Volcanic or Fluvial Channels on Ascraeus Mons: Focus on the Source Area of Sinuous Channels on the Southeast Rift Apron

NASA Technical Reports Server (NTRS)

Signorella, Julia D.; deWet, A.; Bleacher, J. E.; Collins, A.; Schierl, Z. P.; Schwans, B.

2012-01-01

Deciphering the Mars water history is important to understanding the planet's geological evolution and whether it could have sustained life. Channel features on Mars, such as the features documented in Kasei Valles, are generally accepted as evidence for water flowing over the Mars surface in the past [1]. However, not all channels are the product of fluvial processes and many can be interpreted as having a volcanic origin [2]. This research involves studying channel features on the flanks of the Ascraeus Mons volcano, which is a part of the Tharsis province. Numerous sinuous channels exist on the rift apron of Ascraeus Mons and they have been interpreted as either fluvial [3] or volcanic [4,5]. The channels originate from pits and linear depressions and extend for many 100 s of km downslope. Mapping the proximal to distal morphology of the complete channel and determining its relationship with other features on the apron provides evidence for the processes of formation and their relative temporal relationships. This study focused on sinuous channels located on the south-east part of the Ascraeus rift apron (Fig. 1). Observations of possible analogous features on Hawaii are used to provide insights into the processes of formation of the Mars features.

Can Processed Foods Be Part of a Healthy Diet?

MedlinePlus

... Simple Cooking and Recipes Dining Out Choosing a Restaurant Deciphering the Menu Ordering Your Meal Eating Fast ... make smart choices in the grocery store and restaurants. Choose healthier processed foods. Read food labels. This ...

Isotope Variations in Terrestrial Carbonates and Thermal Springs as Biomarkers: Analogs for Martian Processes

NASA Technical Reports Server (NTRS)

Socki, Richard A.; Gibson, Everett K., Jr.; Bissada, K. K.

2006-01-01

Stable isotope measurements of carbonate minerals contained within ALH84001 [1] suggest that fluids were present at 3.9 Gy on Mars [2, 3, 4, 5]. Both oxygen and carbon isotopes provide independent means of deciphering paleoenvironmental conditions at the time of carbonate mineral precipitation. In terrestrial carbonate rocks oxygen isotopes not only indicate the paleotemperature of the precipitating fluid, but also provide clues to environmental conditions that affected the fluid chemistry. Carbon isotopes, on the other hand, can indicate the presence or absence of organic compounds during precipitation (i.e. biogenically vs. thermogenically-generated methane), thus serving as a potential biomarker. We have undertaken a study of micro scale stable isotope variations measured in some terrestrial carbonates and the influence of organic compounds associated with the formation of these carbonates. Preliminary results indicate that isotope variations occur within narrow and discrete intervals, providing clues to paleoenvironmental conditions that include both biological and non-biological activity. These results carry implications for deciphering Martian isotope data and therefore potential biological prospecting on the planet Mars. Recently, Fourier Transform Spectrometer observations have detected methane occurring in the Martian atmosphere [6] that could be attributed to a possible biogenic source. Indeed, Mars Express has detected the presence of methane in the Martian atmosphere [7], with evidence indicating that methane abundances are greatest above those basins with high water concentrations.

Deciphering the influence of the thermal processes on the early passive margins formation

NASA Astrophysics Data System (ADS)

Bousquet, Romain; Nalpas, Thierry; Ballard, Jean-François; Ringenbach, Jean-Claude; Chelalou, Roman; Clerc, Camille

2015-04-01

Many large-scale dynamic processes, from continental rifting to plate subduction, are intimately linked to metamorphic reactions. This close relation between geodynamic processes and metamorphic reactions is, in spite of appearances, yet poorly understood. For example, during extension processes, rocks will be exposed to important temperature, pressures and stress changes. Meanwhile less attention has been paid to other important aspects of the metamorphic processes. When reacting rocks expand and contract, density and volume changes will set up in the surrounding material. While several tectonic models are proposed to explain the formation of extensive basins and passive margins ( simple shear detachment mantle exhumation .... ) a single thermal model (McKenzie , 1978), as a dogma, is used to understanding and modeling the formation and evolution of sedimentary basins . This model is based on the assumption that the extension is only by pure shear and it is instantaneous. Under this approach, the sedimentary deposits occur in two stages. i) A short step , 1 to 10 Ma , controlled by tectonics. ii) A longer step , at least 50 Ma as a result of the thermal evolution of the lithosphere.
However, most stratigraphic data indicate that less thermal model can account for documented vertical movements. The study of the thermal evolution , coupled with other tectonic models , and its consequences have never been studied in detail , although the differences may be significant and it is clear that the petrological changes associated with changes in temperature conditions , influence changes reliefs.
In addition, it seems that the relationship between basin formation and thermal evolution is not always the same:
- Sometimes the temperature rise above 50 to 100 Ma tectonic extension. In the Alps, a significant rise in geothermal gradient Permo -Triassic followed by a "cold" extension , leading to the opening of the Ligurian- Piedmont ocean, from the Middle Jurassic .
- Other examples show that temperature changes are synchronous with basin formation . For example, extensive ponds Cretaceous North Pyrenean clearly indicate that the "cooking" of contemporary sediment deposit. In the light of new models, we discuss the consequences of the formation of LP-granulites during rifting on deformation and the subsidence processes.

Fluid mechanics as a driver of tissue-scale mechanical signaling in organogenesis.

PubMed

Gilbert, Rachel M; Morgan, Joshua T; Marcin, Elizabeth S; Gleghorn, Jason P

2016-12-01

Organogenesis is the process during development by which cells self-assemble into complex, multi-scale tissues. Whereas significant focus and research effort has demonstrated the importance of solid mechanics in organogenesis, less attention has been given to the fluid forces that provide mechanical cues over tissue length scales. Fluid motion and pressure is capable of creating spatial gradients of forces acting on cells, thus eliciting distinct and localized signaling patterns essential for proper organ formation. Understanding the multi-scale nature of the mechanics is critically important to decipher how mechanical signals sculpt developing organs. This review outlines various mechanisms by which tissues generate, regulate, and sense fluid forces and highlights the impact of these forces and mechanisms in case studies of normal and pathological development.

Mass Spectrometric Distinction of In-Source and In-Solution Pyroglutamate and Succinimide in Proteins: A Case Study on rhG-CSF

NASA Astrophysics Data System (ADS)

Kumar, Mukesh; Chatterjee, Amarnath; Khedkar, Anand P.; Kusumanchi, Mutyalasetty; Adhikary, Laxmi

2013-02-01

Formation of cyclic intermediates involving water or ammonia loss is a common occurrence in any reaction involving terminal amines or hydroxyl group containing species. Proteins that have both these functional groups in abundance are no exception, and presence of amino acids such as asparagine, glutamines, aspartic acids, and glutamic acids aid in formation of such intermediates. In the biopharma scenario, such intermediates lead to product- or process-related impurities that might be immunogenic. Mass spectroscopy is a powerful technique that is used to decipher the presence and physicochemical characteristics of such impurities. However, such intermediates can also form in situ during mass spectrometric analysis. We present here the detection of in-source and in-solution formation of succinimide and pyroglutamate in the protein granulocyte colony stimulating factor. We also propose an approach for quick differentiation of such in-situ species from the tangible impurities. We believe that this will not only reduce the time spent in unambiguous identification of succinimide- and/or pyroglutamate-related impurity in bio-pharmaceutics but also provide a platform for similar studies on other impurities that may form due to stabilized intermediates.

Whole genome sequence to decipher the resistome of Shewanella algae, a multidrug-resistant bacterium responsible for pneumonia, Marseille, France.

PubMed

Cimmino, Teresa; Olaitan, Abiola Olumuyiwa; Rolain, Jean-Marc

2016-01-01

We characterize and decipher the resistome and the virulence factors of Shewanella algae MARS 14, a multidrug-resistant clinical strain using the whole genome sequencing (WGS) strategy. The bacteria were isolated from the bronchoalveolar lavage of a hospitalized patient in the Timone Hospital in Marseille, France who developed pneumonia after plunging into the Mediterranean Sea. The genome size of S. algae MARS 14 was 5,005,710 bp with 52.8% guanine cytosine content. The resistome includes members of class C and D beta-lactamases and numerous multidrug-efflux pumps. We also found the presence of several hemolysins genes, a complete flagellum system gene cluster and genes responsible for biofilm formation. Moreover, we reported for the first time in a clinical strain of Shewanella spp. the presence of a bacteriocin (marinocin). The WGS analysis of this pathogen provides insight into its virulence factors and resistance to antibiotics.

Integrated stratigraphy of Paleocene lignite seams of the fluvial Tullock Formation, Montana (USA).

NASA Astrophysics Data System (ADS)

Noorbergen, Lars J.; Kuiper, Klaudia F.; Hilgen, Frederik J.; Krijgsman, Wout; Dekkers, Mark J.; Smit, Jan; Abels, Hemmo A.

2015-04-01

Coal-bearing fluvial sedimentation is generally thought to be dominated by autogenic processes that are processes intrinsic to the sedimentary system. Ongoing research however suggests that several fluvial processes such as floodplain inundation and avulsion, can also be controlled by external forcing such as orbital climate change. Still, the exact role of orbital climate forcing in fluvial sediments is difficult to decipher since riverine deposits are complicated by variable sedimentation rates including erosion of previously deposited material, by lateral heterogeneity of sedimentation, and by scarcity of independent dating methods. The early Paleocene lignite-bearing Tullock Formation of the Williston Basin in eastern Montana represents a record of fluvial sedimentation that is perfectly exposed and, displays a seemingly regular alternation of sandstones and lignite seams. These coal beds contain multiple volcanic ash layers. Here, we use an integrated stratigraphic approach (litho- and magnetostratigraphy, geochemical fingerprinting and radio-isotope dating of volcanic ash layers) to establish a high-resolution time frame for the early Paleocene fluvial sediments. First age estimations indicate that the Tullock Formation in Eastern Montana was deposited over a time span of ~ 1000 kyr subsequent to the Cretaceous - Paleogene boundary, dated at ~ 65.95 Ma [1]. Initial high-resolution magnetostratigraphy revealed the occurrence of the C29r/C29n polarity reversal which was stratigraphic consistent at different field locations. We investigate the regional significance of sedimentary change at multiple sites of the same age in order to provide improved insight on the role of orbital forcing in fluvial coal formation. References: [1] Kuiper, K.F., Deino, A., Hilgen, F.J., Krijgsman, W., Renne, P.R., Wijbrans, J.R. (2008). Synchronizing Rock Clocks of Earth History. Science 320, 500-504.

Learning Processes in Man, Machine and Society

ERIC Educational Resources Information Center

Malita, Mircea

1977-01-01

Deciphering the learning mechanism which exists in man remains to be solved. This article examines the learning process with respect to association and cybernetics. It is recommended that research should focus on the transdisciplinary processes of learning which could become the next key concept in the science of man. (Author/MA)

Fluid mechanics as a driver of tissue-scale mechanical signaling in organogenesis

PubMed Central

Gilbert, Rachel M.; Morgan, Joshua T.; Marcin, Elizabeth S.; Gleghorn, Jason P.

2016-01-01

Purpose of Review Organogenesis is the process during development by which cells self-assemble into complex, multi-scale tissues. Whereas significant focus and research effort has demonstrated the importance of solid mechanics in organogenesis, less attention has been given to the fluid forces that provide mechanical cues over tissue length scales. Recent Findings Fluid motion and pressure is capable of creating spatial gradients of forces acting on cells, thus eliciting distinct and localized signaling patterns essential for proper organ formation. Understanding the multi-scale nature of the mechanics is critically important to decipher how mechanical signals sculpt developing organs. Summary This review outlines various mechanisms by which tissues generate, regulate, and sense fluid forces and highlights the impact of these forces and mechanisms in case studies of normal and pathological development. PMID:28163984

Observations of Nitrogen Fractionation in Prestellar Cores: Nitriles Tracing Interstellar Chemistry

NASA Technical Reports Server (NTRS)

Milam, S. N.; Charnley, S. B.

2012-01-01

Primitive materials provide important clues on the processes that occurred during the formation and early evolution of the Solar System. Space-based and ground-based observations of cometary comae show that comets appear to contain a mixture of the products of both interstellar and nebular chemistries. Significant 15-nitrogen enrichments have been measured in CN and HCN towards a number of comets and may suggest an origin of interstellar chemical fractionation. Additionally, large N-15 enhancements are found in meteorites and has also led to to the view that the N-15 traces material formed in the interstellar medium (ISM), although multiple sources cannot be excluded. Here, we show the results of observations of the nitrogen and carbon fractionation in prestellar cores for various N-bearing species to decipher the origin of primitive material isotopic enrichments.

The role of electrostatics and temperature on morphological transitions of hydrogel nanostructures self-assembled by peptide amphiphiles via molecular dynamics simulations.

PubMed

Fu, Iris W; Markegard, Cade B; Chu, Brian K; Nguyen, Hung D

2013-10-01

Smart biomaterials that are self-assembled from peptide amphiphiles (PA) are known to undergo morphological transitions in response to specific physiological stimuli. The design of such customizable hydrogels is of significant interest due to their potential applications in tissue engineering, biomedical imaging, and drug delivery. Using a novel coarse-grained peptide/polymer model, which has been validated by comparison of equilibrium conformations from atomistic simulations, large-scale molecular dynamics simulations are performed to examine the spontaneous self-assembly process. Starting from initial random configurations, these simulations result in the formation of nanostructures of various sizes and shapes as a function of the electrostatics and temperature. At optimal conditions, the self-assembly mechanism for the formation of cylindrical nanofibers is deciphered involving a series of steps: (1) PA molecules quickly undergo micellization whose driving force is the hydrophobic interactions between alkyl tails; (2) neighboring peptide residues within a micelle engage in a slow ordering process that leads to the formation of β-sheets exposing the hydrophobic core; (3) spherical micelles merge together through an end-to-end mechanism to form cylindrical nanofibers that exhibit high structural fidelity to the proposed structure based on experimental data. As the temperature and electrostatics vary, PA molecules undergo alternative kinetic mechanisms, resulting in the formation of a wide spectrum of nanostructures. A phase diagram in the electrostatics-temperature plane is constructed delineating regions of morphological transitions in response to external stimuli. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geochemical patterns and microbial contribution to iron plaque formation in the rice plant rhizosphere

NASA Astrophysics Data System (ADS)

Maisch, Markus; Murata, Chihiro; Unger, Julia; Kappler, Andreas; Schmidt, Caroline

2015-04-01

Rice is the major food source for more than half of the world population and 80 percent of the worldwide rice cultivation is performed on water logged paddy soils. The establishment of reducing conditions in the soil and across the soil-water interface not only stimulates the microbial production and release of the greenhouse gas methane. These settings also create optimal conditions for microbial iron(III) reduction and therefore saturate the system with reduced ferrous iron. Through the reduction and dissolution of ferric minerals that are characterized by their high surface activity, sorbed nutrients and contaminants (e.g. arsenic) will be mobilized and are thus available for uptake by plants. Rice plants have evolved a strategy to release oxygen from their roots in order to prevent iron toxification in highly ferrous environments. The release of oxygen to the reduced paddy soil causes ferric iron plaque formation on the rice roots and finally increases the sorption capacity for toxic metals. To this date the geochemical and microbiological processes that control the formation of iron plaque are not deciphered. It has been hypothesized that iron(II)-oxidizing bacteria play a potential role in the iron(III) mineral formation along the roots. However, not much is known about the actual processes, mineral products, and geochemical gradients that establish within the rhizosphere. In the present study we have developed a growth set-up that allows the co-cultivation of rice plants and iron(II)-oxidizing bacteria, as well as the visual observation and in situ measurement of geochemical parameters. Oxygen and dissolved iron(II) gradients have been measured using microelectrodes and show geochemical hot spots that offer optimal growth conditions for microaerophilic iron(II) oxidizers. First mineral identification attempts of iron plaque have been performed using Mössbauer spectroscopy and microscopy. The obtained results on mineraology and crystallinity have been compared to mineralogical data from purely biotic (microaerophilic) and abiotic iron mineral formation processes.

Formation of Authigenic Sulfates in Cold Dry Glaciers: Terrestrial and Planetary Implications of Sublimites

NASA Astrophysics Data System (ADS)

Massé, M.; Rondeau, B.; Ginot, P.; Schmitt, B.; Bourgeois, O.; Mitri, G.

2015-12-01

Salts are common on planetary surfaces, and sulfates have been widely observed on Earth, Mars (Gendrin et al., 2005) and on some of Jupiter's and Saturn's icy moons like Europa (Dalton et al., 2007). These minerals can form under a wide range of conditions, and the determination of sulfate formation processes can provide key elements for deciphering past planetary surface conditions. Most terrestrial sulfates form as evaporites in warm environments with high water/rock ratios, but these conditions are rarely encountered on other planets. Here we describe the formation of cryogenic sulfates in an extreme cold and dry environment: the Guanaco glacier located in the Chilean Andes (Fig.1a, Rabatel et al., 2011). Field analyses reveal that it is a cold-based glacier, its surface temperature remains below 0°C throughout the year, and ablation occurs mostly by sublimation. Ablation creates ice cliffs punctuated of pluricentimetric whitish, tapered crystals embedded in the ice (Fig.1b, c). By Raman and chemistry, they proved to be gypsum, covered by micrometric crystals of jarosite, halotrichite and native sulfur. The euhedral morphology of these soft minerals indicates that they are neoformed and have not been transported in the ice. This is supported by the absence of gypsum crystals in ice cores drilled through the glacier. We infer that the crystallization thus occurred at the glacier surface during ice sublimation and does not involve liquid water. To distinguish this original salt formation process from the more common evaporites, we name these minerals "sublimites". Though this formation process is uncommon and generates minor quantities of sulfates on Earth, it may be dominant on other bodies in the Solar System where sublimation is effective. Examples of planetary sublimites may include gypsum on the North Polar Cap of Mars (Massé et al., 2012), and other sulfates on icy moons where sublimation has been observed (Howard et al., 2008).

