the active components as predicted even against a background of other inactive contaminants. When none of the mixture components showed any activity by themselves then the mixture also was without effects. The mixture effects observed using apical endpoints fell in the middle of a prediction window defined by the additivity predictions for concentration addition and independent action, reflecting well the diversity of the anticipated modes of action. In one case, an unexpectedly reduced solubility of one of the mixture components led to mixture responses that fell short of the predictions of both additivity mixture models. The majority of the specific cell- and organism-based endpoints produced mixture responses in agreement with the additivity expectation of concentration addition. Exceptionally, expected (additive) mixture response did not occur due to masking effects such as general toxicity from other compounds. Generally, deviations from an additivity expectation could be explained due to experimental factors, specific limitations of the effect endpoint or masking side effects such as cytotoxicity in in vitro assays. The majority of bioassays were able to quantitatively detect the predicted non-interactive, additive combined effect of the specifically bioactive compounds against a background of complex mixture of other chemicals in the sample. This supports the use of a combination of chemical and bioanalytical monitoring tools for the identification of chemicals that drive a specific mixture effect. Furthermore, we demonstrated that a panel of bioassays can provide a diverse profile of effect responses to a complex contaminated sample. This could be extended towards representing mixture adverse outcome pathways. Our findings support the ongoing development of bioanalytical tools for (i) compiling comprehensive effect-based batteries for water quality assessment, (ii) designing tailored surveillance methods to safeguard specific water uses, and (iii) devising strategies for effect-based diagnosis of complex contamination. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Organics in the atmosphere: From air pollution to biogeochemical cycles and climate (Vilhelm Bjerknes Medal)

NASA Astrophysics Data System (ADS)

Kanakidou, Maria

2016-04-01

Organics are key players in the biosphere-atmosphere-climate interactions. They have also a significant anthropogenic component due to primary emissions or interactions with pollution. The organic pool in the atmosphere is a complex mixture of compounds of variable reactivity and properties, variable content in C, H, O, N and other elements depending on their origin and their history in the atmosphere. Multiphase atmospheric chemistry is known to produce organic acids with high oxygen content, like oxalic acid. This water soluble organic bi-acid is used as indicator for cloud processing and can form complexes with atmospheric Iron, affecting Iron solubility. Organics are also carriers of other nutrients like nitrogen and phosphorus. They also interact with solar radiation and with atmospheric water impacting on climate. In line with this vision for the role of organics in the atmosphere, we present results from a global 3-dimensional chemistry-transport model on the role of gaseous and particulate organics in atmospheric chemistry, accounting for multiphase chemistry and aerosol ageing in the atmosphere as well as nutrients emissions, atmospheric transport and deposition. Historical simulations and projections highlight the human impact on air quality and atmospheric deposition to the oceans. The results are put in the context of climate change. Uncertainties and implications of our findings for biogeochemical and climate modeling are discussed.

Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics.

PubMed

Sardiu, Mihaela E; Gilmore, Joshua M; Carrozza, Michael J; Li, Bing; Workman, Jerry L; Florens, Laurence; Washburn, Michael P

2009-10-06

Protein complexes are key molecular machines executing a variety of essential cellular processes. Despite the availability of genome-wide protein-protein interaction studies, determining the connectivity between proteins within a complex remains a major challenge. Here we demonstrate a method that is able to predict the relationship of proteins within a stable protein complex. We employed a combination of computational approaches and a systematic collection of quantitative proteomics data from wild-type and deletion strain purifications to build a quantitative deletion-interaction network map and subsequently convert the resulting data into an interdependency-interaction model of a complex. We applied this approach to a data set generated from components of the Saccharomyces cerevisiae Rpd3 histone deacetylase complexes, which consists of two distinct small and large complexes that are held together by a module consisting of Rpd3, Sin3 and Ume1. The resulting representation reveals new protein-protein interactions and new submodule relationships, providing novel information for mapping the functional organization of a complex.

The Pseudomonas aeruginosa AlgZR two-component system coordinates multiple phenotypes

PubMed Central

Okkotsu, Yuta; Little, Alexander S.; Schurr, Michael J.

2014-01-01

Pseudomonas aeruginosa is an opportunistic pathogen that causes a multitude of infections. These infections can occur at almost any site in the body and are usually associated with a breach of the innate immune system. One of the prominent sites where P. aeruginosa causes chronic infections is within the lungs of cystic fibrosis patients. P. aeruginosa uses two-component systems that sense environmental changes to differentially express virulence factors that cause both acute and chronic infections. The P. aeruginosa AlgZR two component system is one of its global regulatory systems that affects the organism's fitness in a broad manner. This two-component system is absolutely required for two P. aeruginosa phenotypes: twitching motility and alginate production, indicating its importance in both chronic and acute infections. Additionally, global transcriptome analyses indicate that it regulates the expression of many different genes, including those associated with quorum sensing, type IV pili, type III secretion system, anaerobic metabolism, cyanide and rhamnolipid production. This review examines the complex AlgZR regulatory network, what is known about the structure and function of each protein, and how it relates to the organism's ability to cause infections. PMID:24999454

Error and attack tolerance of complex networks

NASA Astrophysics Data System (ADS)

Albert, Réka; Jeong, Hawoong; Barabási, Albert-László

2000-07-01

Many complex systems display a surprising degree of tolerance against errors. For example, relatively simple organisms grow, persist and reproduce despite drastic pharmaceutical or environmental interventions, an error tolerance attributed to the robustness of the underlying metabolic network. Complex communication networks display a surprising degree of robustness: although key components regularly malfunction, local failures rarely lead to the loss of the global information-carrying ability of the network. The stability of these and other complex systems is often attributed to the redundant wiring of the functional web defined by the systems' components. Here we demonstrate that error tolerance is not shared by all redundant systems: it is displayed only by a class of inhomogeneously wired networks, called scale-free networks, which include the World-Wide Web, the Internet, social networks and cells. We find that such networks display an unexpected degree of robustness, the ability of their nodes to communicate being unaffected even by unrealistically high failure rates. However, error tolerance comes at a high price in that these networks are extremely vulnerable to attacks (that is, to the selection and removal of a few nodes that play a vital role in maintaining the network's connectivity). Such error tolerance and attack vulnerability are generic properties of communication networks.

Transcription-Coupled Repair and Complex Biology.

PubMed

Portman, James R; Strick, Terence R

2018-05-04

All active living organisms mitigate DNA damage via DNA repair, and the so-called nucleotide excision repair pathway (NER) represents a functionally major part of the cell's DNA repair repertoire [1]. In this pathway, the damaged strand of DNA is incised and removed before being resynthesized. This form of DNA repair requires a multitude of proteins working in a complex choreography. Repair thus typically involves detection of a DNA lesion; validation of that detection event; search for an appropriate incision site and subsequent DNA incision; DNA unwinding/removal; and DNA resynthesis and religation. These activities are ultimately the result of molecules randomly diffusing and bumping into each other and acting in succession. It is also true however that repair components are often assembled into functional complexes which may be more efficient or regular in their mode of action. Studying DNA repair complexes for their mechanisms of assembly, action, and disassembly can help address fundamental questions such as whether DNA repair pathways are branched or linear; whether for instance they tolerate fluctuations in numbers of components; and more broadly how search processes between macromolecules take place or can be enhanced. Copyright © 2018. Published by Elsevier Ltd.

Stereotypic and complex phrase types provide structural evidence for a multi-message display in humpback whales (Megaptera novaeangliae).

PubMed

Murray, Anita; Dunlop, Rebecca A; Noad, Michael J; Goldizen, Anne W

2018-02-01

Male humpback whales produce a mating display called "song." Behavioral studies indicate song has inter- and/or intra-sexual functionality, suggesting song may be a multi-message display. Multi-message displays often include stereotypic components that convey group membership for mate attraction and/or male-male interactions, and complex components that convey individual quality for courtship. Humpback whale song contains sounds ("units") arranged into sequences ("phrases"). Repetitions of a specific phrase create a "theme." Within a theme, imperfect phrase repetitions ("phrase variants") create variability among phrases of the same type ("phrase type"). The hypothesis that song contains stereotypic and complex phrase types, structural characteristics consistent with a multi-message display, is investigated using recordings of 17 east Australian males (8:2004, 9:2011). Phrase types are categorized as stereotypic or complex using number of unit types, number of phrase variants, and the proportion of phrases that is unique to an individual versus shared amongst males. Unit types are determined using self-organizing maps. Phrase variants are determined by Levenshtein distances between phrases. Stereotypic phrase types have smaller numbers of unit types and shared phrase variants. Complex phrase types have larger numbers of unit types and unique phrase variants. This study supports the hypothesis that song could be a multi-message display.

Network Physiology: How Organ Systems Dynamically Interact

PubMed Central

Bartsch, Ronny P.; Liu, Kang K. L.; Bashan, Amir; Ivanov, Plamen Ch.

2015-01-01

We systematically study how diverse physiologic systems in the human organism dynamically interact and collectively behave to produce distinct physiologic states and functions. This is a fundamental question in the new interdisciplinary field of Network Physiology, and has not been previously explored. Introducing the novel concept of Time Delay Stability (TDS), we develop a computational approach to identify and quantify networks of physiologic interactions from long-term continuous, multi-channel physiological recordings. We also develop a physiologically-motivated visualization framework to map networks of dynamical organ interactions to graphical objects encoded with information about the coupling strength of network links quantified using the TDS measure. Applying a system-wide integrative approach, we identify distinct patterns in the network structure of organ interactions, as well as the frequency bands through which these interactions are mediated. We establish first maps representing physiologic organ network interactions and discover basic rules underlying the complex hierarchical reorganization in physiologic networks with transitions across physiologic states. Our findings demonstrate a direct association between network topology and physiologic function, and provide new insights into understanding how health and distinct physiologic states emerge from networked interactions among nonlinear multi-component complex systems. The presented here investigations are initial steps in building a first atlas of dynamic interactions among organ systems. PMID:26555073

Plant and algal cell walls: diversity and functionality

PubMed Central

Popper, Zoë A.; Ralet, Marie-Christine; Domozych, David S.

2014-01-01

Background Although plants and many algae (e.g. the Phaeophyceae, brown, and Rhodophyceae, red) are only very distantly related they are united in their possession of carbohydrate-rich cell walls, which are of integral importance being involved in many physiological processes. Furthermore, wall components have applications within food, fuel, pharmaceuticals, fibres (e.g. for textiles and paper) and building materials and have long been an active topic of research. As shown in the 27 papers in this Special Issue, as the major deposit of photosynthetically fixed carbon, and therefore energy investment, cell walls are of undisputed importance to the organisms that possess them, the photosynthetic eukaryotes (plants and algae). The complexities of cell wall components along with their interactions with the biotic and abiotic environment are becoming increasingly revealed. Scope The importance of plant and algal cell walls and their individual components to the function and survival of the organism, and for a number of industrial applications, are illustrated by the breadth of topics covered in this issue, which includes papers concentrating on various plants and algae, developmental stages, organs, cell wall components, and techniques. Although we acknowledge that there are many alternative ways in which the papers could be categorized (and many would fit within several topics), we have organized them as follows: (1) cell wall biosynthesis and remodelling, (2) cell wall diversity, and (3) application of new technologies to cell walls. Finally, we will consider future directions within plant cell wall research. Expansion of the industrial uses of cell walls and potentially novel uses of cell wall components are both avenues likely to direct future research activities. Fundamentally, it is the continued progression from characterization (structure, metabolism, properties and localization) of individual cell wall components through to defining their roles in almost every aspect of plant and algal physiology that will present many of the major challenges in future cell wall research. PMID:25453142

Plant and algal cell walls: diversity and functionality.

PubMed

Popper, Zoë A; Ralet, Marie-Christine; Domozych, David S

2014-10-01

Although plants and many algae (e.g. the Phaeophyceae, brown, and Rhodophyceae, red) are only very distantly related they are united in their possession of carbohydrate-rich cell walls, which are of integral importance being involved in many physiological processes. Furthermore,wall components have applications within food, fuel, pharmaceuticals, fibres (e.g. for textiles and paper) and building materials and have long been an active topic of research. As shown in the 27 papers in this Special Issue, as the major deposit of photosynthetically fixed carbon, and therefore energy investment, cell walls are of undisputed importance to the organisms that possess them, the photosynthetic eukaryotes ( plants and algae). The complexities of cell wall components along with their interactions with the biotic and abiotic environment are becoming increasingly revealed. The importance of plant and algal cell walls and their individual components to the function and survival of the organism, and for a number of industrial applications, are illustrated by the breadth of topics covered in this issue, which includes papers concentrating on various plants and algae, developmental stages, organs, cell wall components, and techniques. Although we acknowledge that there are many alternative ways in which the papers could be categorized (and many would fit within several topics), we have organized them as follows: (1) cell wall biosynthesis and remodelling, (2) cell wall diversity, and (3) application of new technologies to cell walls. Finally, we will consider future directions within plant cell wall research. Expansion of the industrial uses of cell walls and potentially novel uses of cell wall components are both avenues likely to direct future research activities. Fundamentally, it is the continued progression from characterization (structure, metabolism, properties and localization) of individual cell wall components through to defining their roles in almost every aspect of plant and algal physiology that will present many of the major challenges in future cell wall research.

1991 Annual report on scientific programs: A broad research program on the sciences of complexity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1991-01-01

1991 was continued rapid growth for the Santa Fe Institute (SFI) as it broadened its interdisciplinary research into the organization, evolution and operation of complex systems and sought deeply the principles underlying their dynamic behavior. Research on complex systems--the focus of work at SFI--involves an extraordinary range of topics normally studied in seemingly disparate fields. Natural systems displaying complex behavior range upwards from proteins and DNA through cells and evolutionary systems to human societies. Research models exhibiting complexity include nonlinear equations, spin glasses, cellular automata, genetic algorithms, classifier systems, and an array of other computational models. Some of the majormore » questions facing complex systems researchers are: (1) explaining how complexity arises from the nonlinear interaction of simples components, (2) describing the mechanisms underlying high-level aggregate behavior of complex systems (such as the overt behavior of an organism, the flow of energy in an ecology, the GNP of an economy), and (3) creating a theoretical framework to enable predictions about the likely behavior of such systems in various conditions. The importance of understanding such systems in enormous: many of the most serious challenges facing humanity--e.g., environmental sustainability, economic stability, the control of disease--as well as many of the hardest scientific questions--e.g., protein folding, the distinction between self and non-self in the immune system, the nature of intelligence, the origin of life--require deep understanding of complex systems.« less

1991 Annual report on scientific programs: A broad research program on the sciences of complexity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1991-12-31

1991 was continued rapid growth for the Santa Fe Institute (SFI) as it broadened its interdisciplinary research into the organization, evolution and operation of complex systems and sought deeply the principles underlying their dynamic behavior. Research on complex systems--the focus of work at SFI--involves an extraordinary range of topics normally studied in seemingly disparate fields. Natural systems displaying complex behavior range upwards from proteins and DNA through cells and evolutionary systems to human societies. Research models exhibiting complexity include nonlinear equations, spin glasses, cellular automata, genetic algorithms, classifier systems, and an array of other computational models. Some of the majormore » questions facing complex systems researchers are: (1) explaining how complexity arises from the nonlinear interaction of simples components, (2) describing the mechanisms underlying high-level aggregate behavior of complex systems (such as the overt behavior of an organism, the flow of energy in an ecology, the GNP of an economy), and (3) creating a theoretical framework to enable predictions about the likely behavior of such systems in various conditions. The importance of understanding such systems in enormous: many of the most serious challenges facing humanity--e.g., environmental sustainability, economic stability, the control of disease--as well as many of the hardest scientific questions--e.g., protein folding, the distinction between self and non-self in the immune system, the nature of intelligence, the origin of life--require deep understanding of complex systems.« less

Diagenetic changes in Concholepas concholepas shells (Gastropoda, Muricidae) in the hyper-arid conditions of Northern Chile - implications for palaeoenvironmental reconstructions

NASA Astrophysics Data System (ADS)

Guzmán, N.; Dauphin, Y.; Cuif, J. P.; Denis, A.; Ortlieb, L.

2009-02-01

Variations in the chemical composition of fossil biogenic carbonates, and in particular of mollusc shells, have been used in a range of palaeoenvironmental reconstructions. It is of primary importance, therefore, to detect and understand the diagenetic processes that may modify the original chemical signature. This microstructural and biogeochemical study focuses on modern and fossil (Holocene and Pleistocene) shells of a littoral gastropod of Northern Chile, and on the characterization of mineral component transformations at the nanometric scale and concomitant intracrystalline organic compound modifications. The inner aragonite layer of the shell exhibits more complex deteriorations than the calcite layer. This preliminary study confirms that physical and chemical alterations of various components of mollusc shell biocrystals are complex and might manifest in different ways even within a single individual. The single criterion of determining the mineralogical composition to verify the conservation state of shell samples is insufficient.

Diagenetic changes in Concholepas concholepas shells (Gastropoda, Muricidae) in the hyper-arid conditions of Northern Chile - implications for palaeoenvironmental reconstructions

NASA Astrophysics Data System (ADS)

Guzman, N.; Dauphin, Y.; Cuif, J. P.; Denis, A.; Ortlieb, L.

2008-02-01

Variations on chemical composition in fossil biogenic carbonates, and in particular of mollusk shells, have been used in a range of palaeoenvironmental reconstructions. Therefore, it is of primary importance to detect and understand the diagenetic processes that may modify the original chemical signature. This microstructural and biogeochemical study focuses on modern and fossil (Pleistocene and Holocene) shells of a littoral gastropod of Northern Chile, and on the characterization of mineral component transformations at the nanometric scale and concomitant intracrystalline organic compound modifications. The inner aragonite layer of the shell exhibits more complex deteriorations than the calcite layer. This preliminary study confirms that physical and chemical alterations of various components of mollusk shell biocrystals are complex and might manifest in different ways even within a single individual. The single criterion of determining the mineralogical composition to attest shell sample conservation state should not be considered as sufficient.

A Novel Framework for the Comparative Analysis of Biological Networks

PubMed Central

Pache, Roland A.; Aloy, Patrick

2012-01-01

Genome sequencing projects provide nearly complete lists of the individual components present in an organism, but reveal little about how they work together. Follow-up initiatives have deciphered thousands of dynamic and context-dependent interrelationships between gene products that need to be analyzed with novel bioinformatics approaches able to capture their complex emerging properties. Here, we present a novel framework for the alignment and comparative analysis of biological networks of arbitrary topology. Our strategy includes the prediction of likely conserved interactions, based on evolutionary distances, to counter the high number of missing interactions in the current interactome networks, and a fast assessment of the statistical significance of individual alignment solutions, which vastly increases its performance with respect to existing tools. Finally, we illustrate the biological significance of the results through the identification of novel complex components and potential cases of cross-talk between pathways and alternative signaling routes. PMID:22363585

Autoantibodies against complement components in systemic lupus erythematosus - role in the pathogenesis and clinical manifestations.

PubMed

Hristova, M H; Stoyanova, V S

2017-12-01

Many complement structures and a number of additional factors, i.e. autoantibodies, receptors, hormones and cytokines, are implicated in the complex pathogenesis of systemic lupus erythematosus. Genetic defects in the complement as well as functional deficiency due to antibodies against its components lead to different pathological conditions, usually clinically presented. Among them hypocomplementemic urticarial vasculitis, different types of glomerulonephritis as dense deposit disease, IgA nephropathy, atypical haemolytic uremic syndrome and lupus nephritis are very common. These antibodies cause conformational changes leading to pathological activation or inhibition of complement with organ damage and/or limited capacity of the immune system to clear immune complexes and apoptotic debris. Finally, we summarize the role of complement antibodies in the pathogenesis of systemic lupus erythematosus and discuss the mechanism of some related clinical conditions such as infections, thyroiditis, thrombosis, acquired von Willebrand disease, etc.

Intraflagellar transport genes are essential for differentiation and survival of vertebrate sensory neurons.

PubMed

Tsujikawa, Motokazu; Malicki, Jarema

2004-06-10

Cilia play diverse roles in vertebrate and invertebrate sensory neurons. We show that a mutation of the zebrafish oval (ovl) locus affects a component of the ciliary transport (IFT) mechanism, the IFT88 polypeptide. In mutant retina, cilia are generated but not maintained, producing the absence of photoreceptor outer segments. A loss of cilia also occurs in auditory hair cells and olfactory sensory neurons. In all three sense organs, cilia defects are followed by degeneration of sensory cells. Similar phenotypes are induced by the absence of the IFT complex B polypeptides, ift52 and ift57, but not by the loss of complex A protein, ift140. The degeneration of mutant photoreceptor cells is caused, at least partially, by the ectopic accumulation of opsins. These studies reveal an essential role for IFT genes in vertebrate sensory neurons and implicate the molecular components of intraflagellar transport in degenerative disorders of these cells.

The regulatory software of cellular metabolism.

PubMed

Segrè, Daniel

2004-06-01

Understanding the regulation of metabolic pathways in the cell is like unraveling the 'software' that is running on the 'hardware' of the metabolic network. Transcriptional regulation of enzymes is an important component of this software. A recent systematic analysis of metabolic gene-expression data in Saccharomyces cerevisiae reveals a complex modular organization of co-expressed genes, which could increase our ability to understand and engineer cellular metabolic functions.

All-organic optoelectronic sensor for pulse oximetry

NASA Astrophysics Data System (ADS)

Lochner, Claire M.; Khan, Yasser; Pierre, Adrien; Arias, Ana C.

2014-12-01

Pulse oximetry is a ubiquitous non-invasive medical sensing method for measuring pulse rate and arterial blood oxygenation. Conventional pulse oximeters use expensive optoelectronic components that restrict sensing locations to finger tips or ear lobes due to their rigid form and area-scaling complexity. In this work, we report a pulse oximeter sensor based on organic materials, which are compatible with flexible substrates. Green (532 nm) and red (626 nm) organic light-emitting diodes (OLEDs) are used with an organic photodiode (OPD) sensitive at the aforementioned wavelengths. The sensor’s active layers are deposited from solution-processed materials via spin-coating and printing techniques. The all-organic optoelectronic oximeter sensor is interfaced with conventional electronics at 1 kHz and the acquired pulse rate and oxygenation are calibrated and compared with a commercially available oximeter. The organic sensor accurately measures pulse rate and oxygenation with errors of 1% and 2%, respectively.

Protein machines and self assembly in muscle organization

NASA Technical Reports Server (NTRS)

Barral, J. M.; Epstein, H. F.

1999-01-01

The remarkable order of striated muscle is the result of a complex series of protein interactions at different levels of organization. Within muscle, the thick filament and its major protein myosin are classical examples of functioning protein machines. Our understanding of the structure and assembly of thick filaments and their organization into the regular arrays of the A-band has recently been enhanced by the application of biochemical, genetic, and structural approaches. Detailed studies of the thick filament backbone have shown that the myosins are organized into a tubular structure. Additional protein machines and specific myosin rod sequences have been identified that play significant roles in thick filament structure, assembly, and organization. These include intrinsic filament components, cross-linking molecules of the M-band and constituents of the membrane-cytoskeleton system. Muscle organization is directed by the multistep actions of protein machines that take advantage of well-established self-assembly relationships. Copyright 1999 John Wiley & Sons, Inc.

Metallic elements in fossil fuel combustion products: amounts and form of emissions and evaluation of carcinogenicity and mutagenicity.

PubMed

Vouk, V B; Piver, W T

1983-01-01

Metallic elements contained in coal, oil and gasoline are mobilized by combustion processes and may be emitted into the atmosphere, mainly as components of submicron particles. The information about the amounts, composition and form of metal compounds is reviewed for some fuels and combustion processes. Since metal compounds are always contained in urban air pollutants, they have to be considered whenever an evaluation of biological impact of air pollutants is made. The value of currently used bioassays for the evaluation of the role of trace metal compounds, either as major biologically active components or as modifiers of biological effects of organic compounds is assessed. The whole animal bioassays for carcinogenicity do not seem to be an appropriate approach. They are costly, time-consuming and not easily amenable to the testing of complex mixtures. Some problems related to the application and interpretation of short-term bioassays are considered, and the usefulness of such bioassays for the evaluation of trace metal components contained in complex air pollution mixtures is examined.

Individual differences in components of impulsivity and effortful control moderate the relation between borderline personality disorder traits and emotion recognition in a sample of university students.

PubMed

Preti, Emanuele; Richetin, Juliette; Suttora, Chiara; Pisani, Alberto

2016-04-30

Dysfunctions in social cognition characterize personality disorders. However, mixed results emerged from literature on emotion processing. Borderline Personality Disorder (BPD) traits are either associated with enhanced emotion recognition, impairments, or equal functioning compared to controls. These apparent contradictions might result from the complexity of emotion recognition tasks used and from individual differences in impulsivity and effortful control. We conducted a study in a sample of undergraduate students (n=80), assessing BPD traits, using an emotion recognition task that requires the processing of only visual information or both visual and acoustic information. We also measured individual differences in impulsivity and effortful control. Results demonstrated the moderating role of some components of impulsivity and effortful control on the capability of BPD traits in predicting anger and happiness recognition. We organized the discussion around the interaction between different components of regulatory functioning and task complexity for a better understanding of emotion recognition in BPD samples. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The synaptonemal complex of basal metazoan hydra: more similarities to vertebrate than invertebrate meiosis model organisms.

PubMed

Fraune, Johanna; Wiesner, Miriam; Benavente, Ricardo

2014-03-20

The synaptonemal complex (SC) is an evolutionarily well-conserved structure that mediates chromosome synapsis during prophase of the first meiotic division. Although its structure is conserved, the characterized protein components in the current metazoan meiosis model systems (Drosophila melanogaster, Caenorhabditis elegans, and Mus musculus) show no sequence homology, challenging the question of a single evolutionary origin of the SC. However, our recent studies revealed the monophyletic origin of the mammalian SC protein components. Many of them being ancient in Metazoa and already present in the cnidarian Hydra. Remarkably, a comparison between different model systems disclosed a great similarity between the SC components of Hydra and mammals while the proteins of the ecdysozoan systems (D. melanogaster and C. elegans) differ significantly. In this review, we introduce the basal-branching metazoan species Hydra as a potential novel invertebrate model system for meiosis research and particularly for the investigation of SC evolution, function and assembly. Also, available methods for SC research in Hydra are summarized. Copyright © 2014. Published by Elsevier Ltd.

Metallic elements in fossil fuel combustion products: amounts and form of emissions and evaluation of carcinogenicity and mutagenicity.

PubMed Central

Vouk, V B; Piver, W T

1983-01-01

Metallic elements contained in coal, oil and gasoline are mobilized by combustion processes and may be emitted into the atmosphere, mainly as components of submicron particles. The information about the amounts, composition and form of metal compounds is reviewed for some fuels and combustion processes. Since metal compounds are always contained in urban air pollutants, they have to be considered whenever an evaluation of biological impact of air pollutants is made. The value of currently used bioassays for the evaluation of the role of trace metal compounds, either as major biologically active components or as modifiers of biological effects of organic compounds is assessed. The whole animal bioassays for carcinogenicity do not seem to be an appropriate approach. They are costly, time-consuming and not easily amenable to the testing of complex mixtures. Some problems related to the application and interpretation of short-term bioassays are considered, and the usefulness of such bioassays for the evaluation of trace metal components contained in complex air pollution mixtures is examined. PMID:6337825

Absorption spectrum analysis based on singular value decomposition for photoisomerization and photodegradation in organic dyes

NASA Astrophysics Data System (ADS)

Kawabe, Yutaka; Yoshikawa, Toshio; Chida, Toshifumi; Tada, Kazuhiro; Kawamoto, Masuki; Fujihara, Takashi; Sassa, Takafumi; Tsutsumi, Naoto

2015-10-01

In order to analyze the spectra of inseparable chemical mixtures, many mathematical methods have been developed to decompose them into the components relevant to species from series of spectral data obtained under different conditions. We formulated a method based on singular value decomposition (SVD) of linear algebra, and applied it to two example systems of organic dyes, being successful in reproducing absorption spectra assignable to cis/trans azocarbazole dyes from the spectral data after photoisomerization and to monomer/dimer of cyanine dyes from those during photodegaradation process. For the example of photoisomerization, polymer films containing the azocarbazole dyes were prepared, which have showed updatable holographic stereogram for real images with high performance. We made continuous monitoring of absorption spectrum after optical excitation and found that their spectral shapes varied slightly after the excitation and during recovery process, of which fact suggested the contribution from a generated photoisomer. Application of the method was successful to identify two spectral components due to trans and cis forms of azocarbazoles. Temporal evolution of their weight factors suggested important roles of long lifetimed cis states in azocarbazole derivatives. We also applied the method to the photodegradation of cyanine dyes doped in DNA-lipid complexes which have shown efficient and durable optical amplification and/or lasing under optical pumping. The same SVD method was successful in the extraction of two spectral components presumably due to monomer and H-type dimer. During the photodegradation process, absorption magnitude gradually decreased due to decomposition of molecules and their decaying rates strongly depended on the spectral components, suggesting that the long persistency of the dyes in DNA-complex related to weak tendency of aggregate formation.

The National Environmental Respiratory Center (NERC) experiment in multi-pollutant air quality health research: III. Components of diesel and gasoline engine exhausts, hardwood smoke and simulated downwind coal emissions driving non-cancer biological responses in rodents.

PubMed

Mauderly, Joe L; Seilkop, Steven K

2014-09-01

An approach to identify causal components of complex air pollution mixtures was explored. Rats and mice were exposed by inhalation 6 h daily for 1 week or 6 months to dilutions of simulated downwind coal emissions, diesel and gasoline exhausts and wood smoke. Organ weights, hematology, serum chemistry, bronchoalveolar lavage, central vascular and respiratory allergic responses were measured. Multiple additive regression tree (MART) analysis of the combined database ranked 45 exposure (predictor) variables for importance to models best fitting 47 significant responses. Single-predictor concentration-response data were examined for evidence of single response functions across all exposure groups. Replication of the responses by the combined influences of the two most important predictors was tested. Statistical power was limited by inclusion of only four mixtures, albeit in multiple concentrations each and with particles removed for some groups. Results gave suggestive or strong evidence of causation of 19 of the 47 responses. The top two predictors of the 19 responses included only 12 organic and 6 inorganic species or classes. An increase in red blood cell count of rats by ammonia and pro-atherosclerotic vascular responses of mice by inorganic gases yielded the strongest evidence for causation and the best opportunity for confirmation. The former was a novel finding; the latter was consistent with other results. The results demonstrated the plausibility of identifying putative causal components of highly complex mixtures, given a database in which the ratios of the components are varied sufficiently and exposures and response measurements are conducted using a consistent protocol.

Synthesis, Spectral Characterization, Thermal and Optical Studies of Novel Complexes: 4-(Dimethylamino)benzylidene-4-acetamideaniline and 4-(Dimethylamino)benzylidene-4-nitroaniline.

PubMed

Neupane, Umesh; Rai, R N

2017-11-01

The phase diagram representing solid-liquid equilibrium of entire range of composition and thermodynamic studies of two binary organic systems of 4-dimethylaminobenzaldehyde (DMAB) with two NLO active compounds, p-aminoacetanilide (PAA) and p-nitroaniline (PNA), have been studied by solid state synthetic route. Both systems are independently forming a new entity called intermolecular complex (IMC) and two eutectics on either side of intermolecular complexes. The various thermodynamic parameters such as heat of mixing, entropy of fusion, roughness parameter, interfacial energy and excess thermodynamic functions of IMCs and eutectics were calculated using the heat of fusion values. The TGA and DTA studies were performed to understand the physico-chemical, thermal behavior and unique identity of newly synthesized organic complexes, 4-(dimethylamino)benzylidene-4-acetamideaniline (DMABPAA) and 4-(dimethylamino)benzylidene-4-nitroaniline (DMABPNA), and their respective enthalpy of fusion values were found to be 30.01 and 37.26 kJ mol - 1 . The higher melting point of both the novel complexes than their parent's compounds reveal the strong molecular interaction between parent components to yield the complex. The FTIR spectral analysis predicts the disappearance of aldehyde peaks of DMAB and NH 2 peaks of PAA and PNA while the appearance of entirely new peaks than that of parent's compounds are the supportive for the formation of new molecular entities. These findings are further supported by FTNMR spectrum studies by observation of disappearance of proton peak of aldehyde of DMAB and amine peaks of PAA and PNA rather formation of new imine proton peak or peaks were observed. The appearance of new peaks in Powder XRD of complexes than those of parent components is further indicative for the formation of complexes. The absorption spectrum of DMABPAA and DMABPNA showed intra-molecular charge-transfer (ICT) excited state absorption at 258 and 241 nm, respectively. Both the IMCs, DMABPAA and DMABPNA, show strong fluorescence with quantum yield 0.66 and 0.93, respectively, in methanol solution.

Sustainability and the health care manager: part I.

PubMed

Ramirez, Bernardo; Oetjen, Reid M; Malvey, Donna

2011-01-01

Given the current operating climate, organizations are coming under pressure to develop and implement sustainability programs and projects, yet few managers truly understand what is meant by sustainability and its implications for managing organizations. This article examines the concept of sustainability and provides a broader definition of the term than going "green." Using a puzzle metaphor, the authors outline and explain the different components of sustainability and provide a checklist for achieving sustainability goals. In addition, resources such as guides and tools are reviewed and offered to assist managers in gaining more insight into the challenges and complexity of sustainability.

The microbial nitrogen-cycling network.

PubMed

Kuypers, Marcel M M; Marchant, Hannah K; Kartal, Boran

2018-05-01

Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet. By far, the largest inventory of freely accessible nitrogen is atmospheric dinitrogen, but most organisms rely on more bioavailable forms of nitrogen, such as ammonium and nitrate, for growth. The availability of these substrates depends on diverse nitrogen-transforming reactions that are carried out by complex networks of metabolically versatile microorganisms. In this Review, we summarize our current understanding of the microbial nitrogen-cycling network, including novel processes, their underlying biochemical pathways, the involved microorganisms, their environmental importance and industrial applications.

Small-Scale Fabrication of Biomimetic Structures for Periodontal Regeneration

PubMed Central

Green, David W.; Lee, Jung-Seok; Jung, Han-Sung

2016-01-01

The periodontium is the supporting tissues for the tooth organ and is vulnerable to destruction, arising from overpopulating pathogenic bacteria and spirochaetes. The presence of microbes together with host responses can destroy large parts of the periodontium sometimes leading tooth loss. Permanent tissue replacements are made possible with tissue engineering techniques. However, existing periodontal biomaterials cannot promote proper tissue architectures, necessary tissue volumes within the periodontal pocket and a “water-tight” barrier, to become clinically acceptable. New kinds of small-scale engineered biomaterials, with increasing biological complexity are needed to guide proper biomimetic regeneration of periodontal tissues. So the ability to make compound structures with small modules, filled with tissue components, is a promising design strategy for simulating the anatomical complexity of the periodotium attachment complexes along the tooth root and the abutment with the tooth collar. Anatomical structures such as, intima, adventitia, and special compartments such as the epithelial cell rests of Malassez or a stellate reticulum niche need to be engineered from the start of regeneration to produce proper periodontium replacement. It is our contention that the positioning of tissue components at the origin is also necessary to promote self-organizing cell–cell connections, cell–matrix connections. This leads to accelerated, synchronized and well-formed tissue architectures and anatomies. This strategy is a highly effective preparation for tackling periodontitis, periodontium tissue resorption, and to ultimately prevent tooth loss. Furthermore, such biomimetic tissue replacements will tackle problems associated with dental implant support and perimimplantitis. PMID:26903872

On-line coupling of counter-current chromatography and macroporous resin chromatography for continuous isolation of arctiin from the fruit of Arctium lappa L.

PubMed

Guo, Mengzhe; Liang, Junling; Wu, Shihua

2010-08-13

In this work, we have developed a novel hybrid two-dimensional counter-current chromatography and liquid chromatography (2D CCC x LC) system for the continuous purification of arctiin from crude extract of Arctium lappa. The first dimensional CCC column has been designed to fractionalize crude complex extract into pure arctiin effluent using a one-component organic/salt-containing system, and the second dimensional LC column has been packed with macroporous resin for on-line adsorption, desalination and desorption of arctiin which was effluent purified from the first CCC dimension. Thus, the crude arctiin mixture has been purified efficiently and conveniently by on-line CCC x LC in spite of the use of a salt-containing solvent system in CCC separation. As a result, high purity (more than 97%) of arctiin has been isolated by repeated injections both using the ethyl acetate-8% sodium chloride aqueous solution and butanol-1% sodium chloride aqueous solution. By contrast with the traditional CCC processes using multi-component organic/aqueous solvent systems, the present on-line CCC x LC process only used a one-component organic solvent and thus the solvent is easier to recover and regenerate. All of used solvents such as ethyl acetate, n-butanol and NaCl aqueous solution are low toxicity and environment-friendly. Moreover, the lower phase of salt-containing aqueous solution used as mobile phase, only contained minor organic solvent, which will save much organic solvent in continuous separation. In summary, our results indicated that the on-line hybrid 2D CCC x LC system using one-component organic/salt-containing aqueous solution is very promising and powerful tool for high-throughput purification of arctiin from fruits of A. lappa. 2010 Elsevier B.V. All rights reserved.

Sphingolipids from the human fungal pathogen Aspergillus fumigatus.

PubMed

Fontaine, Thierry

2017-10-01

Sphingolipids (SPLs) are key components of the plasma membrane in yeast and filamentous fungi. These molecules are involved in a number of cellular processes, and particularly, SGLs are essential components of the highly polarized fungal growth where they are required for the formation of the polarisome organization at the hyphal apex. Aspergillus fumigatus, a human fungal pathogen, produce SGLs that are discriminated into neutral cerebrosides, glycosylinositolphosphoceramides (GIPCs) and glycosylphosphatidylinositol (GPI) anchors. In addition to complex hydrophilic head groups of GIPCs, A. fumigatus is, to date, the sole fungus that produces a GPI-anchored polysaccharide. These SPLs follow three different biosynthetic pathways. Genetics blockage leading to the inhibition of any SPL biosynthesis or to the alteration of the structure of SPL induces growth and virulence defects. The complete lipid moiety of SPLs is essential for the lipid microdomain organization and their biosynthetic pathways are potential antifungal targets but remains understudied. Copyright © 2017. Published by Elsevier B.V.

Untargeted Identification of Wood Type-Specific Markers in Particulate Matter from Wood Combustion.

PubMed

Weggler, Benedikt A; Ly-Verdu, Saray; Jennerwein, Maximilian; Sippula, Olli; Reda, Ahmed A; Orasche, Jürgen; Gröger, Thomas; Jokiniemi, Jorma; Zimmermann, Ralf

2016-09-20

Residential wood combustion emissions are one of the major global sources of particulate and gaseous organic pollutants. However, the detailed chemical compositions of these emissions are poorly characterized due to their highly complex molecular compositions, nonideal combustion conditions, and sample preparation steps. In this study, the particulate organic emissions from a masonry heater using three types of wood logs, namely, beech, birch, and spruce, were chemically characterized using thermal desorption in situ derivatization coupled to a GCxGC-ToF/MS system. Untargeted data analyses were performed using the comprehensive measurements. Univariate and multivariate chemometric tools, such as analysis of variance (ANOVA), principal component analysis (PCA), and ANOVA simultaneous component analysis (ASCA), were used to reduce the data to highly significant and wood type-specific features. This study reveals substances not previously considered in the literature as meaningful markers for differentiation among wood types.

Cell-free synthetic biology for environmental sensing and remediation.