Deciphering Dynamical Patterns of Growth Processes

ERIC Educational Resources Information Center

Kolakowska, A.

2009-01-01

Large systems of statistical physics often display properties that are independent of particulars that characterize their microscopic components. Universal dynamical patterns are manifested by the presence of scaling laws, which provides a common insight into governing physics of processes as vastly diverse as, e.g., growth of geological…

The Cremeomycin Biosynthetic Gene Cluster Encodes a Pathway for Diazo Formation.

PubMed

Waldman, Abraham J; Pechersky, Yakov; Wang, Peng; Wang, Jennifer X; Balskus, Emily P

2015-10-12

Diazo groups are found in a range of natural products that possess potent biological activities. Despite longstanding interest in these metabolites, diazo group biosynthesis is not well understood, in part because of difficulties in identifying specific genes linked to diazo formation. Here we describe the discovery of the gene cluster that produces the o-diazoquinone natural product cremeomycin and its heterologous expression in Streptomyces lividans. We used stable isotope feeding experiments and in vitro characterization of biosynthetic enzymes to decipher the order of events in this pathway and establish that diazo construction involves late-stage N-N bond formation. This work represents the first successful production of a diazo-containing metabolite in a heterologous host, experimentally linking a set of genes with diazo formation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

BASIC Language Flow Charting Program (BASCHART). Technical Note 3-82.

ERIC Educational Resources Information Center

Johnson, Charles C.; And Others

This document describes BASCHART, a computer aid designed to decipher and automatically flow chart computer program logic; it also provides the computer code necessary for this process. Developed to reduce the labor intensive manual process of producing a flow chart for an undocumented or inadequately documented program, BASCHART will…

Transgenesis in axolotl (Ambystoma mexicanum).

PubMed

Khattak, Shahryar; Tanaka, Elly M

2015-01-01

Transgenic animals have been indispensable in elucidating and deciphering mechanisms underlying various biological phenomena. In regeneration, transgenic animals expressing fluorescent protein genes have been crucial for identifying the source cells for regeneration and the mechanism of blastema formation. Animals are usually generated by manipulating their genome using various techniques at/in one cell embryo/fertilized egg stage. Here, we describe the generation of germline transgenic axolotls (Ambystoma mexicanum) using the I-SceI meganuclease and Tol2 transposase.

["Migration of Thoughts". Ludwik Fleck's morphology of knowledge].

PubMed

Neumann, Michael

2014-01-01

This article traces some of the transformation that the fields of folk psychology (Völkerpsychologie) and anthropology underwent in the late nineteenth century. Ludwik Fleck, in developing his sociology of knowledge, drew on both of these fields; a legacy that makes it possible to conceive of his epistemology as a theory of communication. Fleck, in grounding his understanding of the relationship between sociality and communication on insights from these two disciplines, proposed the morphological concept of an organic formation of all scientific knowledge. Naturalising knowledge production in this manner, Fleck postulated a program of deciphering, reading, and translation that would relate all forms of knowledge back to the rules and conditions of its making. In this morphological conception of the processes of knowledge production, Fleck’s sociology bears significant similarities with the description of social institutions by French sociologists Marcel Mauss and Emile Durkheim, who also drew on insights from late-nineteenth-century folk psychology and anthropology.

A peptide extension dictates IgM assembly.

PubMed

Pasalic, Dzana; Weber, Benedikt; Giannone, Chiara; Anelli, Tiziana; Müller, Roger; Fagioli, Claudio; Felkl, Manuel; John, Christine; Mossuto, Maria Francesca; Becker, Christian F W; Sitia, Roberto; Buchner, Johannes

2017-10-10

Professional secretory cells can produce large amounts of high-quality complex molecules, including IgM antibodies. Owing to their multivalency, polymeric IgM antibodies provide an efficient first-line of defense against pathogens. To decipher the mechanisms of IgM assembly, we investigated its biosynthesis in living cells and faithfully reconstituted the underlying processes in vitro. We find that a conserved peptide extension at the C-terminal end of the IgM heavy (Ig-μ) chains, termed the tailpiece, is necessary and sufficient to establish the correct geometry. Alanine scanning revealed that hydrophobic amino acids in the first half of the tailpiece contain essential information for generating the correct topology. Assembly is triggered by the formation of a disulfide bond linking two tailpieces. This induces conformational changes in the tailpiece and the adjacent domain, which drive further polymerization. Thus, the biogenesis of large and topologically challenging IgM complexes is dictated by a local conformational switch in a peptide extension.

Modern terrestrial analogues for the carbonate globules in Martian meteorite ALH84001.

PubMed

Kazmierczak, Józef; Kempe, Stephan

2003-04-01

Modern carbonate globules, located in cracks of submerged volcanic rocks and in calcareous pinnacles in alkaline (sodic) Lake Van, Turkey, appear to be analogues for the approximately 3.9 billion-year-old carbonate globules in Martian meteorite ALH84001. These terrestrial globules have similar diameters and are chemically and mineralogically zoned. Furthermore, they display surface and etching structures similar to those described from ALH84001, which were interpreted as fossilized microbial forms. These terrestrial carbonates formed at low temperatures where Ca-rich groundwaters enter the lake. Chemical, mineralogical, microbiological, and biomolecular methods were used in an attempt to decipher the process responsible for the genesis of these structures. Although the exact mode of formation of Lake Van carbonates remains an enigma, their similarity to the Martian globules indicates that the ALH84001 carbonates may have formed in similar setting on ancient Mars.

The influence of attention on holistic face encoding.

PubMed

Boutet, Isabelle; Gentes-Hawn, Alyson; Chaudhuri, Avi

2002-07-01

We examined the influence of attention on the formation of holistic face representations using the composite effect (Perception 16 (1987) 747). In Experiment 1, stimuli composed of a face superimposed on a house were shown during encoding. Subjects delineated either the face or the house, thus manipulating attention away or toward the face. In Experiment 2, an intact face image was presented with letters scrolling from top to bottom. Subjects were asked to either ignore the letters or read them and decipher the words that they formed. Aligned and misaligned composites were shown at testing. Recognition performance was consistently better for misaligned than aligned stimuli, regardless of the allocation of attention during encoding. In Experiment 3, we show that the composite effect can be eliminated by a disruption in holistic processing at the time of encoding. We conclude that holistic encoding is one aspect of face analysis that occurs equally well with or without attention.

A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication.

PubMed

Kolar, Katja; Wischhusen, Hanna M; Müller, Konrad; Karlsson, Maria; Weber, Wilfried; Zurbriggen, Matias D

2015-12-30

Multicellular organisms depend on the exchange of information between specialized cells. This communication is often difficult to decipher in its native context, but synthetic biology provides tools to engineer well-defined systems that allow the convenient study and manipulation of intercellular communication networks. Here, we present the first mammalian synthetic network for reciprocal cell-cell communication to compute the border between a sender/receiver and a processing cell population. The two populations communicate via L-tryptophan and interleukin-4 to highlight the population border by the production of a fluorescent protein. The sharpness of that visualized edge can be adjusted by modulating key parameters of the network. We anticipate that this network will on the one hand be a useful tool to gain deeper insights into the mechanisms of tissue formation in nature and will on the other hand contribute to our ability to engineer artificial tissues.

Depositional history of the Late Barremian deposits (Sidi Aïch Formation) in central Tunisia and adjacent parts of Algeria: A geostatistical revelation

NASA Astrophysics Data System (ADS)

Aloui, Tahar; Ounis, Anouar; Dasgupta, Prabir; Lourimi, Wijden; Chaabani, Fredj

2018-07-01

The lithofacies analysis of the Sidi Aïch Formation and equivalents in Tunisia and adjacent parts of Algeria was carried out using probabilistic and quantitative approach as Discrete Time Markov Chain (DTMC) and entropy functions coupled with detailed sedimentary analyses with a view to decipher the Late Barremian depositional history. The Late Barremian successions exhibit asymmetric, fining-upward and retrograding to aggrading cycles in both outcrop and borehole data. Complete cycles typically start with intraformational conglomerates or trough and planar cross-stratified coarse sands, overlain by fine-grained sands, which are succeeded, in turn, by laminated sands, silts, clays and carbonates, and ends with paleosoils. Such ideal succession of lithofacies is observed at Zemlet el Baidha Hill in Tunisia and OuM.1 borehole in northeast Algeria marked by high values of entropy. The entropy analysis indicates deposition in a neritic environment with interplay of fluvial (and rarely alluvial) processes. The facies associations observed at Zemlet el Baidha Hill document evidences of wave and tide dominated coast with complex-gradient of environments that graded from neritic (upper to lower shoreface) to coastal settings (lagoons, embayments, restricted bays, mires, swamps etc.). The architecture of lithofacies appears to have been controlled by autocyclic processes (effects of local tectonics, basin bathymetry, lateral redistribution of deposits by longshore waves and tide currents) and allocyclic processes (global decrease of relative sea-level and sediments supply). Due to large salinity variations, wave action, ephemeral and local aspects of these marginal environments, the ichnodiversity was often limited in time and space, and inhibited the development of fossils during the onset of deposition of Sidi Aïch Formation and its equivalents.

Physical Heterogeneity and Aquatic Community Function in River Networks

EPA Science Inventory

The geomorphological character of a river network provides the template upon which evolution acts to create unique biological communities. Deciphering commonly observed patterns and processes within riverine landscapes resulting from the interplay between physical and biological...

Capturing extracellular matrix properties in vitro: Microengineering materials to decipher cell and tissue level processes.

PubMed

Abdeen, Amr A; Lee, Junmin; Kilian, Kristopher A

2016-05-01

Rapid advances in biology have led to the establishment of new fields with tremendous translational potential including regenerative medicine and immunoengineering. One commonality to these fields is the need to extract cells for manipulation in vitro; however, results obtained in laboratory cell culture will often differ widely from observations made in vivo. To more closely emulate native cell biology in the laboratory, designer engineered environments have proved a successful methodology to decipher the properties of the extracellular matrix that govern cellular decision making. Here, we present an overview of matrix properties that affect cell behavior, strategies for recapitulating important parameters in vitro, and examples of how these properties can affect cell and tissue level processes, with emphasis on leveraging these tools for immunoengineering. © 2016 by the Society for Experimental Biology and Medicine.

Structural Features of the Western Taiwan Foreland Basin in the Eastern Taiwan Strait since Late Miocene

NASA Astrophysics Data System (ADS)

WANG, J. H.; Liu, C. S.; Chang, J. H.; Yang, E. Y.

2017-12-01

The western Taiwan Foreland Basin lies on the eastern part of Taiwan Strait. The structures in this region are dominated by crustal stretch and a series of flexural normal faults have been developed since Late Miocene owing to the flexural of Eurasia Plate. Through deciphering multi-channel seismic data and drilling data, these flexural features are observed in the offshore Changhua coastal area. The flexure normal faults are important features to realize structural activity in the western Taiwan Foreland Basin. Yang et al. (2016) mention that the reactivated normal faults are found north of the Zhushuixi estuary. It should be a significant issue to decipher whether these faults are still active. In this study, we have analyzed all the available seismic reflections profiles in the central part of the Taiwan Strait, and have observed many pre-Pliocene normal faults that are mainly distributed in the middle of the Taiwan Strait to Changyun Rise, and we tentatively suggest that the formation of these faults may be associated with the formation of the foreland basal unconformity. Furthermore, we will map the distribution of these normal faults and examine whether the reactivated normal faults have extended to south of the Zhushuixi estuary. Finally, we discuss the relation between the reactivated normal faults in the Taiwan Strait and those faults onshore. Key words: Multichannel seismic reflection profile, Taiwan Strait, Foreland basin, normal fault.

Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)

PubMed Central

Hsu, Chun-Nan; Lai, Jin-Mei; Liu, Chia-Hung; Tseng, Huei-Hun; Lin, Chih-Yun; Lin, Kuan-Ting; Yeh, Hsu-Hua; Sung, Ting-Yi; Hsu, Wen-Lian; Su, Li-Jen; Lee, Sheng-An; Chen, Chang-Han; Lee, Gen-Cher; Lee, DT; Shiue, Yow-Ling; Yeh, Chang-Wei; Chang, Chao-Hui; Kao, Cheng-Yan; Huang, Chi-Ying F

2007-01-01

Background The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers and cellular pathways. We aim to collect and decipher the HCC-related genes at the systems level. Results Here, we build an integrative platform, the Encyclopedia of Hepatocellular Carcinoma genes Online, dubbed EHCO , to systematically collect, organize and compare the pileup of unsorted HCC-related studies by using natural language processing and softbots. Among the eight gene set collections, ranging across PubMed, SAGE, microarray, and proteomics data, there are 2,906 genes in total; however, more than 77% genes are only included once, suggesting that tremendous efforts need to be exerted to characterize the relationship between HCC and these genes. Of these HCC inventories, protein binding represents the largest proportion (~25%) from Gene Ontology analysis. In fact, many differentially expressed gene sets in EHCO could form interaction networks (e.g. HBV-associated HCC network) by using available human protein-protein interaction datasets. To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes in HCC. 47 out of 120 queries can form a highly interactive network with 18 queries serving as hubs. Conclusion This architectural map may represent the first step toward the attempt to decipher the hepatocarcinogenesis at the systems level. Targeting hubs and/or disruption of the network formation might reveal novel strategy for HCC treatment. PMID:17326819

Tests of various colorants for application of a Fourier transform infrared imaging system to deciphering obliterated writings

NASA Astrophysics Data System (ADS)

Sugawara, Shigeru

2015-10-01

Obliterated writing is writing that has been obscured by different-colored materials. There are obliterated writings that cannot be detected by conventional methods. A method for deciphering such obliterated writings was developed in this study. Mid-infrared spectroscopic imaging in the wavelength range of 2.5-14 μm was used for deciphering because the infrared spectrum differs among different brands of colorants. Obliterated writings were made by pressing information protection stamps onto characters written by 4 kinds of colorants. The samples were tested for deciphering by the Fourier-transform infrared imaging system. Two peak areas of two specific wavenumber regions of each reflectance spectrum were calculated and the ratio of the two values is displayed as a unique gray scale in the spectroscopic image. As a result, the absorption peak at various wavenumbers could be used to decipher obliterated writings that could not be detected by the conventional methods. Ten different parameters for deciphering obliterated writing were found in this study.

Energetics of dendrimer binding to HIV-1 gp120-CD4 complex and mechanismic aspects of its role as an entry-inhibitor

NASA Astrophysics Data System (ADS)

Saurabh, Suman; Sahoo, Anil Kumar; Maiti, Prabal K.

2016-10-01

Experiments and computational studies have established that de-protonated dendrimers (SPL7013 and PAMAM) act as entry-inhibitors of HIV. SPL7013 based Vivagel is currently under clinical development. The dendrimer binds to gp120 in the gp120-CD4 complex, destabilizes it by breaking key contacts between gp120 and CD4 and prevents viral entry into target cells. In this work, we provide molecular details and energetics of the formation of the SPL7013-gp120-CD4 ternary complex and decipher modes of action of the dendrimer in preventing viral entry. It is also known from experiments that the dendrimer binds weakly to gp120 that is not bound to CD4. It binds even more weakly to the CD4-binding region of gp120 and thus cannot directly block gp120-CD4 complexation. In this work, we examine the feasibility of dendrimer binding to the gp120-binding region of CD4 and directly blocking gp120-CD4 complex formation. We find that the process of the dendrimer binding to CD4 can compete with gp120-CD4 binding due to comparable free energy change for the two processes, thus creating a possibility for the dendrimer to directly block gp120-CD4 complexation by binding to the gp120-binding region of CD4.

Lunar and Planetary Science XXXV: Moon and Mercury

NASA Technical Reports Server (NTRS)

2004-01-01

The session" Moon and Mercury" included the following reports:Helium Production of Prompt Neutrinos on the Moon; Vapor Deposition and Solar Wind Implantation on Lunar Soil-Grain Surfaces as Comparable Processes; A New Lunar Geologic Mapping Program; Physical Backgrounds to Measure Instantaneous Spin Components of Terrestrial Planets from Earth with Arcsecond Accuracy; Preliminary Findings of a Study of the Lunar Global Megaregolith; Maps Characterizing the Lunar Regolith Maturity; Probable Model of Anomalies in the Polar Regions of Mercury; Parameters of the Maximum of Positive Polarization of the Moon; Database Structure Development for Space Surveying Results by Moon -Zond Program; CM2-type Micrometeoritic Lunar Winds During the Late Heavy Bombardment; A Comparison of Textural and Chemical Features of Spinel Within Lunar Mare Basalts; The Reiner Gamma Formation as Characterized by Earth-based Photometry at Large Phase Angles; The Significance of the Geometries of Linear Graben for the Widths of Shallow Dike Intrusions on the Moon; Lunar Prospector Data, Surface Roughness and IR Thermal Emission of the Moon; The Influence of a Magma Ocean on the Lunar Global Stress Field Due to Tidal Interaction Between the Earth and Moon; Variations of the Mercurian Photometric Relief; A Model of Positive Polarization of Regolith; Ground Truth and Lunar Global Thorium Map Calibration: Are We There Yet?;and Space Weathering of Apollo 16 Sample 62255: Lunar Rocks as Witness Plates for Deciphering Regolith Formation Processes.