PubMed

Karig, David K

2017-06-01

The fields of biosensing and bioremediation leverage the phenomenal array of sensing and metabolic capabilities offered by natural microbes. Synthetic biology provides tools for transforming these fields through complex integration of natural and novel biological components to achieve sophisticated sensing, regulation, and metabolic function. However, the majority of synthetic biology efforts are conducted in living cells, and concerns over releasing genetically modified organisms constitute a key barrier to environmental applications. Cell-free protein expression systems offer a path towards leveraging synthetic biology, while preventing the spread of engineered organisms in nature. Recent efforts in the areas of cell-free approaches for sensing, regulation, and metabolic pathway implementation, as well as for preserving and deploying cell-free expression components, embody key steps towards realizing the potential of cell-free systems for environmental sensing and remediation. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

Distribution and dynamics of electron transport complexes in cyanobacterial thylakoid membranes☆

PubMed Central

Liu, Lu-Ning

2016-01-01

The cyanobacterial thylakoid membrane represents a system that can carry out both oxygenic photosynthesis and respiration simultaneously. The organization, interactions and mobility of components of these two electron transport pathways are indispensable to the biosynthesis of thylakoid membrane modules and the optimization of bioenergetic electron flow in response to environmental changes. These are of fundamental importance to the metabolic robustness and plasticity of cyanobacteria. This review summarizes our current knowledge about the distribution and dynamics of electron transport components in cyanobacterial thylakoid membranes. Global understanding of the principles that govern the dynamic regulation of electron transport pathways in nature will provide a framework for the design and synthetic engineering of new bioenergetic machinery to improve photosynthesis and biofuel production. This article is part of a Special Issue entitled: Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux. PMID:26619924

Distribution and dynamics of electron transport complexes in cyanobacterial thylakoid membranes.

PubMed

Liu, Lu-Ning

2016-03-01

The cyanobacterial thylakoid membrane represents a system that can carry out both oxygenic photosynthesis and respiration simultaneously. The organization, interactions and mobility of components of these two electron transport pathways are indispensable to the biosynthesis of thylakoid membrane modules and the optimization of bioenergetic electron flow in response to environmental changes. These are of fundamental importance to the metabolic robustness and plasticity of cyanobacteria. This review summarizes our current knowledge about the distribution and dynamics of electron transport components in cyanobacterial thylakoid membranes. Global understanding of the principles that govern the dynamic regulation of electron transport pathways in nature will provide a framework for the design and synthetic engineering of new bioenergetic machinery to improve photosynthesis and biofuel production. This article is part of a Special Issue entitled: Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux. Copyright © 2015 The Author. Published by Elsevier B.V. All rights reserved.

Effects of thermal treatment on high solid anaerobic digestion of swine manure: Enhancement assessment and kinetic analysis.

PubMed

Wu, Jing; Hu, Yu-Ying; Wang, Shi-Feng; Cao, Zhi-Ping; Li, Huai-Zhi; Fu, Xin-Mei; Wang, Kai-Jun; Zuo, Jian-E

2017-04-01

Anaerobic digestion (AD), which is a process for generating biogas, can be applied to the treatment of organic wastes. Owing to its smaller footprint, lower energy consumption, and less digestate, high solid anaerobic digestion (HSAD) has attracted increasing attention. However, its biogas production is poor. In order to improve biogas production and decrease energy consumption, an improved thermal treatment process was proposed. Raw swine manure (>20% solid content) without any dilution was thermally treated at 70±1°C for different retention times, and then its effect on HSAD was investigated via batch AD experiments at 8.9% solid content. Results showed that the main organic components of swine manure hydrolyzed significantly during the thermal treatment, and HSAD's methane production rate was improved by up to 39.5%. Analysis using two kinetic models confirmed that the treatment could increase biodegradable organics (especially the readily biodegradable organics) in swine manure rather than upgrading its hydrolysis rate. It is worth noting that the superimposed first-order kinetics model was firstly applied in AD, and was a good tool to reveal the AD kinetics mechanism of substrates with complex components. Copyright © 2017 Elsevier Ltd. All rights reserved.

Organic compounds in circumstellar and interstellar environments.

PubMed

Kwok, Sun

2015-06-01

Recent research has discovered that complex organic matter is prevalent throughout the Universe. In the Solar System, it is found in meteorites, comets, interplanetary dust particles, and planetary satellites. Spectroscopic signatures of organics with aromatic/aliphatic structures are also found in stellar ejecta, diffuse interstellar medium, and external galaxies. From space infrared spectroscopic observations, we have found that complex organics can be synthesized in the late stages of stellar evolution. Shortly after the nuclear synthesis of the element carbon, organic gas-phase molecules are formed in the stellar winds, which later condense into solid organic particles. This organic synthesis occurs over very short time scales of about a thousand years. In order to determine the chemical structures of these stellar organics, comparisons are made with particles produced in the laboratory. Using the technique of chemical vapor deposition, artificial organic particles have been created by injecting energy into gas-phase hydrocarbon molecules. These comparisons led us to believe that the stellar organics are best described as amorphous carbonaceous nanoparticles with mixed aromatic and aliphatic components. The chemical structures of the stellar organics show strong similarity to the insoluble organic matter found in meteorites. Isotopic analysis of meteorites and interplanetary dust collected in the upper atmospheres have revealed the presence of pre-solar grains similar to those formed in old stars. This provides a direct link between star dust and the Solar System and raises the possibility that the early Solar System was chemically enriched by stellar ejecta with the potential of influencing the origin of life on Earth.

Eutectics as improved pharmaceutical materials: design, properties and characterization.

PubMed

Cherukuvada, Suryanarayan; Nangia, Ashwini

2014-01-28

Eutectics are a long known class of multi-component solids with important and useful applications in daily life. In comparison to other multi-component crystalline solids, such as salts, solid solutions, molecular complexes and cocrystals, eutectics are less studied in terms of molecular structure organization and bonding interactions. Classically, a eutectic is defined based on its low melting point compared to the individual components. In this article, we attempt to define eutectics not just based on thermal methods but from a structural organization view point, and discuss their microstructures and properties as organic materials vis-a-vis solid solutions and cocrystals. The X-ray crystal structure of a cocrystal is different from that of the individual components whereas the unit cell of a solid solution is similar to that of one of the components. Eutectics are closer to the latter species in that their crystalline arrangement is similar to the parent components but they are different with respect to the structural integrity. A solid solution possesses structural homogeneity throughout the structure (single phase) but a eutectic is a heterogeneous ensemble of individual components whose crystal structures are like discontinuous solid solutions (phase separated). Thus, a eutectic may be better defined as a conglomerate of solid solutions. A structural analysis of cocrystals, solid solutions and eutectics has led to an understanding that materials with strong adhesive (hetero) interactions between the unlike components will lead to cocrystals whereas those having stronger cohesive (homo/self) interactions will more often give rise to solid solutions (for similar structures of components) and eutectics (for different structures of components). We demonstrate that the same crystal engineering principles which have been profitably utilized for cocrystal design in the past decade can now be applied to make eutectics as novel composite materials, illustrated by stable eutectics of the hygroscopic salt of the anti-tuberculosis drug ethambutol as a case study. A current gap in the characterization of eutectic microstructure may be fulfilled through pair distribution function (PDF) analysis of X-ray diffraction data, which could be a rapid signature technique to differentiate eutectics from their components.

Two dimensional Blue Native-/SDS-PAGE analysis of SLP family adaptor protein complexes.

PubMed

Swamy, Mahima; Kulathu, Yogesh; Ernst, Sandra; Reth, Michael; Schamel, Wolfgang W A

2006-04-15

SH2 domain containing leukocyte protein (SLP) adaptor proteins serve a central role in the antigen-mediated activation of lymphocytes by organizing multiprotein signaling complexes. Here, we use two dimensional native-/SDS-gel electrophoresis to study the number, size and relative abundance of protein complexes containing SLP family proteins. In non-stimulated T cells all SLP-76 proteins are in a approximately 400 kDa complex with the small adaptor protein Grb2-like adaptor protein downstream of Shc (Gads), whereas half of Gads is monomeric. This constitutive SLP-76/Gads complex could be reconstituted in Drosophila S2 cells expressing both components, suggesting that it might not contain additional subunits. In contrast, in B cells SLP-65 exists in a 180 kDa complex as well as in monomeric form. Since the complex was not found in S2 cells expressing only SLP-65, it was not di/trimeric SLP-65. Upon antigen-stimulation only the complexed SLP-65 was phosphorylated. Surprisingly, stimulation-induced alteration of SLP complexes could not be detected, suggesting that active signaling complexes form only transiently, and are of low abundance.

Soil Organic Matter in Its Native State: Unravelling the Most Complex Biomaterial on Earth.

PubMed

Masoom, Hussain; Courtier-Murias, Denis; Farooq, Hashim; Soong, Ronald; Kelleher, Brian P; Zhang, Chao; Maas, Werner E; Fey, Michael; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Simpson, Myrna J; Simpson, André J

2016-02-16

Since the isolation of soil organic matter in 1786, tens of thousands of publications have searched for its structure. Nuclear magnetic resonance (NMR) spectroscopy has played a critical role in defining soil organic matter but traditional approaches remove key information such as the distribution of components at the soil-water interface and conformational information. Here a novel form of NMR with capabilities to study all physical phases termed Comprehensive Multiphase NMR, is applied to analyze soil in its natural swollen-state. The key structural components in soil organic matter are identified to be largely composed of macromolecular inputs from degrading biomass. Polar lipid heads and carbohydrates dominate the soil-water interface while lignin and microbes are arranged in a more hydrophobic interior. Lignin domains cannot be penetrated by aqueous solvents even at extreme pH indicating they are the most hydrophobic environment in soil and are ideal for sequestering hydrophobic contaminants. Here, for the first time, a complete range of physical states of a whole soil can be studied. This provides a more detailed understanding of soil organic matter at the molecular level itself key to develop the most efficient soil remediation and agricultural techniques, and better predict carbon sequestration and climate change.

Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex

PubMed Central

Ohashi, Yohei; Soler, Nicolas; García Ortegón, Miguel; Zhang, Lufei; Kirsten, Marie L.; Perisic, Olga; Masson, Glenn R.; Burke, John E.; Jakobi, Arjen J.; Apostolakis, Apostolos A.; Johnson, Christopher M.; Ohashi, Maki; Ktistakis, Nicholas T.; Sachse, Carsten; Williams, Roger L.

2016-01-01

ABSTRACT The phosphatidylinositol 3-kinase Vps34 is part of several protein complexes. The structural organization of heterotetrameric complexes is starting to emerge, but little is known about organization of additional accessory subunits that interact with these assemblies. Combining hydrogen-deuterium exchange mass spectrometry (HDX-MS), X-ray crystallography and electron microscopy (EM), we have characterized Atg38 and its human ortholog NRBF2, accessory components of complex I consisting of Vps15-Vps34-Vps30/Atg6-Atg14 (yeast) and PIK3R4/VPS15-PIK3C3/VPS34-BECN1/Beclin 1-ATG14 (human). HDX-MS shows that Atg38 binds the Vps30-Atg14 subcomplex of complex I, using mainly its N-terminal MIT domain and bridges the coiled-coil I regions of Atg14 and Vps30 in the base of complex I. The Atg38 C-terminal domain is important for localization to the phagophore assembly site (PAS) and homodimerization. Our 2.2 Å resolution crystal structure of the Atg38 C-terminal homodimerization domain shows 2 segments of α-helices assembling into a mushroom-like asymmetric homodimer with a 4-helix cap and a parallel coiled-coil stalk. One Atg38 homodimer engages a single complex I. This is in sharp contrast to human NRBF2, which also forms a homodimer, but this homodimer can bridge 2 complex I assemblies. PMID:27630019

Complexation- and ligand-induced metal release from 316L particles: importance of particle size and crystallographic structure.

PubMed

Hedberg, Yolanda; Hedberg, Jonas; Liu, Yi; Wallinder, Inger Odnevall

2011-12-01

Iron, chromium, nickel, and manganese released from gas-atomized AISI 316L stainless steel powders (sized <45 and <4 μm) were investigated in artificial lysosomal fluid (ALF, pH 4.5) and in solutions of its individual inorganic and organic components to determine its most aggressive component, elucidate synergistic effects, and assess release mechanisms, in dependence of surface changes using atomic absorption spectroscopy, Raman, XPS, and voltammetry. Complexation is the main reason for metal release from 316L particles immersed in ALF. Iron was mainly released, while manganese was preferentially released as a consequence of the reduction of manganese oxide on the surface. These processes resulted in highly complexing media in a partial oxidation of trivalent chromium to hexavalent chromium on the surface. The extent of metal release was partially controlled by surface properties (e.g., availability of elements on the surface and structure of the outermost surface) and partially by the complexation capacity of the different metals with the complexing agents of the different media. In general, compared to the coarse powder (<45 μm), the fine (<4 μm) powder displayed significantly higher released amounts of metals per surface area, increased with increased solution complexation capacity, while less amounts of metals were released into non-complexing solutions. Due to the ferritic structure of lower solubility for nickel of the fine powder, more nickel was released into all solutions compared with the coarser powder.

Bioavailability of cyanide and metal-cyanide mixtures to aquatic life.

PubMed

Redman, Aaron; Santore, Robert

2012-08-01

Cyanide can be toxic to aquatic organisms, and the U.S. Environmental Protection Agency has developed ambient water-quality criteria to protect aquatic life. Recent work suggests that considering free, rather than total, cyanide provides a more accurate measure of the biological effects of cyanides and provides a basis for water-quality criteria. Aquatic organisms are sensitive to free cyanide, although certain metals can form stable complexes and reduce the amount of free cyanide. As a result, total cyanide is less toxic when complexing metals are present. Cyanide is often present in complex effluents, which requires understanding how other components within these complex effluents can affect cyanide speciation and bioavailability. The authors have developed a model to predict the aqueous speciation of cyanide and have shown that this model can predict the toxicity of metal-cyanide complexes in terms of free cyanide in solutions with varying water chemistry. Toxicity endpoints based on total cyanide ranged over several orders of magnitude for various metal-cyanide mixtures. However, predicted free cyanide concentrations among these same tests described the observed toxicity data to within a factor of 2. Aquatic toxicity can be well-described using free cyanide, and under certain conditions the toxicity was jointly described by free cyanide and elevated levels of bioavailable metals. Copyright © 2012 SETAC.

Evolution and diversity of plant cell walls: from algae to flowering plants.

PubMed

Popper, Zoë A; Michel, Gurvan; Hervé, Cécile; Domozych, David S; Willats, William G T; Tuohy, Maria G; Kloareg, Bernard; Stengel, Dagmar B

2011-01-01

All photosynthetic multicellular Eukaryotes, including land plants and algae, have cells that are surrounded by a dynamic, complex, carbohydrate-rich cell wall. The cell wall exerts considerable biological and biomechanical control over individual cells and organisms, thus playing a key role in their environmental interactions. This has resulted in compositional variation that is dependent on developmental stage, cell type, and season. Further variation is evident that has a phylogenetic basis. Plants and algae have a complex phylogenetic history, including acquisition of genes responsible for carbohydrate synthesis and modification through a series of primary (leading to red algae, green algae, and land plants) and secondary (generating brown algae, diatoms, and dinoflagellates) endosymbiotic events. Therefore, organisms that have the shared features of photosynthesis and possession of a cell wall do not form a monophyletic group. Yet they contain some common wall components that can be explained increasingly by genetic and biochemical evidence.

Understanding Structure and Bonding of Multilayered Metal–Organic Nanostructures

PubMed Central

2013-01-01

For organic and hybrid electronic devices, the physicochemical properties of the contained interfaces play a dominant role. To disentangle the various interactions occurring at such heterointerfaces, we here model a complex, yet prototypical, three-component system consisting of a Cu–phthalocyanine (CuPc) film on a 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) monolayer adsorbed on Ag(111). The two encountered interfaces are similar, as in both cases there would be no bonding without van der Waals interactions. Still, they are also distinctly different, as only at the Ag(111)–PTCDA interface do massive charge-rearrangements occur. Using recently developed theoretical tools, we show that it has become possible to provide atomistic insight into the physical and chemical processes in this comparatively complex nanostructure distinguishing between interactions involving local rearrangements of the charge density and long-range van der Waals attraction. PMID:23447750

Adsorption of humic acids and trace metals in natural waters

NASA Technical Reports Server (NTRS)

Leung, W. H.

1982-01-01

Studies concerning the interactions between suspended hydrous iron oxide and dissolved humic acids and trace metals are reported. As a major component of dissolved organic matters and its readiness for adsorption at the solid/water interface, humic acids may play a very important role in the organometallic geochemistry of suspended sediments and in determining the fate and distribution of trace metals, pesticides and anions in natural water systems. Most of the solid phases in natural waters contain oxides and hydroxides. The most simple promising theory to describe the interactions of hydrous iron oxide interface is the surface complex formation model. In this model, the adsorptions of humic acids on hydrous iron oxide may be interpreted as complex formation of the organic bases (humic acid oxyanions) with surface Fe ions. Measurements on adsorptions were made in both fresh water and seawater. Attempts have been made to fit our data to Langmuir adsorption isotherm. Adsorption equilibrium constants were determined.

SSB as an organizer/mobilizer of genome maintenance complexes

PubMed Central

Shereda, Robert D.; Kozlov, Alexander G.; Lohman, Timothy M.; Cox, Michael M.; Keck, James L.

2008-01-01

When duplex DNA is altered in almost any way (replicated, recombined, or repaired), single strands of DNA are usually intermediates, and single-stranded DNA binding (SSB) proteins are present. These proteins have often been described as inert, protective DNA coatings. Continuing research is demonstrating a far more complex role of SSB that includes the organization and/or mobilization of all aspects of DNA metabolism. Escherichia coli SSB is now known to interact with at least 14 other proteins that include key components of the elaborate systems involved in every aspect of DNA metabolism. Most, if not all, of these interactions are mediated by the amphipathic C-terminus of SSB. In this review, we summarize the extent of the eubacterial SSB interaction network, describe the energetics of interactions with SSB, and highlight the roles of SSB in the process of recombination. Similar themes to those highlighted in this review are evident in all biological systems. PMID:18937104

Inorganic salts interact with oxalic acid in submicron particles to form material with low hygroscopicity and volatility

NASA Astrophysics Data System (ADS)

Drozd, G.; Woo, J.; Häkkinen, S. A. K.; Nenes, A.; McNeill, V. F.

2014-05-01

Volatility and hygroscopicity are two key properties of organic aerosol components, and both are strongly related to chemical identity. While the hygroscopicities of pure salts, di-carboxylic acids (DCA), and DCA salts are known, the hygroscopicity of internal mixtures of these components, as they are typically found in the atmosphere, has not been fully characterized. Here we show that inorganic-organic component interactions typically not considered in atmospheric models can lead to very strongly bound metal-organic complexes and greatly affect aerosol volatility and hygroscopicity; in particular, the bi-dentate binding of DCA to soluble inorganic ions. We have studied the volatility of pure, dry organic salt particles and the hygroscopicity of internal mixtures of oxalic acid (OxA, the dominant DCA in the atmosphere) and a number of salts, both mono- and di-valent. The formation of very low volatility organic salts was confirmed, with minimal evaporation of oxalate salt particles below 75 °C. Dramatic increases in the cloud condensation nuclei (CCN) activation diameter for particles with di-valent salts (e.g., CaCl2) and relatively small particle volume fractions of OxA indicate that standard volume additivity rules for hygroscopicity do not apply. Thus small organic compounds with high O : C ratios are capable of forming low-volatility and very low hygroscopicity particles. Given current knowledge of the formation mechanisms of OxA and M-Ox salts, surface enrichment of insoluble M-Ox salts is expected. The resulting formation of an insoluble coating of metal-oxalate salts can explain low-particle hygroscopicities. The formation of particles with a hard coating could offer an alternative explanation for observations of glass-like particles without the need for a phase transition.

Role of Organic Matter in the Removal of Heavy Metals in Stormwater Runoff

NASA Astrophysics Data System (ADS)

Barrett, M.; Ingenloff, C.; Katz, L.

2011-12-01

Heavy metals (copper, zinc, and lead) are common constituents in highway runoff and concentrations in runoff from highway facilities are particularly high. These concentrations are also generally higher than observed in natural water bodies and several studies have demonstrated acute and chronic toxicity to aquatic ecosystems. One focus of this project is to assess the potential of sorption to reduce the concentration of metals in runoff. The difficulty evaluating adsorption in multi-component systems is to capture the impacts of background organic matter and other complexing ions on adsorption behavior. Very few studies have evaluated the ability of surface complexation models to predict adsorption in systems that contain organic matter from highway runoff. Moreover, the composition of the organic matter in stormwater runoff can be significantly different from natural organic matter typically used to assess the impact of background organics on metal ion adsorption. This research project specifically addresses these concerns and examines the impact of highway runoff on the adsorption behavior to determine whether existing surface complexation and chemical speciation models and parameter databases can be used to predict adsorption of target metal ions in these waters. Previous research has employed both actual storm water that has been obtained from actual field highway runoff sites as well as synthetic storm water compositions that have attempted to mimic the major components of natural storm water. Researchers and practitioners in the field generally agree on the importance of capturing the background water matrix; however, concerns associated with required volumes, holding times, aging, consistency and temporal and spatial variability often favor the use of synthetic formulations. While synthetic storm water can achieve the required consistency, numerous artifacts can be introduced due to the high reactivity of trace metal ions with background inorganic and organic ligands. Of particular concern, is the background organic matrix associated with stormwater. While most of the inorganic composition of natural stormwater can be adequately characterized using routine analytical procedures, characterization of organic matter to the same level of detail is not possible. Indeed, methods for characterization of natural organic matter typically only provide operational definitions of the composition. A compromise between using natural and synthetic storm water was therefore made by recognizing the importance of capturing the organic matter from natural storm water, but adding the flexibility of using synthetic storm water to provide the ionic composition. To alleviate concerns associated with storing large volumes and aging of organic solutions, the storm water was concentrated within twenty-four hours of collection using reverse osmosis and then freeze-dried. The freeze-dried organic matter will be reconstituted as needed at concentrations that mimic the initial total organic concentration of the stormwater when it was collected. This paper provides detailed guidance for the preparation of a synthetic water that can be used to simulate stormwater composition.

Point process models for localization and interdependence of punctate cellular structures.

PubMed

Li, Ying; Majarian, Timothy D; Naik, Armaghan W; Johnson, Gregory R; Murphy, Robert F

2016-07-01

Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures. © 2016 International Society for Advancement of Cytometry. © 2016 International Society for Advancement of Cytometry.

The Role of Ultrahigh Resolution Fourier Transform Mass Spectrometry (FT-MS) in Astrobiology-Related Research: Analysis of Meteorites and Tholins.

PubMed

Somogyi, Árpád; Thissen, Roland; Orthous-Daunay, Francois-Régis; Vuitton, Véronique

2016-03-24

It is an important but also a challenging analytical problem to understand the chemical composition and structure of prebiotic organic matter that is present in extraterrestrial materials. Its formation, evolution and content in the building blocks ("seeds") for more complex molecules, such as proteins and DNA, are key questions in the field of exobiology. Ultrahigh resolution mass spectrometry is one of the best analytical techniques that can be applied because it provides reliable information on the chemical composition and structure of individual components of complex organic mixtures. Prebiotic organic material is delivered to Earth by meteorites or generated in laboratories in simulation (model) experiments that mimic space or atmospheric conditions. Recent representative examples for ultrahigh resolution mass spectrometry studies using Fourier-transform (FT) mass spectrometers such as Orbitrap and ion cyclotron resonance (ICR) mass spectrometers are shown and discussed in the present article, including: (i) the analysis of organic matter of meteorites; (ii) modeling atmospheric processes in ICR cells; and (iii) the structural analysis of laboratory made tholins that might be present in the atmosphere and surface of Saturn's largest moon, Titan.

The Role of Ultrahigh Resolution Fourier Transform Mass Spectrometry (FT-MS) in Astrobiology-Related Research: Analysis of Meteorites and Tholins

PubMed Central

Somogyi, Árpád; Thissen, Roland; Orthous-Daunay, Francois-Régis; Vuitton, Véronique

2016-01-01

It is an important but also a challenging analytical problem to understand the chemical composition and structure of prebiotic organic matter that is present in extraterrestrial materials. Its formation, evolution and content in the building blocks (“seeds”) for more complex molecules, such as proteins and DNA, are key questions in the field of exobiology. Ultrahigh resolution mass spectrometry is one of the best analytical techniques that can be applied because it provides reliable information on the chemical composition and structure of individual components of complex organic mixtures. Prebiotic organic material is delivered to Earth by meteorites or generated in laboratories in simulation (model) experiments that mimic space or atmospheric conditions. Recent representative examples for ultrahigh resolution mass spectrometry studies using Fourier-transform (FT) mass spectrometers such as Orbitrap and ion cyclotron resonance (ICR) mass spectrometers are shown and discussed in the present article, including: (i) the analysis of organic matter of meteorites; (ii) modeling atmospheric processes in ICR cells; and (iii) the structural analysis of laboratory made tholins that might be present in the atmosphere and surface of Saturn’s largest moon, Titan. PMID:27023520

The Redox Code.

PubMed

Jones, Dean P; Sies, Helmut

2015-09-20

The redox code is a set of principles that defines the positioning of the nicotinamide adenine dinucleotide (NAD, NADP) and thiol/disulfide and other redox systems as well as the thiol redox proteome in space and time in biological systems. The code is richly elaborated in an oxygen-dependent life, where activation/deactivation cycles involving O₂ and H₂O₂ contribute to spatiotemporal organization for differentiation, development, and adaptation to the environment. Disruption of this organizational structure during oxidative stress represents a fundamental mechanism in system failure and disease. Methodology in assessing components of the redox code under physiological conditions has progressed, permitting insight into spatiotemporal organization and allowing for identification of redox partners in redox proteomics and redox metabolomics. Complexity of redox networks and redox regulation is being revealed step by step, yet much still needs to be learned. Detailed knowledge of the molecular patterns generated from the principles of the redox code under defined physiological or pathological conditions in cells and organs will contribute to understanding the redox component in health and disease. Ultimately, there will be a scientific basis to a modern redox medicine.

Mitochondrial phenotype during torpor: Modulation of mitochondrial electron transport system in the Chilean mouse-opossum Thylamys elegans.

PubMed

Cortes, Pablo A; Bozinovic, Francisco; Blier, Pierre U

2018-07-01

Mammalian torpor is a phenotype characterized by a controlled decline of metabolic rate, generally followed by a reduction in body temperature. During arousal from torpor, both metabolic rate and body temperature rapidly returns to resting levels. Metabolic rate reduction experienced by torpid animals is triggered by active suppression of mitochondrial respiration, which is rapidly reversed during rewarming process. In this study, we analyzed the changes in the maximal activity of key enzymes related to electron transport system (complexes I, III and IV) in six tissues of torpid, arousing and euthermic Chilean mouse-opossums (Thylamys elegans). We observed higher maximal activities of complexes I and IV during torpor in brain, heart and liver, the most metabolically active organs in mammals. On the contrary, higher enzymatic activities of complexes III were observed during torpor in kidneys and lungs. Moreover, skeletal muscle was the only tissue without significant differences among stages in all complexes evaluated, suggesting no modulation of oxidative capacities of electron transport system components in this thermogenic tissue. In overall, our data suggest that complexes I and IV activity plays a major role in initiation and maintenance of metabolic suppression during torpor in Chilean mouse-opossum, whereas improvement of oxidative capacities in complex III might be critical to sustain metabolic machinery in organs that remains metabolically active during torpor. Copyright © 2018 Elsevier Inc. All rights reserved.

The Bio-Logic and machinery of plant morphogenesis.

PubMed

Niklas, Karl J

2003-04-01

Morphogenesis (the development of organic form) requires signal-trafficking and cross-talking across all levels of organization to coordinate the operation of metabolic and genomic networked systems. Many biologists are currently converging on the pictorial conventions of computer scientists to render biological signaling as logic circuits supervising the operation of one or more signal-activated metabolic or gene networks. This approach can redact and simplify complex morphogenetic phenomena and allows for their aggregation into diagrams of larger, more "global" networked systems. This conceptualization is discussed in terms of how logic circuits and signal-activated subsystems work, and it is illustrated for examples of increasingly more complex morphogenetic phenomena, e.g., auxin-mediated cell expansion, entry into the mitotic cell cycle phases, and polar/lateral intercellular auxin transport. For each of these phenomena, a posited circuit/subsystem diagram draws rapid attention to missing components, either in the logic circuit or in the subsystem it supervises. These components must be identified experimentally if each of these basic phenomena is to be fully understood. Importantly, the power of the circuit/subsystem approach to modeling developmental phenomena resides not in its pictorial appeal but in the mathematical tools that are sufficiently strong to reveal and quantify the synergistics of networked systems and thus foster a better understanding of morphogenesis.

Fluorescence spectroscopy as a specific tool for the interaction study of two surfactants with natural and synthetic organic compounds

NASA Astrophysics Data System (ADS)

Jung, Aude-Valérie; Frochot, Céline; Bersillon, Jean-Luc

2016-04-01

Four different techniques were used to study the binding of cationic cetyltrimethylammonium bromide (CTAB) and non-ionic nonylphenylethoxyl (NPE) surfactants to three synthetic organic components that mimic humic-like aggregates and to two natural aggregated humic substances (HS) extracted from aquatic suspended matter. The composition of synthetic organic components were chosen to be similar to high molecular weight highly processed terrigenous HS and low and high molecular weight less processed terrigenous (or aquatic terrigenous) HS. The natural HS were extracted under two different meteorological conditions (rainy and dry periods). No significant interaction between the non-ionic surfactant and any of the studied compounds was found. Concerning CTAB; pH, conductivity and turbidity measurements, along with fluorescence spectroscopy were combined to provide a better understanding of interactions between organic aggregates and the surfactant. The spectroscopic data show that a "highly processed terrigenous HS" fluorophore interacts in a different way with the cationic surfactant than an "aquatic terrigenous (or less processed terrigenous) HS" fluorophore does. Under similar conditions, some spectral changes in the fluorescence signal are correlated to changes in non-specific physical-chemical parameters (pH, turbidity, conductivity) for the organic compounds tested. The complexation mechanism is essentially governed by charge neutralization, which can be monitored specifically by the fluorescence of the organic moieties.

Exciton-Dominated Core-Level Absorption Spectra of Hybrid Organic-Inorganic Lead Halide Perovskites.

PubMed

Vorwerk, Christian; Hartmann, Claudia; Cocchi, Caterina; Sadoughi, Golnaz; Habisreutinger, Severin N; Félix, Roberto; Wilks, Regan G; Snaith, Henry J; Bär, Marcus; Draxl, Claudia

2018-04-19

In a combined theoretical and experimental work, we investigate X-ray absorption near-edge structure spectroscopy of the I L 3 and the Pb M 5 edges of the methylammonium lead iodide (MAPbI 3 ) hybrid inorganic-organic perovskite and its binary phase PbI 2 . The absorption onsets are dominated by bound excitons with sizable binding energies of a few hundred millielectronvolts and pronounced anisotropy. The spectra of both materials exhibit remarkable similarities, suggesting that the fingerprints of core excitations in MAPbI 3 are essentially given by its inorganic component, with negligible influence from the organic groups. The theoretical analysis complementing experimental observations provides the conceptual insights required for a full characterization of this complex material.

Adaptive Variability in Skilled Human Movements

NASA Astrophysics Data System (ADS)

Kudo, Kazutoshi; Ohtsuki, Tatsuyuki

Human movements are produced in variable external/internal environments. Because of this variability, the same motor command can result in quite different movement patterns. Therefore, to produce skilled movements humans must coordinate the variability, not try to exclude it. In addition, because human movements are produced in redundant and complex systems, a combination of variability should be observed in different anatomical/physiological levels. In this paper, we introduce our research about human movement variability that shows remarkable coordination among components, and between organism and environment. We also introduce nonlinear dynamical models that can describe a variety of movements as a self-organization of a dynamical system, because the dynamical systems approach is a major candidate to understand the principle underlying organization of varying systems with huge degrees-of-freedom.

Light-Induced Conversion of Chemical Permeability to Enhance Electron and Molecular Transfer in Nanoscale Assemblies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balgley, Renata; de Ruiter, Graham; Evmenenko, Guennadi

In this paper, we demonstrate how photochemically enhancing the permeability of metal–organic assemblies results in a significant enhancement of the electrochemical activity of metal complexes located within the assembly. The molecular assemblies consist of different layers of redox-active metal complexes ([M(mbpy-py)3][PF6]2; M = Ru or Os) that are separated by redox-inactive spacers consisting of 1,4-bis[2-(4-pyridyl)ethenyl]benzene (BPEB) and PdCl2 of variable thicknesses (0–13.4 nm). UV-irradiation (λ = 254 nm) of our assemblies induces a photochemical reaction in the redox-inactive spacer increasing the permeability of the assembly. The observed increase was evident by trapping organic (nBu4NBF4) and inorganic (NiCl2) salts inside themore » assemblies, and by evaluating the electrochemical response of quinones absorbed inside the molecular assemblies before and after UV irradiation. The increase in permeability is reflected by higher currents and a change in the directionality of electron transfer, i.e., from mono- to bidirectional, between the redox-active metal complexes and the electrode surface. The supramolecular structure of the assemblies dominates the overall electron transfer properties and overrules possible electron transfer mediated by the extensive π-conjugation of its individual organic components.« less

Crustacean-derived biomimetic components and nanostructured composites.

PubMed

Grunenfelder, Lessa Kay; Herrera, Steven; Kisailus, David

2014-08-27

Over millions of years, the crustacean exoskeleton has evolved into a rigid, tough, and complex cuticle that is used for structural support, mobility, protection of vital organs, and defense against predation. The crustacean cuticle is characterized by a hierarchically arranged chitin fiber scaffold, mineralized predominately by calcium carbonate and/or calcium phosphate. The structural organization of the mineral and organic within the cuticle occurs over multiple length scales, resulting in a strong and tough biological composite. Here, the ultrastructural details observed in three species of crustacean are reviewed: the American lobster (Homarus americanus), the edible crab (Cancer pagurus), and the peacock mantis shrimp (Odontodactylus scyllarus). The Review concludes with a discussion of recent advances in the development of biomimetics with controlled organic scaffolding, mineralization, and the construction of nanoscale composites, inspired by the organization and formation of the crustacean cuticle. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Many-body perturbation theory for understanding optical excitations in organic molecules and solids

NASA Astrophysics Data System (ADS)

Sharifzadeh, Sahar

2018-04-01

Semiconductors composed of organic molecules are promising as components for flexible and inexpensive optoelectronic devices, with many recent studies aimed at understanding their electronic and optical properties. In particular, computational modeling of these complex materials has provided new understanding of the underlying properties which give rise to their excited-state phenomena. This article provides an overview of recent many-body perturbation theory (MBPT) studies of optical excitations within organic molecules and solids. We discuss the accuracy of MBPT within the GW/BSE approach in predicting excitation energies and absorption spectra, and assess the impact of two commonly used approximations, the DFT starting point and the Tamm–Dancoff approximation. Moreover, we summarize studies that elucidate the role of solid-state structure on the nature of excitons in organic crystals. These studies show that a rich physical understanding of organic materials can be obtained from GW/BSE.

Structural Insights into the PorK and PorN Components of the Porphyromonas gingivalis Type IX Secretion System.

PubMed

Gorasia, Dhana G; Veith, Paul D; Hanssen, Eric G; Glew, Michelle D; Sato, Keiko; Yukitake, Hideharu; Nakayama, Koji; Reynolds, Eric C

2016-08-01

The type IX secretion system (T9SS) has been recently discovered and is specific to Bacteroidetes species. Porphyromonas gingivalis, a keystone pathogen for periodontitis, utilizes the T9SS to transport many proteins including the gingipain virulence factors across the outer membrane and attach them to the cell surface via a sortase-like mechanism. At least 11 proteins have been identified as components of the T9SS including PorK, PorL, PorM, PorN and PorP, however the precise roles of most of these proteins have not been elucidated and the structural organization of these components is unknown. In this study, we purified PorK and PorN complexes from P. gingivalis and using electron microscopy we have shown that PorN and the PorK lipoprotein interact to form a 50 nm diameter ring-shaped structure containing approximately 32-36 subunits of each protein. The formation of these rings was dependent on both PorK and PorN, but was independent of PorL, PorM and PorP. PorL and PorM were found to form a separate stable complex. PorK and PorN were protected from proteinase K cleavage when present in undisrupted cells, but were rapidly degraded when the cells were lysed, which together with bioinformatic analyses suggests that these proteins are exposed in the periplasm and anchored to the outer membrane via the PorK lipid. Chemical cross-linking and mass spectrometry analyses confirmed the interaction between PorK and PorN and further revealed that they interact with the PG0189 outer membrane protein. Furthermore, we established that PorN was required for the stable expression of PorK, PorL and PorM. Collectively, these results suggest that the ring-shaped PorK/N complex may form part of the secretion channel of the T9SS. This is the first report showing the structural organization of any T9SS component.

Structural Insights into the PorK and PorN Components of the Porphyromonas gingivalis Type IX Secretion System

PubMed Central

Gorasia, Dhana G.; Veith, Paul D.; Hanssen, Eric G.; Glew, Michelle D.; Sato, Keiko; Yukitake, Hideharu; Nakayama, Koji; Reynolds, Eric C.

2016-01-01

The type IX secretion system (T9SS) has been recently discovered and is specific to Bacteroidetes species. Porphyromonas gingivalis, a keystone pathogen for periodontitis, utilizes the T9SS to transport many proteins including the gingipain virulence factors across the outer membrane and attach them to the cell surface via a sortase-like mechanism. At least 11 proteins have been identified as components of the T9SS including PorK, PorL, PorM, PorN and PorP, however the precise roles of most of these proteins have not been elucidated and the structural organization of these components is unknown. In this study, we purified PorK and PorN complexes from P. gingivalis and using electron microscopy we have shown that PorN and the PorK lipoprotein interact to form a 50 nm diameter ring-shaped structure containing approximately 32–36 subunits of each protein. The formation of these rings was dependent on both PorK and PorN, but was independent of PorL, PorM and PorP. PorL and PorM were found to form a separate stable complex. PorK and PorN were protected from proteinase K cleavage when present in undisrupted cells, but were rapidly degraded when the cells were lysed, which together with bioinformatic analyses suggests that these proteins are exposed in the periplasm and anchored to the outer membrane via the PorK lipid. Chemical cross-linking and mass spectrometry analyses confirmed the interaction between PorK and PorN and further revealed that they interact with the PG0189 outer membrane protein. Furthermore, we established that PorN was required for the stable expression of PorK, PorL and PorM. Collectively, these results suggest that the ring-shaped PorK/N complex may form part of the secretion channel of the T9SS. This is the first report showing the structural organization of any T9SS component. PMID:27509186

PHB Associates with the HIRA Complex to Control an Epigenetic-Metabolic Circuit in Human ESCs.