Cometary Dust

NASA Astrophysics Data System (ADS)

Levasseur-Regourd, Anny-Chantal; Agarwal, Jessica; Cottin, Hervé; Engrand, Cécile; Flynn, George; Fulle, Marco; Gombosi, Tamas; Langevin, Yves; Lasue, Jérémie; Mannel, Thurid; Merouane, Sihane; Poch, Olivier; Thomas, Nicolas; Westphal, Andrew

2018-04-01

This review presents our understanding of cometary dust at the end of 2017. For decades, insight about the dust ejected by nuclei of comets had stemmed from remote observations from Earth or Earth's orbit, and from flybys, including the samples of dust returned to Earth for laboratory studies by the Stardust return capsule. The long-duration Rosetta mission has recently provided a huge and unique amount of data, obtained using numerous instruments, including innovative dust instruments, over a wide range of distances from the Sun and from the nucleus. The diverse approaches available to study dust in comets, together with the related theoretical and experimental studies, provide evidence of the composition and physical properties of dust particles, e.g., the presence of a large fraction of carbon in macromolecules, and of aggregates on a wide range of scales. The results have opened vivid discussions on the variety of dust-release processes and on the diversity of dust properties in comets, as well as on the formation of cometary dust, and on its presence in the near-Earth interplanetary medium. These discussions stress the significance of future explorations as a way to decipher the formation and evolution of our Solar System.

The Gaseous Phase as a Probe of the Astrophysical Solid Phase Chemistry

NASA Astrophysics Data System (ADS)

Abou Mrad, Ninette; Duvernay, Fabrice; Isnard, Robin; Chiavassa, Thierry; Danger, Grégoire

2017-09-01

In support of space missions and spectroscopic observations, laboratory experiments on ice analogs enable a better understanding of organic matter formation and evolution in astrophysical environments. Herein, we report the monitoring of the gaseous phase of processed astrophysical ice analogs to determine if the gaseous phase can elucidate the chemical mechanisms and dominant reaction pathways occurring in the solid ice subjected to vacuum ultra-violet (VUV) irradiation at low temperature and subsequently warmed. Simple (CH3OH), binary (H2O:CH3OH, CH3OH:NH3), and ternary ice analogs (H2O:CH3OH:NH3) were VUV-processed and warmed. The evolution of volatile organic compounds in the gaseous phase shows a direct link between their relative abundances in the gaseous phase, and the radical and thermal chemistries modifying the initial ice composition. The correlation between the gaseous and solid phases may play a crucial role in deciphering the organic composition of astrophysical objects. As an example, possible solid compositions of the comet Lovejoy are suggested using the abundances of organics in its comae.

Sordaria macrospora, a model organism to study fungal cellular development.

PubMed

Engh, Ines; Nowrousian, Minou; Kück, Ulrich

2010-12-01

During the development of multicellular eukaryotes, the processes of cellular growth and organogenesis are tightly coordinated. Since the 1940s, filamentous fungi have served as genetic model organisms to decipher basic mechanisms underlying eukaryotic cell differentiation. Here, we focus on Sordaria macrospora, a homothallic ascomycete and important model organism for developmental biology. During its sexual life cycle, S. macrospora forms three-dimensional fruiting bodies, a complex process involving the formation of different cell types. S. macrospora can be used for genetic, biochemical and cellular experimental approaches since diverse tools, including fluorescence microscopy, a marker recycling system and gene libraries, are available. Moreover, the genome of S. macrospora has been sequenced and allows functional genomics analyses. Over the past years, our group has generated and analysed a number of developmental mutants which has greatly enhanced our fundamental understanding about fungal morphogenesis. In addition, our recent research activities have established a link between developmental proteins and conserved signalling cascades, ultimately leading to a regulatory network controlling differentiation processes in a eukaryotic model organism. This review summarizes the results of our recent findings, thus advancing current knowledge of the general principles and paradigms underpinning eukaryotic cell differentiation and development. Copyright © 2010 Elsevier GmbH. All rights reserved.

Trichinella spiralis: the evolution of adaptation and parasitism

USDA-ARS?s Scientific Manuscript database

Parasitism among nematodes has occurred in multiple, independent events. Deciphering processes that drive species diversity and adaptation are keys to understanding parasitism and advancing control strategies. Studies have been put forth on morphological and physiological aspects of parasitism and a...

SYMPOSIUM SESSION PROPOSAL: INCORPORATION OF MODE OF ACTION INTO MECHANISTICALLY-BASED QUANTITATIVE MODELS

EPA Science Inventory

The biological processes by which environmental pollutants induce adverse health effects is most likely regulated by complex interactions dependent upon the route of exposure, dose, kinetics of distribution, and multiple cellular responses. To further complicate deciphering thes...

Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy.

PubMed

Kedrov, Alexej; Janovjak, Harald; Sapra, K Tanuj; Müller, Daniel J

2007-01-01

Molecular interactions are the basic language of biological processes. They establish the forces interacting between the building blocks of proteins and other macromolecules, thus determining their functional roles. Because molecular interactions trigger virtually every biological process, approaches to decipher their language are needed. Single-molecule force spectroscopy (SMFS) has been used to detect and characterize different types of molecular interactions that occur between and within native membrane proteins. The first experiments detected and localized molecular interactions that stabilized membrane proteins, including how these interactions were established during folding of alpha-helical secondary structure elements into the native protein and how they changed with oligomerization, temperature, and mutations. SMFS also enables investigators to detect and locate molecular interactions established during ligand and inhibitor binding. These exciting applications provide opportunities for studying the molecular forces of life. Further developments will elucidate the origins of molecular interactions encoded in their lifetimes, interaction ranges, interplay, and dynamics characteristic of biological systems.

Deciphering the Adaptive Immune Response to Ovarian Cancer

DTIC Science & Technology

2013-10-01

Additionally, anti-cancer drugs such as 2-phenyl benzimidazole (2- PB) disrupt the Golgi apparatus, which leads to reduced cell proliferation and tumour...of Golgi processing by 2-phenyl benzimidazole analogs blocks cell proliferation and slows tumor growth. Cancer Chemother Pharmacol 2008; 61: 1045–1058

Applications of Maple To Algebraic Cryptography.

ERIC Educational Resources Information Center

Sigmon, Neil P.

1997-01-01

Demonstrates the use of technology to enhance the appreciation of applications involving abstract algebra. The symbolic manipulator Maple can perform computations required for a linear cryptosystem. One major benefit of this process is that students can encipher and decipher messages using a linear cryptosystem without becoming confused and…

Exploring metazoan evolution through dynamic and holistic changes in protein families and domains

USDA-ARS?s Scientific Manuscript database

Understanding proteome evolution is important for deciphering processes that drive species diversity and adaptation. Herein, the dynamics of change in protein families and protein domains over the course of metazoan evolution was explored. Change, as defined by birth/death and duplication/deletion ...

On cooperative effects and aggregation of GNNQQNY and NNQQNY peptides

NASA Astrophysics Data System (ADS)

Nochebuena, Jorge; Ireta, Joel

2015-10-01

Some health disturbances like neurodegenerative diseases are associated to the presence of amyloids. GNNQQNY and NNQQNY peptides are considered as prototypical examples for studying the formation of amyloids. These exhibit quite different aggregation behaviors despite they solely differ in size by one residue. To get insight into the reasons for such difference, we have examined association energies of aggregates (parallel β-sheets, fibril-spines, and crystal structures) from GNNQQNY and NNQQY using density functional theory. As we found that GNNQQNY tends to form a zwitterion in the crystal structure, we have investigated the energetics of parallel β-sheets and fibril-spines in the canonical and zwitterionic states. We found that the formation of GNNQQNY aggregates is energetically more favored than the formation of the NNQQNY ones. We show that the latter is connected to the network of hydrogen bonds formed by each aggregate. Moreover, we found that the formation of some NNQQNY aggregates is anticooperative, whereas cooperative with GNNQQNY. These results have interesting implications for deciphering the factors determining peptide aggregation propensities.

Deciphering Front-Side Complex Formation in SN2 Reactions via Dynamics Mapping.

PubMed

Szabó, István; Olasz, Balázs; Czakó, Gábor

2017-07-06

Due to their importance in organic chemistry, the atomistic understanding of bimolecular nucleophilic substitution (S N 2) reactions shows exponentially growing interest. In this publication, the effect of front-side complex (FSC) formation is uncovered via quasi-classical trajectory computations combined with a novel analysis method called trajectory orthogonal projection (TOP). For both F - + CH 3 Y [Y = Cl,I] reactions, the lifetime distributions of the F - ···YCH 3 front-side complex revealed weakly trapped nucleophiles (F - ). However, only the F - + CH 3 I reaction features strongly trapped nucleophiles in the front-side region of the prereaction well. Interestingly, both back-side and front-side attack show propensity to long-lived FSC formation. Spatial distributions of the nucleophile demonstrate more prominent FSC formation in case of the F - + CH 3 I reaction compared to F - + CH 3 Cl. The presence of front-side intermediates and the broad spatial distribution in the back-side region may explain the indirect nature of the F - + CH 3 I reaction.

Deciphering the mechanism of interaction of edifenphos with calf thymus DNA

NASA Astrophysics Data System (ADS)

Ahmad, Ajaz; Ahmad, Masood

2018-01-01

Edifenphos is an important organophosphate pesticide with many antifungal and anti-insecticidal properties but it may cause potential hazards to human health. In this work, we have tried to explore the binding mode of action and mechanism of edifenphos to calf thymus DNA (CT-DNA). Several experiments such as ultraviolet-visible absorption spectra and emission spectroscopy showed complex formation between edifenphos and CT-DNA and low binding constant values supporting groove binding mode. These results were further confirmed by circular dichroism (CD), CT-DNA melting studies, viscosity measurements, density functional theory and molecular docking. CD study suggests that edifenphos does not alter native structure of CT-DNA. Isothermal calorimetry reveals that binding of edifenphos with CT-DNA is enthalpy driven process. Competitive binding assay and effect of ionic strength showed that edifenphos binds to CT-DNA via groove binding manner. Hence, edifenphos is a minor groove binder preferably interacting with A-T regions with docking score - 6.84 kJ/mol.

Simulating the Solar Wind Interaction with Comet 67P/Churyumov-Gerasimenko: Latest Results

NASA Astrophysics Data System (ADS)

Deca, J.; Divin, A. V.; Henri, P.; Eriksson, A. I.; Markidis, S.; Olshevsky, V.; Goldstein, R.; Myllys, M. E.; Horanyi, M.

2017-12-01

First observed in 1969, comet 67P/Churyumov-Gerasimenko was escorted for almost two years along its 6.45-yr elliptical orbit by ESA's Rosetta orbiter spacecraft. When a comet is sufficiently close to the Sun, the sublimation of ice leads to an outgassing atmosphere and the formation of a coma, and a dust and plasma tail. Comets are critical to decipher the physics of gas release processes in space. The latter result in mass-loaded plasmas, which more than three decades after the Active Magnetospheric Particle Tracer Explorers (AMPTE) space release experiments are still not fully understood. Using a 3D fully kinetic approach, we study the solar wind interaction with comet 67P/Churyumov-Gerasimenko, focusing in particular on the ion-electron dynamics for various outgassing rates. A detailed kinetic treatment of the electron dynamics is critical to fully capture the complex physics of mass-loading plasmas and to describe the strongly inhomogeneous plasma dynamics observed by Rosetta, down to electron kinetic scales.

A peptide extension dictates IgM assembly

PubMed Central

Pasalic, Dzana; Weber, Benedikt; Giannone, Chiara; Anelli, Tiziana; Müller, Roger; Fagioli, Claudio; Felkl, Manuel; John, Christine; Mossuto, Maria Francesca; Sitia, Roberto; Buchner, Johannes

2017-01-01

Professional secretory cells can produce large amounts of high-quality complex molecules, including IgM antibodies. Owing to their multivalency, polymeric IgM antibodies provide an efficient first-line of defense against pathogens. To decipher the mechanisms of IgM assembly, we investigated its biosynthesis in living cells and faithfully reconstituted the underlying processes in vitro. We find that a conserved peptide extension at the C-terminal end of the IgM heavy (Ig-μ) chains, termed the tailpiece, is necessary and sufficient to establish the correct geometry. Alanine scanning revealed that hydrophobic amino acids in the first half of the tailpiece contain essential information for generating the correct topology. Assembly is triggered by the formation of a disulfide bond linking two tailpieces. This induces conformational changes in the tailpiece and the adjacent domain, which drive further polymerization. Thus, the biogenesis of large and topologically challenging IgM complexes is dictated by a local conformational switch in a peptide extension. PMID:28973899

Application of Circular Dichroism Spectroscopy to the Analysis of the Interaction Between the Estrogen Receptor Alpha and Coactivators: The Case of Calmodulin.

PubMed

Miclet, Emeric; Bourgoin-Voillard, Sandrine; Byrne, Cillian; Jacquot, Yves

2016-01-01

The estrogen receptor α ligand-binding domain (ERα-LBD) binds the natural hormone 17β-estradiol (E2) to induce transcription and cell proliferation. This process occurs with the contribution of protein and peptide partners (also called coactivators) that can modulate the structure of ERα, and therefore its specificity of action. As with most transcription factors, ERα exhibits a high content of α helix, making it difficult to routinely run spectroscopic studies capable of deciphering the secondary structure of the different partners under binding conditions. Ca(2+)-calmodulin, a protein also highly structured in α-helix, is a key coactivator for ERα activity. Here, we show how circular dichroism can be used to study the interaction of ERα with Ca(2+)-calmodulin. Our approach allows the determination not only of the conformational changes induced upon complex formation but also the dissociation constant (K d) of this interaction.

Human Factors in the Design and Evaluation of Air Traffic Control Systems

DTIC Science & Technology

1995-04-01

the controller must filter through and decipher. Fortunately, some of this is done without the need for conscious attention ; fcr example, a clear...components of an information-processing model ? ...................... 166 5.3 ATTENTION ......................................... 172 0 5.3.1 What is...processing? support of our performance of daily activities, including our (,) job tasks. Two models of attention currently in use assume that human infor

Deciphering skeletal patterning: clues from the limb.

PubMed

Mariani, Francesca V; Martin, Gail R

2003-05-15

Even young children can distinguish a Tyrannosaurus rex from a Brontosaurus by observing differences in bone size, shape, number and arrangement, that is, skeletal pattern. But despite our extensive knowledge about cartilage and bone formation per se, it is still largely a mystery how skeletal pattern is established. Much of what we do know has been learned from studying limb development in chicken and mouse embryos. Based on the data from such studies, models for how limb skeletal pattern is established have been proposed and continue to be hotly debated.

twzPEA: A Topology and Working Zone Based Pathway Enrichment Analysis Framework

USDA-ARS?s Scientific Manuscript database

Sensitive detection of involvement and adaptation of key signaling, regulatory, and metabolic pathways holds the key to deciphering molecular mechanisms such as those in the biomass-to-biofuel conversion process in yeast. Typical gene set enrichment analyses often do not use topology information in...

Notas para la decodificacion de lesicos desconocidos en el campo del ingles cientifico (Notes for Deciphering Unknown Lexical Items in Scientific English).

ERIC Educational Resources Information Center

Perez, Cesar Morales

1991-01-01

This article outlines strategies for the inferring of English scientific terms by Spanish speakers. The article considers factors affecting the process of inference, the use of context morphology, and word origin in inferring word meaning. (SR)

Pulse - Accelerator Science in Medicine

Science.gov Websites

the structure of biological molecules. They use the energy that charged particles emit when powerful than the sun and focused on a pinpoint. Deciphering the structure of proteins is key to understanding biological processes and healing disease. To determine a protein’s structure, researchers direct

Deciphering Late-Pleistocence landscape evolution: linking proxies by combining pedo-stratigraphy and luminescence dating

NASA Astrophysics Data System (ADS)

Kreutzer, Sebastian; Meszner, Sascha; Faust, Dominik; Fuchs, Markus

2014-05-01

Interpreting former landscape evolution asks for understanding the processes that sculpt such landforms by means of deciphering complex systems. For reconstructing terrestrial Quaternary environments based on loess archives this might be considered, at least, as a three step process: (1) Identifying valuable records in appropriate morphological positions in a previously defined research area, (2) analysing the profiles by field work and laboratory methods and finally (3) linking the previously considered pseudo-isolated systems to set up a comprehensive picture. Especially the first and the last step might bring some pitfalls, as it is tempting to specify single records as pseudo-isolated, closed systems. They might be, with regard to their preservation in their specific morphological position, but in fact they are part of a complex, open system. Between 2008 and 2013, Late-Pleistocene loess archives in Saxony have been intensively investigated by field and laboratory methods. Linking pedo- and luminescence dating based chronostratigraphies, a composite profile for the entire Saxonian Loess Region has been established. With this, at least, two-fold approach we tried to avoid misinterpretations that might appear when focussing on one standard profile in an open morphological system. Our contribution focuses on this multi-proxy approach to decipher the Late-Pleistocene landscape evolution in the Saxonian Loess Region. Highlighting the challenges and advantages of combining different methods, we believe that (1) this multi-proxy approach is without alternative, (2) the combination of different profiles may simplify the more complex reality, but it may be a useful generalisation to understand and reveal the stratigraphical significance of the landscape evolution in this region.

Deciphering the complexation process of a fluoroquinolone antibiotic, levofloxacin, with bovine serum albumin in the presence of additives

NASA Astrophysics Data System (ADS)

Kaur, Amandeep; Khan, Imran Ahmd; Banipal, Parampaul Kaur; Banipal, Tarlok Singh

2018-02-01

The current work aims to explore the thermodynamic and conformational aspects for the binding of fluoroquinolone antibacterial drug, levofloxacin (LFC), with bovine serum albumin (BSA) using calorimetric, spectroscopic (UV-visible, fluorescence, circular dichroism, and 1H NMR), dynamic light scattering (DLS) and computational methods (molecular docking). The binding of LFC with BSA at two sequential sites with higher affinity ( 103 M- 1) at the first site has been explored by calorimetry whereas the binding at a single site with affinity of the order of 104 M- 1 has been observed from fluorescence spectroscopy. The calorimetric study in the presence of additives along with docking analysis reveals the significant role of electrostatic, hydrogen bonding, and hydrophobic interactions in the association process. The slight conformational changes in protein as well as the changes in the water network structure around the binding cavity of protein have been observed from spectroscopic and DLS measurements. The LFC induced quenching of BSA fluorescence was observed to be initiated mainly through the static quenching process and this suggests the formation of ground state LFC-BSA association complex. The stronger interactions of LFC in the cavity of Sudlow site I (subdomain IIA) of protein have been explored from site marker calorimetric and molecular docking study.