PubMed

Zhu, Zhexin; Li, Chunliang; Zeng, Yanwu; Ding, Jianyi; Qu, Zepeng; Gu, Junjie; Ge, Laixiang; Tang, Fan; Huang, Xin; Zhou, Chenlin; Wang, Ping; Zheng, Deyou; Jin, Ying

2017-02-02

The chromatin landscape and cellular metabolism both contribute to cell fate determination, but their interplay remains poorly understood. Using genome-wide siRNA screening, we have identified prohibitin (PHB) as an essential factor in self-renewal of human embryonic stem cells (hESCs). Mechanistically, PHB forms protein complexes with HIRA, a histone H3.3 chaperone, and stabilizes the protein levels of HIRA complex components. Like PHB, HIRA is required for hESC self-renewal. PHB and HIRA act together to control global deposition of histone H3.3 and gene expression in hESCs. Of particular note, PHB and HIRA regulate the chromatin architecture at the promoters of isocitrate dehydrogenase genes to promote transcription and, thus, production of α-ketoglutarate, a key metabolite in the regulation of ESC fate. Our study shows that PHB has an unexpected nuclear role in hESCs that is required for self-renewal and that it acts with HIRA in chromatin organization to link epigenetic organization to a metabolic circuit. Copyright © 2017 Elsevier Inc. All rights reserved.

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies.

PubMed

Youn, Ji-Young; Dunham, Wade H; Hong, Seo Jung; Knight, James D R; Bashkurov, Mikhail; Chen, Ginny I; Bagci, Halil; Rathod, Bhavisha; MacLeod, Graham; Eng, Simon W M; Angers, Stéphane; Morris, Quaid; Fabian, Marc; Côté, Jean-François; Gingras, Anne-Claude

2018-02-01

mRNA processing, transport, translation, and ultimately degradation involve a series of dedicated protein complexes that often assemble into large membraneless structures such as stress granules (SGs) and processing bodies (PBs). Here, systematic in vivo proximity-dependent biotinylation (BioID) analysis of 119 human proteins associated with different aspects of mRNA biology uncovers 7424 unique proximity interactions with 1,792 proteins. Classical bait-prey analysis reveals connections of hundreds of proteins to distinct mRNA-associated processes or complexes, including the splicing and transcriptional elongation machineries (protein phosphatase 4) and the CCR4-NOT deadenylase complex (CEP85, RNF219, and KIAA0355). Analysis of correlated patterns between endogenous preys uncovers the spatial organization of RNA regulatory structures and enables the definition of 144 core components of SGs and PBs. We report preexisting contacts between most core SG proteins under normal growth conditions and demonstrate that several core SG proteins (UBAP2L, CSDE1, and PRRC2C) are critical for the formation of microscopically visible SGs. Copyright © 2017 Elsevier Inc. All rights reserved.

Self-determined mechanisms in complex networks

NASA Astrophysics Data System (ADS)

Liu, Yang; Yuan, Jian; Shan, Xiuming; Ren, Yong; Ma, Zhengxin

2008-03-01

Self-organized networks are pervasive in communication systems such as the Internet, overlay networks, peer-to-peer networks, and cluster-based services. These networks evolve into complex topologies, under specific driving forces, i.e. user demands, technological innovations, design objectives and so on. Our study focuses on the driving forces behind individual evolutions of network components, and their stimulation and domination to the self-organized networks which are defined as self-determined mechanisms in this paper. Understanding forces underlying the evolution of networks should enable informed design decisions and help to avoid unwanted surprises, such as congestion collapse. A case study on the macroscopic evolution of the Internet topology of autonomous systems under a specific driving force is then presented. Using computer simulations, it is found that the power-law degree distribution can originate from a connection preference to larger numbers of users, and that the small-world property can be caused by rapid growth in the number of users. Our results provide a new feasible perspective to understand intrinsic fundamentals in the topological evolution of complex networks.

A Bacillus megaterium System for the Production of Recombinant Proteins and Protein Complexes.

PubMed

Biedendieck, Rebekka

2016-01-01

For many years the Gram-positive bacterium Bacillus megaterium has been used for the production and secretion of recombinant proteins. For this purpose it was systematically optimized. Plasmids with different inducible promoter systems, with different compatible origins, with small tags for protein purification and with various specific signals for protein secretion were combined with genetically improved host strains. Finally, the development of appropriate cultivation conditions for the production strains established this organism as a bacterial cell factory even for large proteins. Along with the overproduction of individual proteins the organism is now also used for the simultaneous coproduction of up to 14 recombinant proteins, multiple subsequently interacting or forming protein complexes. Some of these recombinant strains are successfully used for bioconversion or the biosynthesis of valuable components including vitamins. The titers in the g per liter scale for the intra- and extracellular recombinant protein production prove the high potential of B. megaterium for industrial applications. It is currently further enhanced for the production of recombinant proteins and multi-subunit protein complexes using directed genetic engineering approaches based on transcriptome, proteome, metabolome and fluxome data.

The molecular origins of specificity in the assembly of a multienzyme complex.

PubMed

Frank, René A W; Pratap, J Venkatesh; Pei, Xue Y; Perham, Richard N; Luisi, Ben F

2005-08-01

The pyruvate dehydrogenase (PDH) multienzyme complex is central to oxidative metabolism. We present the first crystal structure of a complex between pyruvate decarboxylase (E1) and the peripheral subunit binding domain (PSBD) of the dihydrolipoyl acetyltransferase (E2). The interface is dominated by a "charge zipper" of networked salt bridges. Remarkably, the PSBD uses essentially the same zipper to alternately recognize the dihydrolipoyl dehydrogenase (E3) component of the PDH assembly. The PSBD achieves this dual recognition largely through the addition of a network of interfacial water molecules unique to the E1-PSBD complex. These structural comparisons illuminate our observations that the formation of this water-rich E1-E2 interface is largely enthalpy driven, whereas that of the E3-PSBD complex (from which water is excluded) is entropy driven. Interfacial water molecules thus diversify surface complementarity and contribute to avidity, enthalpically. Additionally, the E1-PSBD structure provides insight into the organization and active site coupling within the approximately 9 MDa PDH complex.

Sc65-Null Mice Provide Evidence for a Novel Endoplasmic Reticulum Complex Regulating Collagen Lysyl Hydroxylation

PubMed Central

Weis, MaryAnn; Rai, Jyoti; Hudson, David M.; Dimori, Milena; Zimmerman, Sarah M.; Hogue, William R.; Swain, Frances L.; Burdine, Marie S.; Mackintosh, Samuel G.; Tackett, Alan J.; Suva, Larry J.; Eyre, David R.

2016-01-01

Collagen is a major component of the extracellular matrix and its integrity is essential for connective tissue and organ function. The importance of proteins involved in intracellular collagen post-translational modification, folding and transport was recently highlighted from studies on recessive forms of osteogenesis imperfecta (OI). Here we describe the critical role of SC65 (Synaptonemal Complex 65, P3H4), a leprecan-family member, as part of an endoplasmic reticulum (ER) complex with prolyl 3-hydroxylase 3. This complex affects the activity of lysyl-hydroxylase 1 potentially through interactions with the enzyme and/or cyclophilin B. Loss of Sc65 in the mouse results in instability of this complex, altered collagen lysine hydroxylation and cross-linking leading to connective tissue defects that include low bone mass and skin fragility. This is the first indication of a prolyl-hydroxylase complex in the ER controlling lysyl-hydroxylase activity during collagen synthesis. PMID:27119146

A method for multiprotein assembly in cells reveals independent action of kinesins in complex

PubMed Central

Norris, Stephen R.; Soppina, Virupakshi; Dizaji, Aslan S.; Schimert, Kristin I.; Sept, David; Cai, Dawen; Sivaramakrishnan, Sivaraj

2014-01-01

Teams of processive molecular motors are critical for intracellular transport and organization, yet coordination between motors remains poorly understood. Here, we develop a system using protein components to generate assemblies of defined spacing and composition inside cells. This system is applicable to studying macromolecular complexes in the context of cell signaling, motility, and intracellular trafficking. We use the system to study the emergent behavior of kinesin motors in teams. We find that two kinesin motors in complex act independently (do not help or hinder each other) and can alternate their activities. For complexes containing a slow kinesin-1 and fast kinesin-3 motor, the slow motor dominates motility in vitro but the fast motor can dominate on certain subpopulations of microtubules in cells. Both motors showed dynamic interactions with the complex, suggesting that motor–cargo linkages are sensitive to forces applied by the motors. We conclude that kinesin motors in complex act independently in a manner regulated by the microtubule track. PMID:25365993

Approach to estimation of level of information security at enterprise based on genetic algorithm

NASA Astrophysics Data System (ADS)

V, Stepanov L.; V, Parinov A.; P, Korotkikh L.; S, Koltsov A.

2018-05-01

In the article, the way of formalization of different types of threats of information security and vulnerabilities of an information system of the enterprise and establishment is considered. In a type of complexity of ensuring information security of application of any new organized system, the concept and decisions in the sphere of information security are expedient. One of such approaches is the method of a genetic algorithm. For the enterprises of any fields of activity, the question of complex estimation of the level of security of information systems taking into account the quantitative and qualitative factors characterizing components of information security is relevant.

[Neuronal and synaptic properties: fundamentals of network plasticity].

PubMed

Le Masson, G

2000-02-01

Neurons, within the nervous system, are organized in different neural networks through synaptic connections. Two fundamental components are dynamically interacting in these functional units. The first one are the neurons themselves, and far from being simple action potential generators, they are capable of complex electrical integrative properties due to various types, number, distribution and modulation of voltage-gated ionic channels. The second elements are the synapses where a similar complexity and plasticity is found. Identifying both cellular and synaptic intrinsic properties is necessary to understand the links between neural networks behavior and physiological function, and is a useful step towards a better control of neurological diseases.

Biodegradation of Metal-EDTA Complexes by an Enriched Microbial Population

PubMed Central

Thomas, Russell A. P.; Lawlor, Kirsten; Bailey, Mark; Macaskie, Lynne E.

1998-01-01

A mixed culture utilizing EDTA as the sole carbon source was isolated from a mixed inoculum of water from the River Mersey (United Kingdom) and sludge from an industrial effluent treatment plant. Fourteen component organisms were isolated from the culture, including representatives of the genera Methylobacterium, Variovorax, Enterobacter, Aureobacterium, and Bacillus. The mixed culture biodegraded metal-EDTA complexes slowly; the biodegradability was in the order Fe>Cu>Co>Ni>Cd. By incorporation of inorganic phosphate into the medium as a precipitant ligand, heavy metals were removed in parallel to EDTA degradation. The mixed culture also utilized a number of possible EDTA degradation intermediates as carbon sources. PMID:9546167

A Systematic Classification for HVAC Systems and Components

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Han; Chen, Yan; Zhang, Jian

Depending on the application, the complexity of an HVAC system can range from a small fan coil unit to a large centralized air conditioning system with primary and secondary distribution loops, and central plant components. Currently, the taxonomy of HVAC systems and the components has various aspects, which can get quite complex because of the various components and system configurations. For example, based on cooling and heating medium delivered to terminal units, systems can be classified as either air systems, water systems or air-water systems. In addition, some of the system names might be commonly used in a confusing manner,more » such as “unitary system” vs. “packaged system.” Without a systematic classification, these components and system terminology can be confusing to understand or differentiate from each other, and it creates ambiguity in communication, interpretation, and documentation. It is valuable to organize and classify HVAC systems and components so that they can be easily understood and used in a consistent manner. This paper aims to develop a systematic classification of HVAC systems and components. First, we summarize the HVAC component information and definitions based on published literature, such as ASHRAE handbooks, regulations, and rating standards. Then, we identify common HVAC system types and map them to the collected components in a meaningful way. Classification charts are generated and described based on the component information. Six main categories are identified for the HVAC components and equipment, i.e., heating and cooling production, heat extraction and rejection, air handling process, distribution system, terminal use, and stand-alone system. Components for each main category are further analyzed and classified in detail. More than fifty system names are identified and grouped based on their characteristics. The result from this paper will be helpful for education, communication, and systems and component documentation.« less

GIFTed Demons: deformable image registration with local structure-preserving regularization using supervoxels for liver applications

PubMed Central

Gleeson, Fergus V.; Brady, Michael; Schnabel, Julia A.

2018-01-01

Abstract. Deformable image registration, a key component of motion correction in medical imaging, needs to be efficient and provides plausible spatial transformations that reliably approximate biological aspects of complex human organ motion. Standard approaches, such as Demons registration, mostly use Gaussian regularization for organ motion, which, though computationally efficient, rule out their application to intrinsically more complex organ motions, such as sliding interfaces. We propose regularization of motion based on supervoxels, which provides an integrated discontinuity preserving prior for motions, such as sliding. More precisely, we replace Gaussian smoothing by fast, structure-preserving, guided filtering to provide efficient, locally adaptive regularization of the estimated displacement field. We illustrate the approach by applying it to estimate sliding motions at lung and liver interfaces on challenging four-dimensional computed tomography (CT) and dynamic contrast-enhanced magnetic resonance imaging datasets. The results show that guided filter-based regularization improves the accuracy of lung and liver motion correction as compared to Gaussian smoothing. Furthermore, our framework achieves state-of-the-art results on a publicly available CT liver dataset. PMID:29662918

GIFTed Demons: deformable image registration with local structure-preserving regularization using supervoxels for liver applications.

PubMed

Papież, Bartłomiej W; Franklin, James M; Heinrich, Mattias P; Gleeson, Fergus V; Brady, Michael; Schnabel, Julia A

2018-04-01

Deformable image registration, a key component of motion correction in medical imaging, needs to be efficient and provides plausible spatial transformations that reliably approximate biological aspects of complex human organ motion. Standard approaches, such as Demons registration, mostly use Gaussian regularization for organ motion, which, though computationally efficient, rule out their application to intrinsically more complex organ motions, such as sliding interfaces. We propose regularization of motion based on supervoxels, which provides an integrated discontinuity preserving prior for motions, such as sliding. More precisely, we replace Gaussian smoothing by fast, structure-preserving, guided filtering to provide efficient, locally adaptive regularization of the estimated displacement field. We illustrate the approach by applying it to estimate sliding motions at lung and liver interfaces on challenging four-dimensional computed tomography (CT) and dynamic contrast-enhanced magnetic resonance imaging datasets. The results show that guided filter-based regularization improves the accuracy of lung and liver motion correction as compared to Gaussian smoothing. Furthermore, our framework achieves state-of-the-art results on a publicly available CT liver dataset.

iMarNet: an ocean biogeochemistry model inter-comparison project within a common physical ocean modelling framework

NASA Astrophysics Data System (ADS)

Kwiatkowski, L.; Yool, A.; Allen, J. I.; Anderson, T. R.; Barciela, R.; Buitenhuis, E. T.; Butenschön, M.; Enright, C.; Halloran, P. R.; Le Quéré, C.; de Mora, L.; Racault, M.-F.; Sinha, B.; Totterdell, I. J.; Cox, P. M.

2014-07-01

Ocean biogeochemistry (OBGC) models span a wide range of complexities from highly simplified, nutrient-restoring schemes, through nutrient-phytoplankton-zooplankton-detritus (NPZD) models that crudely represent the marine biota, through to models that represent a broader trophic structure by grouping organisms as plankton functional types (PFT) based on their biogeochemical role (Dynamic Green Ocean Models; DGOM) and ecosystem models which group organisms by ecological function and trait. OBGC models are now integral components of Earth System Models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here, we present an inter-comparison of six OBGC models that were candidates for implementation within the next UK Earth System Model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the Nucleus for the European Modelling of the Ocean (NEMO) ocean general circulation model (GCM), and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform or underperform all other models across all metrics. Nonetheless, the simpler models that are easier to tune are broadly closer to observations across a number of fields, and thus offer a high-efficiency option for ESMs that prioritise high resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low resolution climate dynamics and high complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry-climate interactions.

iMarNet: an ocean biogeochemistry model intercomparison project within a common physical ocean modelling framework

NASA Astrophysics Data System (ADS)

Kwiatkowski, L.; Yool, A.; Allen, J. I.; Anderson, T. R.; Barciela, R.; Buitenhuis, E. T.; Butenschön, M.; Enright, C.; Halloran, P. R.; Le Quéré, C.; de Mora, L.; Racault, M.-F.; Sinha, B.; Totterdell, I. J.; Cox, P. M.

2014-12-01

Ocean biogeochemistry (OBGC) models span a wide variety of complexities, including highly simplified nutrient-restoring schemes, nutrient-phytoplankton-zooplankton-detritus (NPZD) models that crudely represent the marine biota, models that represent a broader trophic structure by grouping organisms as plankton functional types (PFTs) based on their biogeochemical role (dynamic green ocean models) and ecosystem models that group organisms by ecological function and trait. OBGC models are now integral components of Earth system models (ESMs), but they compete for computing resources with higher resolution dynamical setups and with other components such as atmospheric chemistry and terrestrial vegetation schemes. As such, the choice of OBGC in ESMs needs to balance model complexity and realism alongside relative computing cost. Here we present an intercomparison of six OBGC models that were candidates for implementation within the next UK Earth system model (UKESM1). The models cover a large range of biological complexity (from 7 to 57 tracers) but all include representations of at least the nitrogen, carbon, alkalinity and oxygen cycles. Each OBGC model was coupled to the ocean general circulation model Nucleus for European Modelling of the Ocean (NEMO) and results from physically identical hindcast simulations were compared. Model skill was evaluated for biogeochemical metrics of global-scale bulk properties using conventional statistical techniques. The computing cost of each model was also measured in standardised tests run at two resource levels. No model is shown to consistently outperform all other models across all metrics. Nonetheless, the simpler models are broadly closer to observations across a number of fields and thus offer a high-efficiency option for ESMs that prioritise high-resolution climate dynamics. However, simpler models provide limited insight into more complex marine biogeochemical processes and ecosystem pathways, and a parallel approach of low-resolution climate dynamics and high-complexity biogeochemistry is desirable in order to provide additional insights into biogeochemistry-climate interactions.

Complex conductivity of organic-rich shales

NASA Astrophysics Data System (ADS)

Woodruff, W. F.; Revil, A.; Torres-Verdin, C.

2013-12-01

We can accurately determine the intrinsic anisotropy and material properties in the laboratory, providing empirical evidence of transverse isotropy and the polarization of the organic and metallic fractions in saturated and unsaturated shales. We develop two distinct approaches to obtain the complex conductivity tensor from spectral induced polarization (SIP) measurements. Experimental results indicate clear anisotropy, and characterize the effects of thermal maturation, TOC, and pyrite, aiding in the calibration and interpretation of geophysical data. SIP is a non-intrusive measurement, sensitive to the surface conductance of mineral grains, frequency-dependent polarization of the electrical double layer, and bulk conductivity of the pore water. The in-phase and quadrature components depend upon parameters of principal importance in unconventional shale formation evaluation (e.g., the distribution of pore throat sizes, formation factor, permeability, salinity and cation exchange capacity (CEC), fluid saturation and wettability). In addition to the contribution of the electrical double layer of non-conducting minerals to surface conductivity, we have observed a clear relaxation associated with kerogen pyrolysis, pyrite distribution, and evidence that the CEC of the kerogen fraction may also contribute, depending on thermal maturation history. We utilize a recent model for anisotropic complex conductivity, and rigorous experimental protocols to quantify the role of kerogen and pyrolysis on surface and quadrature conductivity in mudrocks. The complex conductivity tensor σ* describes the directional dependence of electrical conduction in a porous medium, and accounts for both conduction and polarization. The complex-valued tensor components are given as σ*ij , where σ'ij represents in-phase and σ"ij denotes quadrature conductivities. The directional dependence of the complex conductivity tensor is relegated to the textural properties of the material. The components of the formation factor and connectivity (tortuosity) tensors Fij and Tij (affecting the bulk and surface conductivity, respectively) are correlated as Fij=TijΦ. Both conductivity and connectivity tensors share the same eigenvectors; the anisotropy ratio is equivalent in TI media. At high pore water salinity, surface and quadrature conductivity share the same bulk tortuosity; when surface conductivity dominates (low salinity), conductivity is controlled by the surface conductance, and the tortuosity of electrical current along mineral surfaces usually higher than that of the pore water. We developed two distinct SIP measurement protocols to obtain the tensor: (1) azimuthal sampling and inversion of phasor potentials through the full-field solution of the Laplace equation; (2) direct measurement of complex conductivity eigenvalues by polarized, single-component stimulus current. Experiments also include unsaturated and saturated measurements with three brines of known salinity and pH, at log-distributed frequencies ranging 1 mHz to 45 kHz. Both azimuthal spectra and eigenvalue spectra validate the theoretical model and illustrate the effectiveness of the protocols themselves. We obtain the textural tensors and invert key parameters including Archie exponents and CEC, and characterize the relaxation phenomena associated with kerogen content and maturity for multiphase fluid systems.

Liquid-liquid phase separation in atmospheric aerosol particles: dependence on organic functionalities and mixture complexity

NASA Astrophysics Data System (ADS)

Song, M.; Marcolli, C.; Krieger, U. K.; Zuend, A.; Peter, T.

2012-04-01

In the troposphere, aerosol particles undergo phase transitions such as deliquescence and efflorescence during humidity cycles (Marcolli and Krieger, 2006). In addition, interactions between organic and inorganic compounds lead to liquid-liquid phase separation (LLPS) (Ciobanu et al., 2009). Recent studies on a limited number of model systems have shown that oxygen-to-carbon ratios (O:C) of the organic aerosol fraction might be a good predictor for LLPS in mixed organic/ammonium sulfate (AS) particles (Bertram et al., 2011; Song et al., 2011). However, in order to corroborate this hypothesis experiments with an organic fraction that consists of a higher number of components with different O:C ratios and functional groups are needed. In order to determine the influence of O:C ratio, the specific organic functionalities and the mixture complexity on LLPS, we subjected organic/AS particles deposited on a hydrophobically coated substrate to relative humidity (RH) cycles and observed phase changes using optical microscopy and micro-Raman spectroscopy. To determine the influence of mixture complexity, we mixed together up to 10 organic compounds. We also prepared mixtures that were rich in different types of functional groups like polyols, aromatics and dicarboxylic acids which were identified from field measurements. We screened for a miscibility gap by varying the organic-to-inorganic ratio from 2:1 to 1:6. AS in the investigated single particles effloresced at 27 - 50 %RH and deliquesced at 72 - 79 %RH during humidity cycles. The occurrence of LLPS is determined to a high degree by the O:C of the organics: there was no LLPS for mixtures with O:C > 0.8 and there was always LLPS for mixtures with O:C < 0.57. In the range in between, we observed a dependence on the specific functional groups: a high share of aromatic functionalities shifts the range of O:C for which LLPS occurs to lower values. A correlation was also found for the onset RH of LLPS as a function of O:C. We did not find any dependence of LLPS on the complexity of the mixture. Overall, the RH range of coexistence of two liquid phases depends in first place on the O:C ratio of the particles and in second place also on the specific organic functionalities.

Genome complexity in the coelacanth is reflected in its adaptive immune system

USGS Publications Warehouse

Saha, Nil Ratan; Ota, Tatsuya; Litman, Gary W.; Hansen, John; Parra, Zuly; Hsu, Ellen; Buonocore, Francesco; Canapa, Adriana; Cheng, Jan-Fang; Amemiya, Chris T.

2014-01-01

We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

Elaborate cellulosome architecture of Acetivibrio cellulolyticus revealed by selective screening of cohesin-dockerin interactions.

PubMed

Hamberg, Yuval; Ruimy-Israeli, Vered; Dassa, Bareket; Barak, Yoav; Lamed, Raphael; Cameron, Kate; Fontes, Carlos M G A; Bayer, Edward A; Fried, Daniel B

2014-01-01

Cellulosic waste represents a significant and underutilized carbon source for the biofuel industry. Owing to the recalcitrance of crystalline cellulose to enzymatic degradation, it is necessary to design economical methods of liberating the fermentable sugars required for bioethanol production. One route towards unlocking the potential of cellulosic waste lies in a highly complex class of molecular machines, the cellulosomes. Secreted mainly by anaerobic bacteria, cellulosomes are structurally diverse, cell surface-bound protein assemblies that can contain dozens of catalytic components. The key feature of the cellulosome is its modularity, facilitated by the ultra-high affinity cohesin-dockerin interaction. Due to the enormous number of cohesin and dockerin modules found in a typical cellulolytic organism, a major bottleneck in understanding the biology of cellulosomics is the purification of each cohesin- and dockerin-containing component, prior to analyses of their interaction. As opposed to previous approaches, the present study utilized proteins contained in unpurified whole-cell extracts. This strategy was made possible due to an experimental design that allowed for the relevant proteins to be "purified" via targeted affinity interactions as a function of the binding assay. The approach thus represents a new strategy, appropriate for future medium- to high-throughput screening of whole genomes, to determine the interactions between cohesins and dockerins. We have selected the cellulosome of Acetivibrio cellulolyticus for this work due to its exceptionally complex cellulosome systems and intriguing diversity of its cellulosomal modular components. Containing 41 cohesins and 143 dockerins, A. cellulolyticus has one of the largest number of potential cohesin-dockerin interactions of any organism, and contains unusual and novel cellulosomal features. We have surveyed a representative library of cohesin and dockerin modules spanning the cellulosome's total cohesin and dockerin sequence diversity, emphasizing the testing of unusual and previously-unknown protein modules. The screen revealed several novel cell-bound cellulosome architectures, thus expanding on those previously known, as well as soluble cellulose systems that are not bound to the bacterial cell surface. This study sets the stage for screening the entire complement of cellulosomal components from A. cellulolyticus and other organisms with large cellulosome systems. The knowledge gained by such efforts brings us closer to understanding the exceptional catalytic abilities of cellulosomes and will allow the use of novel cellulosomal components in artificial assemblies and in enzyme cocktails for sustainable energy-related research programs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Authors, Various

Planning a rational energy future requires anticipating the environmental consequences of various technologies. This is difficult to do with precision as the effects of pollutants are often determined by interactions between and among complex physical (abiotic) and biological (biotic) systems. A given pollutant may affect human beings through direct exposure or indirectly through inducing changes to biological systems which humans need to utilize. The concentration of a toxin in the food chain or the destruction of organisms necessary for the maintenance of high quality water are examples of indirect effects. Pollutants can be transformed and/or degraded as they establish residencemore » in various components of an ecosystem. Anticipation and amelioration of pollutant effects involves the integration of a vast range of data. This data includes: (1) physical and chemical characterization cf the pollutant as it enters the environment; (2) determining effects on the various components (biotic and abiotic) within the context of the functioning ecosystem of interest; (3) transformation in movements and/or degradation of the pollutant within that ecosystem and within specific organisms and physical components; and (4) determining a detailed biochemical and biological picture of the interactions of pollutants with particular organisms and/or their cellular components judged salient for various processes. The major programs described below are designed to answer parts of the above fundamental questions relevant to pollutants generated by energy related technologies. Their emphasis is on anticipating consequences to the biological components of various ecosystems. The work ranges from studies involving parts of a single cell (the membranes) to studies involving the whole ecosystem (in the pelagic zone of a lake). The programs take advantage of expertise and technical abilities present at LBL. Two small exploratory projects which were of brief duration and not related to anticipating biological effects of pollutants are included in this section. They concern geothermal technology and its improvement using techniques based on organic and physical properties of certain materials.« less

Complex adaptive systems: concept analysis.

PubMed

Holden, Lela M

2005-12-01

The aim of this paper is to explicate the concept of complex adaptive systems through an analysis that provides a description, antecedents, consequences, and a model case from the nursing and health care literature. Life is more than atoms and molecules--it is patterns of organization. Complexity science is the latest generation of systems thinking that investigates patterns and has emerged from the exploration of the subatomic world and quantum physics. A key component of complexity science is the concept of complex adaptive systems, and active research is found in many disciplines--from biology to economics to health care. However, the research and literature related to these appealing topics have generated confusion. A thorough explication of complex adaptive systems is needed. A modified application of the methods recommended by Walker and Avant for concept analysis was used. A complex adaptive system is a collection of individual agents with freedom to act in ways that are not always totally predictable and whose actions are interconnected. Examples include a colony of termites, the financial market, and a surgical team. It is often referred to as chaos theory, but the two are not the same. Chaos theory is actually a subset of complexity science. Complexity science offers a powerful new approach--beyond merely looking at clinical processes and the skills of healthcare professionals. The use of complex adaptive systems as a framework is increasing for a wide range of scientific applications, including nursing and healthcare management research. When nursing and other healthcare managers focus on increasing connections, diversity, and interactions they increase information flow and promote creative adaptation referred to as self-organization. Complexity science builds on the rich tradition in nursing that views patients and nursing care from a systems perspective.

Disentangling multidimensional spatio-temporal data into their common and aberrant responses

DOE PAGES

Chang, Young Hwan; Korkola, James; Amin, Dhara N.; ...

2015-04-22

With the advent of high-throughput measurement techniques, scientists and engineers are starting to grapple with massive data sets and encountering challenges with how to organize, process and extract information into meaningful structures. Multidimensional spatio-temporal biological data sets such as time series gene expression with various perturbations over different cell lines, or neural spike trains across many experimental trials, have the potential to acquire insight about the dynamic behavior of the system. For this potential to be realized, we need a suitable representation to understand the data. A general question is how to organize the observed data into meaningful structures andmore » how to find an appropriate similarity measure. A natural way of viewing these complex high dimensional data sets is to examine and analyze the large-scale features and then to focus on the interesting details. Since the wide range of experiments and unknown complexity of the underlying system contribute to the heterogeneity of biological data, we develop a new method by proposing an extension of Robust Principal Component Analysis (RPCA), which models common variations across multiple experiments as the lowrank component and anomalies across these experiments as the sparse component. We show that the proposed method is able to find distinct subtypes and classify data sets in a robust way without any prior knowledge by separating these common responses and abnormal responses. Thus, the proposed method provides us a new representation of these data sets which has the potential to help users acquire new insight from data.« less

Multistate and phase change selection in constitutional multivalent systems.

PubMed

Barboiu, Mihail

2012-01-01

Molecular architectures and materials can be constitutionally self-sorted in the presence of different biomolecular targets or external physical stimuli or chemical effectors, thus responding to an external selection pressure. The high selectivity and specificity of different bioreceptors or self-correlated internal interactions may be used to describe the complex constitutional behaviors through multistate component selection from a dynamic library. The self-selection may result in the dynamic amplification of self-optimized architectures during the phase change process. The sol-gel resolution of dynamic molecular/supramolecular libraries leads to higher self-organized constitutional hybrid materials, in which organic (supramolecular)/inorganic domains are reversibily connected.

Imaging complex nutrient dynamics in mycelial networks.

PubMed

Fricker, M D; Lee, J A; Bebber, D P; Tlalka, M; Hynes, J; Darrah, P R; Watkinson, S C; Boddy, L

2008-08-01

Transport networks are vital components of multi-cellular organisms, distributing nutrients and removing waste products. Animal cardiovascular and respiratory systems, and plant vasculature, are branching trees whose architecture is thought to determine universal scaling laws in these organisms. In contrast, the transport systems of many multi-cellular fungi do not fit into this conceptual framework, as they have evolved to explore a patchy environment in search of new resources, rather than ramify through a three-dimensional organism. These fungi grow as a foraging mycelium, formed by the branching and fusion of threadlike hyphae, that gives rise to a complex network. To function efficiently, the mycelial network must both transport nutrients between spatially separated source and sink regions and also maintain its integrity in the face of continuous attack by mycophagous insects or random damage. Here we review the development of novel imaging approaches and software tools that we have used to characterise nutrient transport and network formation in foraging mycelia over a range of spatial scales. On a millimetre scale, we have used a combination of time-lapse confocal imaging and fluorescence recovery after photobleaching to quantify the rate of diffusive transport through the unique vacuole system in individual hyphae. These data then form the basis of a simulation model to predict the impact of such diffusion-based movement on a scale of several millimetres. On a centimetre scale, we have used novel photon-counting scintillation imaging techniques to visualize radiolabel movement in small microcosms. This approach has revealed novel N-transport phenomena, including rapid, preferential N-resource allocation to C-rich sinks, induction of simultaneous bi-directional transport, abrupt switching between different pre-existing transport routes, and a strong pulsatile component to transport in some species. Analysis of the pulsatile transport component using Fourier techniques shows that as the colony forms, it self-organizes into well demarcated domains that are identifiable by differences in the phase relationship of the pulses. On the centimetre to metre scale, we have begun to use techniques borrowed from graph theory to characterize the development and dynamics of the network, and used these abstracted network models to predict the transport characteristics, resilience, and cost of the network.

Beyond the G-spot: clitourethrovaginal complex anatomy in female orgasm.

PubMed

Jannini, Emmanuele A; Buisson, Odile; Rubio-Casillas, Alberto

2014-09-01

The search for the legendary, highly erogenous vaginal region, the Gräfenberg spot (G-spot), has produced important data, substantially improving understanding of the complex anatomy and physiology of sexual responses in women. Modern imaging techniques have enabled visualization of dynamic interactions of female genitals during self-sexual stimulation or coitus. Although no single structure consistent with a distinct G-spot has been identified, the vagina is not a passive organ but a highly dynamic structure with an active role in sexual arousal and intercourse. The anatomical relationships and dynamic interactions between the clitoris, urethra, and anterior vaginal wall have led to the concept of a clitourethrovaginal (CUV) complex, defining a variable, multifaceted morphofunctional area that, when properly stimulated during penetration, could induce orgasmic responses. Knowledge of the anatomy and physiology of the CUV complex might help to avoid damage to its neural, muscular, and vascular components during urological and gynaecological surgical procedures.

Amoeboid organism solves complex nutritional challenges

PubMed Central

Dussutour, Audrey; Latty, Tanya; Beekman, Madeleine; Simpson, Stephen J.

2010-01-01

A fundamental question in nutritional biology is how distributed systems maintain an optimal supply of multiple nutrients essential for life and reproduction. In the case of animals, the nutritional requirements of the cells within the body are coordinated by the brain in neural and chemical dialogue with sensory systems and peripheral organs. At the level of an insect society, the requirements for the entire colony are met by the foraging efforts of a minority of workers responding to cues emanating from the brood. Both examples involve components specialized to deal with nutrient supply and demand (brains and peripheral organs, foragers and brood). However, some of the most species-rich, largest, and ecologically significant heterotrophic organisms on earth, such as the vast mycelial networks of fungi, comprise distributed networks without specialized centers: How do these organisms coordinate the search for multiple nutrients? We address this question in the acellular slime mold Physarum polycephalum and show that this extraordinary organism can make complex nutritional decisions, despite lacking a coordination center and comprising only a single vast multinucleate cell. We show that a single slime mold is able to grow to contact patches of different nutrient quality in the precise proportions necessary to compose an optimal diet. That such organisms have the capacity to maintain the balance of carbon- and nitrogen-based nutrients by selective foraging has considerable implications not only for our understanding of nutrient balancing in distributed systems but for the functional ecology of soils, nutrient cycling, and carbon sequestration. PMID:20142479

Organization of rescue behaviour sequences in ants, Cataglyphis cursor, reflects goal-directedness, plasticity and memory.

PubMed

Duhoo, Thierry; Durand, Jean-Luc; Hollis, Karen L; Nowbahari, Elise

2017-06-01

The experimental study of rescue behaviour in ants, behaviour in which individuals help entrapped nestmates in distress, has revealed that rescuers respond to victims with very precisely targeted behaviour. In Cataglyphis cursor, several different components of rescue behaviour have been observed, demonstrating the complexity of this behaviour, including sand digging and sand transport to excavate the victim, followed by pulling on the victim's limbs as well as the object holding the victim in place, behaviour that serves to free the victim. Although previous work suggested that rescue was optimally organized, first to expose and then to extricate the victim under a variety of differing circumstances, experimental analysis of that organization has been lacking. Here, using experimental data, we characterize the pattern of individual rescue behaviour in C. cursor by analysing the probabilities of transitions from one behavioural component to another. The results show that the execution of each behavioural component is determined by the interplay of previous acts. In particular, we show not only that ants move sand away from the victim in an especially efficient sequence of behaviour that greatly minimizes energy expenditure, but also that ants appear to form some kind of memory of what they did in the past, a memory that directs their future behaviour. Copyright © 2017 Elsevier B.V. All rights reserved.

Imaging Cytoskeleton Components by Electron Microscopy.

PubMed

Svitkina, Tatyana

2016-01-01

The cytoskeleton is a complex of detergent-insoluble components of the cytoplasm playing critical roles in cell motility, shape generation, and mechanical properties of a cell. Fibrillar polymers-actin filaments, microtubules, and intermediate filaments-are major constituents of the cytoskeleton, which constantly change their organization during cellular activities. The actin cytoskeleton is especially polymorphic, as actin filaments can form multiple higher order assemblies performing different functions. Structural information about cytoskeleton organization is critical for understanding its functions and mechanisms underlying various forms of cellular activity. Because of the nanometer-scale thickness of cytoskeletal fibers, electron microscopy (EM) is a key tool to determine the structure of the cytoskeleton. This article describes application of rotary shadowing (or metal replica) EM for visualization of the cytoskeleton. The procedure is applicable to thin cultured cells growing on glass coverslips and consists of detergent extraction of cells to expose their cytoskeleton, chemical fixation to provide stability, ethanol dehydration and critical point drying to preserve three-dimensionality, rotary shadowing with platinum to create contrast, and carbon coating to stabilize replicas. This technique provides easily interpretable three-dimensional images, in which individual cytoskeletal fibers are clearly resolved, and individual proteins can be identified by immunogold labeling. More importantly, replica EM is easily compatible with live cell imaging, so that one can correlate the dynamics of a cell or its components, e.g., expressed fluorescent proteins, with high resolution structural organization of the cytoskeleton in the same cell.

Ultrafine particle libraries for exploring mechanisms of PM2.5-induced toxicity in human cells.

PubMed

Bai, Xue; Liu, Yin; Wang, Shenqing; Liu, Chang; Liu, Fang; Su, Gaoxing; Peng, Xiaowu; Yuan, Chungang; Jiang, Yiguo; Yan, Bing

2018-08-15

Air pollution worldwide, especially in China and India, has caused serious health issues. Because PM 2.5 particles consist of solid particles of diverse properties with payloads of inorganic, organic and biological pollutants, it is still not known what the major toxic components are and how these components induce toxicities. To explore this complex issue, we apply reductionism principle and an ultrafine particle library approach in this work. From investigation of 63 diversely functionalized ultrafine particles (FUPs) with adsorbed key pollutants, our findings indicate that 1) only certain pollutants in the payloads of PM 2.5 are responsible for causing cellular oxidative stress, cell apoptosis, and cytotoxicity while the particle carriers are much less toxic; 2) pollutant-induced cellular oxidative stress and oxidative stress-triggered apoptosis are identified as one of the dominant mechanisms for PM 2.5 -induced cytotoxicity; 3) each specific toxic component on PM 2.5 (such as As, Pb, Cr or BaP) mainly affects its specific target organ(s) and, adding together, these pollutants may cause synergistic or just additive effects. Our findings demonstrate that reductionism concept and model PM 2.5 particle library approach are very effective in our endeavor to search for a better understanding of PM 2.5 -induced health effects. Copyright © 2018 Elsevier Inc. All rights reserved.

Characterisation of glycoconjugate sugar residues in the vomeronasal organ of the armadillo Chaetophractus villosus (Mammalia, xenarthra)

PubMed Central

CARMANCHAHI, P. D.; FERRARI, C. C.; ALDANA MARCOS, H. J.; AFFANNI, J. M.; SONEZ, C. A.; PAZ, D. A.