Non-aqueous Electrode Processing and Construction of Lithium-ion Coin Cells.

PubMed

Stein, Malcolm; Chen, Chien-Fan; Robles, Daniel J; Rhodes, Christopher; Mukherjee, Partha P

2016-02-01

Research into new and improved materials to be utilized in lithium-ion batteries (LIB) necessitates an experimental counterpart to any computational analysis. Testing of lithium-ion batteries in an academic setting has taken on several forms, but at the most basic level lies the coin cell construction. In traditional LIB electrode preparation, a multi-phase slurry composed of active material, binder, and conductive additive is cast out onto a substrate. An electrode disc can then be punched from the dried sheet and used in the construction of a coin cell for electrochemical evaluation. Utilization of the potential of the active material in a battery is critically dependent on the microstructure of the electrode, as an appropriate distribution of the primary components are crucial to ensuring optimal electrical conductivity, porosity, and tortuosity, such that electrochemical and transport interaction is optimized. Processing steps ranging from the combination of dry powder, wet mixing, and drying can all critically affect multi-phase interactions that influence the microstructure formation. Electrochemical probing necessitates the construction of electrodes and coin cells with the utmost care and precision. This paper aims at providing a step-by-step guide of non-aqueous electrode processing and coin cell construction for lithium-ion batteries within an academic setting and with emphasis on deciphering the influence of drying and calendaring.

Non-aqueous Electrode Processing and Construction of Lithium-ion Coin Cells

PubMed Central

Stein, Malcolm; Chen, Chien-Fan; Robles, Daniel J.; Rhodes, Christopher; Mukherjee, Partha P.

2016-01-01

Research into new and improved materials to be utilized in lithium-ion batteries (LIB) necessitates an experimental counterpart to any computational analysis. Testing of lithium-ion batteries in an academic setting has taken on several forms, but at the most basic level lies the coin cell construction. In traditional LIB electrode preparation, a multi-phase slurry composed of active material, binder, and conductive additive is cast out onto a substrate. An electrode disc can then be punched from the dried sheet and used in the construction of a coin cell for electrochemical evaluation. Utilization of the potential of the active material in a battery is critically dependent on the microstructure of the electrode, as an appropriate distribution of the primary components are crucial to ensuring optimal electrical conductivity, porosity, and tortuosity, such that electrochemical and transport interaction is optimized. Processing steps ranging from the combination of dry powder, wet mixing, and drying can all critically affect multi-phase interactions that influence the microstructure formation. Electrochemical probing necessitates the construction of electrodes and coin cells with the utmost care and precision. This paper aims at providing a step-by-step guide of non-aqueous electrode processing and coin cell construction for lithium-ion batteries within an academic setting and with emphasis on deciphering the influence of drying and calendaring. PMID:26863503

The implication of DNA bending energy for nucleosome positioning and sliding.

PubMed

Liu, Guoqing; Xing, Yongqiang; Zhao, Hongyu; Cai, Lu; Wang, Jianying

2018-06-11

Nucleosome not only directly affects cellular processes, such as DNA replication, recombination, and transcription, but also severs as a fundamentally important target of epigenetic modifications. Our previous study indicated that the bending property of DNA is important in nucleosome formation, particularly in predicting the dyad positions of nucleosomes on a DNA segment. Here, we investigated the role of bending energy in nucleosome positioning and sliding in depth to decipher sequence-directed mechanism. The results show that bending energy is a good physical index to predict the free energy in the process of nucleosome reconstitution in vitro. Our data also imply that there are at least 20% of the nucleosomes in budding yeast do not adopt canonical positioning, in which underlying sequences wrapped around histones are structurally symmetric. We also revealed distinct patterns of bending energy profile for distinctly organized chromatin structures, such as well-positioned nucleosomes, fuzzy nucleosomes, and linker regions and discussed nucleosome sliding in terms of bending energy. We proposed that the stability of a nucleosome is positively correlated with the strength of the bending anisotropy of DNA segment, and both accessibility and directionality of nucleosome sliding is likely to be modulated by diverse patterns of DNA bending energy profile.

The Gaseous Phase as a Probe of the Astrophysical Solid Phase Chemistry

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

Abou Mrad, Ninette; Duvernay, Fabrice; Isnard, Robin

2017-09-10

In support of space missions and spectroscopic observations, laboratory experiments on ice analogs enable a better understanding of organic matter formation and evolution in astrophysical environments. Herein, we report the monitoring of the gaseous phase of processed astrophysical ice analogs to determine if the gaseous phase can elucidate the chemical mechanisms and dominant reaction pathways occurring in the solid ice subjected to vacuum ultra-violet (VUV) irradiation at low temperature and subsequently warmed. Simple (CH{sub 3}OH), binary (H{sub 2}O:CH{sub 3}OH, CH{sub 3}OH:NH{sub 3}), and ternary ice analogs (H{sub 2}O:CH{sub 3}OH:NH{sub 3}) were VUV-processed and warmed. The evolution of volatile organic compoundsmore » in the gaseous phase shows a direct link between their relative abundances in the gaseous phase, and the radical and thermal chemistries modifying the initial ice composition. The correlation between the gaseous and solid phases may play a crucial role in deciphering the organic composition of astrophysical objects. As an example, possible solid compositions of the comet Lovejoy are suggested using the abundances of organics in its comae.« less

Electrochemical lectin based biosensors as a label-free tool in glycomics

PubMed Central

Bertók, Tomáš; Katrlík, Jaroslav; Gemeiner, Peter; Tkac, Jan

2016-01-01

Glycans and other saccharide moieties attached to proteins and lipids, or present on the surface of a cell, are actively involved in numerous physiological or pathological processes. Their structural flexibility (that is based on the formation of various kinds of linkages between saccharides) is making glycans superb “identity cards”. In fact, glycans can form more “words” or “codes” (i.e., unique sequences) from the same number of “letters” (building blocks) than DNA or proteins. Glycans are physicochemically similar and it is not a trivial task to identify their sequence, or - even more challenging - to link a given glycan to a particular physiological or pathological process. Lectins can recognise differences in glycan compositions even in their bound state and therefore are most useful tools in the task to decipher the “glycocode”. Thus, lectin-based biosensors working in a label-free mode can effectively complement the current weaponry of analytical tools in glycomics. This review gives an introduction into the area of glycomics and then focuses on the design, analytical performance, and practical utility of lectin-based electrochemical label-free biosensors for the detection of isolated glycoproteins or intact cells. PMID:27239071

Mantle Wedge formation during Subduction Initiation: evidence from the refertilized base of the Oman ophiolitic mantle

NASA Astrophysics Data System (ADS)

Prigent, C.; Guillot, S.; Agard, P.; Godard, M.; Lemarchand, D.; Ulrich, M.

2015-12-01

Although the Oman ophiolite is classically regarded as being the direct analog of oceanic lithosphere created at fast spreading ridges, the geodynamic context of its formation is still highly debated. The other alternative end-member model suggests that this ophiolite entirely formed in a supra-subduction zone setting. The latter one is supported by studies on volcanic sequences whereas studies dealing on the mantle section do not involve a significant influence of subduction processes on its structure and composition. We herein focus on basal peridotites from all along the ophiolite strike in order to decipher and characterize potential fluid/melt transfers relate to subduction processes. Samples were taken across the basal banded unit directly overlying the amphibolitic/granulitic metamorphic sole which represents an accreted part of the lower plate. We carried out a petrological, structural and geochemical study on these rocks and their constitutive minerals. Our results show that basal peridotites range from lherzolites to highly depleted harzburgites in composition. Clinopyroxenes (cpx) display melt impregnation textures and co-crystallized with HT/HP amphiboles (amph), spinels and sulfurs. Major and trace elements of the constitutive minerals indicate that these minerals represent trapped incremental partial melt after hydrous melting. Different cpx-bearing lithologies then result from varying degrees of partial melting and melt extraction. Combined with Boron isotopic data, we demonstrate that fluids responsible for hydrous melting of these ophiolitic basal peridotites are subduction-related, most likely derived from dehydration of the metamorphic sole during its formation in subduction initiation. From these observations and thermal constraints, we interpret the occurrence of these basal lherzolites as representing a freezing front developed by thermal re-equilibration (cooling) during subduction processes: subduction-related hydrous partial melts were extracted at different degrees until getting ultimately trapped, and crystallized cpx, amph and other associated minerals. If our interpretation is correct, the base of the Oman ophiolite could provide the best proxy for the composition of a frozen-in, incipiently forming mantle wedge.

Broad neutralization of calcium-permeable amyloid pore channels with a chimeric Alzheimer/Parkinson peptide targeting brain gangliosides.

PubMed

Di Scala, Coralie; Yahi, Nouara; Flores, Alessandra; Boutemeur, Sonia; Kourdougli, Nazim; Chahinian, Henri; Fantini, Jacques

2016-02-01

Growing evidence supports a role for brain gangliosides in the pathogenesis of neurodegenerative diseases including Alzheimer's and Parkinson's. Recently we deciphered the ganglioside-recognition code controlling specific ganglioside binding to Alzheimer's β-amyloid (Aβ1-42) peptide and Parkinson's disease-associated protein α-synuclein. Cracking this code allowed us to engineer a short chimeric Aβ/α-synuclein peptide that recognizes all brain gangliosides. Here we show that ganglioside-deprived neural cells do no longer sustain the formation of zinc-sensitive amyloid pore channels induced by either Aβ1-42 or α-synuclein, as assessed by single-cell Ca(2+) fluorescence microscopy. Thus, amyloid channel formation, now considered a key step in neurodegeneration, is a ganglioside-dependent process. Nanomolar concentrations of chimeric peptide competitively inhibited amyloid pore formation induced by Aβ1-42 or α-synuclein in cultured neural cells. Moreover, this peptide abrogated the intracellular calcium increases induced by Parkinson's-associated mutant forms of α-synuclein (A30P, E46K and A53T). The chimeric peptide also prevented the deleterious effects of Aβ1-42 on synaptic vesicle trafficking and decreased the Aβ1-42-induced impairment of spontaneous activity in rat hippocampal slices. Taken together, these data show that the chimeric peptide has broad anti-amyloid pore activity, suggesting that a common therapeutic strategy based on the prevention of amyloid-ganglioside interactions is a reachable goal for both Alzheimer's and Parkinson's diseases. Copyright © 2015 Elsevier B.V. All rights reserved.

Deciphering systemic lupus erythematosus-associated serum biomarkers reflecting apoptosis and disease activity.

PubMed

Delfani, P; Sturfelt, G; Gullstrand, B; Carlsson, A; Kassandra, M; Borrebaeck, C A K; Bengtsson, A A; Wingren, C

2017-04-01

Systemic lupus erythematosus (SLE) is a severe chronic inflammatory autoimmune connective tissue disease. Despite major efforts, SLE remains a poorly understood disease with unpredictable course, unknown etiology and complex pathogenesis. Apoptosis combined with deficiency in clearing apoptotic cells is an important etiopathogenic event in SLE, which could contribute to the increased load of potential autoantigen(s); however, the lack of disease-specific protein signatures deciphering SLE and the underlying biological processes is striking and represents a key limitation. In this retrospective pilot study, we explored the immune system as a specific sensor for disease, in order to advance our understanding of SLE. To this end, we determined multiplexed serum protein expression profiles of crude SLE serum samples, using antibody microarrays. The aim was to identify differential immunoprofiles, or snapshots of the immune response modulated by the disease, reflecting apoptosis, a key process in the etiology of SLE and disease activity. The results showed that multiplexed panels of SLE-associated serum biomarkers could be decoded, in particular reflecting disease activity, but potentially the apoptosis process as well. While the former biomarkers could display a potential future use for prognosis, the latter biomarkers might help shed further light on the apoptosis process taking place in SLE.

Network analysis reveals the recognition mechanism for complex formation of mannose-binding lectins

NASA Astrophysics Data System (ADS)

Jian, Yiren; Zhao, Yunjie; Zeng, Chen

The specific carbohydrate binding of lectin makes the protein a powerful molecular tool for various applications including cancer cell detection due to its glycoprotein profile on the cell surface. Most biologically active lectins are dimeric. To understand the structure-function relation of lectin complex, it is essential to elucidate the short- and long-range driving forces behind the dimer formation. Here we report our molecular dynamics simulations and associated dynamical network analysis on a particular lectin, i.e., the mannose-binding lectin from garlic. Our results, further supported by sequence coevolution analysis, shed light on how different parts of the complex communicate with each other. We propose a general framework for deciphering the recognition mechanism underlying protein-protein interactions that may have potential applications in signaling pathways.

Deciphering Martian climatic history using returned samples

NASA Technical Reports Server (NTRS)

Paige, D. A.; Krieger, D. B.; Brigham, C. A.

1988-01-01

By necessity, a Mars sample return mission must sample the upper few meters of the Martian surface. This material was subjected to a wide variety of physical processes. Presently, the most important processes are believed to be wind-driven erosion and deposition, and water ice accumulation at higher latitudes. A sample return mission represents an opportunity to better understand and quantify these important geological processes. By obtaining sample cores at key locations, it may be possible to interpret much of recent Martian climatic history.

Time to Translate: Deciphering the Codon in the Classroom

ERIC Educational Resources Information Center

Firooznia, Fardad

2015-01-01

I describe and evaluate a fun and simple role-playing exercise that allows students to actively work through the process of translation. This exercise can easily be completed during a 50-minute class period, with time to review the steps and contemplate complications such as the effects of various types of mutations.

Gene screening of Wharton's jelly derived stem cells.

PubMed

Mechiche Alami, S; Velard, F; Draux, F; Siu Paredes, F; Josse, J; Lemaire, F; Gangloff, S C; Graesslin, O; Laurent-Maquin, D; Kerdjoudj, H

2014-01-01

Stem cells are the most powerful candidate for the treatment of various diseases. Suitable stem cell source should be harvested with minimal invasive procedure, found in great quantity, and transplanted with no risk of immune response and tumor formation. Fetal derived stem cells have been introduced as an excellent alternative to adult and embryonic stem cells use, but unfortunately, their degree of "stemness" and molecular characterization is still unclear. Several studies have been performed deciphering whether fetal stem cells meet the needs of regenerative medicine. We believe that a transcriptomic screening of Wharton's jelly stem cells will bring insights on cell population features.

Network Analysis Reveals the Recognition Mechanism for Mannose-binding Lectins

NASA Astrophysics Data System (ADS)

Zhao, Yunjie; Jian, Yiren; Zeng, Chen; Computational Biophysics Lab Team

The specific carbohydrate binding of mannose-binding lectin (MBL) protein in plants makes it a very useful molecular tool for cancer cell detection and other applications. The biological states of most MBL proteins are dimeric. Using dynamics network analysis on molecular dynamics (MD) simulations on the model protein of MBL, we elucidate the short- and long-range driving forces behind the dimer formation. The results are further supported by sequence coevolution analysis. We propose a general framework for deciphering the recognition mechanism underlying protein-protein interactions that may have potential applications in signaling pathways.

Chemical protein synthesis: Inventing synthetic methods to decipher how proteins work.

PubMed

Kent, Stephen

2017-09-15

Total chemical synthesis of proteins has been rendered practical by the chemical ligation principle: chemoselective condensation of unprotected peptide segments equipped with unique, mutually reactive functional groups, enabled by formation of a non-native replacement for the peptide bond. Ligation chemistries are briefly described, including native chemical ligation - thioester-mediated, amide-forming reaction at Xaa-Cys sites - and its extensions. Case studies from the author's own works are used to illustrate the utility and applications of chemical protein synthesis. Selected recent developments in the field are briefly discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

A ‘tool box’ for deciphering neuronal circuits in the developing chick spinal cord

PubMed Central

Hadas, Yoav; Etlin, Alex; Falk, Haya; Avraham, Oshri; Kobiler, Oren; Panet, Amos; Lev-Tov, Aharon; Klar, Avihu

2014-01-01

The genetic dissection of spinal circuits is an essential new means for understanding the neural basis of mammalian behavior. Molecular targeting of specific neuronal populations, a key instrument in the genetic dissection of neuronal circuits in the mouse model, is a complex and time-demanding process. Here we present a circuit-deciphering ‘tool box’ for fast, reliable and cheap genetic targeting of neuronal circuits in the developing spinal cord of the chick. We demonstrate targeting of motoneurons and spinal interneurons, mapping of axonal trajectories and synaptic targeting in both single and populations of spinal interneurons, and viral vector-mediated labeling of pre-motoneurons. We also demonstrate fluorescent imaging of the activity pattern of defined spinal neurons during rhythmic motor behavior, and assess the role of channel rhodopsin-targeted population of interneurons in rhythmic behavior using specific photoactivation. PMID:25147209

Identification of the first diphenyl ether gene cluster for pestheic acid biosynthesis in plant endophyte Pestalotiopsis fici.