2000-01-01

Conventional carbohydrate histochemistry and the binding patterns of 21 lectins were analysed to characterise the glycoconjugate content in the components of the vomeronasal organ of the armadillo Chaetophractus villosus. The mucomicrovillous complex of the sensory epithelium bound most of the lectins studied. No reaction was observed with Con A, PSA, S-Con A and SBA, and the sustentacular cells were stained with UEA-I, DSL, LEL, STL and Con A. The vomeronasal receptor neurons were labelled with S-WGA, WGA, PNA, UEA-I, STL, Con A, S-Con A, ECL and RCA120. The basal cell layer reacted with S-WGA, WGA, LCA, UEA-I, DSL, LEL, STL, Con A, JAC and VVA. The nonsensory epithelium exhibited a differential staining in relation to the different components. The mucociliary complex stained with ECL, DBA, JAC, RCA120, STL, LCA, PHA-E, PHA-L, LEL, BSL-I and VVA. However, SJA and UEA-I stained the mucus complex lining a subpopulation of columnar cells. The cytoplasm and cell membranes of columnar cells was labelled with DBA, DSL and LCA. The apical region of these cells exhibited moderate reactivity with LEL and SJA. None of the lectins bound specifically to secretory granules of the nonsecretory cells. Basal cells of the nonsensory epithelium were labelled with DSL, LEL, LCA, BSL-I and STL. The vomeronasal glands showed a positive reaction with WGA, DSL, LEL, LCA, DBA, PNA, RCA120 and SBA. Subpopulations of acinar cells were observed with ECL, S-WGA, Con A, S-Con A and DBA. PNA and RCA120 stained the cells lining the glandular ducts. In comparison with previous results obtained in the olfactory mucosa of the same group of armadillos, the carbohydrate composition of the vomeronasal organ sensory epithelium differed from the olfactory sensory epithelium. This is probably related to the different nature of molecules involved in the perireceptor processes. PMID:10853958

GPI-anchored protein organization and dynamics at the cell surface

PubMed Central

Saha, Suvrajit; Anilkumar, Anupama Ambika; Mayor, Satyajit

2016-01-01

The surface of eukaryotic cells is a multi-component fluid bilayer in which glycosylphosphatidylinositol (GPI)-anchored proteins are an abundant constituent. In this review, we discuss the complex nature of the organization and dynamics of GPI-anchored proteins at multiple spatial and temporal scales. Different biophysical techniques have been utilized for understanding this organization, including fluorescence correlation spectroscopy, fluorescence recovery after photobleaching, single particle tracking, and a number of super resolution methods. Major insights into the organization and dynamics have also come from exploring the short-range interactions of GPI-anchored proteins by fluorescence (or Förster) resonance energy transfer microscopy. Based on the nanometer to micron scale organization, at the microsecond to the second time scale dynamics, a picture of the membrane bilayer emerges where the lipid bilayer appears inextricably intertwined with the underlying dynamic cytoskeleton. These observations have prompted a revision of the current models of plasma membrane organization, and suggest an active actin-membrane composite. PMID:26394904

Molecular and mass spectroscopic analysis of isotopically labeled organic residues

NASA Technical Reports Server (NTRS)

Mendoza-Gomez, Celia X.; Greenberg, J. Mayo; Mccain, P.; Ferris, J. P.; Briggs, R.; Degroot, M. S.; Schutte, Willem A.

1989-01-01

Experimental studies aimed at understanding the evolution of complex organic molecules on interstellar grains were performed. The photolysis of frozen gas mixtures of various compositions containing H2O, CO, NH3, and CH4 was studied. These species were chosen because of their astrophysical importance as deducted from observational as well as theoretical studies of ice mantles on interstellar grains. These ultraviolet photolyzed ices were warmed up in order to produce refractory organic molecules like the ones formed in molecular clouds when the icy mantles are being irradiated and warmed up either by a nearby stellar source or impulsive heating. The laboratory studies give estimates of the efficiency of production of such organic material under interstellar conditions. It is shown that the gradual carbonization of organic mantles in the diffuse cloud phase leads to higher and higher visual absorptivity - yellow residues become brown in the laboratory. The obtained results can be applied to explaining the organic components of comets and their relevance to the origin of life.

GPI-anchored protein organization and dynamics at the cell surface.

PubMed

Saha, Suvrajit; Anilkumar, Anupama Ambika; Mayor, Satyajit

2016-02-01

The surface of eukaryotic cells is a multi-component fluid bilayer in which glycosylphosphatidylinositol (GPI)-anchored proteins are an abundant constituent. In this review, we discuss the complex nature of the organization and dynamics of GPI-anchored proteins at multiple spatial and temporal scales. Different biophysical techniques have been utilized for understanding this organization, including fluorescence correlation spectroscopy, fluorescence recovery after photobleaching, single particle tracking, and a number of super resolution methods. Major insights into the organization and dynamics have also come from exploring the short-range interactions of GPI-anchored proteins by fluorescence (or Förster) resonance energy transfer microscopy. Based on the nanometer to micron scale organization, at the microsecond to the second time scale dynamics, a picture of the membrane bilayer emerges where the lipid bilayer appears inextricably intertwined with the underlying dynamic cytoskeleton. These observations have prompted a revision of the current models of plasma membrane organization, and suggest an active actin-membrane composite. Copyright © 2016 by the American Society for Biochemistry and Molecular Biology, Inc.

LDRD final report on imaging self-organization of proteins in membranes by photocatalytic nano-tagging.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zavadil, Kevin Robert; Shelnutt, John Allen; Sasaki, Darryl Yoshio

We have developed a new nanotagging technology for detecting and imaging the self-organization of proteins and other components of membranes at nanometer resolution for the purpose of investigating cell signaling and other membrane-mediated biological processes. We used protein-, lipid-, or drug-bound porphyrin photocatalysts to grow in-situ nanometer-sized metal particles, which reveal the location of the porphyrin-labeled molecules by electron microscopy. We initially used photocatalytic nanotagging to image assembled multi-component proteins and to monitor the distribution of lipids and porphyrin labels in liposomes. For example, by exchanging the heme molecules in hemoproteins with a photocatalytic tin porphyrin, a nanoparticle was grownmore » at each heme site of the protein. The result obtained from electron microscopy for a tagged multi-subunit protein such as hemoglobin is a symmetric constellation of a specific number of nanoparticle tags, four in the case of the hemoglobin tetramer. Methods for covalently linking photocatalytic porphyrin labels to lipids and proteins were also developed to detect and image the self-organization of lipids, protein-protein supercomplexes, and membrane-protein complexes. Procedures for making photocatalytic porphyrin-drug, porphyrin-lipid, and porphyrin-protein hybrids for non-porphyrin-binding proteins and membrane components were pursued and the first porphyrin-labeled lipids was investigated in liposomal membrane models. Our photocatalytic nanotagging technique may ultimately allow membrane self-organization and cell signaling processes to be imaged in living cells. Fluorescence and plasmonic spectra of the tagged proteins might also provide additional information about protein association and membrane organization. In addition, a porphyrin-aspirin or other NSAID hybrid may be used to grow metal nanotags for the pharmacologically important COX enzymes in membranes so that the distribution of the protein can be imaged at the nanometer scale.« less

A priming effect of benthic gastropod mucus on sedimentary organic matter remineralization

NASA Astrophysics Data System (ADS)

Hannides, A. K.; Aller, R. C.

2016-02-01

Mucous gels are produced by benthic animals rapidly and in copious amounts, and have previously been shown to significantly affect diffusion rates of redox-sensitive ions and organic compounds in sediment pore waters. They are also a highly likely priming substrate whose addition in modest amounts affects sedimentary organic matter remineralization. We tested the priming effect of benthic infaunal mucus using secretions of the common gastropod Neverita duplicata as model substrate. Their composition is typical of marine molluscan mucus, consisting primarily of water (>96% by weight), which is in relative equilibrium with seawater. Salt-free dry weight constitutes 0.7% and 0.6% of total pedal and hypobranchial mucus, respectively. The C:N ratios of pedal and hypobranchial mucus indicate that the organic component consists of a mucopolysaccharide-glycoprotein complex that varies depending on its function, while low C:S ratios of the insoluble component and positive staining with Alcian Blue dye are indicative of S-ester and alkyl-SO42- groups bridging mucopolysaccharide and glycoprotein components. Anoxic incubations of pedal mucus of N. duplicata, sediment, and mucus-sediment mixture, resulted in the anaerobic generation of ΣCO2 and NH4+ at ratios lower than initial C:N ratios, indicating the preferential decomposition of N-rich moieties. Production rates of SCO2 and NH4+ in mucus-sediment incubations are higher, by 9±16% and 29±11%, respectively, than those predicted from linear addition of mucus-only and sediment-only rates. The statistically significant accelerated remineralization rate of N in the presence of modest mucus contribution (0.2% of total N), suggests that benthic mucus addition affects sedimentary organic matter remineralization processes through a "priming" effect.

Counting numbers of synaptic proteins: absolute quantification and single molecule imaging techniques

PubMed Central

Patrizio, Angela; Specht, Christian G.

2016-01-01

Abstract. The ability to count molecules is essential to elucidating cellular mechanisms, as these often depend on the absolute numbers and concentrations of molecules within specific compartments. Such is the case at chemical synapses, where the transmission of information from presynaptic to postsynaptic terminals requires complex interactions between small sets of molecules. Be it the subunit stoichiometry specifying neurotransmitter receptor properties, the copy numbers of scaffold proteins setting the limit of receptor accumulation at synapses, or protein packing densities shaping the molecular organization and plasticity of the postsynaptic density, all of these depend on exact quantities of components. A variety of proteomic, electrophysiological, and quantitative imaging techniques have yielded insights into the molecular composition of synaptic complexes. In this review, we compare the different quantitative approaches and consider the potential of single molecule imaging techniques for the quantification of synaptic components. We also discuss specific neurobiological data to contextualize the obtained numbers and to explain how they aid our understanding of synaptic structure and function. PMID:27335891

Counting numbers of synaptic proteins: absolute quantification and single molecule imaging techniques.

PubMed

Patrizio, Angela; Specht, Christian G

2016-10-01

The ability to count molecules is essential to elucidating cellular mechanisms, as these often depend on the absolute numbers and concentrations of molecules within specific compartments. Such is the case at chemical synapses, where the transmission of information from presynaptic to postsynaptic terminals requires complex interactions between small sets of molecules. Be it the subunit stoichiometry specifying neurotransmitter receptor properties, the copy numbers of scaffold proteins setting the limit of receptor accumulation at synapses, or protein packing densities shaping the molecular organization and plasticity of the postsynaptic density, all of these depend on exact quantities of components. A variety of proteomic, electrophysiological, and quantitative imaging techniques have yielded insights into the molecular composition of synaptic complexes. In this review, we compare the different quantitative approaches and consider the potential of single molecule imaging techniques for the quantification of synaptic components. We also discuss specific neurobiological data to contextualize the obtained numbers and to explain how they aid our understanding of synaptic structure and function.

About problematic peculiarities of Fault Tolerance digital regulation organization

NASA Astrophysics Data System (ADS)

Rakov, V. I.; Zakharova, O. V.

2018-05-01

The solution of problems concerning estimation of working capacity of regulation chains and possibilities of preventing situations of its violation in three directions are offered. The first direction is working out (creating) the methods of representing the regulation loop (circuit) by means of uniting (combining) diffuse components and forming algorithmic tooling for building predicates of serviceability assessment separately for the components and the for regulation loops (circuits, contours) in general. The second direction is creating methods of Fault Tolerance redundancy in the process of complex assessment of current values of control actions, closure errors and their regulated parameters. The third direction is creating methods of comparing the processes of alteration (change) of control actions, errors of closure and regulating parameters with their standard models or their surroundings. This direction allows one to develop methods and algorithmic tool means, aimed at preventing loss of serviceability and effectiveness of not only a separate digital regulator, but also the whole complex of Fault Tolerance regulation.

Inorganic salts interact with organic di-acids in sub-micron particles to form material with low hygroscopicity and volatility

NASA Astrophysics Data System (ADS)

Drozd, G.; Woo, J.; Häkkinen, S. A. K.; Nenes, A.; McNeill, V. F.

2013-11-01

Volatility and hygroscopicity are two key properties of organic aerosol components, and both are strongly related to chemical identity. Here we show that inorganic-organic component interactions typically not considered in atmospheric models may strongly affect aerosol volatility and hygroscopicity. In particular, bi-dentate binding of di-carboxylic acids (DCA) to soluble inorganic ions can lead to very strongly bound metal-organic complexes with largely undetermined hygroscopicity and volatility. These reactions profoundly impact particle hygroscopicity, transforming hygroscopic components into irreversibly non-hygroscopic material. While the hygroscopicities of pure salts, DCA, and DCA salts are known, the hygroscopicity of internal mixtures of hygroscopic salts and DCA, as they are typically found in the atmosphere, has not been fully characterized. We have studied the volatility of pure, dry organic salt particles and the hygroscopicity of internal mixtures of oxalic acid (OxA, the dominant DCA in the atmosphere) and a number of salts, both mono- and di-valent. The formation of very low volatility organic salts was confirmed, with minimal evaporation of oxalate salt particles below 75 °C. Dramatic increases in the CCN activation diameter for particles with divalent salts (e.g. CaCl2) and relatively small particle mass fractions of OxA indicate that standard volume additivity rules for hygroscopicity do not apply. Thus small organic compounds with high O:C are capable of forming low volatility and very low hygroscopicity particles. Given current knowledge of the formation mechanisms of OxA and M-Ox salts, surface enrichment of insoluble M-Ox salts is expected. The resulting formation of an insoluble coating of metal-oxalate salts can explain low particle hygroscopicities. The formation of particles with a hard coating could offer an alternative explanation for observations of glass-like particles with very low viscosity.

Recognition as a patient-centered medical home: fundamental or incidental?

PubMed

Dohan, Daniel; McCuistion, Mary Honodel; Frosch, Dominick L; Hung, Dorothy Y; Tai-Seale, Ming

2013-01-01

Little is known about reasons why a medical group would seek recognition as a patient-centered medical home (PCMH). We examined the motivations for seeking recognition in one group and assessed why the group allowed recognition to lapse 3 years later. As part of a larger mixed methods case study, we conducted 38 key informant interviews with executives, clinicians, and front-line staff. Interviews were conducted according to a guide that evolved during the project and were audio-recorded and fully transcribed. Transcripts were analyzed and thematically coded. PCMH principles were consistent with the organization's culture and mission, which valued innovation and putting patients first. Motivations for implementing specific PCMH components varied; some components were seen as part of the organization's patient-centered culture, whereas others helped the practice compete in its local market. Informants consistently reported that National Committee for Quality Assurance recognition arose incidentally because of a 1-time incentive from a local group of large employers and because the organization decided to allocate some organizational resources to respond to the complex reporting requirements for about one-half of its clinics. Becoming patient centered and seeking recognition as such ran along separate but parallel tracks within this organization. As the Affordable Care Act continues to focus attention on primary care redesign, this apparent disconnect should be borne in mind.

Interactions between natural organic ligands and trace metals studied by fluorescence lifetime and fluorescence quenching

NASA Astrophysics Data System (ADS)

Nouhi, Ayoub; Hajjoul, Houssam; Redon, Roland; Gagné, Jean-Pierre; Mounier, Stéphane

2017-04-01

Improved insight on the interactions between natural organic ligands and trace metals is of paramount importance for better understanding transport and toxicity pathways of metal ions in the environment. Fluorescence spectroscopy allows introspecting ligands-metals interactions. Time-resolved laser fluorescence spectroscopy (TRLFS) measures fluorophore lifetime probing the local molecular environment. Excitation Emission Fluorescence Matrices (EEFMs) and their statistical treatment : parallel factor analysis (PARAFAC) using PROGMEEF Matlab homemade program, can give insight on the number or nature of organic fluorophores involved in the interactions. Quenching of fluorescence by metals can occur following two processes: dynamic and static quenching (Lakowicz, 2013). In the first case, quenching is caused by physical collisions among molecules and in the second case fluorophores can form nonfluorescent complexes with quenchers. It is possible to identify the different mechanisms because each type of quenching corresponds to a different mathematical model (Lakowicz, 2013; Valeur and Berberan-Santos, 2012). In TRLFS, the study of fluorescence decay's laws induced by nanosecond pulsed laser will allow to exactly qualify the type of interaction. The crucial point of the temporal deconvolution will be the evaluation of the best fitting between the different physical models and the decays measured. From the most suitable time decay model, it will be possible to deduce the quenching which modifies the fluorescence. The aim of this study was to characterize interactions between natural organic ligands and trace metals using fluorescence tools to evaluate the fluorescence lifetime of the fluorophore, the occurrence of quenching in presence of metal, discuss its mechanism and estimate conditional stability constants if a complex organic ligand-metal is formed. This study has been done in two steps. First, we have examined the interactions between salicylic acid and copper in order to calibrate our assays and compare our results with literature. Several studies have shown that static quenching occurs in that case (Brun and Schröder, 1975; Lavrik and Mulloev, 2010; Ventry et al., 1991; Babko, 1968). Indeed, after processing the EEFMs and TRLFS data, we found a fluorescence intensity decay by about 50% and a constant lifetime for the fluorophore suggesting a static quenching, in agreement with the literature. In the second step, we have studied the interactions between metal and different types of natural organic matters. In this case, EEMFs and TRLFS experiments were done on samples prepared by dissolving copper in four different fractions of organic matter extracted from estuarine water (St. Lawrence Estuary, Canada). Organic matter was obtained using DAX-8 and XAD-4 resins in series. Humic and fulvic acids are obtained following the IHSS protocol. The results of interaction between humic substances and copper gathered after processing data on PROGMEEF have shown a fluorescence intensity decay by about 57% for the first component and 88% for the second component. The fluorescence lifetime for both components were close to 2 ns and 6 ns respectively and the pH range was stable and close to 6. This means that a static quenching takes place in this case in agreement with the literature. Our study also focused on the investigation of complexation of organic matter by other metals in particular Aluminum, Arsenic, Europium and Uranium.

Stoichiometry for binding and transport by the twin arginine translocation system.

PubMed

Celedon, Jose M; Cline, Kenneth

2012-05-14

Twin arginine translocation (Tat) systems transport large folded proteins across sealed membranes. Tat systems accomplish this feat with three membrane components organized in two complexes. In thylakoid membranes, cpTatC and Hcf106 comprise a large receptor complex containing an estimated eight cpTatC-Hcf106 pairs. Protein transport occurs when Tha4 joins the receptor complex as an oligomer of uncertain size that is thought to form the protein-conducting structure. Here, binding analyses with intact membranes or purified complexes indicate that each receptor complex could bind eight precursor proteins. Kinetic analysis of translocation showed that each precursor-bound site was independently functional for transport, and, with sufficient Tha4, all sites were concurrently active for transport. Tha4 titration determined that ∼26 Tha4 protomers were required for transport of each OE17 (oxygen-evolving complex subunit of 17 kD) precursor protein. Our results suggest that, when fully saturated with precursor proteins and Tha4, the Tat translocase is an ∼2.2-megadalton complex that can individually transport eight precursor proteins or cooperatively transport multimeric precursors.

Positioning cell wall synthetic complexes by the bacterial morphogenetic proteins MreB and MreD.

PubMed

White, Courtney L; Kitich, Aleksandar; Gober, James W

2010-05-01

In Caulobacter crescentus, intact cables of the actin homologue, MreB, are required for the proper spatial positioning of MurG which catalyses the final step in peptidoglycan precursor synthesis. Similarly, in the periplasm, MreC controls the spatial orientation of the penicillin binding proteins and a lytic transglycosylase. We have now found that MreB cables are required for the organization of several other cytosolic murein biosynthetic enzymes such as MraY, MurB, MurC, MurE and MurF. We also show these proteins adopt a subcellular pattern of localization comparable to MurG, suggesting the existence of cytoskeletal-dependent interactions. Through extensive two-hybrid analyses, we have now generated a comprehensive interaction map of components of the bacterial morphogenetic complex. In the cytosol, this complex contains both murein biosynthetic enzymes and morphogenetic proteins, including RodA, RodZ and MreD. We show that the integral membrane protein, MreD, is essential for lateral peptidoglycan synthesis, interacts with the precursor synthesizing enzymes MurG and MraY, and additionally, determines MreB localization. Our results suggest that the interdependent localization of MreB and MreD functions to spatially organize a complex of peptidoglycan precursor synthesis proteins, which is required for propagation of a uniform cell shape and catalytically efficient peptidoglycan synthesis.

Multiscale structure in eco-evolutionary dynamics

NASA Astrophysics Data System (ADS)

Stacey, Blake C.

In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

Quaternary Structure of the Oxaloacetate Decarboxylase Membrane Complex and Mechanistic Relationships to Pyruvate Carboxylases*

PubMed Central

Balsera, Monica; Buey, Ruben M.; Li, Xiao-Dan

2011-01-01

The oxaloacetate decarboxylase primary Na+ pump (OAD) is an essential membrane protein complex that functions in the citrate fermentation pathway of some pathogenic bacteria under anaerobic conditions. OAD contains three different subunits: Oad-α, a biotinylated extrinsic protein that catalyzes the α-ketodecarboxylation of oxaloacetate; Oad-γ, a structural bitopic membrane protein whose cytosolic tail (named as Oad-γ′) binds tightly to Oad-α; and Oad-β, a multispan transmembrane α-helical protein that constitutes the Na+ channel. How OAD is organized structurally at the membrane and what the molecular determinants are that lead to an efficient energy coupling mechanism remain elusive. In the present work, we elucidate the stoichiometry of the native complex as well as the low resolution structure of the peripheral components of OAD (Oad-α and Oad-γ′) by small angle x-ray scattering. Our results point to a quaternary assembly similar to the pyruvate carboxylase complex organization. Herein, we propose a model in which the association in pairs of Oad-α dimers, mediated by Oad-γ, results in the acquisition of a functional oligomeric state at the bacterial membrane. New structural insights for the conformational rearrangements associated with the carboxylbiotin transfer reaction within OAD are provided. PMID:21209096

Self-assembled virus-membrane complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Lihua; Liang, Hongjun; Angelini, Thomas

Anionic polyelectrolytes and cationic lipid membranes can self-assemble into lamellar structures ranging from alternating layers of membranes and polyelectrolytes to 'missing layer' superlattice structures. We show that these structural differences can be understood in terms of the surface-charge-density mismatch between the polyelectrolyte and membrane components by examining complexes between cationic membranes and highly charged M13 viruses, a system that allowed us to vary the polyelectrolyte diameter independently of the charge density. Such virus-membrane complexes have pore sizes that are about ten times larger in area than DNA-membrane complexes, and can be used to package and organize large functional molecules; correlatedmore » arrays of Ru(bpy){sub 3}{sup 2+} macroionic dyes have been directly observed within the virus-membrane complexes using an electron-density reconstruction. These observations elucidate fundamental design rules for rational control of self-assembled polyelectrolyte-membrane structures, which have applications ranging from non-viral gene therapy to biomolecular templates for nanofabrication.« less

Molecular architecture of the TRAPPII complex and implications for vesicle tethering.

PubMed

Yip, Calvin K; Berscheminski, Julia; Walz, Thomas

2010-11-01

Multisubunit tethering complexes participate in the process of vesicle tethering--the initial interaction between transport vesicles and their acceptor compartments. TRAPPII (named for transport protein particle II) is a highly conserved tethering complex that functions in the late Golgi apparatus and consists of all of the subunits of TRAPPI and three additional, specific subunits. We have purified native yeast TRAPPII and characterized its structure and subunit organization by single-particle EM. Our data show that the nine TRAPPII components form a core complex that dimerizes into a three-layered, diamond-shaped structure. The TRAPPI subunits assemble into TRAPPI complexes that form the outer layers. The three TRAPPII-specific subunits cap the ends of TRAPPI and form the middle layer, which is responsible for dimerization. TRAPPII binds the Ypt1 GTPase and probably uses the TRAPPI catalytic core to promote guanine nucleotide exchange. We discuss the implications of the structure of TRAPPII for coat interaction and TRAPPII-associated human pathologies.

Reprint of "How do components of real cloud water affect aqueous pyruvate oxidation?"

NASA Astrophysics Data System (ADS)

Boris, Alexandra J.; Desyaterik, Yury; Collett, Jeffrey L.

2015-01-01

Chemical oxidation of dissolved volatile or semi-volatile organic compounds within fog and cloud droplets in the atmosphere could be a major pathway for secondary organic aerosol (SOA) formation. This proposed pathway consists of: (1) dissolution of organic chemicals from the gas phase into a droplet; (2) reaction with an aqueous phase oxidant to yield low volatility products; and (3) formation of particle phase organic matter as the droplet evaporates. The common approach to simulating aqueous SOA (aqSOA) reactions is photo-oxidation of laboratory standards in pure water. Reactions leading to aqSOA formation should be studied within real cloud and fog water to determine whether additional competing processes might alter apparent rates of reaction as indicated by rates of reactant loss or product formation. To evaluate and identify the origin of any cloud water matrix effects on one example of observed aqSOA production, pyruvate oxidation experiments simulating aqSOA formation were monitored within pure water, real cloud water samples, and an aqueous solution of inorganic salts. Two analysis methods were used: online electrospray ionization high-resolution time-of-flight mass spectrometry (ESI-HR-ToF-MS), and offline anion exchange chromatography (IC) with quantitative conductivity and qualitative ESI-HR-ToF-MS detection. The apparent rate of oxidation of pyruvate was slowed in cloud water matrices: overall measured degradation rates of pyruvate were lower than in pure water. This can be at least partially accounted for by the observed formation of pyruvate from reactions of other cloud water components. Organic constituents of cloud water also compete for oxidants and/or UV light, contributing to the observed slowed degradation rates of pyruvate. The oxidation of pyruvate was not significantly affected by the presence of inorganic anions (nitrate and sulfate) at cloud-relevant concentrations. Future bulk studies of aqSOA formation reactions using simplified simulated cloud solutions and model estimates of generated aqSOA mass should take into account possible generation of, or competition for, oxidant molecules by organic components found in the complex matrices typically associated with real atmospheric water droplets. Additionally, it is likely that some components of real atmospheric waters have not yet been identified as aqSOA precursors, but could be distinguished through further simplified bulk oxidations of known atmospheric water components.

Interactions of specific extracellular organic matter and polyaluminum chloride and their roles in the algae-polluted water treatment.

PubMed

Tang, Xiaomin; Zheng, Huaili; Gao, Baoyu; Zhao, Chuanliang; Liu, Bingzhi; Chen, Wei; Guo, Jinsong

2017-06-15

Extracellular organic matter (EOM) is ubiquitous in the algae-polluted water and has a significant impact on the human health and drinking water treatment. We investigate the different characteristics of dissolved extracellular organic matter (dEOM) and bound extracellular organic matter (bEOM) recovered from the various growth period of Microcystis aeruginosa and the interactions of them and polyaluminum chloride (PACl). The roles of the different EOM in the algae-polluted water treatment are also discussed. The functional groups of aromatic, OH, NH, CN and NO in bEOM possessing the stronger interaction with hydroxyl aluminum compared with dEOM is responsible for bEOM and algae removal. Some low molecular weight (MW) organic components and protein-like substances in bEOM are most easily removed. And dEOM weakly reacts with PACl or inhibits coagulation, especially dEOM with the high MW organic components. The main coagulation mechanisms of bEOM are the generation of insoluble Al-bEOM through complexation, the bridge of AlO 4 Al 12 (OH) 24 (H 2 O) 12 7+ (Al 13 ), the adsorption of Al(OH) 3(am) and the entrapment of flocs. The adsorption of Al 13 and Al(OH) 3(am) mainly contribute to dEOM removal. It is also recommended to treat the algae with dEOM and bEOM at the initial stage. Copyright © 2017 Elsevier B.V. All rights reserved.

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

PubMed Central

Stegen, James C.; Fredrickson, James K.; Wilkins, Michael J.; Konopka, Allan E.; Nelson, William C.; Arntzen, Evan V.; Chrisler, William B.; Chu, Rosalie K.; Danczak, Robert E.; Fansler, Sarah J.; Kennedy, David W.; Resch, Charles T.; Tfaily, Malak

2016-01-01

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater–surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater–surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds. PMID:27052662

Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover.

PubMed

Stegen, James C; Fredrickson, James K; Wilkins, Michael J; Konopka, Allan E; Nelson, William C; Arntzen, Evan V; Chrisler, William B; Chu, Rosalie K; Danczak, Robert E; Fansler, Sarah J; Kennedy, David W; Resch, Charles T; Tfaily, Malak

2016-04-07

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater-surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater-surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds.

Characterization of selected municipal solid waste components to estimate their biodegradability.

PubMed

Bayard, R; Benbelkacem, H; Gourdon, R; Buffière, P

2018-06-15

Biological treatments of Residual Municipal Solid Waste (RMSW) allow to divert biodegradable materials from landfilling and recover valuable alternative resources. The biodegradability of the waste components needs however to be assessed in order to design the bioprocesses properly. The present study investigated complementary approaches to aerobic and anaerobic biotests for a more rapid evaluation. A representative sample of residual MSW was collected from a Mechanical Biological Treatment (MBT) plant and sorted out into 13 fractions according to the French standard procedure MODECOM™. The different fractions were analyzed for organic matter content, leaching behavior, contents in biochemical constituents (determined by Van Soest's acid detergent fiber method), Biochemical Oxygen Demand (BOD) and Bio-Methane Potential (BMP). Experimental data were statistically treated by Principal Components Analysis (PCA). Cumulative oxygen consumption from BOD tests and cumulative methane production from BMP tests were found to be positively correlated in all waste fractions. No correlation was observed between the results from BOD or BMP bioassays and the contents in cellulose-like, hemicelluloses-like or labile organic compounds. No correlation was observed either with the results from leaching tests (Soluble COD). The contents in lignin-like compounds, evaluated as the non-extracted RES fraction in Van Soest's method, was found however to impact negatively the biodegradability assessed by BOD or BMP tests. Since cellulose, hemicelluloses and lignin are the polymers responsible for the structuration of lignocellulosic complexes, it was concluded that the structural organization of the organic matter in the different waste fractions was more determinant on biodegradability than the respective contents in individual biopolymers. Copyright © 2017 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, Koushik; Balog, Eva Rose M.; Sista, Prakash

We report a method for creating hybrid organic-inorganic “nanoflowers” using calcium or copper ions as the inorganic component and a recombinantly expressed elastin-like polypeptide (ELP) as the organic component. Polypeptides provide binding sites for the dynamic coordination with metal ions, and then such noncovalent complexes become nucleation sites for primary crystals of metal phosphates. We have shown that the interaction between the stimuli-responsive ELP and Ca{sup 2+} or Cu{sup 2+}, in the presence of phosphate, leads to the growth of micrometer-sized particles featuring nanoscale patterns shaped like flower petals. The morphology of these flower-like composite structures is dependent upon themore » temperature of growth and has been characterized by scanning electron microscopy. The composition of nanoflowers has also been analyzed by energy-dispersive X-ray spectroscopy, X-ray photoelectron spectroscopy, and X-ray diffraction. The temperature-dependent morphologies of these hybrid nanostructures, which arise from the controllable phase transition of ELPs, hold potential for morphological control of biomaterials in emerging applications such as tissue engineering and biocatalysis.« less

The Diffuse Interstellar Bands: an Elderly Astro-Puzzle Rejuvenated

NASA Astrophysics Data System (ADS)

Cox, Nick L. J.

2011-12-01

The interstellar medium constitutes a physically and chemically complex component of galaxies and is important in the cycle of matter and the evolution of stars. From various spectroscopic clues we now know that the interstellar medium is rich in organic compounds. However, identifying the exact nature of all these components remains a challenge. In particular the identification of the so-called diffuse band carriers has been alluding astronomers for almost a century. In recent decades, observational, experimental and theoretical advances have rapidly lead to renewed interest in the diffuse interstellar bands (DIBs). This has been instigated partly by their perceived relation to the infrared aromatic emission bands, the UV extinction bump and far-UV rise, and the growing number of (small) organic molecules identified in space. This chapter gives an overview of the observational properties and behaviour of the DIBs, and their presence throughout the Universe. I will highlight recent progress in identifying their carriers and discuss their potential as tracers and probes of (extra)-Galactic ISM conditions.

A node organization in the actomyosin contractile ring generates tension and aids stability

PubMed Central

Thiyagarajan, Sathish; Wang, Shuyuan; O’Shaughnessy, Ben

2017-01-01

During cytokinesis, a contractile actomyosin ring constricts and divides the cell in two. How the ring marshals actomyosin forces to generate tension is not settled. Recently, a superresolution microscopy study of the fission yeast ring revealed that myosins and formins that nucleate actin filaments colocalize in plasma membrane-anchored complexes called nodes in the constricting ring. The nodes move bidirectionally around the ring. Here we construct and analyze a coarse-grained mathematical model of the fission yeast ring to explore essential consequences of the recently discovered ring ultrastructure. The model reproduces experimentally measured values of ring tension, explains why nodes move bidirectionally, and shows that tension is generated by myosin pulling on barbed-end-anchored actin filaments in a stochastic sliding-filament mechanism. This mechanism is not based on an ordered sarcomeric organization. We show that the ring is vulnerable to intrinsic contractile instabilities, and protection from these instabilities and organizational homeostasis require both component turnover and anchoring of components to the plasma membrane. PMID:28954859

Effects of diesel exhaust-derived secondary organic aerosol (SOA) on oocytes: Potential risks to meiotic maturation.

PubMed

Udagawa, Osamu; Furuyama, Akiko; Imai, Koji; Fujitani, Yuji; Hirano, Seishiro

2018-01-01

Particulate air pollution (PM 2.5) is a worldwide concern. Growing epidemiological evidence has shown pathophysiological effects of PM 2.5, not only on cardiovascular system but also on reproductive performance. The composition and physicochemical properties of PM 2.5 vary depending on the emission sources, climate conditions, and complex chemical reactions in the air. These factors make it difficult to understand the cause and mechanistic details of the adverse health effects of PM 2.5. Here, we show potential impacts of PM 2.5 on oocyte maturation in mice by utilizing diesel exhaust-derived secondary organic aerosol (SOA), a major component of urban PM 2.5. We found that the SOA destabilized microtubules of mouse oocytes and p-benzoquinone is one of the candidates for the microtubule-destabilizing compounds. We propose that some biologically reactive components of PM 2.5 should be prioritized for the regulation of atmospheric quality. Copyright © 2017 Elsevier Inc. All rights reserved.

Super-Resolution Microscopy: Shedding Light on the Cellular Plasma Membrane.

PubMed

Stone, Matthew B; Shelby, Sarah A; Veatch, Sarah L

2017-06-14

Lipids and the membranes they form are fundamental building blocks of cellular life, and their geometry and chemical properties distinguish membranes from other cellular environments. Collective processes occurring within membranes strongly impact cellular behavior and biochemistry, and understanding these processes presents unique challenges due to the often complex and myriad interactions between membrane components. Super-resolution microscopy offers a significant gain in resolution over traditional optical microscopy, enabling the localization of individual molecules even in densely labeled samples and in cellular and tissue environments. These microscopy techniques have been used to examine the organization and dynamics of plasma membrane components, providing insight into the fundamental interactions that determine membrane functions. Here, we broadly introduce the structure and organization of the mammalian plasma membrane and review recent applications of super-resolution microscopy to the study of membranes. We then highlight some inherent challenges faced when using super-resolution microscopy to study membranes, and we discuss recent technical advancements that promise further improvements to super-resolution microscopy and its application to the plasma membrane.

Multiscale Modeling of Cardiac Cellular Energetics

PubMed Central

BASSINGTHWAIGHTE, JAMES B.; CHIZECK, HOWARD J.; ATLAS, LES E.; QIAN, HONG

2010-01-01

Multiscale modeling is essential to integrating knowledge of human physiology starting from genomics, molecular biology, and the environment through the levels of cells, tissues, and organs all the way to integrated systems behavior. The lowest levels concern biophysical and biochemical events. The higher levels of organization in tissues, organs, and organism are complex, representing the dynamically varying behavior of billions of cells interacting together. Models integrating cellular events into tissue and organ behavior are forced to resort to simplifications to minimize computational complexity, thus reducing the model’s ability to respond correctly to dynamic changes in external conditions. Adjustments at protein and gene regulatory levels shortchange the simplified higher-level representations. Our cell primitive is composed of a set of subcellular modules, each defining an intracellular function (action potential, tricarboxylic acid cycle, oxidative phosphorylation, glycolysis, calcium cycling, contraction, etc.), composing what we call the “eternal cell,” which assumes that there is neither proteolysis nor protein synthesis. Within the modules are elements describing each particular component (i.e., enzymatic reactions of assorted types, transporters, ionic channels, binding sites, etc.). Cell subregions are stirred tanks, linked by diffusional or transporter-mediated exchange. The modeling uses ordinary differential equations rather than stochastic or partial differential equations. This basic model is regarded as a primitive upon which to build models encompassing gene regulation, signaling, and long-term adaptations in structure and function. During simulation, simpler forms of the model are used, when possible, to reduce computation. However, when this results in error, the more complex and detailed modules and elements need to be employed to improve model realism. The processes of error recognition and of mapping between different levels of model form complexity are challenging but are essential for successful modeling of large-scale systems in reasonable time. Currently there is to this end no established methodology from computational sciences. PMID:16093514

Promoting Conceptual Change for Complex Systems Understanding: Outcomes of an Agent-Based Participatory Simulation

NASA Astrophysics Data System (ADS)

Rates, Christopher A.; Mulvey, Bridget K.; Feldon, David F.

2016-08-01

Components of complex systems apply across multiple subject areas, and teaching these components may help students build unifying conceptual links. Students, however, often have difficulty learning these components, and limited research exists to understand what types of interventions may best help improve understanding. We investigated 32 high school students' understandings of complex systems components and whether an agent-based simulation could improve their understandings. Pretest and posttest essays were coded for changes in six components to determine whether students showed more expert thinking about the complex system of the Chesapeake Bay watershed. Results showed significant improvement for the components Emergence ( r = .26, p = .03), Order ( r = .37, p = .002), and Tradeoffs ( r = .44, p = .001). Implications include that the experiential nature of the simulation has the potential to support conceptual change for some complex systems components, presenting a promising option for complex systems instruction.

Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming

DOE PAGES

Feng, Wenting; Liang, Junyi; Hale, Lauren E.; ...

2017-06-09

Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon–climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming.more » Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the decomposition of SOC components with slow turnover rates and thus amplify the positive feedback to climate change.« less

Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Wenting; Liang, Junyi; Hale, Lauren E.

Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon–climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming.more » Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the decomposition of SOC components with slow turnover rates and thus amplify the positive feedback to climate change.« less

Enhanced decomposition of stable soil organic carbon and microbial catabolic potentials by long-term field warming.

PubMed

Feng, Wenting; Liang, Junyi; Hale, Lauren E; Jung, Chang Gyo; Chen, Ji; Zhou, Jizhong; Xu, Minggang; Yuan, Mengting; Wu, Liyou; Bracho, Rosvel; Pegoraro, Elaine; Schuur, Edward A G; Luo, Yiqi

2017-11-01

Quantifying soil organic carbon (SOC) decomposition under warming is critical to predict carbon-climate feedbacks. According to the substrate regulating principle, SOC decomposition would decrease as labile SOC declines under field warming, but observations of SOC decomposition under warming do not always support this prediction. This discrepancy could result from varying changes in SOC components and soil microbial communities under warming. This study aimed to determine the decomposition of SOC components with different turnover times after subjected to long-term field warming and/or root exclusion to limit C input, and to test whether SOC decomposition is driven by substrate lability under warming. Taking advantage of a 12-year field warming experiment in a prairie, we assessed the decomposition of SOC components by incubating soils from control and warmed plots, with and without root exclusion for 3 years. We assayed SOC decomposition from these incubations by combining inverse modeling and microbial functional genes during decomposition with a metagenomic technique (GeoChip). The decomposition of SOC components with turnover times of years and decades, which contributed to 95% of total cumulative CO 2 respiration, was greater in soils from warmed plots. But the decomposition of labile SOC was similar in warmed plots compared to the control. The diversity of C-degradation microbial genes generally declined with time during the incubation in all treatments, suggesting shifts of microbial functional groups as substrate composition was changing. Compared to the control, soils from warmed plots showed significant increase in the signal intensities of microbial genes involved in degrading complex organic compounds, implying enhanced potential abilities of microbial catabolism. These are likely responsible for accelerated decomposition of SOC components with slow turnover rates. Overall, the shifted microbial community induced by long-term warming accelerates the decomposition of SOC components with slow turnover rates and thus amplify the positive feedback to climate change. © 2017 John Wiley & Sons Ltd.