PubMed

Xu, Xinxin; Liu, Ling; Zhang, Fan; Wang, Wenzhao; Li, Jinyang; Guo, Liangdong; Che, Yongsheng; Liu, Gang

2014-01-24

The diphenyl ether pestheic acid was isolated from the endophytic fungus Pestalotiopsis fici, which is proposed to be the biosynthetic precursor of the unique chloropupukeananes. The pestheic acid biosynthetic gene (pta) cluster was identified in the fungus through genome scanning. Sequence analysis revealed that this gene cluster encodes a nonreducing polyketide synthase, a number of modification enzymes, and three regulators. Gene disruption and intermediate analysis demonstrated that the biosynthesis proceeded through formation of the polyketide backbone, cyclization of a polyketo acid to a benzophenone, chlorination, and formation of the diphenyl ether skeleton through oxidation and hydrolyzation. A dihydrogeodin oxidase gene, ptaE, was essential for diphenyl ether formation, and ptaM encoded a flavin-dependent halogenase catalyzing chlorination in the biosynthesis. Identification of the pta cluster laid the foundation to decipher the genetic and biochemical mechanisms involved in the pathway. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Permian Whitehill Formation (Karoo Basin, South Africa): deciphering the complexity and potential of an unconventional gas resource

NASA Astrophysics Data System (ADS)

Götz, Annette E.

2014-05-01

A key energy policy objective of the South African government is to diversify its energy mix from coal which constitutes 85% of the current mix. Gas will play a key role in the future South African economy with demand coming from electricity generation and gas-to-liquids projects. A study on world shale reserves conducted by the Energy Information Agency (EIA) in 2011 concluded that there could be as much as 485 Tcf recoverable reserves of shale gas in the South African Karoo Basin. However, the true extent and commercial viability is still unknown, due to the lack of exploration drilling and modern 3D seismic. The present study compiles existing data from literature review and new data from outcrop analogue studies on the Permian Whitehill Formation, the main target formation for future shale gas production, including thickness, depth, maturity, TOC, lithologies, sedimentary and organic facies, and dolerite occurrence to provide a first reference dataset for further investigations and resource estimates.

Career Survival: Strategic Job and Role Planning. Pfeiffer Career Series.

ERIC Educational Resources Information Center

Schein, Edgar H.

This book was designed to help managers and employees to decipher the two crucial elements in work design and human resource planning: the role network that surrounds every position and the key stakeholders whose expectations define the essence of the job. It provides a structured process for analyzing one's own job as well as the jobs of…

Decoding transcriptional enhancers: Evolving from annotation to functional interpretation

PubMed Central

Engel, Krysta L.; Mackiewicz, Mark; Hardigan, Andrew A.; Myers, Richard M.; Savic, Daniel

2016-01-01

Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research. PMID:27224938

Decoding transcriptional enhancers: Evolving from annotation to functional interpretation.

PubMed

Engel, Krysta L; Mackiewicz, Mark; Hardigan, Andrew A; Myers, Richard M; Savic, Daniel

2016-09-01

Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research. Copyright © 2016 Elsevier Ltd. All rights reserved.

Amyloidosis

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

Glenner, G.G.; Osserman, E.F.

1986-01-01

The subjects covered in this Symposium range through almost every clinical medical specialty. From an average of one paper in each of the past three Symposiums, the explosive interest in cerebral amyloidosis has led to the presentation of 12 papers on this subject in the present volume. The genetically predisposed familial amyloidotic processes, such as the polyneuropathies and familial Mediterranean fever have also stimulated extensive and intriguing investigations which have revealed the striking effect of a single amino acid substitution in transforming a normal protein into a lethal ''amyloidogenic'' one. This Symposium clearly depicts the advances since the first amyloidmore » fibril protein was definitively identified and defined 14 years ago. Since all amyloid fibril proteins so far described are variants of normal proteins, attention to gene abnormalities now becomes a significant focus as well as the pathogenic sequences which lead in these cases to twisted BETA-pleated sheet (amyloid) fibril formation. Tentative concepts such as the ''amyloidogenic protein precursor of the fibril,'' ''proteolysis as one mechanism of fibril formation,'' ''Congo red birefringence as a marker for the twisted BETA-pleated sheet protein'' are now substantiated by recurring confirmation. Even a prophylactic treatment for one of the amyloidotic conditions, familial Mediterranean fever, is now available. Predictably, as the pathogeneses of the amyloid diseases are individually deciphered, highly specific and directed therapies will evolve to treat their devastated victims.« less

Primitive Fine-Grained Matrix in the Unequilbrated Enstatite Chondrites

NASA Technical Reports Server (NTRS)

Weisberg, M. K.; Zolensky, M. E.; Kimura, M.; Ebel, D. S.

2014-01-01

Enstatite chondrites (EC) have important implications for constraining conditions in the early solar system and for understanding the evolution of the Earth and other inner planets. They are among the most reduced solar system materials as reflected in their mineral compositions and assemblage. They are the only chondrites with oxygen as well as Cr, Ti, Ni and Zn stable isotope compositions similar to the earth and moon and most are completely dry, lacking any evidence of hydrous alteration; the only exception are EC clasts in the Kaidun breccia which have hydrous minerals. Thus, ECs likely formed within the snow line and are good candidates to be building blocks of the inner planets. Our goals are to provide a more detailed characterization the fine-grained matrix in E3 chondrites, understand its origin and relationship to chondrules, decipher the relationship between EH and EL chondrites and compare E3 matrix to matrices in C and O chondrites as well as other fine-grained solar system materials. Is E3 matrix the dust remaining from chondrule formation or a product of parent body processing or both?

Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses.

PubMed

Amrani, Amira; van Helden, Jacques; Bergon, Aurélie; Aouane, Aicha; Ben Hania, Wajdi; Tamburini, Christian; Loriod, Béatrice; Imbert, Jean; Ollivier, Bernard; Pradel, Nathalie; Dolla, Alain

2016-08-01

Desulfovibrio piezophilus strain C1TLV30(T) is a mesophilic piezophilic sulfate-reducer isolated from Wood Falls at 1700 m depth in the Mediterranean Sea. In this study, we analysed the effect of the hydrostatic pressure on this deep-sea living bacterium at the physiologic and transcriptomic levels. Our results showed that lactate oxidation and energy metabolism were affected by the hydrostatic pressure. Especially, acetyl-CoA oxidation pathway and energy conservation through hydrogen and formate recycling would be more important when the hydrostatic pressure is above (26 MPa) than below (0.1 MPa) the optimal one (10 MPa). This work underlines also the role of the amino acid glutamate as a piezolyte for the Desulfovibrio genus. The transcriptomic analysis revealed 146 differentially expressed genes emphasizing energy production and conversion, amino acid transport and metabolism and cell motility and signal transduction mechanisms as hydrostatic pressure responding processes. This dataset allowed us to identify a sequence motif upstream of a subset of differentially expressed genes as putative pressure-dependent regulatory element. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Deciphering Debris Disk Structure with the Submillimeter Array

NASA Astrophysics Data System (ADS)

MacGregor, Meredith Ann

2018-01-01

More than 20% of nearby main sequence stars are surrounded by dusty disks continually replenished via the collisional erosion of planetesimals, larger bodies similar to asteroids and comets in our own Solar System. The material in these ‘debris disks’ is directly linked to the larger bodies such as planets in the system. As a result, the locations, morphologies, and physical properties of dust in these disks provide important probes of the processes of planet formation and subsequent dynamical evolution. Observations at millimeter wavelengths are especially critical to our understanding of these systems, since they are dominated by larger grains that do not travel far from their origin and therefore reliably trace the underlying planetesimal distribution. The Submillimeter Array (SMA) plays a key role in advancing our understanding of debris disks by providing sensitivity at the short baselines required to determine the structure of wide-field disks, such as the HR 8799 debris disk. Many of these wide-field disks are among the closest systems to us, and will serve as cornerstone templates for the interpretation of more distant, less accessible systems.

A family affair: A Ral-exocyst-centered network links Ras, Rac, Rho signaling to control cell migration.

PubMed

Zago, Giulia; Biondini, Marco; Camonis, Jacques; Parrini, Maria Carla

2017-05-12

Cell migration is central to many developmental, physiologic and pathological processes, including cancer progression. The Ral GTPases (RalA and RalB) which act down-stream the Ras oncogenes, are key players in the coordination between membrane trafficking and actin polymerization. A major direct effector of Ral, the exocyst complex, works in polarized exocytosis and is at the center of multiple protein-protein interactions that support cell migration by promoting protrusion formation, front-rear polarization, and extra-cellular matrix degradation. In this review we describe the recent advancements in deciphering the molecular mechanisms underlying this role of Ral via exocyst on cell migration. Among others, we will discuss the recently identified cross-talk between Ral and Rac1 pathways: exocyst binds to a negative regulator (the RacGAP SH3BP1) and to the major effector (the Wave Regulatory Complex, WRC) of Rac1, the master regulator of protrusions. Next challenge will be to better characterize the dynamics in space and in time of these molecular interplays, to better understand the pleiotropic functions of Ral in both normal and cancer cells.

Deposition dynamics of multi-solvent bioinks

NASA Astrophysics Data System (ADS)

Kaneelil, Paul; Pack, Min; Cui, Chunxiao; Han, Li-Hsin; Sun, Ying

2017-11-01

Inkjet printing cellular scaffolds using bioinks is gaining popularity due to the advancement of printing technology as well as the growing demands of regenerative medicine. Numerous studies have been conducted on printing scaffolds of biomimetic structures that support the cell production of human tissues. However, the underlying physics of the deposition dynamics of bioinks remains elusive. Of particular interest is the unclear deposition dynamics of multi-solvent bioinks, which is often used to tune the micro-architecture formation. Here we systematically studied the effects of jetting frequency, solvent properties, substrate wettability, and temperature on the three-dimensional deposition patterns of bioinks made of Methacrylated Gelatin and Carboxylated Gelatin. The microflows inside the inkjet-printed picolitre drops were visualized using fluorescence tracer particles to decipher the complex processes of multi-solvent evaporation and solute self-assembly. The evolution of droplet shape was observed using interferometry. With the integrated techniques, the interplay of solvent evaporation, biopolymer deposition, and multi-drop interactions were directly observed for various ink and substrate properties, and printing conditions. Such knowledge enables the design and fabrication of a variety of tissue engineering scaffolds for potential use in regenerative medicine.

SHIP2 Regulates Lumen Generation, Cell Division, and Ciliogenesis through the Control of Basolateral to Apical Lumen Localization of Aurora A and HEF 1.

PubMed

Hamze-Komaiha, Ola; Sarr, Sokavuth; Arlot-Bonnemains, Yannick; Samuel, Didier; Gassama-Diagne, Ama

2016-12-06

Lumen formation during epithelial morphogenesis requires the creation of a luminal space at cell interfaces named apical membrane-initiation sites (AMISs). This is dependent upon integrated signaling from mechanical and biochemical cues, vesicle trafficking, cell division, and processes tightly coupled to ciliogenesis. Deciphering relationships between polarity determinants and lumen or cilia generation remains a fundamental issue. Here, we report that Src homology 2 domain-containing inositol 5-phosphatase 2 (SHIP2), a basolateral determinant of polarity, regulates RhoA-dependent actin contractility and cell division to form AMISs. SHIP2 regulates mitotic spindle alignment. SHIP2 is expressed in G1 phase, whereas Aurora A kinase is enriched in mitosis. SHIP2 binds Aurora A kinase and the scaffolding protein HEF1 and promotes their basolateral localization at the expense of their luminal expression connected with cilia resorption. Furthermore, SHIP2 expression increases cilia length. Thus, our findings offer new insight into the relationships among basolateral proteins, lumen generation, and ciliogenesis. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

An Interaction Landscape of Ubiquitin Signaling.

PubMed

Zhang, Xiaofei; Smits, Arne H; van Tilburg, Gabrielle B A; Jansen, Pascal W T C; Makowski, Matthew M; Ovaa, Huib; Vermeulen, Michiel

2017-03-02

Intracellular signaling via the covalent attachment of different ubiquitin linkages to protein substrates is fundamental to many cellular processes. Although linkage-selective ubiquitin interactors have been studied on a case-by-case basis, proteome-wide analyses have not been conducted yet. Here, we present ubiquitin interactor affinity enrichment-mass spectrometry (UbIA-MS), a quantitative interaction proteomics method that makes use of chemically synthesized diubiquitin to enrich and identify ubiquitin linkage interactors from crude cell lysates. UbIA-MS reveals linkage-selective diubiquitin interactions in multiple cell types. For example, we identify TAB2 and TAB3 as novel K6 diubiquitin interactors and characterize UCHL3 as a K27-linkage selective interactor that regulates K27 polyubiquitin chain formation in cells. Additionally, we show a class of monoubiquitin and K6 diubiquitin interactors whose binding is induced by DNA damage. We expect that our proteome-wide diubiquitin interaction landscape and established workflows will have broad applications in the ongoing efforts to decipher the complex language of ubiquitin signaling. Copyright © 2017 Elsevier Inc. All rights reserved.

A biplanar X-ray approach for studying the 3D dynamics of human track formation.

PubMed

Hatala, Kevin G; Perry, David A; Gatesy, Stephen M

2018-05-09

Recent discoveries have made hominin tracks an increasingly prevalent component of the human fossil record, and these data have the capacity to inform long-standing debates regarding the biomechanics of hominin locomotion. However, there is currently no consensus on how to decipher biomechanical variables from hominin tracks. These debates can be linked to our generally limited understanding of the complex interactions between anatomy, motion, and substrate that give rise to track morphology. These interactions are difficult to study because direct visualization of the track formation process is impeded by foot and substrate opacity. To address these obstacles, we developed biplanar X-ray and computer animation methods, derived from X-ray Reconstruction of Moving Morphology (XROMM), to analyze the 3D dynamics of three human subjects' feet as they walked across four substrates (three deformable muds and rigid composite panel). By imaging and reconstructing 3D positions of external markers, we quantified the 3D dynamics at the foot-substrate interface. Foot shape, specifically heel and medial longitudinal arch deformation, was significantly affected by substrate rigidity. In deformable muds, we found that depths measured across tracks did not directly reflect the motions of the corresponding regions of the foot, and that track outlines were not perfectly representative of foot size. These results highlight the complex, dynamic nature of track formation, and the experimental methods presented here offer a promising avenue for developing and refining methods for accurately inferring foot anatomy and gait biomechanics from fossil hominin tracks. Copyright © 2018 Elsevier Ltd. All rights reserved.

Deciphering cGMP signatures and cGMP-dependent pathways in plant defence

PubMed Central

Meier, Stuart; Madeo, Laura; Ederli, Luisa; Donaldson, Lara; Gehring, Chris

2009-01-01

The second messenger, 3′,5′-cyclic monophosphate (cGMP), is a critical component of many different processes in plants while guanylyl cyclases that catalyse the formation of cGMP from GTP have remained somewhat elusive in higher plants. Consequently, two major aims are the discovery of novel GCs and the identification of cGMP mediated processes. Recently, we have reported temporal signatures of ozone (O3)-induced hydrogen peroxide (H2O2) and nitric oxide (NO) generation, their effect on cGMP generation, and consequent transcriptional changes of genes diagnostic for stress responses in tobacco. We demonstrated that O3 and NO induced early transcriptional activation of the scavenger encoding proteins, alternative oxidase (AOX1a), glutathione peroxidase (GPX) and the induction of ethylene production through aminocyclopropancarboxylic acid synthase (ACS2) are cGMP-independent. By contrast, the early response of the phenylalanine ammonia lyase gene (PALa) and the late response of the gene encoding the pathogenesis-related protein (PR1a) show critical dependence on cGMP. Here we show differential cGMP responses to virulent and avirulent Pseudomonas syringae strains and propose that host-pathogen recognition and/or down-stream processes are transduced by complex cGMP signatures. This is in accordance with the identification of a growing number of multi-domain molecules in Arabidopsis that are reported to contain putative functional GC catalytic centers. PMID:19794847

Ca-Mediated Electroformation of Cell-Sized Lipid Vesicles

PubMed Central

Tao, Fei; Yang, Peng

2015-01-01

Cell-sized lipid giant unilamellar vesicles (GUVs) are formed when lipid molecules self-assemble to construct a single bilayer compartment with similar morphology to living cells. The physics of self-assembly process is only generally understood and the size distribution of GUVs tends to be very polydisperse. Herein we report a strategy for the production of controlled size distributions of GUVs by a novel mechanism dissecting the mediation ability of calcium (Ca) on the conventional electroformation of GUVs. We finely construct both of the calcium ion (Ca2+) and calcium carbonate (CaCO3) mineral adsorption layers on a lipid film surface respectively during the electroformation of GUVs. It is found that Ca2+ Slip plane polarized by alternating electric field could induce a pattern of electroosmotic flow across the surface, and thus confine the fusion and growth of GUVs to facilitate the formation of uniform GUVs. The model is further improved by directly using CaCO3 that is in situ formed on a lipid film surface, providing a GUV population with narrow polydispersity. The two models deciphers the new biological function of calcium on the birth of cell-like lipid vesicles, and thus might be potentially relevant to the construction of new model to elucidate the cellular development process. PMID:25950604

Ca-mediated electroformation of cell-sized lipid vesicles.

PubMed

Tao, Fei; Yang, Peng

2015-05-07

Cell-sized lipid giant unilamellar vesicles (GUVs) are formed when lipid molecules self-assemble to construct a single bilayer compartment with similar morphology to living cells. The physics of self-assembly process is only generally understood and the size distribution of GUVs tends to be very polydisperse. Herein we report a strategy for the production of controlled size distributions of GUVs by a novel mechanism dissecting the mediation ability of calcium (Ca) on the conventional electroformation of GUVs. We finely construct both of the calcium ion (Ca(2+)) and calcium carbonate (CaCO3) mineral adsorption layers on a lipid film surface respectively during the electroformation of GUVs. It is found that Ca(2+) Slip plane polarized by alternating electric field could induce a pattern of electroosmotic flow across the surface, and thus confine the fusion and growth of GUVs to facilitate the formation of uniform GUVs. The model is further improved by directly using CaCO3 that is in situ formed on a lipid film surface, providing a GUV population with narrow polydispersity. The two models deciphers the new biological function of calcium on the birth of cell-like lipid vesicles, and thus might be potentially relevant to the construction of new model to elucidate the cellular development process.

Simulating Electrophoresis.

ERIC Educational Resources Information Center

Moertel, Cheryl; Frutiger, Bruce

1996-01-01

Describes a DNA fingerprinting simulation that uses vegetable food coloring and plastic food containers instead of DNA and expensive gel electrophoresis chambers. Allows students to decipher unknown combinations of dyes in a method similar to that used to decipher samples of DNA in DNA fingerprint techniques. (JRH)

Cooperative Interactions between 480 kDa Ankyrin-G and EB Proteins Assemble the Axon Initial Segment.

PubMed

Fréal, Amélie; Fassier, Coralie; Le Bras, Barbara; Bullier, Erika; De Gois, Stéphanie; Hazan, Jamilé; Hoogenraad, Casper C; Couraud, François

2016-04-20

The axon initial segment (AIS) is required for generating action potentials and maintaining neuronal polarity. Significant progress has been made in deciphering the basic building blocks composing the AIS, but the underlying mechanisms required for AIS formation remains unclear. The scaffolding protein ankyrin-G is the master-organizer of the AIS. Microtubules and their interactors, particularly end-binding proteins (EBs), have emerged as potential key players in AIS formation. Here, we show that the longest isoform of ankyrin-G (480AnkG) selectively associates with EBs via its specific tail domain and that this interaction is crucial for AIS formation and neuronal polarity in cultured rodent hippocampal neurons. EBs are essential for 480AnkG localization and stabilization at the AIS, whereas 480AnkG is required for the specific accumulation of EBs in the proximal axon. Our findings thus provide a conceptual framework for understanding how the cooperative relationship between 480AnkG and EBs induces the assembly of microtubule-AIS structures in the proximal axon. Neuronal polarity is crucial for the proper function of neurons. The assembly of the axon initial segment (AIS), which is the hallmark of early neuronal polarization, relies on the longest 480 kDa ankyrin-G isoform. The microtubule cytoskeleton and its interacting proteins were suggested to be early key players in the process of AIS formation. In this study, we show that the crosstalk between 480 kDa ankyrin-G and the microtubule plus-end tracking proteins, EBs, at the proximal axon is decisive for AIS assembly and neuronal polarity. Our work thus provides insight into the functional mechanisms used by 480 kDa ankyrin-G to drive the AIS formation and thereby to establish neuronal polarity. Copyright © 2016 the authors 0270-6474/16/364421-13$15.00/0.

DECIPHERING NATURALLY-OCCURRING PB CONTAMINATION IMPACTING DRINKING WATER WELLS: SHAKER VILLAGE CATCHMENT, MAINE.

EPA Science Inventory

Trace Pb concentrations in groundwater within glacial deposits across Maine fluctuate considerably. Deciphering the distribution and sources of naturally occurring Pb in groundwater with only the use of conventional anomaly identification techniques presents a challenge. In a rep...

50-Ma Initiation of Hawaiian-Emperor Bend Records Major Change in Pacific Plate Motion

NASA Astrophysics Data System (ADS)

Sharp, Warren D.; Clague, David A.

2006-09-01

The Hawaiian-Emperor bend has played a prominent yet controversial role in deciphering past Pacific plate motions and the tempo of plate motion change. New ages for volcanoes of the central and southern Emperor chain define large changes in volcanic migration rate with little associated change in the chain's trend, which suggests that the bend did not form by slowing of the Hawaiian hot spot. Initiation of the bend near Kimmei seamount about 50 million years ago (MA) was coincident with realignment of Pacific spreading centers and early magmatism in western Pacific arcs, consistent with formation of the bend by changed Pacific plate motion.

Deciphering the glycosaminoglycan code with the help of microarrays.

PubMed

de Paz, Jose L; Seeberger, Peter H

2008-07-01

Carbohydrate microarrays have become a powerful tool to elucidate the biological role of complex sugars. Microarrays are particularly useful for the study of glycosaminoglycans (GAGs), a key class of carbohydrates. The high-throughput chip format enables rapid screening of large numbers of potential GAG sequences produced via a complex biosynthesis while consuming very little sample. Here, we briefly highlight the most recent advances involving GAG microarrays built with synthetic or naturally derived oligosaccharides. These chips are powerful tools for characterizing GAG-protein interactions and determining structure-activity relationships for specific sequences. Thereby, they contribute to decoding the information contained in specific GAG sequences.

Mathematics and biology: a Kantian view on the history of pattern formation theory.

PubMed

Roth, Siegfried

2011-12-01

Driesch's statement, made around 1900, that the physics and chemistry of his day were unable to explain self-regulation during embryogenesis was correct and could be extended until the year 1972. The emergence of theories of self-organisation required progress in several areas including chemistry, physics, computing and cybernetics. Two parallel lines of development can be distinguished which both culminated in the early 1970s. Firstly, physicochemical theories of self-organisation arose from theoretical (Lotka 1910-1920) and experimental work (Bray 1920; Belousov 1951) on chemical oscillations. However, this research area gained broader acceptance only after thermodynamics was extended to systems far from equilibrium (1922-1967) and the mechanism of the prime example for a chemical oscillator, the Belousov-Zhabotinski reaction, was deciphered in the early 1970s. Secondly, biological theories of self-organisation were rooted in the intellectual environment of artificial intelligence and cybernetics. Turing wrote his The chemical basis of morphogenesis (1952) after working on the construction of one of the first electronic computers. Likewise, Gierer and Meinhardt's theory of local activation and lateral inhibition (1972) was influenced by ideas from cybernetics. The Gierer-Meinhardt theory provided an explanation for the first time of both spontaneous formation of spatial order and of self-regulation that proved to be extremely successful in elucidating a wide range of patterning processes. With the advent of developmental genetics in the 1980s, detailed molecular and functional data became available for complex developmental processes, allowing a new generation of data-driven theoretical approaches. Three examples of such approaches will be discussed. The successes and limitations of mathematical pattern formation theory throughout its history suggest a picture of the organism, which has structural similarity to views of the organic world held by the philosopher Immanuel Kant at the end of the eighteenth century. © The Author(s) 2011. This article is published with open access at Springerlink.com

77 FR 24554 - Culturally Significant Objects Imported for Exhibition; Determinations: “Quay Brothers: On...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-24

... DEPARTMENT OF STATE [Public Notice 7855] Culturally Significant Objects Imported for Exhibition; Determinations: ``Quay Brothers: On Deciphering the Pharmacist's Prescription for Lip-Reading Puppets'' AGENCY...: On Deciphering the Pharmacist's Prescription for Lip-Reading Puppets'' imported from abroad for...

Toward a mechanism-based understanding of skeletal formation: Toolbox for biomineralization past, present, and future

NASA Astrophysics Data System (ADS)

Dove, P. M.; Wallace, A. F.; Stephenson, A. E.; Wang, D. E.; Hamm, L.; de Yoreo, J. J.

2008-05-01

Since the onset of the Cambrian radiation (~540 Ma), organisms have developed the ability to control the nucleation and growth of amorphous and crystalline earth materials to form skeletal structures. Observations that similar skeletal materials are utilized across multiple branches on the eukaryotic tree of life are cited as evidence that biomineralization strategies evolved independently by similar biochemical pathways that developed early in evolutionary history (A. Knoll). An understanding of these relations is critical to deciphering earth history, yet until recently, studies of biomineral formation were primarily based upon descriptive approaches focused on morphology. Insights into mineralization processes were inferred largely from macroscopic experiments and structural characterizations. Over the last ten years, we have pursued the long-term goal of establishing a mechanistic understanding of biologically controlled mineralization. Through molecular-scale studies of calcium carbonate growth using in situ atomic force microscopy and computational methods, our approach has been to design simple model systems that link direct measurements of growth with the underlying chemical interactions. Recent additions to the toolbox of insights for mineral formation and compositional signatures include: 1) Shape is a kinetic effect of differential energy barriers to solute attachment/detachment and stereochemical relationships between crystal and growth modifier.; 2) From simple amino acids to peptides and full proteins, acidic biomolecules enhance mineralization rate up to 25X by a systematic relation. This suggests a functional role for aspartate- and glutamate-enriched macromolecules long-known to be associated with calcification.; 3) Acidic biomolecules promote uptake of impurities such as magnesium by 2-3 mol%. This enhancement corresponds to a temperature difference of 7- 14°C in proxy models that correlate Mg content with temperature. Anecdotal evidence suggests water structure in confined biomineralization environments may have important, yet-unrecognized roles in biomolecule-solute- mineral interactions. With the realization that biogenic minerals often form by nonclassical processes from amorphous precursors, new studies are focused on establishing factors that drive the transformation of intermediate phases to final biomineral products. By developing model systems to probe how biological substrates can modulate the onset of mineral formation, we are working to establish 1) Principles of mineral formation by nonclassical processes and influences on resultant signatures; 2) Thermodynamic and kinetic role(s) of the organic matrix as a trigger/inhibitor to the timing and location of mineral formation; and 3) Interplay of solvation and organic matrix in polymorph selection. The next 10 years promise to be an exciting time of uncovering how skeletal formation is modulated by a rich biochemical machinery at sites of mineralization while also providing insights to phylogenetic relations.

The Hubble Deep UV Legacy Survey (HDUV)

NASA Astrophysics Data System (ADS)

Montes, Mireia; Oesch, Pascal

2015-08-01

Deep HST imaging has shown that the overall star formation density and UV light density at z>3 is dominated by faint, blue galaxies. Remarkably, very little is known about the equivalent galaxy population at lower redshifts. Understanding how these galaxies evolve across the epoch of peak cosmic star-formation is key to a complete picture of galaxy evolution. Here, we present a new HST WFC3/UVIS program, the Hubble Deep UV (HDUV) legacy survey. The HDUV is a 132 orbit program to obtain deep imaging in two filters (F275W and F336W) over the two CANDELS Deep fields. We will cover ~100 arcmin2 sampling the rest-frame far-UV at z>~0.5, this will provide a unique legacy dataset with exquisite HST multi-wavelength imaging as well as ancillary HST grism NIR spectroscopy for a detailed study of faint, star-forming galaxies at z~0.5-2. The HDUV will enable a wealth of research by the community, which includes tracing the evolution of the FUV luminosity function over the peak of the star formation rate density from z~3 down to z~0.5, measuring the physical properties of sub-L* galaxies, and characterizing resolved stellar populations to decipher the build-up of the Hubble sequence from sub-galactic clumps. This poster provides an overview of the HDUV survey and presents the reduced data products and catalogs which will be released to the community, reaching down to 27.5-28.0 mag at 5 sigma. By directly sampling the rest-frame far-UV at z>~0.5, this will provide a unique legacy dataset with exquisite HST multi-wavelength imaging as well as ancillary HST grism NIR spectroscopy for a detailed study of faint, star-forming galaxies at z~0.5-2. The HDUV will enable a wealth of research by the community, which includes tracing the evolution of the FUV luminosity function over the peak of the star formation rate density from z~3 down to z~0.5, measuring the physical properties of sub-L* galaxies, and characterizing resolved stellar populations to decipher the build-up of the Hubble sequence from sub-galactic clumps. This poster provides an overview of the HDUV survey and presents reduced data products and catalogs which will be released to the community.

Deciphering the Minimal Algorithm for Development and Information-genesis

NASA Astrophysics Data System (ADS)

Li, Zhiyuan; Tang, Chao; Li, Hao

During development, cells with identical genomes acquires different fates in a highly organized manner. In order to decipher the principles underlining development, we used C.elegans as the model organism. Based on a large set of microscopy imaging, we first constructed a ``standard worm'' in silico: from the single zygotic cell to about 500 cell stage, the lineage, position, cell-cell contact and gene expression dynamics are quantified for each cell in order to investigate principles underlining these intensive data. Next, we reverse-engineered the possible gene-gene/cell-cell interaction rules that are capable of running a dynamic model recapitulating the early fate decisions during C.elegans development. we further formulized the C.elegans embryogenesis in the language of information genesis. Analysis towards data and model uncovered the global landscape of development in the cell fate space, suggested possible gene regulatory architectures and cell signaling processes, revealed diversity and robustness as the essential trade-offs in development, and demonstrated general strategies in building multicellular organisms.

Deciphering the Mode of Action of the Processive Polysaccharide Modifying Enzyme Dermatan Sulfate Epimerase 1 by Hydrogen-Deuterium Exchange Mass Spectrometry.

PubMed

Tykesson, Emil; Mao, Yang; Maccarana, Marco; Pu, Yi; Gao, Jinshan; Lin, Cheng; Zaia, Joseph; Westergren-Thorsson, Gunilla; Ellervik, Ulf; Malmström, Lars; Malmström, Anders

2016-02-01

Distinct from template-directed biosynthesis of nucleic acids and proteins, the enzymatic synthesis of heterogeneous polysaccharides is a complex process that is difficult to study using common analytical tools. Therefore, the mode of action and processivity of those enzymes are largely unknown. Dermatan sulfate epimerase 1 (DS-epi1) is the predominant enzyme during the formation of iduronic acid residues in the glycosaminoglycan dermatan sulfate. Using recombinant DS-epi1 as a model enzyme, we describe a tandem mass spectrometry-based method to study the mode of action of polysaccharide processing enzymes. The enzyme action on the substrate was monitored by hydrogen-deuterium exchange mass spectrometry and the sequence information was then fed into mathematical models with two different assumptions of the mode of action for the enzyme: processive reducing end to non-reducing end, and processive non-reducing end to reducing end. Model data was scored by correlation to experimental data and it was found that DS-epi1 attacks its substrate on a random position, followed by a processive mode of modification towards the non-reducing end and that the substrate affinity of the enzyme is negatively affected by each additional epimerization event. It could also be shown that the smallest active substrate was the reducing end uronic acid in a tetrasaccharide and that octasaccharides and longer oligosaccharides were optimal substrates. The method of using tandem mass spectrometry to generate sequence information of the complex enzymatic products in combination with in silico modeling can be potentially applied to study the mode of action of other enzymes involved in polysaccharide biosynthesis.

Deciphering the Acute Cellular Phosphoproteome Response to Irradiation with X-rays, Protons and Carbon Ions*

PubMed Central

Winter, Martin; Dokic, Ivana; Schlegel, Julian; Warnken, Uwe; Debus, Jürgen; Abdollahi, Amir; Schnölzer, Martina

2017-01-01

Radiotherapy is a cornerstone of cancer therapy. The recently established particle therapy with raster-scanning protons and carbon ions landmarks a new era in the field of high-precision cancer medicine. However, molecular mechanisms governing radiation induced intracellular signaling remain elusive. Here, we present the first comprehensive proteomic and phosphoproteomic study applying stable isotope labeling by amino acids in cell culture (SILAC) in combination with high-resolution mass spectrometry to decipher cellular response to irradiation with X-rays, protons and carbon ions. At protein expression level limited alterations were observed 2 h post irradiation of human lung adenocarcinoma cells. In contrast, 181 phosphorylation sites were found to be differentially regulated out of which 151 sites were not hitherto attributed to radiation response as revealed by crosscheck with the PhosphoSitePlus database. Radiation-induced phosphorylation of the p(S/T)Q motif was the prevailing regulation pattern affecting proteins involved in DNA damage response signaling. Because radiation doses were selected to produce same level of cell kill and DNA double-strand breakage for each radiation quality, DNA damage responsive phosphorylation sites were regulated to same extent. However, differential phosphorylation between radiation qualities was observed for 55 phosphorylation sites indicating the existence of distinct signaling circuitries induced by X-ray versus particle (proton/carbon) irradiation beyond the canonical DNA damage response. This unexpected finding was confirmed in targeted spike-in experiments using synthetic isotope labeled phosphopeptides. Herewith, we successfully validated uniform DNA damage response signaling coexisting with altered signaling involved in apoptosis and metabolic processes induced by X-ray and particle based treatments. In summary, the comprehensive insight into the radiation-induced phosphoproteome landscape is instructive for the design of functional studies aiming to decipher cellular signaling processes in response to radiotherapy, space radiation or ionizing radiation per se. Further, our data will have a significant impact on the ongoing debate about patient treatment modalities. PMID:28302921

Deciphering the Acute Cellular Phosphoproteome Response to Irradiation with X-rays, Protons and Carbon Ions.