Ground experiments for finding principles and working out methods for preventing adverse effects of weightlessness on the human organism

NASA Technical Reports Server (NTRS)

Kakurin, L. I.; Gregoryev, A. I.; Mikhailov, V. M.; Tishler, V. A.

1980-01-01

A comparative assessment of the effectiveness of different prophylactic procedures to prevent the adverse effects of weightlessness is presented. It is concluded that: physical training is most effective but no single method by itself produces the full effect, and an adjustment of regimes to one another enhances the effect. The approved complex of prophylactic procedures affected basic changes occurring in hypokinesia: deficit of muscular activity, no or reduced BP hydrostatic component, reduced volume of blood circulation, reduced hydration level, and the application of various prophylactic complexes during 49 day antiorthostatic hypodynamia eliminated or reduced the adverse effects of weightlessness in simulation.

Charge Segregation and Low Hydrophobicity Are Key Features of Ribosomal Proteins from Different Organisms*

PubMed Central

Fedyukina, Daria V.; Jennaro, Theodore S.; Cavagnero, Silvia

2014-01-01

Ribosomes are large and highly charged macromolecular complexes consisting of RNA and proteins. Here, we address the electrostatic and nonpolar properties of ribosomal proteins that are important for ribosome assembly and interaction with other cellular components and may influence protein folding on the ribosome. We examined 50 S ribosomal subunits from 10 species and found a clear distinction between the net charge of ribosomal proteins from halophilic and non-halophilic organisms. We found that ∼67% ribosomal proteins from halophiles are negatively charged, whereas only up to ∼15% of ribosomal proteins from non-halophiles share this property. Conversely, hydrophobicity tends to be lower for ribosomal proteins from halophiles than for the corresponding proteins from non-halophiles. Importantly, the surface electrostatic potential of ribosomal proteins from all organisms, especially halophiles, has distinct positive and negative regions across all the examined species. Positively and negatively charged residues of ribosomal proteins tend to be clustered in buried and solvent-exposed regions, respectively. Hence, the majority of ribosomal proteins is characterized by a significant degree of intramolecular charge segregation, regardless of the organism of origin. This key property enables the ribosome to accommodate proteins within its complex scaffold regardless of their overall net charge. PMID:24398678

Improved source apportionment of organic aerosols in complex urban air pollution using the multilinear engine (ME-2)

NASA Astrophysics Data System (ADS)

Zhu, Qiao; Huang, Xiao-Feng; Cao, Li-Ming; Wei, Lin-Tong; Zhang, Bin; He, Ling-Yan; Elser, Miriam; Canonaco, Francesco; Slowik, Jay G.; Bozzetti, Carlo; El-Haddad, Imad; Prévôt, André S. H.

2018-02-01

Organic aerosols (OAs), which consist of thousands of complex compounds emitted from various sources, constitute one of the major components of fine particulate matter. The traditional positive matrix factorization (PMF) method often apportions aerosol mass spectrometer (AMS) organic datasets into less meaningful or mixed factors, especially in complex urban cases. In this study, an improved source apportionment method using a bilinear model of the multilinear engine (ME-2) was applied to OAs collected during the heavily polluted season from two Chinese megacities located in the north and south with an Aerodyne high-resolution aerosol mass spectrometer (HR-ToF-AMS). We applied a rather novel procedure for utilization of prior information and selecting optimal solutions, which does not necessarily depend on other studies. Ultimately, six reasonable factors were clearly resolved and quantified for both sites by constraining one or more factors: hydrocarbon-like OA (HOA), cooking-related OA (COA), biomass burning OA (BBOA), coal combustion (CCOA), less-oxidized oxygenated OA (LO-OOA) and more-oxidized oxygenated OA (MO-OOA). In comparison, the traditional PMF method could not effectively resolve the appropriate factors, e.g., BBOA and CCOA, in the solutions. Moreover, coal combustion and traffic emissions were determined to be primarily responsible for the concentrations of PAHs and BC, respectively, through the regression analyses of the ME-2 results.

Adsorption of MCPA on goethite and humic acid-coated goethite.

PubMed

Iglesias, A; López, R; Gondar, D; Antelo, J; Fiol, S; Arce, F

2010-03-01

Anionic pesticides are adsorbed on the mineral oxide fraction of the soil surface but considerably less on the organic fraction, so that the presence of organic matter causes a decrease in the amount of pesticide adsorbed, and may affect the mechanism of adsorption. In the present study we investigated the adsorption of the weak acid pesticide MCPA on the surface of goethite and of humic acid-coated goethite, selected as models of the mineral oxide fraction and organic components present in soil systems. Adsorption of the anionic form of the pesticide on goethite fitted an S-type isotherm and the amount adsorbed increased as the ionic strength decreased and the pH of the medium decreased. Application of the charge distribution multi site complexation model (CD-MUSIC model) enabled interpretation of the results, which suggested the formation of inner and outer sphere complexes between the pesticide and the singly-coordinated surface sites of goethite. Less pesticide was adsorbed on the humic acid-coated goethite than on the bare goethite and the pattern fitted an L-type isotherm, which indicates a change in the mechanism of adsorption. Simplified calculations with the CD-MUSIC model enabled interpretation of the results, which suggested that the pesticide molecules form the same type of surface complexes as in the previous case. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

Synthesis, Photoluminescence Behavior of Green Light Emitting Tb(III) Complexes and Mechanistic Investigation of Energy Transfer Process.

PubMed

Bala, Manju; Kumar, Satish; Devi, Rekha; Khatkar, Avni; Taxak, V B; Boora, Priti; Khatkar, S P

2018-06-04

A series of five new terbium(III) ion complexes with 4,4-difluoro-1-phenylbutane-1,3-dione (HDPBD) and anciliary ligands was synthesized. The composition and properties of complexes were analyzed by elemental analysis, IR, NMR, powder X-ray diffaraction, TG-DTG and photoluminescence spectroscopy. These complexes exhibited ligand sensitized green emission at 546 nm associated with 5 D 4  →  7 F 5 transitions of terbium ion in the emission spectra. The photoluminescence study manifested that the organic ligands act as antenna and facilitate the absorbed energy to emitting levels of Tb(III) ion efficiently. The enhanced luminescence intensity and decay time of ternary C2-C5 complexes observed due to synergistic effect of anciliary ligands. The CIE color coordinates of complexes came under the green region of chromaticity diagram. The mechanistic investigation of intramolecular energy transfer in the complexes was discussed in detail. These terbium(III) complexes can be thrivingly used as one of the green component in light emitting material and in display devices. Graphical Abstract Illustrate the sensitization process of the Tb ion and intramolecular energy transfer process in the Tb 3+ complex.

Sleeping of a Complex Brain Networks with Hierarchical Organization

NASA Astrophysics Data System (ADS)

Zhang, Ying-Yue; Yang, Qiu-Ying; Chen, Tian-Lun

2009-01-01

The dynamical behavior in the cortical brain network of macaque is studied by modeling each cortical area with a subnetwork of interacting excitable neurons. We characterize the system by studying how to perform the transition, which is now topology-dependent, from the active state to that with no activity. This could be a naive model for the wakening and sleeping of a brain-like system, i.e., a multi-component system with two different dynamical behavior.

B-Cell Activation and Tolerance Mediated by B-Cell Receptor, Toll-Like Receptor and Survival Signal Crosstalk in SLE Pathogenesis

DTIC Science & Technology

2015-10-01

reduction in the number of regulatory T cells (Tregs) in STING2/2 lpr/lpr secondary lymphoid organs. Apoptotic debris induces the production of IDO...DNA complex is the exclusive malaria parasite component that activates dendritic cells and triggers innate immune responses. J. Immunol. 184: 4338–4348... cells remain relatively unchanged. Nevertheless, nearly all peripheral lymphoid pools exhibit altered dynamics, shifts in functional subset representation

Immune responses to bioengineered organs

PubMed Central

Ochando, Jordi; Charron, Dominique; Baptista, Pedro M.; Uygun, Basak E.

2017-01-01

Purpose of review Organ donation in the United States registered 9079 deceased organ donors in 2015. This high percentage of donations allowed organ transplantation in 29 851 recipients. Despite increasing numbers of transplants performed in comparison with previous years, the numbers of patients that are in need for a transplant increase every year at a higher rate. This reveals that the discrepancy between the demand and availability of organs remains fundamental problem in organ transplantation. Recent findings Development of bioengineered organs represents a promising approach to increase the pool of organs for transplantation. The technology involves obtaining complex three-dimensional scaffolds that support cellular activity and functional remodeling though tissue recellularization protocols using progenitor cells. This innovative approach integrates cross-thematic approaches from specific areas of transplant immunology, tissue engineering and stem cell biology, to potentially manufacture an unlimited source of donor organs for transplantation. Summary Although bioengineered organs are thought to escape immune recognition, the potential immune reactivity toward each of its components has not been studied in detail. Here, we summarize the host immune response toward different progenitor cells and discuss the potential implications of using nonself biological scaffolds to develop bioengineered organs. PMID:27926545

Harm reduction as a complex adaptive system: A dynamic framework for analyzing Tanzanian policies concerning heroin use

PubMed Central

Ratliff, Eric A.; Kaduri, Pamela; Masao, Frank; Mbwambo, Jessie K.K.; McCurdy, Sheryl A.

2016-01-01

Contrary to popular belief, policies on drug use are not always based on scientific evidence or composed in a rational manner. Rather, decisions concerning drug policies reflect the negotiation of actors’ ambitions, values, and facts as they organize in different ways around the perceived problems associated with illicit drug use. Drug policy is thus best represented as a complex adaptive system (CAS) that is dynamic, self-organizing, and coevolving. In this analysis, we use a CAS framework to examine how harm reduction emerged around heroin trafficking and use in Tanzania over the past thirty years (1985-present). This account is an organizational ethnography based on of the observant participation of the authors as actors within this system. We review the dynamic history and self-organizing nature of harm reduction, noting how interactions among system actors and components have coevolved with patterns of heroin us, policing, and treatment activities over time. Using a CAS framework, we describe harm reduction as a complex process where ambitions, values, facts, and technologies interact in the Tanzanian socio-political environment. We review the dynamic history and self-organizing nature of heroin policies, noting how the interactions within and between competing prohibitionist and harm reduction policies have changed with patterns of heroin use, policing, and treatment activities over time. Actors learn from their experiences to organize with other actors, align their values and facts, and implement new policies. Using a CAS approach provides researchers and policy actors a better understanding of patterns and intricacies in drug policy. This knowledge of how the system works can help improve the policy process through adaptive action to introduce new actors, different ideas, and avenues for communication into the system. PMID:26790689

Harm reduction as a complex adaptive system: A dynamic framework for analyzing Tanzanian policies concerning heroin use.

PubMed

Ratliff, Eric A; Kaduri, Pamela; Masao, Frank; Mbwambo, Jessie K K; McCurdy, Sheryl A

2016-04-01

Contrary to popular belief, policies on drug use are not always based on scientific evidence or composed in a rational manner. Rather, decisions concerning drug policies reflect the negotiation of actors' ambitions, values, and facts as they organize in different ways around the perceived problems associated with illicit drug use. Drug policy is thus best represented as a complex adaptive system (CAS) that is dynamic, self-organizing, and coevolving. In this analysis, we use a CAS framework to examine how harm reduction emerged around heroin trafficking and use in Tanzania over the past thirty years (1985-present). This account is an organizational ethnography based on of the observant participation of the authors as actors within this system. We review the dynamic history and self-organizing nature of harm reduction, noting how interactions among system actors and components have coevolved with patterns of heroin us, policing, and treatment activities over time. Using a CAS framework, we describe harm reduction as a complex process where ambitions, values, facts, and technologies interact in the Tanzanian sociopolitical environment. We review the dynamic history and self-organizing nature of heroin policies, noting how the interactions within and between competing prohibitionist and harm reduction policies have changed with patterns of heroin use, policing, and treatment activities over time. Actors learn from their experiences to organize with other actors, align their values and facts, and implement new policies. Using a CAS approach provides researchers and policy actors a better understanding of patterns and intricacies in drug policy. This knowledge of how the system works can help improve the policy process through adaptive action to introduce new actors, different ideas, and avenues for communication into the system. Copyright © 2015 Elsevier B.V. All rights reserved.

Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression.

PubMed

Maishman, Luke; Obado, Samson O; Alsford, Sam; Bart, Jean-Mathieu; Chen, Wei-Ming; Ratushny, Alexander V; Navarro, Miguel; Horn, David; Aitchison, John D; Chait, Brian T; Rout, Michael P; Field, Mark C

2016-12-15

The nuclear lamina is a filamentous structure subtending the nuclear envelope and required for chromatin organization, transcriptional regulation and maintaining nuclear structure. The trypanosomatid coiled-coil NUP-1 protein is a lamina component functionally analogous to lamins, the major lamina proteins of metazoa. There is little evidence for shared ancestry, suggesting the presence of a distinct lamina system in trypanosomes. To find additional trypanosomatid lamina components we identified NUP-1 interacting proteins by affinity capture and mass-spectrometry. Multiple components of the nuclear pore complex (NPC) and a second coiled-coil protein, which we termed NUP-2, were found. NUP-2 has a punctate distribution at the nuclear periphery throughout the cell cycle and is in close proximity to NUP-1, the NPCs and telomeric chromosomal regions. RNAi-mediated silencing of NUP-2 leads to severe proliferation defects, gross alterations to nuclear structure, chromosomal organization and nuclear envelope architecture. Further, transcription is altered at telomere-proximal variant surface glycoprotein (VSG) expression sites (ESs), suggesting a role in controlling ES expression, although NUP-2 silencing does not increase VSG switching. Transcriptome analysis suggests specific alterations to Pol I-dependent transcription. NUP-1 is mislocalized in NUP-2 knockdown cells and vice versa, implying that NUP-1 and NUP-2 form a co-dependent network and identifying NUP-2 as a second trypanosomatid nuclear lamina component. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Epithelial organization and cyst lumen expansion require efficient Sec13-Sec31-driven secretion.

PubMed

Townley, Anna K; Schmidt, Katy; Hodgson, Lorna; Stephens, David J

2012-02-01

Epithelial morphogenesis is directed by interactions with the underlying extracellular matrix. Secretion of collagen and other matrix components requires efficient coat complex II (COPII) vesicle formation at the endoplasmic reticulum. Here, we show that suppression of the outer layer COPII component, Sec13, in zebrafish embryos results in a disorganized gut epithelium. In human intestinal epithelial cells (Caco-2), Sec13 depletion causes defective epithelial polarity and organization on permeable supports. Defects are seen in the ability of cells to adhere to the substrate, form a monolayer and form intercellular junctions. When embedded in a three-dimensional matrix, Sec13-depleted Caco-2 cells form cysts but, unlike controls, are defective in lumen expansion. Incorporation of primary fibroblasts within the three-dimensional culture substantially restores normal morphogenesis. We conclude that efficient COPII-dependent secretion, notably assembly of Sec13-Sec31, is required to drive epithelial morphogenesis in both two- and three-dimensional cultures in vitro, as well as in vivo. Our results provide insight into the role of COPII in epithelial morphogenesis and have implications for the interpretation of epithelial polarity and organization assays in cell culture.

Epithelial organization and cyst lumen expansion require efficient Sec13–Sec31-driven secretion

PubMed Central

Townley, Anna K.; Schmidt, Katy; Hodgson, Lorna; Stephens, David J.

2012-01-01

Epithelial morphogenesis is directed by interactions with the underlying extracellular matrix. Secretion of collagen and other matrix components requires efficient coat complex II (COPII) vesicle formation at the endoplasmic reticulum. Here, we show that suppression of the outer layer COPII component, Sec13, in zebrafish embryos results in a disorganized gut epithelium. In human intestinal epithelial cells (Caco-2), Sec13 depletion causes defective epithelial polarity and organization on permeable supports. Defects are seen in the ability of cells to adhere to the substrate, form a monolayer and form intercellular junctions. When embedded in a three-dimensional matrix, Sec13-depleted Caco-2 cells form cysts but, unlike controls, are defective in lumen expansion. Incorporation of primary fibroblasts within the three-dimensional culture substantially restores normal morphogenesis. We conclude that efficient COPII-dependent secretion, notably assembly of Sec13–Sec31, is required to drive epithelial morphogenesis in both two- and three-dimensional cultures in vitro, as well as in vivo. Our results provide insight into the role of COPII in epithelial morphogenesis and have implications for the interpretation of epithelial polarity and organization assays in cell culture. PMID:22331354

Following the Footsteps of Chlamydial Gene Regulation

PubMed Central

Domman, D.; Horn, M.

2015-01-01

Regulation of gene expression ensures an organism responds to stimuli and undergoes proper development. Although the regulatory networks in bacteria have been investigated in model microorganisms, nearly nothing is known about the evolution and plasticity of these networks in obligate, intracellular bacteria. The phylum Chlamydiae contains a vast array of host-associated microbes, including several human pathogens. The Chlamydiae are unique among obligate, intracellular bacteria as they undergo a complex biphasic developmental cycle in which large swaths of genes are temporally regulated. Coupled with the low number of transcription factors, these organisms offer a model to study the evolution of regulatory networks in intracellular organisms. We provide the first comprehensive analysis exploring the diversity and evolution of regulatory networks across the phylum. We utilized a comparative genomics approach to construct predicted coregulatory networks, which unveiled genus- and family-specific regulatory motifs and architectures, most notably those of virulence-associated genes. Surprisingly, our analysis suggests that few regulatory components are conserved across the phylum, and those that are conserved are involved in the exploitation of the intracellular niche. Our study thus lends insight into a component of chlamydial evolution that has otherwise remained largely unexplored. PMID:26424812

The Redox Code

PubMed Central

Jones, Dean P.

2015-01-01

Abstract Significance: The redox code is a set of principles that defines the positioning of the nicotinamide adenine dinucleotide (NAD, NADP) and thiol/disulfide and other redox systems as well as the thiol redox proteome in space and time in biological systems. The code is richly elaborated in an oxygen-dependent life, where activation/deactivation cycles involving O2 and H2O2 contribute to spatiotemporal organization for differentiation, development, and adaptation to the environment. Disruption of this organizational structure during oxidative stress represents a fundamental mechanism in system failure and disease. Recent Advances: Methodology in assessing components of the redox code under physiological conditions has progressed, permitting insight into spatiotemporal organization and allowing for identification of redox partners in redox proteomics and redox metabolomics. Critical Issues: Complexity of redox networks and redox regulation is being revealed step by step, yet much still needs to be learned. Future Directions: Detailed knowledge of the molecular patterns generated from the principles of the redox code under defined physiological or pathological conditions in cells and organs will contribute to understanding the redox component in health and disease. Ultimately, there will be a scientific basis to a modern redox medicine. Antioxid. Redox Signal. 23, 734–746. PMID:25891126

Mathematical Modeling of Intestinal Iron Absorption Using Genetic Programming

PubMed Central

Colins, Andrea; Gerdtzen, Ziomara P.; Nuñez, Marco T.; Salgado, J. Cristian

2017-01-01

Iron is a trace metal, key for the development of living organisms. Its absorption process is complex and highly regulated at the transcriptional, translational and systemic levels. Recently, the internalization of the DMT1 transporter has been proposed as an additional regulatory mechanism at the intestinal level, associated to the mucosal block phenomenon. The short-term effect of iron exposure in apical uptake and initial absorption rates was studied in Caco-2 cells at different apical iron concentrations, using both an experimental approach and a mathematical modeling framework. This is the first report of short-term studies for this system. A non-linear behavior in the apical uptake dynamics was observed, which does not follow the classic saturation dynamics of traditional biochemical models. We propose a method for developing mathematical models for complex systems, based on a genetic programming algorithm. The algorithm is aimed at obtaining models with a high predictive capacity, and considers an additional parameter fitting stage and an additional Jackknife stage for estimating the generalization error. We developed a model for the iron uptake system with a higher predictive capacity than classic biochemical models. This was observed both with the apical uptake dataset used for generating the model and with an independent initial rates dataset used to test the predictive capacity of the model. The model obtained is a function of time and the initial apical iron concentration, with a linear component that captures the global tendency of the system, and a non-linear component that can be associated to the movement of DMT1 transporters. The model presented in this paper allows the detailed analysis, interpretation of experimental data, and identification of key relevant components for this complex biological process. This general method holds great potential for application to the elucidation of biological mechanisms and their key components in other complex systems. PMID:28072870

Infrared mapping resolves soft tissue preservation in 50 million year-old reptile skin.

PubMed

Edwards, N P; Barden, H E; van Dongen, B E; Manning, P L; Larson, P L; Bergmann, U; Sellers, W I; Wogelius, R A

2011-11-07

Non-destructive Fourier Transform InfraRed (FTIR) mapping of Eocene aged fossil reptile skin shows that biological control on the distribution of endogenous organic components within fossilized soft tissue can be resolved. Mapped organic functional units within this approximately 50 Myr old specimen from the Green River Formation (USA) include amide and sulphur compounds. These compounds are most probably derived from the original beta keratin present in the skin because fossil leaf- and other non-skin-derived organic matter from the same geological formation do not show intense amide or thiol absorption bands. Maps and spectra from the fossil are directly comparable to extant reptile skin. Furthermore, infrared results are corroborated by several additional quantitative methods including Synchrotron Rapid Scanning X-Ray Fluorescence (SRS-XRF) and Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS). All results combine to clearly show that the organic compound inventory of the fossil skin is different from the embedding sedimentary matrix and fossil plant material. A new taphonomic model involving ternary complexation between keratin-derived organic molecules, divalent trace metals and silicate surfaces is presented to explain the survival of the observed compounds. X-ray diffraction shows that suitable minerals for complex formation are present. Previously, this study would only have been possible with major destructive sampling. Non-destructive FTIR imaging methods are thus shown to be a valuable tool for understanding the taphonomy of high-fidelity preservation, and furthermore, may provide insight into the biochemistry of extinct organisms.

Infrared mapping resolves soft tissue preservation in 50 million year-old reptile skin

PubMed Central

Edwards, N. P.; Barden, H. E.; van Dongen, B. E.; Manning, P. L.; Larson, P. L.; Bergmann, U.; Sellers, W. I.; Wogelius, R. A.

2011-01-01

Non-destructive Fourier Transform InfraRed (FTIR) mapping of Eocene aged fossil reptile skin shows that biological control on the distribution of endogenous organic components within fossilized soft tissue can be resolved. Mapped organic functional units within this approximately 50 Myr old specimen from the Green River Formation (USA) include amide and sulphur compounds. These compounds are most probably derived from the original beta keratin present in the skin because fossil leaf- and other non-skin-derived organic matter from the same geological formation do not show intense amide or thiol absorption bands. Maps and spectra from the fossil are directly comparable to extant reptile skin. Furthermore, infrared results are corroborated by several additional quantitative methods including Synchrotron Rapid Scanning X-Ray Fluorescence (SRS-XRF) and Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS). All results combine to clearly show that the organic compound inventory of the fossil skin is different from the embedding sedimentary matrix and fossil plant material. A new taphonomic model involving ternary complexation between keratin-derived organic molecules, divalent trace metals and silicate surfaces is presented to explain the survival of the observed compounds. X-ray diffraction shows that suitable minerals for complex formation are present. Previously, this study would only have been possible with major destructive sampling. Non-destructive FTIR imaging methods are thus shown to be a valuable tool for understanding the taphonomy of high-fidelity preservation, and furthermore, may provide insight into the biochemistry of extinct organisms. PMID:21429928

Effect of photodegradation and biodegradation on the concentration and composition of dissolved organic matter in diverse waterbodies

NASA Astrophysics Data System (ADS)

Manalilkada Sasidharan, S.; Dash, P.; Singh, S.; Lu, Y.

2017-12-01

The objective of this research was to quantify the effects of photodegradation and biodegradation on the dissolved organic matter (DOM) concentration and composition in five distinct waterbodies with diverse types of watershed land use and land cover in the southeastern United States. The water bodies included an agricultural pond, a lake in a predominantly forested watershed, a man-made reservoir, an estuary, and a bay. Two sets of samples were prepared from these water bodies by dispensing filtered water samples to unfiltered samples in 10:1 ratio. The first set was kept in the sunlight during the day (12 hours), and colored dissolved organic matter (CDOM) absorption and fluorescence were measured periodically over a 30-day period for examining the effects of combined photo- and biodegradation. The second set of samples was kept in the dark for examining the effects of biodegradation alone, and CDOM absorption and fluorescence were measured at the same time as the sunlight-exposed samples. Subsequently, spectrometric results in tandem with multivariate statistical analysis were used to interpret the lability vs. composition of DOM. Parallel factor analysis (PARAFAC) revealed the presence of four DOM components (C1-C4). C1 and C4 were microbial tryptophan-like, labile lighter components, while C2 and C3 were terrestrial humic like or fulvic acid type, larger aromatic refractory components. The principal component analysis (PCA) also revealed two distinct groups of DOM - C1 and C4 vs. C2 and C3. The negative PC1 loadings of C2, C3, HIX, a254 and SUVA indicated humic-like or fulvic-like structurally complex refractory aromatic DOM originated from higher plants in forested areas. C1, C4, SR, FI and BI had positive PC1 loadings, which indicated structurally simpler labile DOM were derived from agricultural areas or microbial activity. There was a decrease in dissolved organic carbon (DOC) due to combined photo- and biodegradation, and transformation of components C2, C3 into components C1, C4 was at a much faster rate than only biodegradation. This observation suggests that the presence of sunlight facilitated the degradation of larger, recalcitrant, terrestrial humic-like compounds into smaller, labile microbial components.

Characterization of the Catalytic Subunits of the RNA Exosome-like Complex in Plasmodium falciparum.

PubMed

Jiang, Ning; Yu, Shengchao; Yang, Na; Feng, Ying; Sang, Xiaoyu; Wang, Yao; Wahlgren, Mats; Chen, Qijun

2018-04-17

The eukaryotic ribonucleic acid (RNA) exosome is a versatile multiribonuclease complex that mediates the processing, surveillance, and degradation of virtually all classes of RNA in both the nucleus and cytoplasm. The complex, composed of 10 to 11 subunits, has been widely described in many organisms. Bioinformatic analyses revealed that there may be also an exosome-like complex in Plasmodium falciparum, a parasite of great importance in public health, with eight predicted subunits having high sequence similarity to their counterparts in yeast and human. In this work, the putative RNA catalytic components, designated as PfRrp4, PfRrp41, PfDis3, and PfRrp6, were identified and systematically analyzed. Quantitative polymerase chain reaction (QPCR) analyses suggested that all of them were transcribed steadily throughout the asexual stage. The expression of these proteins was determined by Western blot, and their localization narrowed to the cytoplasm of the parasite by indirect immunofluorescence. The recombinant proteins of PfRrp41, PfDis3, and PfRrp6 exhibited catalytic activity for single-stranded RNA (ssRNA), whereas PfRrp4 showed no processing activity of both ssRNA and dsRNA. The identification of these putative components of the RNA exosome complex opens up new perspectives for a deep understanding of RNA metabolism in the malarial parasite P. falciparum. © 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

Programmable chemical controllers made from DNA.

PubMed

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2013-10-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.

Probing Complex Free-Radical Reaction Pathways of Fuel Model Compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchanan III, A C; Kidder, Michelle; Beste, Ariana

2012-01-01

Fossil (e.g. coal) and renewable (e.g. woody biomass) organic energy resources have received considerable attention as possible sources of liquid transportation fuels and commodity chemicals. Knowledge of the reactivity of these complex materials has been advanced through fundamental studies of organic compounds that model constituent substructures. In particular, an improved understanding of thermochemical reaction pathways involving free-radical intermediates has arisen from detailed experimental kinetic studies and, more recently, advanced computational investigations. In this presentation, we will discuss our recent investigations of the fundamental pyrolysis pathways of model compounds that represent key substructures in the lignin component of woody biomass withmore » a focus on molecules representative of the dominant beta-O-4 aryl ether linkages. Additional mechanistic insights gleaned from DFT calculations on the kinetics of key elementary reaction steps will also be presented, as well as a few thoughts on the significant contributions of Jim Franz to this area of free radical chemistry.« less

Dlgap1 knockout mice exhibit alterations of the postsynaptic density and selective reductions in sociability.

PubMed

Coba, M P; Ramaker, M J; Ho, E V; Thompson, S L; Komiyama, N H; Grant, S G N; Knowles, J A; Dulawa, S C

2018-02-02

The scaffold protein DLGAP1 is localized at the post-synaptic density (PSD) of glutamatergic neurons and is a component of supramolecular protein complexes organized by PSD95. Gain-of-function variants of DLGAP1 have been associated with obsessive-compulsive disorder (OCD), while haploinsufficient variants have been linked to autism spectrum disorder (ASD) and schizophrenia in human genetic studies. We tested male and female Dlgap1 wild type (WT), heterozygous (HT), and knockout (KO) mice in a battery of behavioral tests: open field, dig, splash, prepulse inhibition, forced swim, nest building, social approach, and sucrose preference. We also used biochemical approaches to examine the role of DLGAP1 in the organization of PSD protein complexes. Dlgap1 KO mice were most notable for disruption of protein interactions in the PSD, and deficits in sociability. Other behavioral measures were largely unaffected. Our data suggest that Dlgap1 knockout leads to PSD disruption and reduced sociability, consistent with reports of DLGAP1 haploinsufficient variants in schizophrenia and ASD.

Programmable chemical controllers made from DNA

NASA Astrophysics Data System (ADS)

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2013-10-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.

Quality control considerations for size exclusion chromatography with online ICP-MS: a powerful tool for evaluating the size dependence of metal-organic matter complexation.

PubMed

McKenzie, Erica R; Young, Thomas M

2013-01-01

Size exclusion chromatography (SEC), which separates molecules based on molecular volume, can be coupled with online inductively coupled plasma mass spectrometry (ICP-MS) to explore size-dependent metal-natural organic matter (NOM) complexation. To make effective use of this analytical dual detector system, the operator should be mindful of quality control measures. Al, Cr, Fe, Se, and Sn all exhibited columnless attenuation, which indicated unintended interactions with system components. Based on signal-to-noise ratio and peak reproducibility between duplicate analyses of environmental samples, consistent peak time and height were observed for Mg, Cl, Mn, Cu, Br, and Pb. Al, V, Fe, Co, Ni, Zn, Se, Cd, Sn, and Sb were less consistent overall, but produced consistent measurements in select samples. Ultrafiltering and centrifuging produced similar peak distributions, but glass fiber filtration produced more high molecular weight (MW) peaks. Storage in glass also produced more high MW peaks than did plastic bottles.

A model for the emergence of cooperation, interdependence, and structure in evolving networks.

PubMed

Jain, S; Krishna, S

2001-01-16

Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of cooperative molecular species arises and evolves to become more complex and structured. The network is modeled by a directed weighted graph whose positive and negative links represent "catalytic" and "inhibitory" interactions among the molecular species, and which evolves as the least populated species (typically those that go extinct) are replaced by new ones. A small autocatalytic set, appearing by chance, provides the seed for the spontaneous growth of connectivity and cooperation in the graph. A highly structured chemical organization arises inevitably as the autocatalytic set enlarges and percolates through the network in a short analytically determined timescale. This self organization does not require the presence of self-replicating species. The network also exhibits catastrophes over long timescales triggered by the chance elimination of "keystone" species, followed by recoveries.

Recent Advances in Bioink Design for 3D Bioprinting of Tissues and Organs.

PubMed

Ji, Shen; Guvendiren, Murat

2017-01-01

There is a growing demand for alternative fabrication approaches to develop tissues and organs as conventional techniques are not capable of fabricating constructs with required structural, mechanical, and biological complexity. 3D bioprinting offers great potential to fabricate highly complex constructs with precise control of structure, mechanics, and biological matter [i.e., cells and extracellular matrix (ECM) components]. 3D bioprinting is an additive manufacturing approach that utilizes a "bioink" to fabricate devices and scaffolds in a layer-by-layer manner. 3D bioprinting allows printing of a cell suspension into a tissue construct with or without a scaffold support. The most common bioinks are cell-laden hydrogels, decellulerized ECM-based solutions, and cell suspensions. In this mini review, a brief description and comparison of the bioprinting methods, including extrusion-based, droplet-based, and laser-based bioprinting, with particular focus on bioink design requirements are presented. We also present the current state of the art in bioink design including the challenges and future directions.

Recent Advances in Bioink Design for 3D Bioprinting of Tissues and Organs

PubMed Central

Ji, Shen; Guvendiren, Murat

2017-01-01

There is a growing demand for alternative fabrication approaches to develop tissues and organs as conventional techniques are not capable of fabricating constructs with required structural, mechanical, and biological complexity. 3D bioprinting offers great potential to fabricate highly complex constructs with precise control of structure, mechanics, and biological matter [i.e., cells and extracellular matrix (ECM) components]. 3D bioprinting is an additive manufacturing approach that utilizes a “bioink” to fabricate devices and scaffolds in a layer-by-layer manner. 3D bioprinting allows printing of a cell suspension into a tissue construct with or without a scaffold support. The most common bioinks are cell-laden hydrogels, decellulerized ECM-based solutions, and cell suspensions. In this mini review, a brief description and comparison of the bioprinting methods, including extrusion-based, droplet-based, and laser-based bioprinting, with particular focus on bioink design requirements are presented. We also present the current state of the art in bioink design including the challenges and future directions. PMID:28424770

Programmable chemical controllers made from DNA

PubMed Central

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2014-01-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language', and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents. PMID:24077029

A model for the emergence of cooperation, interdependence, and structure in evolving networks

NASA Astrophysics Data System (ADS)

Jain, Sanjay; Krishna, Sandeep

2001-01-01

Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of cooperative molecular species arises and evolves to become more complex and structured. The network is modeled by a directed weighted graph whose positive and negative links represent "catalytic" and "inhibitory" interactions among the molecular species, and which evolves as the least populated species (typically those that go extinct) are replaced by new ones. A small autocatalytic set, appearing by chance, provides the seed for the spontaneous growth of connectivity and cooperation in the graph. A highly structured chemical organization arises inevitably as the autocatalytic set enlarges and percolates through the network in a short analytically determined timescale. This self organization does not require the presence of self-replicating species. The network also exhibits catastrophes over long timescales triggered by the chance elimination of "keystone" species, followed by recoveries.

Evolution of complexity in the volvocine algae: transitions in individuality through Darwin's eye.

PubMed

Herron, Matthew D; Michod, Richard E

2008-02-01

The transition from unicellular to differentiated multicellular organisms constitutes an increase in the level complexity, because previously existing individuals are combined to form a new, higher-level individual. The volvocine algae represent a unique opportunity to study this transition because they diverged relatively recently from unicellular relatives and because extant species display a range of intermediate grades between unicellular and multicellular, with functional specialization of cells. Following the approach Darwin used to understand "organs of extreme perfection" such as the vertebrate eye, this jump in complexity can be reduced to a series of small steps that cumulatively describe a gradual transition between the two levels. We use phylogenetic reconstructions of ancestral character states to trace the evolution of steps involved in this transition in volvocine algae. The history of these characters includes several well-supported instances of multiple origins and reversals. The inferred changes can be understood as components of cooperation-conflict-conflict mediation cycles as predicted by multilevel selection theory. One such cycle may have taken place early in volvocine evolution, leading to the highly integrated colonies seen in extant volvocine algae. A second cycle, in which the defection of somatic cells must be prevented, may still be in progress.

Quantifying the Adaptive Cycle | Science Inventory | US EPA

EPA Pesticide Factsheets

The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994–2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and

Calibration of a simple and a complex model of global marine biogeochemistry

NASA Astrophysics Data System (ADS)

Kriest, Iris

2017-11-01

The assessment of the ocean biota's role in climate change is often carried out with global biogeochemical ocean models that contain many components and involve a high level of parametric uncertainty. Because many data that relate to tracers included in a model are only sparsely observed, assessment of model skill is often restricted to tracers that can be easily measured and assembled. Examination of the models' fit to climatologies of inorganic tracers, after the models have been spun up to steady state, is a common but computationally expensive procedure to assess model performance and reliability. Using new tools that have become available for global model assessment and calibration in steady state, this paper examines two different model types - a complex seven-component model (MOPS) and a very simple four-component model (RetroMOPS) - for their fit to dissolved quantities. Before comparing the models, a subset of their biogeochemical parameters has been optimised against annual-mean nutrients and oxygen. Both model types fit the observations almost equally well. The simple model contains only two nutrients: oxygen and dissolved organic phosphorus (DOP). Its misfit and large-scale tracer distributions are sensitive to the parameterisation of DOP production and decay. The spatio-temporal decoupling of nitrogen and oxygen, and processes involved in their uptake and release, renders oxygen and nitrate valuable tracers for model calibration. In addition, the non-conservative nature of these tracers (with respect to their upper boundary condition) introduces the global bias (fixed nitrogen and oxygen inventory) as a useful additional constraint on model parameters. Dissolved organic phosphorus at the surface behaves antagonistically to phosphate, and suggests that observations of this tracer - although difficult to measure - may be an important asset for model calibration.

Comparison of the Organic Composition of Cometary Samples with Residues Formed from the UV Irradiation of Astrophysical Ice Analogs

NASA Technical Reports Server (NTRS)

Milam, S. N.; Nuevo, M.; Sandford, S. A.; Cody, G. D.; Kilcoyne, A. L. D.; Stroud, R. M.; DeGregorio, B. T.

2010-01-01

The NASA Stardust mission successfully collected material from Comet 81P/Wild 2 [1], including authentic cometary grains [2]. X-ray absorption near-edge structure (XANES) spectroscopy analysis of these samples indicates the presence of oxygen-rich and nitrogen-rich organic materials, which contain a broad variety of functional groups (carbonyls, C=C bonds, aliphatic chains, amines, arnides, etc.) [3]. One component of these organics appears to contain very little aromatic carbon and bears some similarity to the organic residues produced by the irradiation of ices of interstellar/cometary composition, Stardust samples were also recently shown to contain glycine, the smallest biological amino acid [4]. Organic residues produced froth the UV irradiation of astrophysical ice analogs are already known to contain a large suite of organic molecules including amino acids [5-7], amphiphilic compounds (fatty acids) [8], and other complex species. This work presents a comparison between XANES spectra measured from organic residues formed in the laboratory with similar data of cometary samples collected by the Stardust mission

Anaerobic Digestion.

PubMed

Liebetrau, Jan; Sträuber, Heike; Kretzschmar, Jörg; Denysenko, Velina; Nelles, Michael

2017-04-09

The term anaerobic digestion usually refers to the microbial conversion of organic material to biogas, which mainly consists of methane and carbon dioxide. The technical application of the naturally-occurring process is used to provide a renewable energy carrier and - as the substrate is often waste material - to reduce the organic matter content of the substrate prior to disposal.Applications can be found in sewage sludge treatment, the treatment of industrial and municipal solid wastes and wastewaters (including landfill gas utilization), and the conversion of agricultural residues and energy crops.For biorefinery concepts, the anaerobic digestion (AD) process is, on the one hand, an option to treat organic residues from other production processes. Concomitant effects are the reduction of organic carbon within the treated substance, the conversion of nitrogen and sulfur components, and the production of an energy-rich gas - the biogas. On the other hand, the multistep conversion of complex organic material offers the possibility of interrupting the conversion chain and locking out intermediates for utilization as basic material within the chemical industry.