PubMed

Winter, Martin; Dokic, Ivana; Schlegel, Julian; Warnken, Uwe; Debus, Jürgen; Abdollahi, Amir; Schnölzer, Martina

2017-05-01

Radiotherapy is a cornerstone of cancer therapy. The recently established particle therapy with raster-scanning protons and carbon ions landmarks a new era in the field of high-precision cancer medicine. However, molecular mechanisms governing radiation induced intracellular signaling remain elusive. Here, we present the first comprehensive proteomic and phosphoproteomic study applying stable isotope labeling by amino acids in cell culture (SILAC) in combination with high-resolution mass spectrometry to decipher cellular response to irradiation with X-rays, protons and carbon ions. At protein expression level limited alterations were observed 2 h post irradiation of human lung adenocarcinoma cells. In contrast, 181 phosphorylation sites were found to be differentially regulated out of which 151 sites were not hitherto attributed to radiation response as revealed by crosscheck with the PhosphoSitePlus database.Radiation-induced phosphorylation of the p(S/T)Q motif was the prevailing regulation pattern affecting proteins involved in DNA damage response signaling. Because radiation doses were selected to produce same level of cell kill and DNA double-strand breakage for each radiation quality, DNA damage responsive phosphorylation sites were regulated to same extent. However, differential phosphorylation between radiation qualities was observed for 55 phosphorylation sites indicating the existence of distinct signaling circuitries induced by X-ray versus particle (proton/carbon) irradiation beyond the canonical DNA damage response. This unexpected finding was confirmed in targeted spike-in experiments using synthetic isotope labeled phosphopeptides. Herewith, we successfully validated uniform DNA damage response signaling coexisting with altered signaling involved in apoptosis and metabolic processes induced by X-ray and particle based treatments.In summary, the comprehensive insight into the radiation-induced phosphoproteome landscape is instructive for the design of functional studies aiming to decipher cellular signaling processes in response to radiotherapy, space radiation or ionizing radiation per se Further, our data will have a significant impact on the ongoing debate about patient treatment modalities. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Large rock-slope failures impacting on lakes - Reconstruction of events and deciphering mobility processes at Lake Oeschinen (CH) and Lake Eibsee (D)

NASA Astrophysics Data System (ADS)

Knapp, Sibylle; Anselmetti, Flavio; Gilli, Adrian; Krautblatter, Michael; Hajdas, Irka

2017-04-01

Among single event landslide disasters large rock-slope failures account for 75% of disasters with more than 1000 casualties. The precise determination of recurrence rates and failure volumes combined with an improved understanding of mobility processes are essential to better constrain runout models and establish early warning systems. Here we present the data sets from the two alpine regions Lake Oeschinen (CH) and Lake Eibsee (D) to show how lake studies can help to decipher the multistage character of rock-slope failures and to improve the understanding of the processes related to rock avalanche runout dynamics. We focus on such that impacted on a (paleo-) lake for two main reasons. First, the lake background sedimentation acts as a natural chronometer, which enables the stratigraphic positioning of events and helps to reconstruct the event history. This way it becomes possible to (i) decipher the multistage character of the failure of a certain rock slope and maybe detect progressive failure, (ii) determine the recurrence rates of failures at that certain rock slope, and (iii) consider energies based on estimated failure volumes, fall heights and deposition patterns. Hence, the interactions between a rock-slope failure, the water reservoir and the altered rock-slope are better understood. Second, picturing a rock avalanche running through and beyond a lake, we assume the entrainment of water and slurry to be crucial for the subsequent flow dynamics. The entrainment consumes a large share of the total energy, and orchestrates the mobility leading to fluidization, a much higher flow velocity and a longer runout-path length than expected. At Lake Oeschinen (CH) we used lake sediment cores and reflection seismic profiles in order to reconstruct the 2.5 kyrs spanning rock-slope failure history including 10 events, six of which detached from the same mountain flank, and correlated them with (pre-) historical data. The Lake Eibsee records provide insights into the impact of the rock-slope failure at Mount Zugspitze on the presumed Eibsee paleolake 3.7 kyrs ago. We have been working on seismic profiles and sediment cores from the lake as well as on geoelectrical profiles and terrestrial sediments in the runout path aiming at the reconstruction of mobility processes related to the impact and leading to an extraordinarily long runout.

Mineralogical, crystallographic and redox features of the earliest stages of fluid alteration in CM chondrites

NASA Astrophysics Data System (ADS)

Pignatelli, Isabella; Marrocchi, Yves; Mugnaioli, Enrico; Bourdelle, Franck; Gounelle, Matthieu

2017-07-01

The CM chondrites represent the largest group of hydrated meteorites and span a wide range of conditions, from less altered (i.e., CM2) down to heavily altered (i.e., CM1). The Paris chondrite is considered the least altered CM and thus enables the earliest stages of aqueous alteration processes to be deciphered. Here, we report results from a nanoscale study of tochilinite/cronstedtite intergrowths (TCIs) in Paris-TCIs being the emblematic secondary mineral assemblages of CM chondrites, formed from the alteration of Fe-Ni metal beads (type-I TCIs) and anhydrous silicates (type-II TCIs). We combined high-resolution transmission electron microscopy, scanning transmission X-ray microscopy and electron diffraction tomography to characterize the crystal structure, crystal chemistry and redox state of TCIs. The data obtained are useful to reconstruct the alteration conditions of Paris and to compare them with those of other meteorites. Our results show that tochilinite in Paris is characterized by a high hydroxide layer content (n = 2.1-2.2) regardless of the silicate precursors. When examined alongside other CMs, it appears that the hydroxide layer and iron contents of tochilinites correlate with the degree of alteration experienced by the chondrites. The Fe3+/ΣFe ratios of TCIs are high: 8-15% in tochilinite, 33-60% in cronstedtite and 70-80% in hydroxides. These observations suggest that alteration of CM chondrites took place under oxidizing conditions that could have been induced by significant H2 release during serpentinization. Similar results were recently reported in CR chondrites (Le Guillou et al., 2015), suggesting that the process(es) controlling the redox state of the secondary mineral assemblages were quite similar in the CM and CR parent bodies despite the different alteration conditions. According to our mineralogical and crystallographic survey, the formation of TCIs in Paris occurred at temperatures lower than 100 °C, under neutral, slightly alkaline conditions that favored the formation of both tochilinite and cronstedtite. During the course of alteration, the reduction in sulfur activity and/or the decrease of temperature prevented tochilinite crystallization and favoured the formation of cronstedtite and iron hydroxides. We suggest that iron hydroxides probably formed as ferrihydrite and then progressively converted to goethite between 50° and 80 °C, a temperature range that is also favorable for cronstedtite formation. The presence of cronstedtite plays a key role in the reconstruction of the alteration history, demonstrating that the alteration of Paris took place by way of serpentinization processes similar to those described on the Earth.

Deciphering indented impressions on plastic.

PubMed

Brown, Sharon; Klein, Asne; Chaikovsky, Alan

2003-07-01

The questioned document laboratory is often called upon to decipher writing that has been erased, obliterated, or that has faded. In cases like these, the original writing is no longer legible to the naked eye, but may be enhanced using various light sources. Certain remnants of the ink's components absorb into the substrate's fibers and can be visualized, usually as luminescence or absorbance. A case is described here that involved the theft of a credit card. An empty plastic credit card holder was found in the possession of a suspect, and as submitted for examination. Indented impressions could be discerned on its clear plastic window and presumably originated from the credit card that had been held in the envelope. These indented impressions were deciphered in the hope that they would reveal enough details from the credit card to establish a connection between the plastic envelope and the stolen credit card. With methods generally utilized in the toolmarks and materials laboratory and the photography laboratory of the Israel Police, most of the indented impressions on the plastic were deciphered and a connection between the plastic envelope and the stolen credit card was demonstrated.

'For our garden of remembrance is somewhere else': Narratives of separation through the eyes of Freud's patients.

PubMed

Mahalel, Anat Tzur

2017-12-01

This article presents a unique collection of narratives of separation - unique because the separation here is from psychoanalysis and from Freud as analyst. These narratives were published as part of memoirs written about Freud by three of his patients. Their narratives of separation give us an innovative point of view on the psychoanalytic process, in particular with respect to the importance they place on the termination phase of the analysis at a time when Freud himself had not given it much consideration. The three autobiographical texts are Abram Kardiner's memoir (1977); the memoir of Sergei Pankejeff, known as the Wolf Man (Gardiner, ); and 'Tribute to Freud', by the poet H.D. (). These three distinguished narratives are discussed here as works of translation, as understood by Walter Benjamin (1968 [1955]), Paul Ricoeur (2006 [2004]), and Jean Laplanche (1999 [1992]). They express translation under three aspects: reconstruction of the past (the work of memory), interpreting the conscious residues of the transference (the work of mourning), and, as a deferred action, deciphering the enigmatic messages received from Freud as the parental figure. This representation of the analysand's writing suggests that the separation from analysis is an endless work of translation within the endless process of deciphering the unconscious. Copyright © 2017 Institute of Psychoanalysis.

Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan).

PubMed

Pazhamala, Lekha T; Agarwal, Gaurav; Bajaj, Prasad; Kumar, Vinay; Kulshreshtha, Akanksha; Saxena, Rachit K; Varshney, Rajeev K

2016-01-01

Seed development is an important event in plant life cycle that has interested humankind since ages, especially in crops of economic importance. Pigeonpea is an important grain legume of the semi-arid tropics, used mainly for its protein rich seeds. In order to understand the transcriptional programming during the pod and seed development, RNA-seq data was generated from embryo sac from the day of anthesis (0 DAA), seed and pod wall (5, 10, 20 and 30 DAA) of pigeonpea variety "Asha" (ICPL 87119) using Illumina HiSeq 2500. About 684 million sequencing reads have been generated from nine samples, which resulted in the identification of 27,441 expressed genes after sequence analysis. These genes have been studied for their differentially expression, co-expression, temporal and spatial gene expression. We have also used the RNA-seq data to identify important seed-specific transcription factors, biological processes and associated pathways during seed development process in pigeonpea. The comprehensive gene expression study from flowering to mature pod development in pigeonpea would be crucial in identifying candidate genes involved in seed traits directly or indirectly related to yield and quality. The dataset will serve as an important resource for gene discovery and deciphering the molecular mechanisms underlying various seed related traits.

Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan)

PubMed Central

Pazhamala, Lekha T.; Agarwal, Gaurav; Bajaj, Prasad; Kumar, Vinay; Kulshreshtha, Akanksha; Saxena, Rachit K.; Varshney, Rajeev K.

2016-01-01

Seed development is an important event in plant life cycle that has interested humankind since ages, especially in crops of economic importance. Pigeonpea is an important grain legume of the semi-arid tropics, used mainly for its protein rich seeds. In order to understand the transcriptional programming during the pod and seed development, RNA-seq data was generated from embryo sac from the day of anthesis (0 DAA), seed and pod wall (5, 10, 20 and 30 DAA) of pigeonpea variety “Asha” (ICPL 87119) using Illumina HiSeq 2500. About 684 million sequencing reads have been generated from nine samples, which resulted in the identification of 27,441 expressed genes after sequence analysis. These genes have been studied for their differentially expression, co-expression, temporal and spatial gene expression. We have also used the RNA-seq data to identify important seed-specific transcription factors, biological processes and associated pathways during seed development process in pigeonpea. The comprehensive gene expression study from flowering to mature pod development in pigeonpea would be crucial in identifying candidate genes involved in seed traits directly or indirectly related to yield and quality. The dataset will serve as an important resource for gene discovery and deciphering the molecular mechanisms underlying various seed related traits. PMID:27760186

Altered cellular localization and hemichannel activities of KID syndrome associated connexin26 I30N and D50Y mutations.

PubMed

Aypek, Hande; Bay, Veysel; Meşe, Gülistan

2016-02-02

Gap junctions facilitate exchange of small molecules between adjacent cells, serving a crucial function for the maintenance of cellular homeostasis. Mutations in connexins, the basic unit of gap junctions, are associated with several human hereditary disorders. For example, mutations in connexin26 (Cx26) cause both non-syndromic deafness and syndromic deafness associated with skin abnormalities such as keratitis-ichthyosis-deafness (KID) syndrome. These mutations can alter the formation and function of gap junction channels through different mechanisms, and in turn interfere with various cellular processes leading to distinct disorders. The KID associated Cx26 mutations were mostly shown to result in elevated hemichannel activities. However, the effects of these aberrant hemichannels on cellular processes are recently being deciphered. Here, we assessed the effect of two Cx26 mutations associated with KID syndrome, Cx26I30N and D50Y, on protein biosynthesis and channel function in N2A and HeLa cells. Immunostaining experiments showed that Cx26I30N and D50Y failed to form gap junction plaques at cell-cell contact sites. Further, these mutations resulted in the retention of Cx26 protein in the Golgi apparatus. Examination of hemichannel function by fluorescent dye uptake assays revealed that cells with Cx26I30N and D50Y mutations had increased dye uptake compared to Cx26WT (wild-type) containing cells, indicating abnormal hemichannel activities. Cells with mutant proteins had elevated intracellular calcium levels compared to Cx26WT transfected cells, which were abolished by a hemichannel blocker, carbenoxolone (CBX), as measured by Fluo-3 AM loading and flow cytometry. Here, we demonstrated that Cx26I30N and D50Y mutations resulted in the formation of aberrant hemichannels that might result in elevated intracellular calcium levels, a process which may contribute to the hyperproliferative epidermal phenotypes of KID syndrome.

Deciphering the late steps of rifamycin biosynthesis.

PubMed

Qi, Feifei; Lei, Chao; Li, Fengwei; Zhang, Xingwang; Wang, Jin; Zhang, Wei; Fan, Zhen; Li, Weichao; Tang, Gong-Li; Xiao, Youli; Zhao, Guoping; Li, Shengying

2018-06-14

Rifamycin-derived drugs, including rifampin, rifabutin, rifapentine, and rifaximin, have long been used as first-line therapies for the treatment of tuberculosis and other deadly infections. However, the late steps leading to the biosynthesis of the industrially important rifamycin SV and B remain largely unknown. Here, we characterize a network of reactions underlying the biosynthesis of rifamycin SV, S, L, O, and B. The two-subunit transketolase Rif15 and the cytochrome P450 enzyme Rif16 are found to mediate, respectively, a unique C-O bond formation in rifamycin L and an atypical P450 ester-to-ether transformation from rifamycin L to B. Both reactions showcase interesting chemistries for these two widespread and well-studied enzyme families.

The Vaguries of Pyroxene Nucleation and the Resulting Chondrule Textures

NASA Technical Reports Server (NTRS)

Lofgren, G. E.; Le, L.

2004-01-01

Pyroxene is a major phase in chondrules, but often follows olivine in the crystallization sequence and depending on the melting temperature and time may not nucleate readily upon cooling. Dynamic crystallization experiments based on total or near total melting were used to study PO (porphyritic olivine) and PP (Porphyritic pyroxene) compositions as defined by. The experiments showed that pyroxene nucleated only at subliquidus temperatures in the PP melts and rarely in the PO melts. Porphyritic chondrules with phenocrysts of both olivine and pyroxene (POP chondrules) were not easily produced in the experiments. POP chondrules are common and it is important for deciphering their formation that we understand pyroxene nucleation properties of chondrule melts.

A Rare Glimpse of Paleoarchean Life: Geobiology of an Exceptionally Preserved Microbial Mat Facies from the 3.4 Ga Strelley Pool Formation, Western Australia.

PubMed

Duda, Jan-Peter; Van Kranendonk, Martin J; Thiel, Volker; Ionescu, Danny; Strauss, Harald; Schäfer, Nadine; Reitner, Joachim

2016-01-01

Paleoarchean rocks from the Pilbara Craton of Western Australia provide a variety of clues to the existence of early life on Earth, such as stromatolites, putative microfossils and geochemical signatures of microbial activity. However, some of these features have also been explained by non-biological processes. Further lines of evidence are therefore required to convincingly argue for the presence of microbial life. Here we describe a new type of microbial mat facies from the 3.4 Ga Strelley Pool Formation, which directly overlies well known stromatolitic carbonates from the same formation. This microbial mat facies consists of laminated, very fine-grained black cherts with discontinuous white quartz layers and lenses, and contains small domical stromatolites and wind-blown crescentic ripples. Light- and cathodoluminescence microscopy, Raman spectroscopy, and time of flight-secondary ion mass spectrometry (ToF-SIMS) reveal a spatial association of carbonates, organic material, and highly abundant framboidal pyrite within the black cherts. Nano secondary ion mass spectrometry (NanoSIMS) confirmed the presence of distinct spheroidal carbonate bodies up to several tens of μm that are surrounded by organic material and pyrite. These aggregates are interpreted as biogenic. Comparison with Phanerozoic analogues indicates that the facies represents microbial mats formed in a shallow marine environment. Carbonate precipitation and silicification by hydrothermal fluids occurred during sedimentation and earliest diagenesis. The deciphered environment, as well as the δ13C signature of bulk organic matter (-35.3‰), are in accord with the presence of photoautotrophs. At the same time, highly abundant framboidal pyrite exhibits a sulfur isotopic signature (δ34S = +3.05‰; Δ33S = 0.268‰; and Δ36S = -0.282‰) that is consistent with microbial sulfate reduction. Taken together, our results strongly support a microbial mat origin of the black chert facies, thus providing another line of evidence for life in the 3.4 Ga Strelley Pool Formation.