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status

PubMed Central

Li, Dongming; Palanca, Ana Marie S; Won, So Youn; Gao, Lei; Feng, Ying; Vashisht, Ajay A; Liu, Li; Zhao, Yuanyuan; Liu, Xigang; Wu, Xiuyun; Li, Shaofang; Le, Brandon; Kim, Yun Ju; Yang, Guodong; Li, Shengben; Liu, Jinyuan; Wohlschlegel, James A; Guo, Hongwei; Mo, Beixin; Chen, Xuemei; Law, Julie A

2017-01-01

DNA methylation is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation are known, relatively little is understood about how DNA methylation influences gene expression. Here we identified a METHYL-CpG-BINDING DOMAIN 7 (MBD7) complex in Arabidopsis thaliana that suppresses the transcriptional silencing of two LUCIFERASE (LUC) reporters via a mechanism that is largely downstream of DNA methylation. Although mutations in components of the MBD7 complex resulted in modest increases in DNA methylation concomitant with decreased LUC expression, we found that these hyper-methylation and gene expression phenotypes can be genetically uncoupled. This finding, along with genome-wide profiling experiments showing minimal changes in DNA methylation upon disruption of the MBD7 complex, places the MBD7 complex amongst a small number of factors acting downstream of DNA methylation. This complex, however, is unique as it functions to suppress, rather than enforce, DNA methylation-mediated gene silencing. DOI: http://dx.doi.org/10.7554/eLife.19893.001 PMID:28452714

Ontology patterns for complex topographic feature yypes

USGS Publications Warehouse

Varanka, Dalia E.

2011-01-01

Complex feature types are defined as integrated relations between basic features for a shared meaning or concept. The shared semantic concept is difficult to define in commonly used geographic information systems (GIS) and remote sensing technologies. The role of spatial relations between complex feature parts was recognized in early GIS literature, but had limited representation in the feature or coverage data models of GIS. Spatial relations are more explicitly specified in semantic technology. In this paper, semantics for topographic feature ontology design patterns (ODP) are developed as data models for the representation of complex features. In the context of topographic processes, component assemblages are supported by resource systems and are found on local landscapes. The topographic ontology is organized across six thematic modules that can account for basic feature types, resource systems, and landscape types. Types of complex feature attributes include location, generative processes and physical description. Node/edge networks model standard spatial relations and relations specific to topographic science to represent complex features. To demonstrate these concepts, data from The National Map of the U. S. Geological Survey was converted and assembled into ODP.

3D Printing of Organs-On-Chips

PubMed Central

Yi, Hee-Gyeong; Lee, Hyungseok; Cho, Dong-Woo

2017-01-01

Organ-on-a-chip engineering aims to create artificial living organs that mimic the complex and physiological responses of real organs, in order to test drugs by precisely manipulating the cells and their microenvironments. To achieve this, the artificial organs should to be microfabricated with an extracellular matrix (ECM) and various types of cells, and should recapitulate morphogenesis, cell differentiation, and functions according to the native organ. A promising strategy is 3D printing, which precisely controls the spatial distribution and layer-by-layer assembly of cells, ECMs, and other biomaterials. Owing to this unique advantage, integration of 3D printing into organ-on-a-chip engineering can facilitate the creation of micro-organs with heterogeneity, a desired 3D cellular arrangement, tissue-specific functions, or even cyclic movement within a microfluidic device. Moreover, fully 3D-printed organs-on-chips more easily incorporate other mechanical and electrical components with the chips, and can be commercialized via automated massive production. Herein, we discuss the recent advances and the potential of 3D cell-printing technology in engineering organs-on-chips, and provides the future perspectives of this technology to establish the highly reliable and useful drug-screening platforms. PMID:28952489

3D Printing of Organs-On-Chips.

PubMed

Yi, Hee-Gyeong; Lee, Hyungseok; Cho, Dong-Woo

2017-01-25

Organ-on-a-chip engineering aims to create artificial living organs that mimic the complex and physiological responses of real organs, in order to test drugs by precisely manipulating the cells and their microenvironments. To achieve this, the artificial organs should to be microfabricated with an extracellular matrix (ECM) and various types of cells, and should recapitulate morphogenesis, cell differentiation, and functions according to the native organ. A promising strategy is 3D printing, which precisely controls the spatial distribution and layer-by-layer assembly of cells, ECMs, and other biomaterials. Owing to this unique advantage, integration of 3D printing into organ-on-a-chip engineering can facilitate the creation of micro-organs with heterogeneity, a desired 3D cellular arrangement, tissue-specific functions, or even cyclic movement within a microfluidic device. Moreover, fully 3D-printed organs-on-chips more easily incorporate other mechanical and electrical components with the chips, and can be commercialized via automated massive production. Herein, we discuss the recent advances and the potential of 3D cell-printing technology in engineering organs-on-chips, and provides the future perspectives of this technology to establish the highly reliable and useful drug-screening platforms.

N-terminal lysines are essential for protein translocation via a modified ERAD system in complex plastids.

PubMed

Lau, Julia B; Stork, Simone; Moog, Daniel; Sommer, Maik S; Maier, Uwe G

2015-05-01

Nuclear-encoded pre-proteins being imported into complex plastids of red algal origin have to cross up to five membranes. Thereby, transport across the second outermost or periplastidal membrane (PPM) is facilitated by SELMA (symbiont-specific ERAD-like machinery), an endoplasmic reticulum-associated degradation (ERAD)-derived machinery. Core components of SELMA are enzymes involved in ubiquitination (E1-E3), a Cdc48 ATPase complex and Derlin proteins. These components are present in all investigated organisms with four membrane-bound complex plastids of red algal origin, suggesting a ubiquitin-dependent translocation process of substrates mechanistically similar to the process of retro-translocation in ERAD. Even if, according to the current model, translocation via SELMA does not end up in the classical poly-ubiquitination, transient mono-/oligo-ubiquitination of pre-proteins might be required for the mechanism of translocation. We investigated the import mechanism of SELMA and were able to show that protein transport across the PPM depends on lysines in the N-terminal but not in the C-terminal part of pre-proteins. These lysines are predicted to be targets of ubiquitination during the translocation process. As proteins lacking the N-terminal lysines get stuck in the PPM, a 'frozen intermediate' of the translocation process could be envisioned and initially characterized. © 2015 John Wiley & Sons Ltd.

Cellulose synthase complexes act in a concerted fashion to synthesize highly aggregated cellulose in secondary cell walls of plants

PubMed Central

Li, Shundai; Bashline, Logan; Zheng, Yunzhen; Xin, Xiaoran; Huang, Shixin; Kong, Zhaosheng; Kim, Seong H.; Cosgrove, Daniel J.; Gu, Ying

2016-01-01

Cellulose, often touted as the most abundant biopolymer on Earth, is a critical component of the plant cell wall and is synthesized by plasma membrane-spanning cellulose synthase (CESA) enzymes, which in plants are organized into rosette-like CESA complexes (CSCs). Plants construct two types of cell walls, primary cell walls (PCWs) and secondary cell walls (SCWs), which differ in composition, structure, and purpose. Cellulose in PCWs and SCWs is chemically identical but has different physical characteristics. During PCW synthesis, multiple dispersed CSCs move along a shared linear track in opposing directions while synthesizing cellulose microfibrils with low aggregation. In contrast, during SCW synthesis, we observed swaths of densely arranged CSCs that moved in the same direction along tracks while synthesizing cellulose microfibrils that became highly aggregated. Our data support a model in which distinct spatiotemporal features of active CSCs during PCW and SCW synthesis contribute to the formation of cellulose with distinct structure and organization in PCWs and SCWs of Arabidopsis thaliana. This study provides a foundation for understanding differences in the formation, structure, and organization of cellulose in PCWs and SCWs. PMID:27647923

Cellulose synthase complexes act in a concerted fashion to synthesize highly aggregated cellulose in secondary cell walls of plants.

PubMed

Li, Shundai; Bashline, Logan; Zheng, Yunzhen; Xin, Xiaoran; Huang, Shixin; Kong, Zhaosheng; Kim, Seong H; Cosgrove, Daniel J; Gu, Ying

2016-10-04

Cellulose, often touted as the most abundant biopolymer on Earth, is a critical component of the plant cell wall and is synthesized by plasma membrane-spanning cellulose synthase (CESA) enzymes, which in plants are organized into rosette-like CESA complexes (CSCs). Plants construct two types of cell walls, primary cell walls (PCWs) and secondary cell walls (SCWs), which differ in composition, structure, and purpose. Cellulose in PCWs and SCWs is chemically identical but has different physical characteristics. During PCW synthesis, multiple dispersed CSCs move along a shared linear track in opposing directions while synthesizing cellulose microfibrils with low aggregation. In contrast, during SCW synthesis, we observed swaths of densely arranged CSCs that moved in the same direction along tracks while synthesizing cellulose microfibrils that became highly aggregated. Our data support a model in which distinct spatiotemporal features of active CSCs during PCW and SCW synthesis contribute to the formation of cellulose with distinct structure and organization in PCWs and SCWs of Arabidopsis thaliana This study provides a foundation for understanding differences in the formation, structure, and organization of cellulose in PCWs and SCWs.

Molecular structure of the pyruvate dehydrogenase complex from Escherichia coli K-12.

PubMed

Vogel, O; Hoehn, B; Henning, U

1972-06-01

The pyruvate dehydrogenase core complex from E. coli K-12, defined as the multienzyme complex that can be obtained with a unique polypeptide chain composition, has a molecular weight of 3.75 x 10(6). All results obtained agree with the following numerology. The core complex consists of 48 polypeptide chains. There are 16 chains (molecular weight = 100,000) of the pyruvate dehydrogenase component, 16 chains (molecular weight = 80,000) of the dihydrolipoamide dehydrogenase component, and 16 chains (molecular weight = 56,000) of the dihydrolipoamide dehydrogenase component. Usually, but not always, pyruvate dehydrogenase complex is produced in vivo containing at least 2-3 mol more of dimers of the pyruvate dehydrogenase component than the stoichiometric ratio with respect to the core complex. This "excess" component is bound differently than are the eight dimers in the core complex.

Unusual features of fibrillarin cDNA and gene structure in Euglena gracilis: evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs throughout the domain Eucarya.

PubMed

Russell, Anthony G; Watanabe, Yoh-ichi; Charette, J Michael; Gray, Michael W

2005-01-01

Box C/D ribonucleoprotein (RNP) particles mediate O2'-methylation of rRNA and other cellular RNA species. In higher eukaryotic taxa, these RNPs are more complex than their archaeal counterparts, containing four core protein components (Snu13p, Nop56p, Nop58p and fibrillarin) compared with three in Archaea. This increase in complexity raises questions about the evolutionary emergence of the eukaryote-specific proteins and structural conservation in these RNPs throughout the eukaryotic domain. In protists, the primarily unicellular organisms comprising the bulk of eukaryotic diversity, the protein composition of box C/D RNPs has not yet been extensively explored. This study describes the complete gene, cDNA and protein sequences of the fibrillarin homolog from the protozoon Euglena gracilis, the first such information to be obtained for a nucleolus-localized protein in this organism. The E.gracilis fibrillarin gene contains a mixture of intron types exhibiting markedly different sizes. In contrast to most other E.gracilis mRNAs characterized to date, the fibrillarin mRNA lacks a spliced leader (SL) sequence. The predicted fibrillarin protein sequence itself is unusual in that it contains a glycine-lysine (GK)-rich domain at its N-terminus rather than the glycine-arginine-rich (GAR) domain found in most other eukaryotic fibrillarins. In an evolutionarily diverse collection of protists that includes E.gracilis, we have also identified putative homologs of the other core protein components of box C/D RNPs, thereby providing evidence that the protein composition seen in the higher eukaryotic complexes was established very early in eukaryotic cell evolution.

Concepts for the material development of phosphorescent organic materials processable from solution and their application in OLEDs

NASA Astrophysics Data System (ADS)

Janietz, S.; Krueger, H.; Thesen, M.; Salert, B.; Wedel, A.

2014-10-01

One example of organic electronics is the application of polymer based light emitting devices (PLEDs). PLEDs are very attractive for large area and fine-pixel displays, lighting and signage. The polymers are more amenable to solution processing by printing techniques which are favourable for low cost production in large areas. With phosphorescent emitters like Ir-complexes higher quantum efficiencies were obtained than with fluorescent systems, especially if multilayer stack systems with separated charge transport and emitting layers were applied in the case of small molecules. Polymers exhibit the ability to integrate all the active components like the hole-, electron-transport and phosphorescent molecules in only one layer. Here, the active components of a phosphorescent system - triplet emitter, hole- and electron transport molecules - can be linked as a side group to a polystyrene main chain. By varying the molecular structures of the side groups as well as the composition of the side chains with respect to the triplet emitter, hole- and electron transport structure, and by blending with suitable glass-forming, so-called small molecules, brightness, efficiency and lifetime of the produced OLEDs can be optimized. By choosing the triplet emitter, such as iridium complexes, different emission colors can be specially set. Different substituted triazine molecules were introduced as side chain into a polystyrene backbone and applied as electron transport material in PLED blend systems. The influence of alkyl chain lengths of the performance will be discussed. For an optimized blend system with a green emitting phosphorescent Ir-complex efficiencies of 60 cd/A and an lifetime improvement of 66.000 h @ 1000 cd/m2 were achieved.

Transformational change in health care systems: an organizational model.

PubMed

Lukas, Carol VanDeusen; Holmes, Sally K; Cohen, Alan B; Restuccia, Joseph; Cramer, Irene E; Shwartz, Michael; Charns, Martin P

2007-01-01

The Institute of Medicine's 2001 report Crossing the Quality Chasm argued for fundamental redesign of the U.S. health care system. Six years later, many health care organizations have embraced the report's goals, but few have succeeded in making the substantial transformations needed to achieve those aims. This article offers a model for moving organizations from short-term, isolated performance improvements to sustained, reliable, organization-wide, and evidence-based improvements in patient care. Longitudinal comparative case studies were conducted in 12 health care systems using a mixed-methods evaluation design based on semistructured interviews and document review. Participating health care systems included seven systems funded through the Robert Wood Johnson Foundation's Pursuing Perfection Program and five systems with long-standing commitments to improvement and high-quality care. Five interactive elements appear critical to successful transformation of patient care: (1) Impetus to transform; (2) Leadership commitment to quality; (3) Improvement initiatives that actively engage staff in meaningful problem solving; (4) Alignment to achieve consistency of organization goals with resource allocation and actions at all levels of the organization; and (5) Integration to bridge traditional intra-organizational boundaries among individual components. These elements drive change by affecting the components of the complex health care organization in which they operate: (1) Mission, vision, and strategies that set its direction and priorities; (2) Culture that reflects its informal values and norms; (3) Operational functions and processes that embody the work done in patient care; and (4) Infrastructure such as information technology and human resources that support the delivery of patient care. Transformation occurs over time with iterative changes being sustained and spread across the organization. The conceptual model holds promise for guiding health care organizations in their efforts to pursue the Institute of Medicine aims of fundamental system redesign to achieve dramatically improved patient care.

Processing Mechanisms for Interstellar Ices: Connections to the Solar System

NASA Technical Reports Server (NTRS)

Pendleton, Y. J.; Cuzzi, Jeffrey N. (Technical Monitor)

1995-01-01

The organic component of the interstellar medium, which has revealed itself through the ubiquitous 3.4 micrometers hydrocarbon absorption feature, is widespread throughout the disk of our galaxy and has been attributed to dust grains residing in the diffuse interstellar medium. The absorption band positions near 3.4 micrometers are characteristic of C-H stretching vibrations in the -CH3 and -CH2- groups of saturated aliphatic hydrocarbons associated with perturbing chemical groups. The production of complex molecules is thought to occur within dense molecular clouds when ice-mantled grains are processed by various energetic mechanisms. Studies of the processing of interstellar ices and the subsequent production of organic residues have relevance to studies of ices in the solar system, because primitive, icy solar system bodies such as those in the Kuiper belt are likely reservoirs of organic material, either preserved from the interstellar medium or produced in situ. Connections between the interstellar medium and the early solar nebula have long been a source of interest. A comparison of the interstellar organics and the Murchison meteorite illustrates the importance of probing the interstellar connection to the solar system, because although the carbonaceous meteorites are undoubtedly highly processed, they do retain specific interstellar signatures (such as diamonds, SiC grains, graphite and enriched D/H). The organic component, while not proven interstellar, has a remarkable similarity to the interstellar organics observed in over a dozen sightlines through our galaxy. This paper compares spectra from laboratory organics produced through the processing of interstellar ice analog materials with the high resolution infrared observations of the interstellar medium in order to investigate the mechanisms (such as ion bombardment, plasma processing, and UV photolysis) that may be producing the organics in the ISM.

Quantifying Sources and Fluxes of Aquatic Carbon in U.S. Streams and Reservoirs Using Spatially Referenced Regression Models

NASA Astrophysics Data System (ADS)

Boyer, E. W.; Smith, R. A.; Alexander, R. B.; Schwarz, G. E.

2004-12-01

Organic carbon (OC) is a critical water quality characteristic in riverine systems that is an important component of the aquatic carbon cycle and energy balance. Examples of processes controlled by OC interactions are complexation of trace metals; enhancement of the solubility of hydrophobic organic contaminants; formation of trihalomethanes in drinking water; and absorption of visible and UV radiation. Organic carbon also can have indirect effects on water quality by influencing internal processes of aquatic ecosystems (e.g. photosynthesis and autotrophic and heterotrophic activity). The importance of organic matter dynamics on water quality has been recognized, but challenges remain in quantitatively addressing OC processes over broad spatial scales in a hydrological context. In this study, we apply spatially referenced watershed models (SPARROW) to statistically estimate long-term mean-annual rates of dissolved- and total- organic carbon export in streams and reservoirs across the conterminous United States. We make use of a GIS framework for the analysis, describing sources, transport, and transformations of organic matter from spatial databases providing characterizations of climate, land use, primary productivity, topography, soils, and geology. This approach is useful because it illustrates spatial patterns of organic carbon fluxes in streamflow, highlighting hot spots (e.g., organic-rich environments in the southeastern coastal plain). Further, our simulations provide estimates of the relative contributions to streams from allochthonous and autochthonous sources. We quantify surface water fluxes of OC with estimates of uncertainty in relation to the overall US carbon budget; our simulations highlight that aquatic sources and sinks of OC may be a more significant component of regional carbon cycling than was previously thought. Further, we are using our simulations to explore the potential role of climate and other changes in the terrestrial environment on OC fluxes in aquatic systems.

Organization of the ER–Golgi interface for membrane traffic control

PubMed Central

Brandizzi, Federica; Barlowe, Charles

2014-01-01

Coat protein complex I (COPI) and COPII are required for bidirectional membrane trafficking between the endoplasmic reticulum (ER) and the Golgi. While these core coat machineries and other transport factors are highly conserved across species, high-resolution imaging studies indicate that the organization of the ER–Golgi interface is varied in eukaryotic cells. Regulation of COPII assembly, in some cases to manage distinct cellular cargo, is emerging as one important component in determining this structure. Comparison of the ER–Golgi interface across different systems, particularly mammalian and plant cells, reveals fundamental elements and distinct organization of this interface. A better understanding of how these interfaces are regulated to meet varying cellular secretory demands should provide key insights into the mechanisms that control efficient trafficking of proteins and lipids through the secretory pathway. PMID:23698585

High molecular diversity of extraterrestrial organic matter in Murchison meteorite revealed 40 years after its fall

PubMed Central

Schmitt-Kopplin, Philippe; Gabelica, Zelimir; Gougeon, Régis D.; Fekete, Agnes; Kanawati, Basem; Harir, Mourad; Gebefuegi, Istvan; Eckel, Gerhard; Hertkorn, Norbert

2010-01-01

Numerous descriptions of organic molecules present in the Murchison meteorite have improved our understanding of the early interstellar chemistry that operated at or just before the birth of our solar system. However, all molecular analyses were so far targeted toward selected classes of compounds with a particular emphasis on biologically active components in the context of prebiotic chemistry. Here we demonstrate that a nontargeted ultrahigh-resolution molecular analysis of the solvent-accessible organic fraction of Murchison extracted under mild conditions allows one to extend its indigenous chemical diversity to tens of thousands of different molecular compositions and likely millions of diverse structures. This molecular complexity, which provides hints on heteroatoms chronological assembly, suggests that the extraterrestrial chemodiversity is high compared to terrestrial relevant biological- and biogeochemical-driven chemical space. PMID:20160129

ORGANIZATION AND FUNCTION OF THE FKBP52 AND FKBP51 GENES

PubMed Central

Cioffi, Donna L.; Hubler, Tina R.; Scammell, Jonathan G.

2011-01-01

Best established as components of steroid hormone receptor complexes, it is now clear that the large molecular weight immunophilins, FKBP52 and FKBP51, play important regulatory roles elsewhere in the cell. This review outlines what is known about the organization of the genes, FKBP4 and FKBP5 respectively, encoding these proteins and describes their diverse actions in the nervous system, reproduction, and cancer. The organization of FKBP4 and FKBP5 is very similar among the chordates, and gene expression is influenced by both genetic and epigenetic mechanisms. Recent studies identifying roles of FKBP52 and FKBP51 in regulation of the microtubule-associated protein tau and microtubule assembly are discussed, as is their interaction with and influence on the transient receptor potential canonical subfamily of ion channel proteins. PMID:21514887

High‐Volume Processed, ITO‐Free Superstrates and Substrates for Roll‐to‐Roll Development of Organic Electronics

PubMed Central

Hösel, Markus; Angmo, Dechan; Søndergaard, Roar R.; dos Reis Benatto, Gisele A.; Carlé, Jon E.; Jørgensen, Mikkel

2014-01-01

The fabrication of substrates and superstrates prepared by scalable roll‐to‐roll methods is reviewed. The substrates and superstrates that act as the flexible carrier for the processing of functional organic electronic devices are an essential component, and proposals are made about how the general availability of various forms of these materials is needed to accelerate the development of the field of organic electronics. The initial development of the replacement of indium‐tin‐oxide (ITO) for the flexible carrier materials is described and a description of how roll‐to‐roll processing development led to simplification from an initially complex make‐up to higher performing materials through a more simple process is also presented. This process intensification through process simplification is viewed as a central strategy for upscaling, increasing throughput, performance, and cost reduction. PMID:27980893

High molecular diversity of extraterrestrial organic matter in Murchison meteorite revealed 40 years after its fall.

PubMed

Schmitt-Kopplin, Philippe; Gabelica, Zelimir; Gougeon, Régis D; Fekete, Agnes; Kanawati, Basem; Harir, Mourad; Gebefuegi, Istvan; Eckel, Gerhard; Hertkorn, Norbert

2010-02-16

Numerous descriptions of organic molecules present in the Murchison meteorite have improved our understanding of the early interstellar chemistry that operated at or just before the birth of our solar system. However, all molecular analyses were so far targeted toward selected classes of compounds with a particular emphasis on biologically active components in the context of prebiotic chemistry. Here we demonstrate that a nontargeted ultrahigh-resolution molecular analysis of the solvent-accessible organic fraction of Murchison extracted under mild conditions allows one to extend its indigenous chemical diversity to tens of thousands of different molecular compositions and likely millions of diverse structures. This molecular complexity, which provides hints on heteroatoms chronological assembly, suggests that the extraterrestrial chemodiversity is high compared to terrestrial relevant biological- and biogeochemical-driven chemical space.

Phenotypic integration in an extended phenotype: among-individual variation in nest-building traits of the alfalfa leafcutting bee (Megachile rotundata).

PubMed

Royauté, Raphaël; Wilson, Elisabeth S; Helm, Bryan R; Mallinger, Rachel E; Prasifka, Jarrad; Greenlee, Kendra J; Bowsher, Julia H

2018-03-02

Structures such as nests and burrows are an essential component of many organisms' life-cycle and require a complex sequence of behaviours. Because behaviours can vary consistently among individuals and be correlated with one another, we hypothesized that these structures would (1) show evidence of among-individual variation, (2) be organized into distinct functional modules and (3) show evidence of trade-offs among functional modules due to limits on energy budgets. We tested these hypotheses using the alfalfa leafcutting bee, Megachile rotundata, a solitary bee and important crop pollinator. Megachile rotundata constructs complex nests by gathering leaf materials to form a linear series of cells in pre-existing cavities. In this study, we examined variation in the following nest construction traits: reproduction (number of cells per nest and nest length), nest protection (cap length and number of leaves per cap), cell construction (cell size and number of leaves per cell) and cell provisioning (cell mass) from 60 nests. We found a general decline in investment in cell construction and provisioning with each new cell built. In addition, we found evidence for both repeatability and plasticity in cell provisioning with little evidence for trade-offs among traits. Instead, most traits were positively, albeit weakly, correlated (r ~ 0.15), and traits were loosely organized into covarying modules. Our results show that individual differences in nest construction are detectable at a level similar to that of other behavioural traits and that these traits are only weakly integrated. This suggests that nest components are capable of independent evolutionary trajectories. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Induction of Biogenic Magnetization and Redox Control by a Component of the Target of Rapamycin Complex 1 Signaling Pathway

PubMed Central

Nishida, Keiji; Silver, Pamela A.

2012-01-01

Most organisms are simply diamagnetic, while magnetotactic bacteria and migratory animals are among organisms that exploit magnetism. Biogenic magnetization not only is of fundamental interest, but also has industrial potential. However, the key factor(s) that enable biogenic magnetization in coordination with other cellular functions and metabolism remain unknown. To address the requirements for induction and the application of synthetic bio-magnetism, we explored the creation of magnetism in a simple model organism. Cell magnetization was first observed by attraction towards a magnet when normally diamagnetic yeast Saccharomyces cerevisiae were grown with ferric citrate. The magnetization was further enhanced by genetic modification of iron homeostasis and introduction of ferritin. The acquired magnetizable properties enabled the cells to be attracted to a magnet, and be trapped by a magnetic column. Superconducting quantum interference device (SQUID) magnetometry confirmed and quantitatively characterized the acquired paramagnetism. Electron microscopy and energy-dispersive X-ray spectroscopy showed electron-dense iron-containing aggregates within the magnetized cells. Magnetization-based screening of gene knockouts identified Tco89p, a component of TORC1 (Target of rapamycin complex 1), as important for magnetization; loss of TCO89 and treatment with rapamycin reduced magnetization in a TCO89-dependent manner. The TCO89 expression level positively correlated with magnetization, enabling inducible magnetization. Several carbon metabolism genes were also shown to affect magnetization. Redox mediators indicated that TCO89 alters the intracellular redox to an oxidized state in a dose-dependent manner. Taken together, we demonstrated that synthetic induction of magnetization is possible and that the key factors are local redox control through carbon metabolism and iron supply. PMID:22389629

Characterization of Whole Porewater Dissolved Organic Matter by 1H NMR

NASA Astrophysics Data System (ADS)

Fox, C.; Lewicki, J. P.; Abdulla, H. A.; Burdige, D.; Magen, C.; Chanton, J.; Komada, T.

2014-12-01

Dissolved organic matter (DOM) is a key intermediate in microbial remineralization of organic matter, but only a small percentage of this complex pool has been fully characterized. We present the results of a novel approach to the characterization of DOM in whole porewater samples from the anoxic sediments of the Santa Barbara Basin, California Borderland, using solution state nuclear magnetic resonance (NMR) techniques. Profiles of porewater DOM were obtained by 1H NMR from 95 to 435 cm sediment depth. 1H NMR spectra of each whole porewater sample showed continuous, broad regions from ~0.5 to ~4.5 ppm, indicative of significant signal overlap inherent to complex mixtures, superimposed on a few highly resolved peaks. The individual samples consist of a broad range of chemical environments with varying relative abundances that show a near linear trend with depth. The normalized spectral data were analyzed by principal component analysis to resolve variations in chemical composition of DOM as a function of depth. In addition to detecting the major components such as carbohydrates, cyclic aliphatics and aromatics, our results demonstrate a negative correlation between carbohydrates concurrent with a relative increase in levels of aliphatics. Furthermore, we have identified a decrease in the abundance of alkenes coupled with an increase in a broad region from ~1.9 to ~3.2 ppm, likely corresponding to signals from carboxylic-rich alicyclic molecules. In both trends, the greatest variation occurs between 115 and 135 cm, which straddles the sulfate-methane transition zone (~125 cm), potentially highlighting a region of relatively high DOM transformation. Our work has also identified thiol species which are thought to be formed by dissolved (inorganic) sulfide incorporation into porewater DOM compounds. The implications of these results with respect to carbon cycling in anaerobic sediments will be discussed.

Journal of the United States Artillery. Volume 56, Number 1, January 1922

DTIC Science & Technology

1922-01-01

its develop- ment and recognitio ,n as a real component of the Army of the United States. At the same time, many of us, believing the National Guard...exist in the Ninth Corps Area it is believed that similar conditions and problems are being faced in other Corps Areas. DECEXTRALIZATIO~ SUGGESTIOX1.-It...Guard organizations should be measured by the same standard. On the face of it, if the standard as to instant readiness and variety and complexity in

IT security evaluation - “hybrid” approach and risk of its implementation

NASA Astrophysics Data System (ADS)

Livshitz, I. I.; Neklyudov, A. V.; Lontsikh, P. A.

2018-05-01

It is relevant to evolve processes of evaluation of the IT security nowadays. Creating and application of the common evaluation approaches for an IT component, which are processed by the governmental and civil organizations, are still not solving problem. It is suggested to create a more precise and complex assessment tool for an IT security – the “hybrid” method of the IT security evaluation for a particular object, which is based on a range of adequate assessment tools.

Abundance, size distributions and trace-element binding of organic and iron-rich nanocolloids in Alaskan rivers, as revealed by field-flow fractionation and ICP-MS

NASA Astrophysics Data System (ADS)

Stolpe, Björn; Guo, Laodong; Shiller, Alan M.; Aiken, George R.

2013-03-01

Water samples were collected from six small rivers in the Yukon River basin in central Alaska to examine the role of colloids and organic matter in the transport of trace elements in Northern high latitude watersheds influenced by permafrost. Concentrations of dissolved organic carbon (DOC), selected elements (Al, Si, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Rb, Sr, Ba, Pb, U), and UV-absorbance spectra were measured in 0.45 μm filtered samples. 'Nanocolloidal size distributions' (0.5-40 nm, hydrodynamic diameter) of humic-type and chromophoric dissolved organic matter (CDOM), Cr, Mn, Fe, Co, Ni, Cu, Zn, and Pb were determined by on-line coupling of flow field-flow fractionation (FFF) to detectors including UV-absorbance, fluorescence, and ICP-MS. Total dissolved and nanocolloidal concentrations of the elements varied considerably between the rivers and between spring flood and late summer base flow. Data on specific UV-absorbance (SUVA), spectral slopes, and the nanocolloidal fraction of the UV-absorbance indicated a decrease in aromaticity and size of CDOM from spring flood to late summer. The nanocolloidal size distributions indicated the presence of different 'components' of nanocolloids. 'Fulvic-rich nanocolloids' had a hydrodynamic diameter of 0.5-3 nm throughout the sampling season; 'organic/iron-rich nanocolloids' occurred in the <8 nm size range during the spring flood; whereas 'iron-rich nanocolloids' formed a discrete 4-40 nm components during summer base flow. Mn, Co, Ni, Cu and Zn were distributed between the nanocolloid components depending on the stability constant of the metal (+II)-organic complexes, while stronger association of Cr to the iron-rich nanocolloids was attributed to the higher oxidation states of Cr (+III or +IV). Changes in total dissolved element concentrations, size and composition of CDOM, and occurrence and size of organic/iron and iron-rich nanocolloids were related to variations in their sources from either the upper organic-rich soil or the deeper mineral layer, depending on seasonal variations in hydrological flow patterns and permafrost dynamics.

Health perceptions of Mexican American women.

PubMed

Mendelson, Cindy

2002-07-01

This article describes the health perceptions of a sample of moderately to highly acculturated Mexican American women. Using an ethnographic design, the author interviewed 13 women to determine their health perceptions. The interviews were guided by the domains of health described in the World Health Organization (WHO) definition of health. Three broad categories of health perceptions were identified: the physical body, the emotional component, and finding balance. With the addition of a spiritual component, the WHO definition was a useful tool for uncovering health perceptions. The process of in-depth ethnographic interviewing provided a contextual view of health in which the complexity of intrafamilial relationships was revealed, as were the importance of spirituality as a coping mechanism and the perception of health as an integrated, holistic experience.

From neural development to cognition: unexpected roles for chromatin

PubMed Central

Ronan, Jehnna L.; Wu, Wei

2014-01-01

Recent genome-sequencing studies in human neurodevelopmental and psychiatric disorders have uncovered mutations in many chromatin regulators. These human genetic studies, along with studies in model organisms, are providing insight into chromatin regulatory mechanisms in neural development and how alterations to these mechanisms can cause cognitive deficits, such as intellectual disability. We discuss several implicated chromatin regulators, including BAF (also known as SWI/SNF) and CHD8 chromatin remodellers, HDAC4 and the Polycomb component EZH2. Interestingly, mutations in EZH2 and certain BAF complex components have roles in both neurodevelopmental disorders and cancer, and overlapping point mutations are suggesting functionally important residues and domains. We speculate on the contribution of these similar mutations to disparate disorders. PMID:23568486

The effect of herbal remedy on the development of Trichinella spiralis infection in mice.

PubMed

Bany, J; Zdanowska, D; Zdanowski, R; Skopińska-Rózewska, E

2003-01-01

The effect of Alchinal (a complex preparation consisting of three substances: Echinacea purpurea extract, Allium sativum extract, cocoa) on the development of Trichinella spiralis infection in mice was studied. The preparation was administered to the animals orally, twice a day in 30 microl doses for 10 days after infecting mice with Trichinella larvae (500 larvae per mouse). It was demonstrated that after Alchinal administration, the number of adult forms (10 dpi--days post infection) and muscular larvae (36 dpi) significantly decreased. It is suggested that the remedy studied causes antiparasitic immunity enhancement in mice. Modulation of immunity by individual component(s) and/or joint action of the substances contained in Alchinal increases the antiparasitic defence of the organism.

The Scenario-Based Engineering Process (SEP): a user-centered approach for the development of health care systems.

PubMed

Harbison, K; Kelly, J; Burnell, L; Silva, J

1995-01-01

The Scenario-based Engineering Process (SEP) is a user-focused methodology for large and complex system design. This process supports new application development from requirements analysis with domain models to component selection, design and modification, implementation, integration, and archival placement. It is built upon object-oriented methodologies, domain modeling strategies, and scenario-based techniques to provide an analysis process for mapping application requirements to available components. We are using SEP in the health care applications that we are developing. The process has already achieved success in the manufacturing and military domains and is being adopted by many organizations. SEP should prove viable in any domain containing scenarios that can be decomposed into tasks.

Sequencing the Cortical Processing of Pitch-Evoking Stimuli using EEG Analysis and Source Estimation

PubMed Central

Butler, Blake E.; Trainor, Laurel J.

2012-01-01

Cues to pitch include spectral cues that arise from tonotopic organization and temporal cues that arise from firing patterns of auditory neurons. fMRI studies suggest a common pitch center is located just beyond primary auditory cortex along the lateral aspect of Heschl’s gyrus, but little work has examined the stages of processing for the integration of pitch cues. Using electroencephalography, we recorded cortical responses to high-pass filtered iterated rippled noise (IRN) and high-pass filtered complex harmonic stimuli, which differ in temporal and spectral content. The two stimulus types were matched for pitch saliency, and a mismatch negativity (MMN) response was elicited by infrequent pitch changes. The P1 and N1 components of event-related potentials (ERPs) are thought to arise from primary and secondary auditory areas, respectively, and to result from simple feature extraction. MMN is generated in secondary auditory cortex and is thought to act on feature-integrated auditory objects. We found that peak latencies of both P1 and N1 occur later in response to IRN stimuli than to complex harmonic stimuli, but found no latency differences between stimulus types for MMN. The location of each ERP component was estimated based on iterative fitting of regional sources in the auditory cortices. The sources of both the P1 and N1 components elicited by IRN stimuli were located dorsal to those elicited by complex harmonic stimuli, whereas no differences were observed for MMN sources across stimuli. Furthermore, the MMN component was located between the P1 and N1 components, consistent with fMRI studies indicating a common pitch region in lateral Heschl’s gyrus. These results suggest that while the spectral and temporal processing of different pitch-evoking stimuli involves different cortical areas during early processing, by the time the object-related MMN response is formed, these cues have been integrated into a common representation of pitch. PMID:22740836

[The occurrence of tumors in the minnow Phoxinus phoxinus (L.), their influence upon the parasite fauna, component community of parasites, and organism of the host].

PubMed

Dorovskikh, G N; Sedriseva, V A; Stepanov, V G; Boznak, E I

2006-01-01

The occurrence of tumors, their influence upon the organism of Phoxinus phoxinus (L.), its parasite fauna, and parasite component community were investigated in the upstream of the Pechora River. According to the data obtained, tumors could occur in the fishes of every age group, but one-year (0+) or two-year (1+) old minnow is affected by tumors more frequently. The tumors lesion extensiveness ranges from 0.02 to 3 %. From 1 to 3 tumors were recorded on one fish specimen. The investigated tumors were in progressive stage (Georgiev, 2000), since the vascular ingrowth and dissemination (in few cases) of the tumors were observed. Tumors are colored in intensive-black and taupe. The taupe tumors usually have a compact capsule at its peripheries, which isolates affected tissue from muscle fibers. In the intensive-black tumors the invasion of tumor cells to the adjacent transversal striated musculature is observed. Distinct symptoms of necrosis are revealed in all slides of the new growths. Blood vessels are formed in most tumors, and the blood flow is recorded before the completion of the vessels forming, that apparently supplies the tumors feeding. Metastases in different organs revealed in several minnow specimens. Tumor affected individuals of the minnow has parasite species complex practically identical (by species list and quantity) with the same of the even-aged unaffected fishes. However, the parasite component communities of the affected individuals are characterized by 4 groups of species, while the parasite component communities of the intact individuals--by 3 groups. The parasite communities of affected and unaffected one-year fishes are similar by the number of the groups of species, but differ in the number of species.

Control of Orientation and Morphology of Crystals Grown Under Organic Templates

NASA Astrophysics Data System (ADS)

Stripe, Benjamin

Living creatures demonstrate an extraordinary ability to both grow and control the growth of inorganic crystals. These biominerals are found almost everywhere in nature from simple plants and plankton to our own teeth and bones. A great deal of research has been focused on how living creatures are able to achieve such control over the shape, size, orientation, and arrangement of these biominerals. Many studies have been done demonstrating the effects the presence of organic molecules can have on the morphology of nucleating inorganic crystals. These studies have led to the use of ordered arrays of biological molecules as templates to select the orientation of the crystals. Such experiments have had amazing success cataloging monolayers, orientations and morphologies of crystals grown beneath them. However, despite several decades of work, the exact mechanisms by which the orientation and morphology of crystals is selected by organic templates are still not known. The present study attempts to explain the complex interactions that take place at the template surface and decide the orientations and morphologies of the crystals that nucleate there. To do this, scanning electron microscopy (SEM), grazing incidence x-ray diffraction (GID), and x-ray reflectivity have been used to probe the templates and nucleating crystals in situ. The experiments described here seek to move beyond the well-studied two-component systems. In many of these two-component systems a single template and a single type of crystal are grown, and often many claims and comparisons are made about monolayer charge, crystal surface energies, stereochemical recognition, and lattice matches. However, almost all of the claims and comparisons are between systems that are different enough that assumptions about relative charge, strain, recognition, and lattice dynamics are either unfounded or poorly supported. To bridge this gap in the comparison of these different two-component systems the studies presented here are tunable three-component systems. These experiments allow for either continuously adjusting the template by means of two miscible monolayers or adjusting the growing crystals by incorporation of secondary ions. In either case, the idea is the same: we can more accurately compare two-component systems and isolate the controlling factor in the selection of orientation and morphology of the nucleating crystals. The results of these studies have shown that there is a complex interplay of charge, lattice parameters and kinetics. Despite this, we have been able to show that well-oriented growth of single non-dendritic crystals is limited to a fairly small range of surface charges and relative growth kinetics. Within this range, variations in the growing crystals can be seen based on changes in the average lattice parameters despite there being no evidence of direct epitaxy. Theories have evolved around the idea of stereochemical matching between the template and nucleating surface. These theories correlate the template molecular tilt to the orientation relative to the nucleation plane. However, these theories are not supported by the results presented in this manuscript. The data presented in this manuscript are suggestive of far more complex interfacial interactions involving an intermediary amorphous precursor, or possible networks of hydrated or hydrogen bonded ions than has been suggested in previous studies. Excitingly, it appears to be possible to control the selection of orientation using these multicomponent systems despite the complex interactions at the surface.

The Fluid-Mosaic Model of Membrane Structure: still relevant to understanding the structure, function and dynamics of biological membranes after more than 40 years.

PubMed

Nicolson, Garth L

2014-06-01

In 1972 the Fluid-Mosaic Membrane Model of membrane structure was proposed based on thermodynamic principals of organization of membrane lipids and proteins and available evidence of asymmetry and lateral mobility within the membrane matrix [S. J. Singer and G. L. Nicolson, Science 175 (1972) 720-731]. After over 40years, this basic model of the cell membrane remains relevant for describing the basic nano-structures of a variety of intracellular and cellular membranes of plant and animal cells and lower forms of life. In the intervening years, however, new information has documented the importance and roles of specialized membrane domains, such as lipid rafts and protein/glycoprotein complexes, in describing the macrostructure, dynamics and functions of cellular membranes as well as the roles of membrane-associated cytoskeletal fences and extracellular matrix structures in limiting the lateral diffusion and range of motion of membrane components. These newer data build on the foundation of the original model and add new layers of complexity and hierarchy, but the concepts described in the original model are still applicable today. In updated versions of the model more emphasis has been placed on the mosaic nature of the macrostructure of cellular membranes where many protein and lipid components are limited in their rotational and lateral motilities in the membrane plane, especially in their natural states where lipid-lipid, protein-protein and lipid-protein interactions as well as cell-matrix, cell-cell and intracellular membrane-associated protein and cytoskeletal interactions are important in restraining the lateral motility and range of motion of particular membrane components. The formation of specialized membrane domains and the presence of tightly packed integral membrane protein complexes due to membrane-associated fences, fenceposts and other structures are considered very important in describing membrane dynamics and architecture. These structures along with membrane-associated cytoskeletal and extracellular structures maintain the long-range, non-random mosaic macro-organization of membranes, while smaller membrane nano- and submicro-sized domains, such as lipid rafts and protein complexes, are important in maintaining specialized membrane structures that are in cooperative dynamic flux in a crowded membrane plane. This Article is Part of a Special Issue Entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy. © 2013.

Molecular Structure of the Pyruvate Dehydrogenase Complex from Escherichia coli K-12

PubMed Central

Vogel, Otto; Hoehn, Barbara; Henning, Ulf

1972-01-01

The pyruvate dehydrogenase core complex from E. coli K-12, defined as the multienzyme complex that can be obtained with a unique polypeptide chain composition, has a molecular weight of 3.75 × 106. All results obtained agree with the following numerology. The core complex consists of 48 polypeptide chains. There are 16 chains (molecular weight = 100,000) of the pyruvate dehydrogenase component, 16 chains (molecular weight = 80,000) of the dihydrolipoamide dehydrogenase component, and 16 chains (molecular weight = 56,000) of the dihydrolipoamide dehydrogenase component. Usually, but not always, pyruvate dehydrogenase complex is produced in vivo containing at least 2-3 mol more of dimers of the pyruvate dehydrogenase component than the stoichiometric ratio with respect to the core complex. This “excess” component is bound differently than are the eight dimers in the core complex. Images PMID:4556465

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

PubMed Central

Barutcu, A. Rasim; Lajoie, Bryan R.; Fritz, Andrew J.; McCord, Rachel P.; Nickerson, Jeffrey A.; van Wijnen, Andre J.; Lian, Jane B.; Stein, Janet L.; Dekker, Job; Stein, Gary S.; Imbalzano, Anthony N.

2016-01-01

The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma-related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucleosomes at target regions. Although the transcriptional role of SMARCA4 at gene promoters is well-studied, less is known about its role in higher-order genome organization. SMARCA4 knockdown in human mammary epithelial MCF-10A cells resulted in 176 up-regulated genes, including many related to lipid and calcium metabolism, and 1292 down-regulated genes, some of which encode extracellular matrix (ECM) components that can exert mechanical forces and affect nuclear structure. ChIP-seq analysis of SMARCA4 localization and SMARCA4-bound super-enhancers demonstrated extensive binding at intergenic regions. Furthermore, Hi-C analysis showed extensive SMARCA4-mediated alterations in higher-order genome organization at multiple resolutions. First, SMARCA4 knockdown resulted in clustering of intra- and inter-subtelomeric regions, demonstrating a novel role for SMARCA4 in telomere organization. SMARCA4 binding was enriched at topologically associating domain (TAD) boundaries, and SMARCA4 knockdown resulted in weakening of TAD boundary strength. Taken together, these findings provide a dynamic view of SMARCA4-dependent changes in higher-order chromatin organization and gene expression, identifying SMARCA4 as a novel component of chromatin organization. PMID:27435934

Quantitative analysis of nucleolar chromatin distribution in the complex convoluted nucleoli of Didinium nasutum (Ciliophora).

PubMed

Leonova, Olga G; Karajan, Bella P; Ivlev, Yuri F; Ivanova, Julia L; Skarlato, Sergei O; Popenko, Vladimir I

2013-01-01

We have earlier shown that the typical Didinium nasutum nucleolus is a complex convoluted branched domain, comprising a dense fibrillar component located at the periphery of the nucleolus and a granular component located in the central part. Here our main interest was to study quantitatively the spatial distribution of nucleolar chromatin structures in these convoluted nucleoli. There are no "classical" fibrillar centers in D.nasutum nucleoli. The spatial distribution of nucleolar chromatin bodies, which play the role of nucleolar organizers in the macronucleus of D.nasutum, was studied using 3D reconstructions based on serial ultrathin sections. The relative number of nucleolar chromatin bodies was determined in macronuclei of recently fed, starved D.nasutum cells and in resting cysts. This parameter is shown to correlate with the activity of the nucleolus. However, the relative number of nucleolar chromatin bodies in different regions of the same convoluted nucleolus is approximately the same. This finding suggests equal activity in different parts of the nucleolar domain and indicates the existence of some molecular mechanism enabling it to synchronize this activity in D. nasutum nucleoli. Our data show that D. nasutum nucleoli display bipartite structure. All nucleolar chromatin bodies are shown to be located outside of nucleoli, at the periphery of the fibrillar component.

Implicit Binding of Facial Features During Change Blindness

PubMed Central

Lyyra, Pessi; Mäkelä, Hanna; Hietanen, Jari K.; Astikainen, Piia

2014-01-01

Change blindness refers to the inability to detect visual changes if introduced together with an eye-movement, blink, flash of light, or with distracting stimuli. Evidence of implicit detection of changed visual features during change blindness has been reported in a number of studies using both behavioral and neurophysiological measurements. However, it is not known whether implicit detection occurs only at the level of single features or whether complex organizations of features can be implicitly detected as well. We tested this in adult humans using intact and scrambled versions of schematic faces as stimuli in a change blindness paradigm while recording event-related potentials (ERPs). An enlargement of the face-sensitive N170 ERP component was observed at the right temporal electrode site to changes from scrambled to intact faces, even if the participants were not consciously able to report such changes (change blindness). Similarly, the disintegration of an intact face to scrambled features resulted in attenuated N170 responses during change blindness. Other ERP deflections were modulated by changes, but unlike the N170 component, they were indifferent to the direction of the change. The bidirectional modulation of the N170 component during change blindness suggests that implicit change detection can also occur at the level of complex features in the case of facial stimuli. PMID:24498165

Implicit binding of facial features during change blindness.

PubMed

Lyyra, Pessi; Mäkelä, Hanna; Hietanen, Jari K; Astikainen, Piia

2014-01-01

Change blindness refers to the inability to detect visual changes if introduced together with an eye-movement, blink, flash of light, or with distracting stimuli. Evidence of implicit detection of changed visual features during change blindness has been reported in a number of studies using both behavioral and neurophysiological measurements. However, it is not known whether implicit detection occurs only at the level of single features or whether complex organizations of features can be implicitly detected as well. We tested this in adult humans using intact and scrambled versions of schematic faces as stimuli in a change blindness paradigm while recording event-related potentials (ERPs). An enlargement of the face-sensitive N170 ERP component was observed at the right temporal electrode site to changes from scrambled to intact faces, even if the participants were not consciously able to report such changes (change blindness). Similarly, the disintegration of an intact face to scrambled features resulted in attenuated N170 responses during change blindness. Other ERP deflections were modulated by changes, but unlike the N170 component, they were indifferent to the direction of the change. The bidirectional modulation of the N170 component during change blindness suggests that implicit change detection can also occur at the level of complex features in the case of facial stimuli.

Photoprotection Conferred by Changes in Photosynthetic Protein Levels and Organization during Dehydration of a Homoiochlorophyllous Resurrection Plant1

PubMed Central

Charuvi, Dana; Nevo, Reinat; Shimoni, Eyal; Naveh, Leah; Zia, Ahmad; Adam, Zach; Farrant, Jill M.; Kirchhoff, Helmut; Reich, Ziv

2015-01-01

During desiccation, homoiochlorophyllous resurrection plants retain most of their photosynthetic apparatus, allowing them to resume photosynthetic activity quickly upon water availability. These plants rely on various mechanisms to prevent the formation of reactive oxygen species and/or protect their tissues from the damage they inflict. In this work, we addressed the issue of how homoiochlorophyllous resurrection plants deal with the problem of excessive excitation/electron pressures during dehydration using Craterostigma pumilum as a model plant. To investigate the alterations in the supramolecular organization of photosynthetic protein complexes, we examined cryoimmobilized, freeze-fractured leaf tissues using (cryo)scanning electron microscopy. These examinations revealed rearrangements of photosystem II (PSII) complexes, including a lowered density during moderate dehydration, consistent with a lower level of PSII proteins, as shown by biochemical analyses. The latter also showed a considerable decrease in the level of cytochrome f early during dehydration, suggesting that initial regulation of the inhibition of electron transport is achieved via the cytochrome b6f complex. Upon further dehydration, PSII complexes are observed to arrange into rows and semicrystalline arrays, which correlates with the significant accumulation of sucrose and the appearance of inverted hexagonal lipid phases within the membranes. As opposed to PSII and cytochrome f, the light-harvesting antenna complexes of PSII remain stable throughout the course of dehydration. Altogether, these results, along with photosynthetic activity measurements, suggest that the protection of retained photosynthetic components is achieved, at least in part, via the structural rearrangements of PSII and (likely) light-harvesting antenna complexes into a photochemically quenched state. PMID:25713340

The Aminoacyl-tRNA Synthetase Complex.

PubMed

Mirande, Marc

2017-01-01

Aminoacyl-tRNA synthetases (AARSs) are essential enzymes that specifically aminoacylate one tRNA molecule by the cognate amino acid. They are a family of twenty enzymes, one for each amino acid. By coupling an amino acid to a specific RNA triplet, the anticodon, they are responsible for interpretation of the genetic code. In addition to this translational, canonical role, several aminoacyl-tRNA synthetases also fulfill nontranslational, moonlighting functions. In mammals, nine synthetases, those specific for amino acids Arg, Asp, Gln, Glu, Ile, Leu, Lys, Met and Pro, associate into a multi-aminoacyl-tRNA synthetase complex, an association which is believed to play a key role in the cellular organization of translation, but also in the regulation of the translational and nontranslational functions of these enzymes. Because the balance between their alternative functions rests on the assembly and disassembly of this supramolecular entity, it is essential to get precise insight into the structural organization of this complex. The high-resolution 3D-structure of the native particle, with a molecular weight of about 1.5 MDa, is not yet known. Low-resolution structures of the multi-aminoacyl-tRNA synthetase complex, as determined by cryo-EM or SAXS, have been reported. High-resolution data have been reported for individual enzymes of the complex, or for small subcomplexes. This review aims to present a critical view of our present knowledge of the aminoacyl-tRNA synthetase complex in 3D. These preliminary data shed some light on the mechanisms responsible for the balance between the translational and nontranslational functions of some of its components.

Ultrastructural analysis of cell component distribution in the apical cell of Ceratodon protonemata

NASA Technical Reports Server (NTRS)

Walker, L. M.; Sack, F. D.

1995-01-01

A distinctive feature of tip-growing plant cells is that cell components are distributed differentially along the length of the cell, although most ultrastructural analyses have been qualitative. The longtitudinal distribution of cell components was studied both qualitatively and quantitatively in the apical cell of dark-grown protonemata of the moss Ceratodon. The first 35 micrometers of the apical cell was analyzed stereologically using transmission electron microscopy. There were four types of distributions along the cell's axis, three of them differential: (1) tubular endoplasmic reticulum was evenly distributed, (2) cisternal endoplasmic reticulum and Golgi vesicles were distributed in a tip-to-base gradient, (3) plastids, vacuoles, and Golgi stacks were enriched in specific areas, although the locations of the enrichments varied, and (4) mitochondria were excluded in the tip-most 5 micrometers and evenly distributed throughout the remaining 30 micrometers. This study provides one of the most comprehensive quantitative, ultrastructural analyses of the distribution of cell components in the apex of any tip-growing plant cell. The finding that almost every component had its own spatial arrangement demonstrates the complexity of the organization and regulation of the distribution of components in tip-growing cells.

An immunoglobulin M monoclonal antibody, recognizing a subset of acetylcholinesterase molecules from electric organs of Electrophorus and Torpedo, belongs to the HNK-1 anti-carbohydrate family.

PubMed

Bon, S; Méflah, K; Musset, F; Grassi, J; Massoulié, J

1987-12-01

An immunoglobulin M (IgM) monoclonal antibody (mAb Elec-39), obtained against asymmetric acetylcholinesterase (AChE) from Electrophorus electric organs, also reacts with a fraction of globular AChE (amphiphilic G2 form) from Torpedo electric organs. This antibody does not react with asymmetric AChE from Torpedo electric organs or with the enzyme from other tissues of Electrophorus or Torpedo. The corresponding epitope is removed by endoglycosidase F, showing that it is a carbohydrate. The subsets of Torpedo G2 that react or do not react with Elec-39 (Elec-39+ and Elec-39-) differ in their electrophoretic mobility under nondenaturing conditions; the Elec-39+ component also binds the lectins from Pisum sativum and Lens culinaris. Whereas the Elec-39- component is present at the earliest developmental stages examined, an Elec-39+ component becomes distinguishable only around the 70-mm stage. Its proportion increases progressively, but later than the rapid accumulation of the total G2 form. In immunoblots, mAb Elec-39 recognizes a number of proteins other than AChE from various tissues of several species. The specificity of Elec-39 resembles that of a family of anti-carbohydrate antibodies that includes HNK-1, L2, NC-1, NSP-4, as well as IgMs that occur in human neuropathies. Although some human neuropathy IgMs that recognize the myelin-associated glycoprotein did not react with Elec-39+ AChE, mAbs HNK-1, NC-1, and NSP-4 showed the same selectivity as Elec-39 for Torpedo G2 AChE, but differed in the formation of immune complexes.

RNAi and retroviruses: are they in RISC?

PubMed

Vasselon, Thierry; Bouttier, Manuella; Saumet, Anne; Lecellier, Charles-Henri

2013-02-01

RNA interference (RNAi) is a potent cellular system against viruses in various organisms. Although common traits are observed in plants, insects, and nematodes, the situation observed in mammals appears more complex. In mammalian somatic cells, RNAi is implicated in endonucleolytic cleavage mediated by artificially delivered small interfering RNAs (siRNAs) as well as in translation repression mediated by microRNAs (miRNAs). Because siRNAs and miRNAs recognize viral mRNAs, RNAi inherently limits virus production and participates in antiviral defense. However, several observations made in the cases of hepatitis C virus and retroviruses (including the human immunodeficiency virus and the primate foamy virus) bring evidence that this relationship is much more complex and that certain components of the RNAi effector complex [called the RNA-induced silencing complex (RISC)], such as AGO2, are also required for viral replication. Here, we summarize recent discoveries that have revealed this dual implication in virus biology. We further discuss their potential implications for the functions of RNAi-related proteins, with special emphasis on retrotransposition and genome stability.

Individual nodeʼs contribution to the mesoscale of complex networks

NASA Astrophysics Data System (ADS)

Klimm, Florian; Borge-Holthoefer, Javier; Wessel, Niels; Kurths, Jürgen; Zamora-López, Gorka

2014-12-01

The analysis of complex networks is devoted to the statistical characterization of the topology of graphs at different scales of organization in order to understand their functionality. While the modular structure of networks has become an essential element to better apprehend their complexity, the efforts to characterize the mesoscale of networks have focused on the identification of the modules rather than describing the mesoscale in an informative manner. Here we propose a framework to characterize the position every node takes within the modular configuration of complex networks and to evaluate their function accordingly. For illustration, we apply this framework to a set of synthetic networks, empirical neural networks, and to the transcriptional regulatory network of the Mycobacterium tuberculosis. We find that the architecture of both neuronal and transcriptional networks are optimized for the processing of multisensory information with the coexistence of well-defined modules of specialized components and the presence of hubs conveying information from and to the distinct functional domains.

Chromatin organization and radio resistance in the bacterium Gemmata obscuriglobus.

PubMed

Lieber, Arnon; Leis, Andrew; Kushmaro, Ariel; Minsky, Abraham; Medalia, Ohad

2009-03-01

The organization of chromatin has a major impact on cellular activities, such as gene expression. For bacteria, it was suggested that the spatial organization of the genetic material correlates with transcriptional levels, implying a specific architecture of the chromosome within the cytoplasm. Accordingly, recent technological advances have emphasized the organization of the genetic material within nucleoid structures. Gemmata obscuriglobus, a member of the phylum Planctomycetes, exhibits a distinctive nucleoid structure in which chromatin is encapsulated within a discrete membrane-bound compartment. Here, we show that this soil and freshwater bacterium tolerates high doses of UV and ionizing radiation. Cryoelectron tomography of frozen hydrated sections and electron microscopy of freeze-substituted cells have indicated a more highly ordered condensed-chromatin organization in actively dividing and stationary-phase G. obscuriglobus cells. These three-dimensional analyses revealed a complex network of double membranes that engulf the condensed DNA. Bioinformatics analysis has revealed the existence of a putative component involved in nonhomologous DNA end joining that presumably plays a role in maintaining chromatin integrity within the bacterium. Thus, our observations further support the notion that packed chromatin organization enhances radiation tolerance.

Crystal structure of a shark single-domain antibody V region in complex with lysozyme.

PubMed

Stanfield, Robyn L; Dooley, Helen; Flajnik, Martin F; Wilson, Ian A

2004-09-17

Cartilaginous fish are the phylogenetically oldest living organisms known to possess components of the vertebrate adaptive immune system. Key to their immune response are heavy-chain, homodimeric immunoglobulins called new antigen receptors (IgNARs), in which the variable (V) domains recognize antigens with only a single immunoglobulin domain, akin to camelid heavy-chain V domains. The 1.45 angstrom resolution crystal structure of the type I IgNAR V domain in complex with hen egg-white lysozyme (HEL) reveals a minimal antigen-binding domain that contains only two of the three conventional complementarity-determining regions but still binds HEL with nanomolar affinity by means of a binding interface comparable in size to conventional antibodies.

Catalytic bismetallative multicomponent coupling reactions: scope, applications, and mechanisms

PubMed Central

Cho, Hee Yeon

2014-01-01

Catalytic reactions have played an indispensable role in organic chemistry for the last several decades. In particular, catalytic multicomponent reactions have attracted a lot of attention due to their efficiency and expediency towards complex molecule synthesis. The presence of bismetallic reagents (e.g. B–B, Si–Si, B–Si, Si–Sn, etc.) in this process renders the products enriched with various functional groups and multiple stereocenters. For this reason, catalytic bismetallative coupling is considered an effective method to generate the functional and stereochemical complexity of simple hydrocarbon substrates. This review highlights key developments of transition-metal catalyzed bismetallative reactions involving multiple π components. Specifically, it will highlight the scope, synthetic applications, and proposed mechanistic pathways of this process. PMID:24736839

Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria.

PubMed

Domínguez-Escobar, Julia; Chastanet, Arnaud; Crevenna, Alvaro H; Fromion, Vincent; Wedlich-Söldner, Roland; Carballido-López, Rut

2011-07-08

The peptidoglycan cell wall and the actin-like MreB cytoskeleton are major determinants of cell shape in rod-shaped bacteria. The prevailing model postulates that helical, membrane-associated MreB filaments organize elongation-specific peptidoglycan-synthesizing complexes along sidewalls. We used total internal reflection fluorescence microscopy to visualize the dynamic relation between MreB isoforms and cell wall synthesis in live Bacillus subtilis cells. During exponential growth, MreB proteins did not form helical structures. Instead, together with other morphogenetic factors, they assembled into discrete patches that moved processively along peripheral tracks perpendicular to the cell axis. Patch motility was largely powered by cell wall synthesis, and MreB polymers restricted diffusion of patch components in the membrane and oriented patch motion.

Bu-2470, a new peptide antibiotic complex. I. Production, isolation and properties of Bu-2470 A, B1 and B2.

PubMed

Konishi, M; Sugawara, K; Tomita, K; Matsumoto, K; Miyaki, T; Fujisawa, K; Tsukiura, H; Kawaguchi, H

1983-06-01

A strain of Bacillus circulans produced a complex of basic peptide antibiotics designated Bu-2470, which was found to contain four active components, A, B1, B2a and B2b. Bu-2470 A specifically inhibited various Pseudomonas species including P. aeruginosa, P. maltophilia and P. putida, but otherwise its antibacterial spectrum was limited to certain Gram-negative organisms. Bu-2470 B1 and B2 (B2a + B2b) showed broad antibiotic activity against Gram-positive and Gram-negative bacteria including Pseudomonas species. The physicochemical and biological properties of Bu-2470 B1 and B2 are very similar to those of the octapeptin group of antibiotics.

Intelligent Agent Architectures: Reactive Planning Testbed

NASA Technical Reports Server (NTRS)

Rosenschein, Stanley J.; Kahn, Philip

1993-01-01

An Integrated Agent Architecture (IAA) is a framework or paradigm for constructing intelligent agents. Intelligent agents are collections of sensors, computers, and effectors that interact with their environments in real time in goal-directed ways. Because of the complexity involved in designing intelligent agents, it has been found useful to approach the construction of agents with some organizing principle, theory, or paradigm that gives shape to the agent's components and structures their relationships. Given the wide variety of approaches being taken in the field, the question naturally arises: Is there a way to compare and evaluate these approaches? The purpose of the present work is to develop common benchmark tasks and evaluation metrics to which intelligent agents, including complex robotic agents, constructed using various architectural approaches can be subjected.

Alternative cytoskeletal landscapes: cytoskeletal novelty and evolution in basal excavate protists

PubMed Central

Dawson, Scott C.; Paredez, Alexander R.

2016-01-01

Microbial eukaryotes encompass the majority of eukaryotic evolutionary and cytoskeletal diversity. The cytoskeletal complexity observed in multicellular organisms appears to be an expansion of components present in genomes of diverse microbial eukaryotes such as the basal lineage of flagellates, the Excavata. Excavate protists have complex and diverse cytoskeletal architectures and life cycles – essentially alternative cytoskeletal “landscapes” – yet still possess conserved microtubule- and actin-associated proteins. Comparative genomic analyses have revealed that a subset of excavates, however, lack many canonical actin-binding proteins central to actin cytoskeleton function in other eukaryotes. Overall, excavates possess numerous uncharacterized and “hypothetical” genes, and may represent an undiscovered reservoir of novel cytoskeletal genes and cytoskeletal mechanisms. The continued development of molecular genetic tools in these complex microbial eukaryotes will undoubtedly contribute to our overall understanding of cytoskeletal diversity and evolution. PMID:23312067

Deciphering the complexity of acute inflammation using mathematical models.

PubMed

Vodovotz, Yoram

2006-01-01

Various stresses elicit an acute, complex inflammatory response, leading to healing but sometimes also to organ dysfunction and death. We constructed both equation-based models (EBM) and agent-based models (ABM) of various degrees of granularity--which encompass the dynamics of relevant cells, cytokines, and the resulting global tissue dysfunction--in order to begin to unravel these inflammatory interactions. The EBMs describe and predict various features of septic shock and trauma/hemorrhage (including the response to anthrax, preconditioning phenomena, and irreversible hemorrhage) and were used to simulate anti-inflammatory strategies in clinical trials. The ABMs that describe the interrelationship between inflammation and wound healing yielded insights into intestinal healing in necrotizing enterocolitis, vocal fold healing during phonotrauma, and skin healing in the setting of diabetic foot ulcers. Modeling may help in understanding the complex interactions among the components of inflammation and response to stress, and therefore aid in the development of novel therapies and diagnostics.

Evolution and development of brain networks: from Caenorhabditis elegans to Homo sapiens.

PubMed

Kaiser, Marcus; Varier, Sreedevi

2011-01-01

Neural networks show a progressive increase in complexity during the time course of evolution. From diffuse nerve nets in Cnidaria to modular, hierarchical systems in macaque and humans, there is a gradual shift from simple processes involving a limited amount of tasks and modalities to complex functional and behavioral processing integrating different kinds of information from highly specialized tissue. However, studies in a range of species suggest that fundamental similarities, in spatial and topological features as well as in developmental mechanisms for network formation, are retained across evolution. 'Small-world' topology and highly connected regions (hubs) are prevalent across the evolutionary scale, ensuring efficient processing and resilience to internal (e.g. lesions) and external (e.g. environment) changes. Furthermore, in most species, even the establishment of hubs, long-range connections linking distant components, and a modular organization, relies on similar mechanisms. In conclusion, evolutionary divergence leads to greater complexity while following essential developmental constraints.

INTERRELATION BETWEEN ACTIVATION AND POLYMERIZATION IN GRAMICIDIN S BIOSYNTHESIS*

PubMed Central

Kleinkauf, Horst; Gevers, Wieland; Lipmann, Fritz

1969-01-01

The nucleic acid-independent biosynthesis of the peptide antibiotic gramicidin S results from the interaction of an enzyme bearing phenylalanine in activated form with a polyenzyme system charged with the other four component amino acids. After reaction with ATP, magnesium, and any or all of its amino acid substrates, the polyenzyme system (mol wt 280,000) yields complexes containing AMP and the respective amino acids in the proportion of 1 to 2. Similar complexes are formed by another enzyme (mol wt 100,000) on incubation with ATP, magnesium, and L- or D-phenylalanine. The amino acids are probably bound as aminoacyl adenylates and then transferred to another function on the enzyme. Initiation of polymerization is achieved by combination of the two complexes. No ATP is needed for completion of synthesis, and free intermediates are not released. Enzyme organization and specificity are responsible for the ordering of the amino acid sequence. PMID:5253659

Hydrosoluble Cu(i)-DAPTA complexes: synthesis, characterization, luminescence thermochromism and catalytic activity for microwave-assisted three-component azide-alkyne cycloaddition click reaction.

PubMed

Mahmoud, Abdallah G; Guedes da Silva, M Fátima C; Sokolnicki, Jerzy; Smoleński, Piotr; Pombeiro, Armando J L

2018-05-16

New hydrosoluble and air-stable Cu(i) halide compounds, viz. [CuX(DAPTA)3] (1) and (2), and [Cu(μ-X)(DAPTA)2]2 (3) and (4) (X = Br or I, in this order), have been prepared by reacting Cu(i) halide (i.e., bromide or iodide) with 3,7-diacetyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane (DAPTA) under mild conditions. They represent the first examples of Cu(i) halide complexes bearing the DAPTA ligand, which have been fully characterized by elemental analysis, IR, 1H, 13C{1H} and 31P{1H} NMR spectroscopies, ESI-MS+ and, for 4, also by single-crystal X-ray diffraction (SCXRD) analyses. Complexes 1-4 are efficient catalysts for the one-pot microwave assisted three-component (terminal alkyne, organic halide and NaN3) Huisgen cycloaddition reaction in aqueous media to afford the corresponding disubstituted triazoles. The catalysis proceeds with a broad alkyne substrate scope and according to "click rules". Photophysical studies of compound 4 showed an unusual reversible thermochromic behaviour exhibiting a blue emission at 298 K due to the halide-to-ligand charge transfer (3XLCT) and a red emission at 77 K because of the {Cu2I2} unit.

Speciation and distribution of cadmium and lead in salinized horizons of antrosols

NASA Astrophysics Data System (ADS)

Bulgariu, D.; Bulgariu, L.; Astefanei, D.

2009-04-01

The utilization of intensive technologies for the vegetable cultivation in glass houses by the administration of high doses of organic fertilizes, the supra-dimensional irrigation and the maintaining of soil at high humidity state, in special in case of vicious drainage have as result the rapid degradation of morphological, chemical and physical characteristics of soils, concretized by: (i) decrease of structural aggregates stability; (ii) more dense packing of soil; (iii) accumulation of easy soluble salts (in special at superior horizons level); (iv) limitation of organic compounds and micro-elements biodisponibility. All these determined a significant reduction of productivity and of exploitation duration of soils from glass houses. These phenomena modified continuously the dynamic of speciation processes and inter-phases distribution, of heavy metals in soils from glass houses, and can determined a non-controlled accumulation of heavy metals, in special as mobile forms with high biodisponibility. Ours studied have been performed using soil profiles drawing from Copou-glass house, Iasi (Romania). Has been followed the modification of distribution for speciation forms of cadmium and lead (two heavy metals with high toxicity degree), between hortic antrosol horizons, and between chemical-mineralogical components of this, with the progressive salinization of superior horizons, in 2007-2008 period. The separation, differentiation and determination of cadmium and lead speciation forms was done by combined solid-liquid sequential extraction (SPE) and extraction in aqueous polymer-inorganic salt two-phase systems (ABS) procedure, presented in some of ours previous studies. After extraction, the total contents of the two heavy metals and fractions from these differential bonded by mineral and organic components of hortic antrosol have been determined by atomic absorption spectrometry. The specific interaction mechanisms of Cd and Pb with organic-mineral components of soils have been estimated on the basis of Raman and FT-IR spectra, recorded for fractions obtained after each extraction step. These data were correlated with those obtained by chemical analysis and UV-VIS spectrometry, and were used for to establish the type and weight of Cd and Pb speciation forms in studied antrosol. Our studies have been show that in medium and inferior horizons of hortic antrosols, the heavy metals have a general accumulation tendency, preferential by binding on organic matter and organic-mineral complexes, components with higher abundance in such type of soils. The selectivity and complexation mechanisms are controlled by speciation forms of the two metals. This phenomenon has two important consequences, the strong fixation of heavy metals in hortic antrosol and significant modification of structure and conformation of organic macromolecules. A specific phenomenon of hortic antrosols is that the accumulation rate of heavy metals is higher than levigation rate, and the mobile forms of these have a higher biodisponibility, being relative easy assimilated by plants. The progressive salinization of superior horizons of soils from glass houses, determined a sever perturbation of equilibrium between Cd and Pb speciation forms. In consequence these will have an accentuated migration tendency in superior horizons, as complexes with inorganic ligands, with a high mobility and biodsiponibility. The accumulation of soluble salts in superior horizons, and the formation of frangipane horizon (horizon of geochemical segregation of hortic antrosols) modified the ionic strength from soil solution and the thermodynamic activity of cadmium and lead species. Under these conditions, the levigation rate of cadmium and lead is higher than the accumulation rate, which means that the migration of these metals in soil solution occurs fast and in high concentrations. Acknowledgments The authors would like to acknowledge the financial support from Romanian Ministry of Education and Research (Project PNCDI 2-D5 no. 51045/07 an Project PNCDI 2-D5 no. 52141 / 08).

Evaluation of microbial transformations of dissolved organic matter - what information can be extracted from high-field FTICR-MS elemental formula data sets?

NASA Astrophysics Data System (ADS)

Herzsprung, Peter; von Tümpling, Wolf; Harir, Mourad; Hertkorn, Norbert; Schmitt-Kopplin, Philippe; Norf, Helge; Weitere, Markus; Kamjunke, Norbert

2017-04-01

Transformation of DOC and DOM was and is widespread investigated (1-3). Due to the complex composition of DOC increased attention was payed to DOM quality change during degradation processes. In order to get a better insight in DOM transformation processes both resolution as a function of time and on a molecular level are promising. The observation of DOM quality changes requires sophisticated evaluation techniques. A new evaluation strategy of FTICR-MS elemental formula data sets is introduced. An experiment with seven flumes and leaf leachate was performed. All flumes were sampled on five dates (within 7 days) and the SPEDOM was characterized using high-field FTICR-MS analysis, resulting in together 35 elemental formula data sets. The time dependent change of components abundance was fitted by a simple linear regression model after normalization of mass peak intensities. All components were categorized by calculation of the slope (change of percent intensity per day) in all seven flumes. A positive slope means product formation, a negative slope means degradation of components. Specific data filtration was developed to find out components with relevant change of relative intensity. About 7000 different components were present in at least one of the 35 samples. Of those about 1800 components were present in all of the 35 samples. About 300 components with significant increase of intensity were identified. They were mainly unsaturated and oxygen-rich components (lignin-like or tannin-like) and had molecular masses less than 450 Dalton. A group of about 70 components was partially degraded (significant negative slope, present in all samples). These components were more saturated and less oxygen-rich compared to the product group and had molecular masses > 450 Dalton. A third group of about 150 components was identified with a tendency to total degradation (significant negative slope, not present in all samples, reduced or no abundance at the end of the experiment). They were highly saturated and oxygen-poor (lipid-like). As a conclusion components of biogeochemical groups (specified by their H/C and O/C coordinates in Van Krevelen diagrams) can be allocated to DOM transformation processes by their tendency of intensity change. References 1) Lechtenfeld, O.J., Kattner, G., Flerus, R., McCallister, S.L., Schmitt-Kopplin, P., Koch, B.P., 2014. Molecular transformation and degradation of refractory dissolved organic matter in the Atlantic and Southern Ocean. Geochim. Cosmochim. Acta 126, 321-337. 2) Morling, K., Herzsprung, P., Kamjunke, N., 2017. Discharge determines production of, decomposition of and quality changes in dissolved organic carbon in pre-dams of drinking water reservoirs. Sci. Tot. Environ. 577, 329-339. 3) Ohno, T., Parr, T.B., Gruselle, M.C.I., Fernandez, I.J., Sleighter, R.L., Hatcher, P.G., 2014. Molecular Composition and Biodegradability of Soil Organic Matter: A Case Study Comparing Two New England Forest Types. Environ. Sci. Technol. 48, 7229 - 7236.

12 CFR 502.27 - How does OTS determine the risk/complexity component for a savings and loan holding company?

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false How does OTS determine the risk/complexity...-Calculation of Assessments § 502.27 How does OTS determine the risk/complexity component for a savings and loan holding company? (a) OTS computes the risk/complexity component for responsible savings and loan...

Physiologically Distributed Loading Patterns Drive the Formation of Zonally Organized Collagen Structures in Tissue-Engineered Meniscus.

PubMed

Puetzer, Jennifer L; Bonassar, Lawrence J

2016-07-01

The meniscus is a dense fibrocartilage tissue that withstands the complex loads of the knee via a unique organization of collagen fibers. Attempts to condition engineered menisci with compression or tensile loading alone have failed to reproduce complex structure on the microscale or anatomic scale. Here we show that axial loading of anatomically shaped tissue-engineered meniscus constructs produced spatial distributions of local strain similar to those seen in the meniscus when the knee is loaded at full extension. Such loading drove formation of tissue with large organized collagen fibers, levels of mechanical anisotropy, and compressive moduli that match native tissue. Loading accelerated the development of native-sized and aligned circumferential and radial collagen fibers. These loading patterns contained both tensile and compressive components that enhanced the major biochemical and functional properties of the meniscus, with loading significantly improved glycosaminoglycan (GAG) accumulation 200-250%, collagen accumulation 40-55%, equilibrium modulus 1000-1800%, and tensile moduli 500-1200% (radial and circumferential). Furthermore, this study demonstrates local changes in mechanical environment drive heterogeneous tissue development and organization within individual constructs, highlighting the importance of recapitulating native loading environments. Loaded menisci developed cartilage-like tissue with rounded cells, a dense collagen matrix, and increased GAG accumulation in the more compressively loaded horns, and fibrous collagen-rich tissue in the more tensile loaded outer 2/3, similar to native menisci. Loaded constructs reached a level of organization not seen in any previous engineered menisci and demonstrate great promise as meniscal replacements.

Self-assembly micro optical filter

NASA Astrophysics Data System (ADS)

Zhang, Ping (Cerina); Le, Kevin; Malalur-Nagaraja-Rao, Smitha; Hsu, Lun-Chen; Chiao, J.-C.

2006-01-01

Optical communication and sensor industry face critical challenges in manufacturing for system integration. Due to the assembly complexity and integration platform variety, micro optical components require costly alignment and assembly procedures, in which many required manual efforts. Consequently, self-assembly device architectures have become a great interest and could provide major advantages over the conventional optical devices. In this paper, we discussed a self-assembly integration platform for micro optical components. To demonstrate the adaptability and flexibility of the proposed optical device architectures, we chose a commercially available MEMS fabrication foundry service - MUMPs (Multi-User MEMS Process). In this work, polysilicon layers of MUMPS are used as the 3-D structural material for construction of micro component framework and actuators. However, because the polysilicon has high absorption in the visible and near infrared wavelength ranges, it is not suitable for optical interaction. To demonstrate the required optical performance, hybrid integration of materials was proposed and implemented. Organic compound materials were applied on the silicon-based framework to form the required optical interfaces. Organic compounds provide good optical transparency, flexibility to form filters or lens and inexpensive manufacturing procedures. In this paper, we have demonstrated a micro optical filter integrated with self-assembly structures. We will discuss the self-assembly mechanism, optical filter designs, fabrication issues and results.

Sorptive fractionation of organic matter and formation of organo-hydroxy-aluminum complexes during litter biodegradation in the presence of gibbsite

NASA Astrophysics Data System (ADS)

Heckman, K.; Grandy, A. S.; Gao, X.; Keiluweit, M.; Wickings, K.; Carpenter, K.; Chorover, J.; Rasmussen, C.

2013-11-01

Solid and aqueous phase Al species are recognized to affect organic matter (OM) stabilization in forest soils. However, little is known about the dynamics of formation, composition and dissolution of organo-Al hydroxide complexes in microbially-active soil systems, where plant litter is subject to microbial decomposition in close proximity to mineral weathering reactions. We incubated gibbsite-quartz mineral mixtures in the presence of forest floor material inoculated with a native microbial consortium for periods of 5, 60 and 154 days. At each time step, samples were density separated into light (<1.6 g cm-3), intermediate (1.6-2.0 g cm-3), and heavy (>2.0 g cm-3) fractions. The light fraction was mainly comprised of particulate organic matter, while the intermediate and heavy density fractions contained moderate and large amounts of Al-minerals, respectively. Multi-method interrogation of the fractions indicated the intermediate and heavy fractions differed both in mineral structure and organic compound composition. X-ray diffraction analysis and SEM/EDS of the mineral component of the intermediate fractions indicated some alteration of the original gibbsite structure into less crystalline Al hydroxide and possibly proto-imogolite species, whereas alteration of the gibbsite structure was not evident in the heavy fraction. DRIFT, Py-GC/MS and STXM/NEXAFS results all showed that intermediate fractions were composed mostly of lignin-derived compounds, phenolics, and polysaccharides. Heavy fraction organics were dominated by polysaccharides, and were enriched in proteins, N-bearing compounds, and lipids. The source of organics appeared to differ between the intermediate and heavy fractions. Heavy fractions were enriched in 13C with lower C/N ratios relative to intermediate fractions, suggesting a microbial origin. The observed differential fractionation of organics among hydroxy-Al mineral types suggests that microbial activity superimposed with abiotic mineral-surface-mediated fractionation leads to strong density differentiation of organo-mineral complex composition even over the short time scales probed in these incubation experiments. The data highlight the strong interdependency of mineral transformation, microbial community activity, and organic matter stabilization during biodegradation.

Classifying organic materials by oxygen-to-carbon elemental ratio to predict the activation regime of cloud condensation nuclei (CCN)

NASA Astrophysics Data System (ADS)

Kuwata, M.; Shao, W.; Lebouteiller, R.; Martin, S. T.

2012-12-01

The governing highly soluble, slightly soluble, or insoluble activation regime of organic compounds as cloud condensation nuclei (CCN) was examined as a function of oxygen-to-carbon elemental ratio (O : C). New data were collected for adipic, pimelic, suberic, azelaic and pinonic acids. Secondary organic materials (SOMs) produced by α-pinene ozonolysis and isoprene photo-oxidation were also included in the analysis. The saturation concentrations C of the organic compounds in aqueous solutions served as the key parameter for delineating regimes of CCN activation, and the values of C were tightly correlated to the O : C ratios. The highly soluble, slightly soluble, and insoluble regimes of CCN activation were found to correspond to ranges of [O : C] > 0.6, 0.2 < [O : C] < 0.6, and [O : C] < 0.2, respectively. These classifications were evaluated against CCN activation data of isoprene-derived SOM (O : C = 0.69-0.72) and α-pinene-derived SOM (O : C = 0.38-0.48). Isoprene-derived SOM had highly soluble activation behavior, consistent with its high O : C ratio. For α-pinene-derived SOM, although CCN activation can be modeled as a highly soluble mechanism, this behavior was not predicted by the O : C ratio, for which a slightly soluble mechanism was anticipated. Complexity in chemical composition, resulting in continuous water uptake and the absence of a deliquescence transition that can thermodynamically limit CCN activation, might explain the differences of α-pinene-derived SOM compared to the behavior of pure organic compounds. The present results suggest that atmospheric particles dominated by hydrocarbon-like organic components do not activate (i.e. insoluble regime) whereas those dominated by oxygenated organic components activate (i.e. highly soluble regime).

Classifying organic materials by oxygen-to-carbon elemental ratio to predict the activation regime of Cloud Condensation Nuclei (CCN)

NASA Astrophysics Data System (ADS)

Kuwata, M.; Shao, W.; Lebouteiller, R.; Martin, S. T.

2013-05-01

The governing highly soluble, slightly soluble, or insoluble activation regime of organic compounds as cloud condensation nuclei (CCN) was examined as a function of oxygen-to-carbon elemental ratio (O : C). New data were collected for adipic, pimelic, suberic, azelaic, and pinonic acids. Secondary organic materials (SOMs) produced by α-pinene ozonolysis and isoprene photo-oxidation were also included in the analysis. The saturation concentrations C of the organic compounds in aqueous solutions served as the key parameter for delineating regimes of CCN activation, and the values of C were tightly correlated to the O : C ratios. The highly soluble, slightly soluble, and insoluble regimes of CCN activation were found to correspond to ranges of [O : C] > 0.6, 0.2 < [O : C] < 0.6, and [O : C] < 0.2, respectively. These classifications were evaluated against CCN activation data of isoprene-derived SOM (O : C = 0.69-0.72) and α-pinene-derived SOM (O : C = 0.38-0.48). Isoprene-derived SOM had highly soluble activation behavior, consistent with its high O : C ratio. For α-pinene-derived SOM, although CCN activation can be modeled as a highly soluble mechanism, this behavior was not predicted by the O : C ratio, for which a slightly soluble mechanism was anticipated. Complexity in chemical composition, resulting in continuous water uptake and the absence of a deliquescence transition that can thermodynamically limit CCN activation, might explain the difference in the behavior of α-pinene-derived SOM compared to that of pure organic compounds. The present results suggest that atmospheric particles dominated by hydrocarbon-like organic components do not activate (i.e., insoluble regime) whereas those dominated by oxygenated organic components activate (i.e., highly soluble regime) for typical atmospheric cloud life cycles.

Centromere Protein (CENP)-W Interacts with Heterogeneous Nuclear Ribonucleoprotein (hnRNP) U and May Contribute to Kinetochore-Microtubule Attachment in Mitotic Cells

PubMed Central

Chun, Younghwa; Kim, Raehyung; Lee, Soojin

2016-01-01

Background Recent studies have shown that heterogeneous nuclear ribonucleoprotein U (hnRNP U), a component of the hnRNP complex, contributes to stabilize the kinetochore-microtubule interaction during mitosis. CENP-W was identified as an inner centromere component that plays crucial roles in the formation of a functional kinetochore complex. Results We report that hnRNP U interacts with CENP-W, and the interaction between hnRNP U and CENP-W mutually increased each other’s protein stability by inhibiting the proteasome-mediated degradation. Further, their co-localization was observed chiefly in the nuclear matrix region and at the microtubule-kinetochore interface during interphase and mitosis, respectively. Both microtubule-stabilizing and microtubule-destabilizing agents significantly decreased the protein stability of CENP-W. Furthermore, loss of microtubules and defects in microtubule organization were observed in CENP-W-depleted cells. Conclusion Our data imply that CENP-W plays an important role in the attachment and interaction between microtubules and kinetochore during mitosis. PMID:26881882

Genotype evaluation of cowpea seeds (Vigna unguiculata) using 1H qNMR combined with exploratory tools and solid-state NMR.

PubMed

Alves Filho, Elenilson G; Silva, Lorena M A; Teofilo, Elizita M; Larsen, Flemming H; de Brito, Edy S

2017-01-01

The ultimate aim of this study was to apply a non-targeted chemometric analysis (principal component analysis and hierarchical clustering analysis using the heat map approach) of NMR data to investigate the variability of organic compounds in nine genotype cowpea seeds, without any complex pre-treatment. In general, both exploratory tools show that Tvu 233, CE-584, and Setentão genotypes presented higher amount mainly of raffinose and Tvu 382 presented the highest content of choline and least content of raffinose. The evaluation of the aromatic region showed the Setentão genotype with highest content of niacin/vitamin B3 whereas Tvu 382 with lowest amount. To investigate rigid and mobile components in the seeds cotyledon, 13 C CP and SP/MAS solid-state NMR experiments were performed. The cotyledon of the cowpea comprised a rigid part consisting of starch as well as a soft portion made of starch, fatty acids, and protein. The variable contact time experiment suggests the presence of lipid-amylose complexes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Between “design” and “bricolage”: Genetic networks, levels of selection, and adaptive evolution

PubMed Central

Wilkins, Adam S.

2007-01-01

The extent to which “developmental constraints” in complex organisms restrict evolutionary directions remains contentious. Yet, other forms of internal constraint, which have received less attention, may also exist. It will be argued here that a set of partial constraints below the level of phenotypes, those involving genes and molecules, influences and channels the set of possible evolutionary trajectories. At the top-most organizational level there are the genetic network modules, whose operations directly underlie complex morphological traits. The properties of these network modules, however, have themselves been set by the evolutionary history of the component genes and their interactions. Characterization of the components, structures, and operational dynamics of specific genetic networks should lead to a better understanding not only of the morphological traits they underlie but of the biases that influence the directions of evolutionary change. Furthermore, such knowledge may permit assessment of the relative degrees of probability of short evolutionary trajectories, those on the microevolutionary scale. In effect, a “network perspective” may help transform evolutionary biology into a scientific enterprise with greater predictive capability than it has hitherto possessed. PMID:17494754

Between "design" and "bricolage": genetic networks, levels of selection, and adaptive evolution.

PubMed

Wilkins, Adam S

2007-05-15

The extent to which "developmental constraints" in complex organisms restrict evolutionary directions remains contentious. Yet, other forms of internal constraint, which have received less attention, may also exist. It will be argued here that a set of partial constraints below the level of phenotypes, those involving genes and molecules, influences and channels the set of possible evolutionary trajectories. At the top-most organizational level there are the genetic network modules, whose operations directly underlie complex morphological traits. The properties of these network modules, however, have themselves been set by the evolutionary history of the component genes and their interactions. Characterization of the components, structures, and operational dynamics of specific genetic networks should lead to a better understanding not only of the morphological traits they underlie but of the biases that influence the directions of evolutionary change. Furthermore, such knowledge may permit assessment of the relative degrees of probability of short evolutionary trajectories, those on the microevolutionary scale. In effect, a "network perspective" may help transform evolutionary biology into a scientific enterprise with greater predictive capability than it has hitherto possessed.

The Giardia cell cycle progresses independently of the anaphase-promoting complex

PubMed Central

Gourguechon, Stéphane; Holt, Liam J.; Cande, W. Zacheus

2013-01-01

Summary Most cell cycle regulation research has been conducted in model organisms representing a very small part of the eukaryotic domain. The highly divergent human pathogen Giardia intestinalis is ideal for studying the conservation of eukaryotic pathways. Although Giardia has many cell cycle regulatory components, its genome lacks all anaphase-promoting complex (APC) components. In the present study, we show that a single mitotic cyclin in Giardia is essential for progression into mitosis. Strikingly, Giardia cyclin B lacks the conserved N-terminal motif required for timely degradation mediated by the APC and ubiquitin conjugation. Expression of Giardia cyclin B in fission yeast is toxic, leading to a prophase arrest, and this toxicity is suppressed by the addition of a fission yeast degradation motif. Cyclin B is degraded during mitosis in Giardia cells, but this degradation appears to be independent of the ubiquitination pathway. Other putative APC substrates, aurora and polo-like kinases, also show no evidence of ubiquitination. This is the first example of mitosis not regulated by the APC and might reflect an evolutionary ancient form of cell cycle regulation. PMID:23525017

RiskChanges Spatial Decision Support system for the analysis of changing multi-hazard risk

NASA Astrophysics Data System (ADS)

van Westen, Cees; Zhang, Kaixi; Bakker, Wim; Andrejchenko, Vera; Berlin, Julian; Olyazadeh, Roya; Cristal, Irina

2015-04-01

Within the framework of the EU FP7 Marie Curie Project CHANGES and the EU FP7 Copernicus project INCREO a spatial decision support system was developed with the aim to analyse the effect of risk reduction planning alternatives on reducing the risk now and in the future, and support decision makers in selecting the best alternatives. Central to the SDSS are the stakeholders. The envisaged users of the system are organizations involved in planning of risk reduction measures, and that have staff capable of visualizing and analyzing spatial data at a municipal scale. The SDSS should be able to function in different countries with different legal frameworks and with organizations with different mandates. These could be subdivided into Civil protection organization with the mandate to design disaster response plans, Expert organizations with the mandate to design structural risk reduction measures (e.g. dams, dikes, check-dams etc), and planning organizations with the mandate to make land development plans. The SDSS can be used in different ways: analyzing the current level of risk, analyzing the best alternatives for risk reduction, the evaluation of the consequences of possible future scenarios to the risk levels, and the evaluation how different risk reduction alternatives will lead to risk reduction under different future scenarios. The SDSS is developed based on open source software and following open standards, for code as well as for data formats and service interfaces. Code development was based upon open source software as well. The architecture of the system is modular. The various parts of the system are loosely coupled, extensible, using standards for interoperability, flexible and web-based. The Spatial Decision Support System is composed of a number of integrated components. The Risk Assessment component allows to carry out spatial risk analysis, with different degrees of complexity, ranging from simple exposure (overlay of hazard and assets maps) to quantitative analysis (using different hazard types, temporal scenarios and vulnerability curves) resulting into risk curves. The platform does not include a component to calculate hazard maps, and existing hazard maps are used as input data for the risk component. The second component of the SDSS is a risk reduction planning component, which forms the core of the platform. This component includes the definition of risk reduction alternatives (related to disaster response planning, risk reduction measures and spatial planning) and links back to the risk assessment module to calculate the new level of risk if the measure is implemented, and a cost-benefit (or cost-effectiveness/ Spatial Multi Criteria Evaluation) component to compare the alternatives and make decision on the optimal one. The third component of the SDSS is a temporal scenario component, which allows to define future scenarios in terms of climate change, land use change and population change, and the time periods for which these scenarios will be made. The component doesn't generate these scenarios but uses input maps for the effect of the scenarios on the hazard and assets maps. The last component is a communication and visualization component, which can compare scenarios and alternatives, not only in the form of maps, but also in other forms (risk curves, tables, graphs)

Identification of the Mitochondrial Heme Metabolism Complex

PubMed Central

Medlock, Amy E.; Shiferaw, Mesafint T.; Marcero, Jason R.; Vashisht, Ajay A.; Wohlschlegel, James A.; Phillips, John D.; Dailey, Harry A.

2015-01-01

Heme is an essential cofactor for most organisms and all metazoans. While the individual enzymes involved in synthesis and utilization of heme are fairly well known, less is known about the intracellular trafficking of porphyrins and heme, or regulation of heme biosynthesis via protein complexes. To better understand this process we have undertaken a study of macromolecular assemblies associated with heme synthesis. Herein we have utilized mass spectrometry with coimmunoprecipitation of tagged enzymes of the heme biosynthetic pathway in a developing erythroid cell culture model to identify putative protein partners. The validity of these data obtained in the tagged protein system is confirmed by normal porphyrin/heme production by the engineered cells. Data obtained are consistent with the presence of a mitochondrial heme metabolism complex which minimally consists of ferrochelatase, protoporphyrinogen oxidase and aminolevulinic acid synthase-2. Additional proteins involved in iron and intermediary metabolism as well as mitochondrial transporters were identified as potential partners in this complex. The data are consistent with the known location of protein components and support a model of transient protein-protein interactions within a dynamic protein complex. PMID:26287972

The Adam and Eve story as exemplar of an early-life variant of the oedipus complex.

PubMed

Osman, M P

2000-01-01

The Adam and Eve story is construed as having an organizing function that facilitates the analytic understanding of certain patients. In this interpretation, the story epitomizes a psychodynamic in which progressive growth, with separation and individuation, of the young is experienced as perilous--not only to them, but also correspondingly to their procreators. In the myth, the increasing psychic and physical maturation of Adam and Eve produced a crisis. Not only was divine authority flouted, but also apprehensions were aroused that God might be humbled or diminished. This threatened him, evoking his wrath and leading to the punishment by abandonment of his youthful wards. It is suggested that the story depicts an emotional complex of widespread application and is an archaic version of the oedipus complex, continuous with the oedipus complex proper, but from an earlier stage of development. This archaic complex is delineated with clinical vignettes, and a clinical explication of its various components is provided. Clinical management is considered, particularly with reference to the challenge that a closed-system perspective (Fairbairn 1958) presents to a patient's development.

Interstellar grain chemistry and organic molecules

NASA Technical Reports Server (NTRS)

Allamandola, L. J.; Sandford, S. A.

1990-01-01

The detection of prominant infrared absorption bands at 3250, 2170, 2138, 1670 and 1470 cm(-1) (3.08, 4.61, 4.677, 5.99 and 6.80 micron m) associated with molecular clouds show that mixed molecular (icy) grain mantles are an important component of the interstellar dust in the dense interstellar medium. These ices, which contain many organic molecules, may also be the production site of the more complex organic grain mantles detected in the diffuse interstellar medium. Theoretical calculations employing gas phase as well as grain surface reactions predict that the ices should be dominated only by the simple molecules H2O, H2CO, N2, CO, O2, NH3, CH4, possibly CH3OH, and their deuterated counterparts. However, spectroscopic observations in the 2500 to 1250 cm(-1)(4 to 8 micron m) range show substantial variation from source reactions alone. By comparing these astronomical spectra with the spectra of laboratory-produced analogs of interstellar ices, one can determine the composition and abundance of the materials frozen on the grains in dense clouds. Experiments are described in which the chemical evolution of an interstellar ice analog is determined during irradiation and subsequent warm-up. Particular attention is paid to the types of moderately complex organic materials produced during these experiments which are likely to be present in interstellar grains and cometary ices.

Evidence for Extended Aqueous Alteration in CR Carbonaceous Chondrites

NASA Technical Reports Server (NTRS)

Trigo-Rodriquez, J. M.; Moyano-Cambero, C. E.; Mestres, N.; Fraxedas, J.; Zolensky, M.; Nakamura, T.; Martins, Z.

2013-01-01

We are currently studying the chemical interrelationships between the main rockforming components of carbonaceous chondrites (hereafter CC), e.g. silicate chondrules, refractory inclusions and metal grains, and the surrounding meteorite matrices. It is thought that the fine-grained materials that form CC matrices are representing samples of relatively unprocessed protoplanetary disk materials [1-3]. In fact, modern non-destructive analytical techniques have shown that CC matrices host a large diversity of stellar grains from many distinguishable stellar sources [4]. Aqueous alteration has played a role in homogeneizing the isotopic content that allows the identification of presolar grains [5]. On the other hand, detailed analytical techniques have found that the aqueously-altered CR, CM and CI chondrite groups contain matrices in which the organic matter has experienced significant processing concomitant to the formation of clays and other minerals. In this sense, clays have been found to be directly associated with complex organics [6, 7]. CR chondrites are particularly relevant in this context as this chondrite group contains abundant metal grains in the interstitial matrix, and inside glassy silicate chondrules. It is important because CR are known for exhibiting a large complexity of organic compounds [8-10], and only metallic Fe is considered essential in Fischer-Tropsch catalysis of organics [11-13]. Therefore, CR chondrites can be considered primitive materials capable to provide clues on the role played by aqueous alteration in the chemical evolution of their parent asteroids.

Use of grape seed and its natural polyphenol extracts as a natural organic coagulant for removal of cationic dyes.

PubMed

Jeon, Jong-Rok; Kim, Eun-Ju; Kim, Young-Mo; Murugesan, Kumarasamy; Kim, Jae-Hwan; Chang, Yoon-Seok

2009-11-01

Natural organic coagulants (NOCs) such as chitosan and Moringa oleifera seeds have been extensively characterized for potential application in water treatment as an alternative to metal-based coagulants. However, the action of both chitosan and M. oleifera seeds is mainly restricted to anionic organic pollutants because of their cationic functional groups affording poor cationic pollutant coagulation by electrostatic repulsion. In this study, we employed ethanolic grape seed extract (GSE) and grape seed-derived polyphenols such as tannic acid and catechin in an effort to find novel NOCs showing stable anionic forms for removal of cationic organic pollutants. The target substances tested were malachite green (MG) and crystal violet (CV), both mutagenic cationic dyes. Polyphenol treatment induced fast decolorization followed by gradual floc formation concomitant with red or blue shifts in maximum absorbance wavelengths of the cationic dyes. Liquid chromatography analysis of flocs formed by polyphenols directly showed that initial supramolecular complexes attributed mainly to electrostatic attraction between polyphenol hydroxyphenyl groups and cationic dyes further progressed into stronger aggregates, leading to precipitation of dye-polyphenol complexes. Consistent with the results obtained using catechin and tannic acid, use of GSE also resulted in effective decolorization and coagulation of soluble MG and CV in aqueous solutions. Screening of several organic GSE components for NOC activity strongly suggested that natural polyphenols are the main organic ingredients causing MG and CV removal via gradual floc formation. The treatment by natural polyphenols and GSE decreased toxicity of MG- or CV-contaminated water.

Coordination of flower development by homeotic master regulators.

PubMed

Ito, Toshiro

2011-02-01

Floral homeotic genes encode transcription factors and act as master regulators of flower development. The homeotic protein complex is expressed in a specific whorl of the floral primordium and determines floral organ identity by the combinatorial action. Homeotic proteins continue to be expressed until late in flower development to coordinate growth and organogenesis. Recent genomic studies have shown that homeotic proteins bind thousands of target sites in the genome and regulate the expression of transcription factors, chromatin components and various proteins involved in hormone biosynthesis and signaling and other physiological activities. Further, homeotic proteins program chromatin to direct the developmental coordination of stem cell maintenance and differentiation in shaping floral organs. Copyright © 2010 Elsevier Ltd. All rights reserved.

[Effect of Charge-Transfer Complex on Ultraviolet-Visible (UV-Vis) Absorption Property of Chromophoric Dissolved Organic Matter (CDOM) in Waters of Typical Water-Level Fluctuation Zones of the Three Gorges Reservoir Areas].

PubMed

Jiang, Tao; Liang, Jian; Zhang, Mu-xue; Wang, Ding-yong; Wei, Shi-qiang; Lu, Song

2016-02-15

As an important fraction of dissolved organic matter (DOM), chromophoric dissolved organic matter (CDOM) plays a key role in decision of the optical properties and photogeochemistry of DOM, and further affects pollutant fate and global carbon cycle. These optical properties are ascribed to two chromophoric systems including superposition of individual chromophores and charge-transfer (CT) complexation between electron donor (e.g., phenols and indoles) and acceptor (e.g., quinones and other oxidized aromatics) in DOM structures. Thus in this study, based on the "double-chromophoric system" model, DOM samples from four typical water-level fluctuation zones of Three Gorges Reservoir (TGR) areas were selected, to investigate the effect and contribution of charge-transfer complex to ultraviolet-visible (UV-Vis) absorption property of CDOM. Using NaBH, reduction method, original featureless absorption curve was classified into two independent curves caused by individual chromophoric group, which were derived from a simple superposition of independent chromophore and charge-transfer complex, respectively. Also, the changes in curve properties and specific parameters before and after NaBH4 reduction were compared. The results showed that in all DOM samples from the four sites of TGR, more than 35% of absorption was attributed from CT complex. Shibaozhai of Zhongxian and Zhenxi of Fuling showed the highest proportion ( > 50%). It suggested that the role of CT complex in CDOM property could not be neglected. After removal of CT complex, absorption curve showed blue-shift and CDOM concentration [a (355)] decreased significantly. Meanwhile, because of deforming of bonds by reduction, DOM structures became more dispersive and the molecular size was decreased, resulting in the lower spectral slope (S) observed, which evidentially supported that the supermolecular association structure of DOM was self-assembled through CT complex. Meanwhile, deceasing hydrophobic components led to decreased apparent aromaticity (lower SUVA values), whereas specific parameters including SUVA, CDOM and SR still were applicable for comparison among different DOM samples instead of the same sample without consideration of "double-cbromopboric system" model involving tbe role of CT complex. Comparatively, S(275-295) was dynamic due to tbe impact of CT effect. Furtbermore, establisbing DOC estimation model by short-wavelength range of CDOM was recommended because of its stability despite of CT complex.

Causality, randomness, intelligibility, and the epistemology of the cell.

PubMed

Dougherty, Edward R; Bittner, Michael L

2010-06-01

Because the basic unit of biology is the cell, biological knowledge is rooted in the epistemology of the cell, and because life is the salient characteristic of the cell, its epistemology must be centered on its livingness, not its constituent components. The organization and regulation of these components in the pursuit of life constitute the fundamental nature of the cell. Thus, regulation sits at the heart of biological knowledge of the cell and the extraordinary complexity of this regulation conditions the kind of knowledge that can be obtained, in particular, the representation and intelligibility of that knowledge. This paper is essentially split into two parts. The first part discusses the inadequacy of everyday intelligibility and intuition in science and the consequent need for scientific theories to be expressed mathematically without appeal to commonsense categories of understanding, such as causality. Having set the backdrop, the second part addresses biological knowledge. It briefly reviews modern scientific epistemology from a general perspective and then turns to the epistemology of the cell. In analogy with a multi-faceted factory, the cell utilizes a highly parallel distributed control system to maintain its organization and regulate its dynamical operation in the face of both internal and external changes. Hence, scientific knowledge is constituted by the mathematics of stochastic dynamical systems, which model the overall relational structure of the cell and how these structures evolve over time, stochasticity being a consequence of the need to ignore a large number of factors while modeling relatively few in an extremely complex environment.

The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling

PubMed Central

Schaap, Pauline; Barrantes, Israel; Minx, Pat; Sasaki, Narie; Anderson, Roger W.; Bénard, Marianne; Biggar, Kyle K.; Buchler, Nicolas E.; Bundschuh, Ralf; Chen, Xiao; Fronick, Catrina; Fulton, Lucinda; Golderer, Georg; Jahn, Niels; Knoop, Volker; Landweber, Laura F.; Maric, Chrystelle; Miller, Dennis; Noegel, Angelika A.; Peace, Rob; Pierron, Gérard; Sasaki, Taeko; Schallenberg-Rüdinger, Mareike; Schleicher, Michael; Singh, Reema; Spaller, Thomas; Storey, Kenneth B.; Suzuki, Takamasa; Tomlinson, Chad; Tyson, John J.; Warren, Wesley C.; Werner, Ernst R.; Werner-Felmayer, Gabriele; Wilson, Richard K.; Winckler, Thomas; Gott, Jonatha M.; Glöckner, Gernot; Marwan, Wolfgang

2016-01-01

Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer. PMID:26615215

In situ analysis of Bacillus licheniformis biofilms: amyloid-like polymers and eDNA are involved in the adherence and aggregation of the extracellular matrix.

PubMed

Randrianjatovo-Gbalou, I; Rouquette, P; Lefebvre, D; Girbal-Neuhauser, E; Marcato-Romain, C-E

2017-05-01

This study attempts to determine which of the exopolymeric substances are involved in the adherence and aggregation of a Bacillus licheniformis biofilm. The involvement of extracellular proteins and eDNA were particularly investigated using DNase and proteinase K treatment. The permeability of the biofilms increased fivefold after DNase I treatment. The quantification of the matrix components showed that, irrespective to the enzyme tested, eDNA and amyloid-like polymers were removed simultaneously. Size-exclusion chromatography analyses supported these observations and revealed the presence of associated nucleic acid and protein complexes in the biofilm lysates. These data suggest that some extracellular DNA and amyloid-like proteins were closely interlaced within the matrix. Finally, confocal laser scanning microscopy imaging gave supplementary clues about the 3D organization of the biofilms, confirming that eDNA and exoproteins were essentially layered under and around the bacterial cells, whereas the amyloid-like fractions were homogeneously distributed within the matrix. These results confirm that some DNA-amyloid complexes play a key role in the modulation of the mechanical resistance of B. licheniformis biofilms. The study highlights the need to consider the whole structure of biofilms and to target the interactions between matrix components. A better understanding of B. licheniformis biofilm physiology and the structural organization of the matrix will strengthen strategies of biofilm control. © 2017 The Society for Applied Microbiology.

Mass fraction assignment of folic acid in a high purity material

NASA Astrophysics Data System (ADS)

Westwood, Steven; Josephs, Ralf; Choteau, Tiphaine; Daireaux, Adeline; Stoppacher, Norbert; Wielgosz, Robert; Davies, Stephen; de Rego, Eliane; Wollinger, Wagner; Garrido, Bruno; Fernandes, Jane; Lima, Jonathan; Oliveira, Rodrigo; de Sena, Rodrigo; Windust, Anthony; Huang, Ting; Dai, Xinhua; Quan, Can; He, Haihong; Zhang, Wei; Wei, Chao; Li, Na; Gao, Dexin; Liu, Zhao; Lo, Man-fung; Wong, Wai-fun; Pfeifer, Dietmar; Koch, Matthias; Dorgerloh, Ute; Rothe, Robert; Philip, Rosemary; Hirari, Nobuyasu; Fazlin Rezali, Mohd; Salazar Arzate, Claudia Marcela; Pedraza Evelina Berenice, Mercado; Serrano Caballero, Victor; Arce Osuna, Mariana; Krylov, A.; Kharitonov, S.; Lopushanskaya, E.; Liu, Qinde; Tang Lin, Teo; Fernandes-Whaley, Maria; Quinn, Laura; Nhlapo, Nontete; Prevoo-Franzsen, Desiree; Archer, Marcelle; Kim, Byungjoo; Baek, Song-Yee; Lee, Sunyoung; Lee, Joonhee; Marbumrung, Sornkrit; Kankaew, Ponhatai; Chaorenpornpukdee, Kanokrat; Chaipet, Thitiphan; Shearman, Kittiya; Ceyhan Goren, Ahmet; Gunduz, Simay; Yilmaz, Hasibe; Un, Ilker; Bilsel, Gokhan; Clarkson, Cailean; Bedner, Mary; Camara, Johanna E.; Lang, Brian E.; Lippa, Katrice A.; Nelson, Michael A.; Toman, Blaza; Yu, Lee L.

2018-01-01

The comparison required the assignment of the mass fraction of folic acid present as the main component in the comparison sample. Performance in the comparison is representative of a laboratory's measurement capability for the purity assignment of organic compounds of medium structural complexity [molecular weight range 300–500] and high polarity (pKOW < ‑2). Methods used by the eighteen participating NMIs or DIs were based on a mass balance (summation of impurities) or qNMR approach, or the combination of data obtained using both methods. The qNMR results tended to give slightly lower values for the content of folic acid, albeit with larger associated uncertainties, compared with the results obtained by mass balance procedures. Possible reasons for this divergence are discussed in the report, without reaching a definitive conclusion as to their origin. The comparison demonstrates that for a structurally complex polar organic compound containing a high water content and presenting a number of additional analytical challenges, the assignment of the mass fraction content property value of the main component can reasonably be achieved with an associated relative standard uncertainty in the assigned value of 0.5% Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Generation and characterization of four dilutions of diesel engine exhaust for a subchronic inhalation study.

PubMed

McDonald, Jacob D; Barr, Edward B; White, Richard K; Chow, Judith C; Schauer, James J; Zielinska, Barbara; Grosjean, Eric

2004-05-01

Exposure atmospheres for a rodent inhalation toxicology study were generated from the exhaust of a 2000 Cummins ISB 5.9L diesel engine coupled to a dynamometer and operated on a slightly modified heavy-duty Federal Test Procedure cycle. Exposures were conducted to one clean air control and four diesel exhaust levels maintained at four different dilution rates (300:1, 100:1, 30:1, 10:1) that yielded particulate mass concentrations of 30, 100, 300, and 1000 microg/m3. Exposures at the four dilutions were characterized for particle mass, particle size distribution (reported elsewhere), detailed chemical speciation of gaseous, semivolatile, and particle-phase inorganic and organic compounds. Target analytes included metals, inorganic ions and gases, organic and elemental carbon, alkanes, alkenes, aromatic and aliphatic acids, aromatic hydrocarbons, polycyclic aromatic hydrocarbons (PAH), oxygenated PAH, nitrogenated PAH, isoprenoids, carbonyls, methoxyphenols, sugar derivatives, and sterols. The majority of the mass of material in the exposure atmospheres was gaseous nitrogen oxides and carbon monoxide, with lesser amounts of volatile organics and particle mass (PM) composed of carbon (approximately 90% of PM) and ions (approximately 10% of PM). Measured particle organic species accounted for about 10% of total organic particle mass and were mostly alkanes and aliphatic acids. Several of the components in the exposure atmosphere scaled in concentration with dilution but did not scale precisely with the dilution rate because of background from the rodents and scrubbed dilution air, interaction of animal derived emissions with diesel exhaust components, and day-to-day variability in the output of the engine. Rodent-derived ammonia reacted with exhaust to form secondary inorganic particles (at different rates dependent on dilution), and rodent respiration accounted for volatile organics (especially carbonyls and acids) in the same range as the diesel exhaust at the lowest exhaust exposure concentrations. Day-to-day variability in the engine output was implicated partially for differences of several components, including some of the particle bound organics. Though these observations have likely occurred in nearly all inhalation exposure atmospheres that contain complex mixtures of material, the speciations conducted here illustrate many of them for the first time.

Concept model of the formation process of humic acid-kaolin complexes deduced by trichloroethylene sorption experiments and various characterizations.

PubMed

Zhu, Xiaojing; He, Jiangtao; Su, Sihui; Zhang, Xiaoliang; Wang, Fei

2016-05-01

To explore the interactions between soil organic matter and minerals, humic acid (HA, as organic matter), kaolin (as a mineral component) and Ca(2+) (as metal ions) were used to prepare HA-kaolin and Ca-HA-kaolin complexes. These complexes were used in trichloroethylene (TCE) sorption experiments and various characterizations. Interactions between HA and kaolin during the formation of their complexes were confirmed by the obvious differences between the Qe (experimental sorbed TCE) and Qe_p (predicted sorbed TCE) values of all detected samples. The partition coefficient kd obtained for the different samples indicated that both the organic content (fom) and Ca(2+) could significantly impact the interactions. Based on experimental results and various characterizations, a concept model was developed. In the absence of Ca(2+), HA molecules first patched onto charged sites of kaolin surfaces, filling the pores. Subsequently, as the HA content increased and the first HA layer reached saturation, an outer layer of HA began to form, compressing the inner HA layer. As HA loading continued, the second layer reached saturation, such that an outer-third layer began to form, compressing the inner layers. In the presence of Ca(2+), which not only can promote kaolin self-aggregation but can also boost HA attachment to kaolin, HA molecules were first surrounded by kaolin. Subsequently, first and second layers formed (with inner layer compression) via the same process as described above in the absence of Ca(2+), except that the second layer continued to load rather than reach saturation, within the investigated conditions, because of enhanced HA aggregation caused by Ca(2+). Copyright © 2016 Elsevier Ltd. All rights reserved.

Fluorescence fingerprints and Cu2+-complexing ability of individual molecular size fractions in soil- and waste-borne DOM.

PubMed

Knoth de Zarruk, K; Scholer, G; Dudal, Y

2007-09-01

Land spreading of organic materials introduces large amounts of dissolved organic matter (DOM) into the soil. DOM has the ability to form stable complexes with heavy metals and can facilitate their transport towards the groundwater. The effects on soil processes are difficult to assess, because different DOM components might react differently towards metal ions. The objective of this study was to investigate the fluorescence signature and the Cu2+-binding capacity of individual molecular size fractions of DOM from various sources. DOM extracted from leaf compost, chicken manure, sugar cane vinasse and a fulvic hypercalcaric cambisol was fractionated by the means of dialysis into four molecular size classes: MW<500, 50012000-14000 Da. Vinasse and leaf compost contained around 80% and 70%, respectively, of the total organic carbon in the fractions with low molecular weight (MW<3500 Da); in chicken manure and soil these fractions accounted for 40% and 50% only. Fluorescence was highest in the fraction MW>12000 Da for leaf compost, chicken manure and soil. The opposite result was obtained for vinasse, where the fractions with low molecular weight showed highest fluorescence intensities, distinguishing it from all other samples. Vinasse showed the greatest ability to bind Cu2+ with a resulting complex concentration of 6.31mgl(-1) while in contact with an excess of Cu2+. Leaf compost, soil and chicken manure followed with 2.69, 1.12, and 0.85mgl(-1), respectively. Within vinasse, the fraction MW<500 Da was able to form the most DOM-Cu complexes, indicating the importance of low molecular weight fractions in metal binding.

Papillae formation on trichome cell walls requires the function of the mediator complex subunit Med25.

PubMed

Fornero, Christy; Suo, Bangxia; Zahde, Mais; Juveland, Katelyn; Kirik, Viktor

2017-11-01

Glassy Hair 1 (GLH1) gene that promotes papillae formation on trichome cell walls was identified as a subunit of the transcriptional mediator complex MED25. The MED25 gene is shown to be expressed in trichomes. The expression of the trichome development marker genes GLABRA2 (GL2) and Ethylene Receptor2 (ETR2) is not affected in the glh1 mutant. Presented data suggest that Arabidopsis MED25 mediator component is likely involved in the transcription of genes promoting papillae deposition in trichomes. The plant cell wall plays an important role in communication, defense, organization and support. The importance of each of these functions varies by cell type. Specialized cells, such as Arabidopsis trichomes, exhibit distinct cell wall characteristics including papillae. To better understand the molecular processes important for papillae deposition on the cell wall surface, we identified the GLASSY HAIR 1 (GLH1) gene, which is necessary for papillae formation. We found that a splice-site mutation in the component of the transcriptional mediator complex MED25 gene is responsible for the near papillae-less phenotype of the glh1 mutant. The MED25 gene is expressed in trichomes. Reporters for trichome developmental marker genes GLABRA2 (GL2) and Ethylene Receptor2 (ETR2) were not affected in the glh1 mutant. Collectively, the presented results show that MED25 is necessary for papillae formation on the cell wall surface of leaf trichomes and suggest that the Arabidopsis MED25 mediator component is likely involved in the transcription of a subset of genes that promote papillae deposition in trichomes.

16S rRNA analysis provides evidence of biofilms on all components of three infected periprosthetic knees including permanent braided suture.

PubMed

Swearingen, Matthew C; DiBartola, Alex C; Dusane, Devendra; Granger, Jeffrey; Stoodley, Paul

2016-10-01

Bacterial biofilms are the main etiological agent of periprosthetic joint infections (PJI); however, it is unclear if biofilms colonize one or multiple components. Because biofilms can colonize a variety of surfaces, we hypothesized that biofilms would be present on all components. 16S ribosomal RNA (rRNA) gene sequencing analysis was used to identify bacteria recovered from individual components and non-absorbable suture material recovered from three PJI total knee revision cases. Bray-Curtis non-metric multidimensional scaling analysis revealed no significant differences in similarity when factoring component, material type, or suture versus non-suture material, but did reveal significant differences in organism profile between patients (P < 0.001) and negative controls (P < 0.001). Confocal microscopy and a novel agar encasement culturing method also confirmed biofilm growth on a subset of components. While 16S sequencing suggested that the microbiology was more complex than revealed by culture contaminating, bacterial DNA generates a risk of false positives. This report highlights that biofilm bacteria may colonize all infected prosthetic components including braided suture material, and provides further evidence that clinical culture can fail to sufficiently identify the full pathogen profile in PJI cases. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Virtual enterprise model for the electronic components business in the Nuclear Weapons Complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferguson, T.J.; Long, K.S.; Sayre, J.A.

1994-08-01

The electronic components business within the Nuclear Weapons Complex spans organizational and Department of Energy contractor boundaries. An assessment of the current processes indicates a need for fundamentally changing the way electronic components are developed, procured, and manufactured. A model is provided based on a virtual enterprise that recognizes distinctive competencies within the Nuclear Weapons Complex and at the vendors. The model incorporates changes that reduce component delivery cycle time and improve cost effectiveness while delivering components of the appropriate quality.