A Rare Glimpse of Paleoarchean Life: Geobiology of an Exceptionally Preserved Microbial Mat Facies from the 3.4 Ga Strelley Pool Formation, Western Australia

PubMed Central

Duda, Jan-Peter; Van Kranendonk, Martin J.; Thiel, Volker; Ionescu, Danny; Strauss, Harald; Schäfer, Nadine; Reitner, Joachim

2016-01-01

Paleoarchean rocks from the Pilbara Craton of Western Australia provide a variety of clues to the existence of early life on Earth, such as stromatolites, putative microfossils and geochemical signatures of microbial activity. However, some of these features have also been explained by non-biological processes. Further lines of evidence are therefore required to convincingly argue for the presence of microbial life. Here we describe a new type of microbial mat facies from the 3.4 Ga Strelley Pool Formation, which directly overlies well known stromatolitic carbonates from the same formation. This microbial mat facies consists of laminated, very fine-grained black cherts with discontinuous white quartz layers and lenses, and contains small domical stromatolites and wind-blown crescentic ripples. Light- and cathodoluminescence microscopy, Raman spectroscopy, and time of flight—secondary ion mass spectrometry (ToF-SIMS) reveal a spatial association of carbonates, organic material, and highly abundant framboidal pyrite within the black cherts. Nano secondary ion mass spectrometry (NanoSIMS) confirmed the presence of distinct spheroidal carbonate bodies up to several tens of μm that are surrounded by organic material and pyrite. These aggregates are interpreted as biogenic. Comparison with Phanerozoic analogues indicates that the facies represents microbial mats formed in a shallow marine environment. Carbonate precipitation and silicification by hydrothermal fluids occurred during sedimentation and earliest diagenesis. The deciphered environment, as well as the δ13C signature of bulk organic matter (-35.3‰), are in accord with the presence of photoautotrophs. At the same time, highly abundant framboidal pyrite exhibits a sulfur isotopic signature (δ34S = +3.05‰; Δ33S = 0.268‰; and Δ36S = -0.282‰) that is consistent with microbial sulfate reduction. Taken together, our results strongly support a microbial mat origin of the black chert facies, thus providing another line of evidence for life in the 3.4 Ga Strelley Pool Formation. PMID:26807732

Alignment of Common Wheat and Other Grass Genomes Establishes a Comparative Genomics Research Platform

PubMed Central

Sun, Sangrong; Wang, Jinpeng; Yu, Jigao; Meng, Fanbo; Xia, Ruiyan; Wang, Li; Wang, Zhenyi; Ge, Weina; Liu, Xiaojian; Li, Yuxian; Liu, Yinzhe; Yang, Nanshan; Wang, Xiyin

2017-01-01

Grass genomes are complicated structures as they share a common tetraploidization, and particular genomes have been further affected by extra polyploidizations. These events and the following genomic re-patternings have resulted in a complex, interweaving gene homology both within a genome, and between genomes. Accurately deciphering the structure of these complicated plant genomes would help us better understand their compositional and functional evolution at multiple scales. Here, we build on our previous research by performing a hierarchical alignment of the common wheat genome vis-à-vis eight other sequenced grass genomes with most up-to-date assemblies, and annotations. With this data, we constructed a list of the homologous genes, and then, in a layer-by-layer process, separated their orthology, and paralogy that were established by speciations and recursive polyploidizations, respectively. Compared with the other grasses, the far fewer collinear outparalogous genes within each of three subgenomes of common wheat suggest that homoeologous recombination, and genomic fractionation should have occurred after its formation. In sum, this work contributes to the establishment of an important and timely comparative genomics platform for researchers in the grass community and possibly beyond. Homologous gene list can be found in Supplemental material. PMID:28912789

A dual origin for water in carbonaceous asteroids revealed by CM chondrites

NASA Astrophysics Data System (ADS)

Piani, Laurette; Yurimoto, Hisayoshi; Remusat, Laurent

2018-04-01

Carbonaceous asteroids represent the principal source of water in the inner Solar System and might correspond to the main contributors for the delivery of water to Earth. Hydrogen isotopes in water-bearing primitive meteorites, for example carbonaceous chondrites, constitute a unique tool for deciphering the sources of water reservoirs at the time of asteroid formation. However, fine-scale isotopic measurements are required to unravel the effects of parent-body processes on the pre-accretion isotopic distributions. Here, we report in situ micrometre-scale analyses of hydrogen isotopes in six CM-type carbonaceous chondrites, revealing a dominant deuterium-poor water component (δD = -350 ± 40‰) mixed with deuterium-rich organic matter. We suggest that this deuterium-poor water corresponds to a ubiquitous water reservoir in the inner protoplanetary disk. A deuterium-rich water signature has been preserved in the least altered part of the Paris chondrite (δDParis ≥ -69 ± 163‰) in hydrated phases possibly present in the CM rock before alteration. The presence of the deuterium-enriched water signature in Paris might indicate that transfers of ice from the outer to the inner Solar System were significant within the first million years of the history of the Solar System.

Polarized Growth in the Absence of F-Actin in Saccharomyces cerevisiae Exiting Quiescence

PubMed Central

Sahin, Annelise; Daignan-Fornier, Bertrand; Sagot, Isabelle

2008-01-01

Background Polarity establishment and maintenance are crucial for morphogenesis and development. In budding yeast, these two intricate processes involve the superposition of regulatory loops between polarity landmarks, RHO GTPases, actin-mediated vesicles transport and endocytosis. Deciphering the chronology and the significance of each molecular step of polarized growth is therefore very challenging. Principal Findings We have taken advantage of the fact that yeast quiescent cells display actin bodies, a non polarized actin structure, to evaluate the role of F-actin in bud emergence. Here we show that upon exit from quiescence, actin cables are not required for the first steps of polarized growth. We further show that polarized growth can occur in the absence of actin patch-mediated endocytosis. We finally establish, using latrunculin-A, that the first steps of polarized growth do not require any F-actin containing structures. Yet, these structures are required for the formation of a bona fide daughter cell and cell cycle completion. We propose that upon exit from quiescence in the absence of F-actin, secretory vesicles randomly reach the plasma membrane but preferentially dock and fuse where polarity cues are localized, this being sufficient to trigger polarized growth. PMID:18596916

Deciphering protein signatures using color, morphological, and topological analysis of immunohistochemically stained human tissues

NASA Astrophysics Data System (ADS)

Zerhouni, Erwan; Prisacari, Bogdan; Zhong, Qing; Wild, Peter; Gabrani, Maria

2016-03-01

Images of tissue specimens enable evidence-based study of disease susceptibility and stratification. Moreover, staining technologies empower the evidencing of molecular expression patterns by multicolor visualization, thus enabling personalized disease treatment and prevention. However, translating molecular expression imaging into direct health benefits has been slow. Two major factors contribute to that. On the one hand, disease susceptibility and progression is a complex, multifactorial molecular process. Diseases, such as cancer, exhibit cellular heterogeneity, impeding the differentiation between diverse grades or types of cell formations. On the other hand, the relative quantification of the stained tissue selected features is ambiguous, tedious and time consuming, prone to clerical error, leading to intra- and inter-observer variability and low throughput. Image analysis of digital histopathology images is a fast-developing and exciting area of disease research that aims to address the above limitations. We have developed a computational framework that extracts unique signatures using color, morphological and topological information and allows the combination thereof. The integration of the above information enables diagnosis of disease with AUC as high as 0.97. Multiple staining show significant improvement with respect to most proteins, and an AUC as high as 0.99.

Cone-Deciphered Modes of Problem Solving Action (MPSA Cone): Alternative Perspectives on Diversified Professions.

ERIC Educational Resources Information Center

Lai, Su-Huei

A conceptual framework of the modes of problem-solving action has been developed on the basis of a simple relationship cone to assist individuals in diversified professions in inquiry and implementation of theory and practice in their professional development. The conceptual framework is referred to as the Cone-Deciphered Modes of Problem Solving…

Quaternary stratigraphy of Bermuda: A high-resolution pre-Sangamonian rock record

NASA Astrophysics Data System (ADS)

Hearty, Paul J.; Vacher, H. Leonard

Carbonate islands such as Bermuda are created by climatic change. Warm climates and high sea levels stimulate carbonate sediment production that may ultimately result in island growth, while cold glacials expose the platforms to weathering, dissolution and soil formation. Of great importance in Quaternary studies is the ability to decipher this climatic history. Mapping and geochronologic studies have established that Bermuda may have one of the most continuous and detailed Quaternary interglacial depositional records on a carbonate platform. Advances in racemization dating (AAR) have offered a means of deciphering this climatic history and generating a high-resolution stratigraphic and age framework for the Quaternary. Bermudian interglacial units consist predominantly of eolianites, with less voluminous occurrences of beach deposits and calcarenite protosols (Entisols). Glacial or stadial-age terra rossa (aluminous laterite) paleosols, whose degree of development is a function of time of exposure, form boundaries between interglacial units. D-alloiso-leucine/ L-isoleucine ( {A}/{I}) ratios have been determined on marine pelecypods, land snails and whole-rock samples from mapped sections; aminozones have been defined for two Sangamonian and at least five pre-Sangamonian depositional intervals. From kinetic models based on calibration with previously published U-series coral dates, estimated ages of middle Pleistocene and older aminozones are: F = 190,000-265,000 years; G = 300,000-400,000 years; H = 400,000-500,000 years; J = >700,000 years; and K = > 900,000 years. Aminozone G, which is correlated with the upper Town Hill Formation and Isotope Stage 9, is volumetrically the most important depositional event of the middle Pleistocene. The great mass of sediment deposited during this period suggests an interglacial of significant duration and prolonged shelf submergence, during which the island grew to over half its present size. Only the Sangamonian ( sensu lato) rivals Stage 9 in volume of eolianite deposited on the island. Sea-level amplitude, as determined from dated outcrops, appears to correlate well with amplitudinal variations in the oxygen isotope record.

CTC Sentinel. Volume 6, Issue 2, February 2013

DTIC Science & Technology

2013-02-01

Use of Militias to Maintain Stability in Abyan Province By Casey L. Coombs 7 Deciphering the Jihadist Presence in Syria: An Analysis of...and impose their authority in their communities . This poses particular challenges for Libya as i t moves through the transit ion process...IssUE 2 5 Yemen’s Use of Militias to Maintain Stability in Abyan Province By Casey L. Coombs in 2011, militants from al-Qa`ida in the Arabian

Preservation of martian organic and environmental records: final report of the Mars biosignature working group.

PubMed

Summons, Roger E; Amend, Jan P; Bish, David; Buick, Roger; Cody, George D; Des Marais, David J; Dromart, Gilles; Eigenbrode, Jennifer L; Knoll, Andrew H; Sumner, Dawn Y

2011-03-01

The Mars Science Laboratory (MSL) has an instrument package capable of making measurements of past and present environmental conditions. The data generated may tell us if Mars is, or ever was, able to support life. However, the knowledge of Mars' past history and the geological processes most likely to preserve a record of that history remain sparse and, in some instances, ambiguous. Physical, chemical, and geological processes relevant to biosignature preservation on Earth, especially under conditions early in its history when microbial life predominated, are also imperfectly known. Here, we present the report of a working group chartered by the Co-Chairs of NASA's MSL Project Science Group, John P. Grotzinger and Michael A. Meyer, to review and evaluate potential for biosignature formation and preservation on Mars. Orbital images confirm that layered rocks achieved kilometer-scale thicknesses in some regions of ancient Mars. Clearly, interplays of sedimentation and erosional processes govern present-day exposures, and our understanding of these processes is incomplete. MSL can document and evaluate patterns of stratigraphic development as well as the sources of layered materials and their subsequent diagenesis. It can also document other potential biosignature repositories such as hydrothermal environments. These capabilities offer an unprecedented opportunity to decipher key aspects of the environmental evolution of Mars' early surface and aspects of the diagenetic processes that have operated since that time. Considering the MSL instrument payload package, we identified the following classes of biosignatures as within the MSL detection window: organism morphologies (cells, body fossils, casts), biofabrics (including microbial mats), diagnostic organic molecules, isotopic signatures, evidence of biomineralization and bioalteration, spatial patterns in chemistry, and biogenic gases. Of these, biogenic organic molecules and biogenic atmospheric gases are considered the most definitive and most readily detectable by MSL. © Mary Ann Liebert, Inc.

What does the fine-scale petrography of IDPs reveal about grain formation and evolution in the early solar system?

NASA Technical Reports Server (NTRS)

Bradley, John

1994-01-01

The 'pyroxene' interplanetary dust particles (IDP's) may be the best samples for investigation of primordial grain-forming reactions because they appear to have experienced negligible post-accretional alteration. They are likely to continue to yield information about gas-to-solid condensation and other grain-forming reactions that may have occurred either in the solar nebular or presolar interstellar environments. An immediate challenge lies in understanding the nanometer-scale petrography of the ultrafine-grained aggregates in 'pyroxene' IDP's. Whether these aggregates contain components from diverse grain-forming environments may ultimately be answered by systematic petrographic studies using electron microscopes capable of high spatial resolution microanalysis. It may be more difficult to decipher evidence of grain formation and evolution in 'olivine' and 'layer silicate' IDP's because they appear to have experienced post-accretional alteration. Most of the studied 'olivine' IDPs have been subjected to heating and equilibration, perhaps during atmospheric entry, while the 'layer silicate' IDP's have experienced aqueous alteration.

Encircling the dark, a simple method to decipher the cosmos

NASA Astrophysics Data System (ADS)

Quirico, Eric

2017-09-01

Asteroids are relics of Solar System formation and host insightful information on physical, chemical, chronological and dynamical conditions that operated, since the formation of the first solids until the Late Heavy Bombardment. Since 2000, our view on these small objects has been deeply transformed due to several space missions and advances in ground-based observations. Near, Dawn (NASA) and Hayabusa 1 (JAXA) have provided extensive characterizations of the surface and interior of asteroids 433Eros, Itokawa, Vesta and Ceres, and revealed a complex morphology driven by collisions and/or internal activity. The samples returned to Earth by Hayabusa 1 provided a firm evidence of the genetic link between S-type asteroids and ordinary chondrites, and valuable clues on the first stage of space weathering. Meanwhile, ground-based observations, dynamical theory and meteoritics have drawn a big picture pointing to a continuum between asteroids and comets. Hopefully, the forthcoming missions Hayabusa2 and Osiris ReX will explore for the first time two C-type asteroids in the next years.

Unraveling the mechanisms of synapse formation and axon regeneration: the awesome power of C. elegans genetics.

PubMed

Jin, YiShi

2015-11-01

Since Caenorhabditis elegans was chosen as a model organism by Sydney Brenner in 1960's, genetic studies in this organism have been instrumental in discovering the function of genes and in deciphering molecular signaling network. The small size of the organism and the simple nervous system enable the complete reconstruction of the first connectome. The stereotypic developmental program and the anatomical reproducibility of synaptic connections provide a blueprint to dissect the mechanisms underlying synapse formation. Recent technological innovation using laser surgery of single axons and in vivo imaging has also made C. elegans a new model for axon regeneration. Importantly, genes regulating synaptogenesis and axon regeneration are highly conserved in function across animal phyla. This mini-review will summarize the main approaches and the key findings in understanding the mechanisms underlying the development and maintenance of the nervous system. The impact of such findings underscores the awesome power of C. elegans genetics.

Computational modeling of chemo-bio-mechanical coupling: a systems-biology approach toward wound healing.

PubMed

Buganza Tepole, A; Kuhl, E

2016-01-01

Wound healing is a synchronized cascade of chemical, biological, and mechanical phenomena, which act in concert to restore the damaged tissue. An imbalance between these events can induce painful scarring. Despite intense efforts to decipher the mechanisms of wound healing, the role of mechanics remains poorly understood. Here, we establish a computational systems biology model to identify the chemical, biological, and mechanical mechanisms of scar formation. First, we introduce the generic problem of coupled chemo-bio-mechanics. Then, we introduce the model problem of wound healing in terms of a particular chemical signal, inflammation, a particular biological cell type, fibroblasts, and a particular mechanical model, isotropic hyperelasticity. We explore the cross-talk between chemical, biological, and mechanical signals and show that all three fields have a significant impact on scar formation. Our model is the first step toward rigorous multiscale, multifield modeling in wound healing. Our formulation has the potential to improve effective wound management and optimize treatment on an individualized patient-specific basis.

Sequence dependent aggregation of peptides and fibril formation

NASA Astrophysics Data System (ADS)

Hung, Nguyen Ba; Le, Duy-Manh; Hoang, Trinh X.

2017-09-01

Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.

Deciphering Sources of Variability in Clinical Pathology.

PubMed

Tripathi, Niraj K; Everds, Nancy E; Schultze, A Eric; Irizarry, Armando R; Hall, Robert L; Provencher, Anne; Aulbach, Adam

2017-01-01

The objectives of this session were to explore causes of variability in clinical pathology data due to preanalytical and analytical variables as well as study design and other procedures that occur in toxicity testing studies. The presenters highlighted challenges associated with such variability in differentiating test article-related effects from the effects of experimental procedures and its impact on overall data interpretation. These presentations focused on preanalytical and analytical variables and study design-related factors and their influence on clinical pathology data, and the importance of various factors that influence data interpretation including statistical analysis and reference intervals. Overall, these presentations touched upon potential effect of many variables on clinical pathology parameters, including animal physiology, sample collection process, specimen handling and analysis, study design, and some discussion points on how to manage those variables to ensure accurate interpretation of clinical pathology data in toxicity studies. This article is a brief synopsis of presentations given in a session entitled "Deciphering Sources of Variability in Clinical Pathology-It's Not Just about the Numbers" that occurred at the 35th Annual Symposium of the Society of Toxicologic Pathology in San Diego, California.

Basaltic Volcanism and Ancient Planetary Crusts

NASA Technical Reports Server (NTRS)

Shervais, John W.

1993-01-01

The purpose of this project is to decipher the origin of rocks which form the ancient lunar crust. Our goal is to better understand how the moon evolved chemically and, more generally, the processes involved in the chemical fractionation of terrestrial planetoids. This research has implications for other planetary bodies besides the Moon, especially smaller planetoids which evolved early in the history of the solar system and are now thermally stable. The three main areas focused on in our work (lunar mare basalts, KREEP basalts, and plutonic rocks of the lunar highlands) provide complementary information on the lunar interior and the processes that formed it.

Mineral systems and the thermodynamics of selenites and selenates in the oxidation zone of sulfide ores - a review

NASA Astrophysics Data System (ADS)

Charykova, Marina V.; Krivovichev, Vladimir G.

2017-02-01

Contemporary mineralogy and geochemistry are concerned with understanding and deciphering processes that occur near the surface of the Earth. These processes are especially important for resolving ecological challenges and developing principles of good environmental management. Selenium oxysalts, selenites and selenates, are relatively rare as minerals; there are presently only 34 known mineral species. Thirty-one "pure" selenites, which contain only selenite anionic groups, are known to occur naturally. The other three minerals each contain two anionic groups: selenate and selenite (schmiederite), selenate and sulphate (olsacherite), and selenate and iodate (carlosruizite).

Tourmaline as a recorder of ore-forming processes

USGS Publications Warehouse

Slack, John F.; Trumbull, Robert B.

2011-01-01

Tourmaline occurs in diverse types of hydrothermal mineral deposits and can be used to constrain the nature and evolution of ore-forming fl uids. Because of its broad range in composition and retention of chemical and isotopic signatures, tourmaline may be the only robust recorder of original mineralizing processes in some deposits. Microtextures and in situ analysis of compositional and isotopic variations in ore-related tourmaline provide valuable insights into hydrothermal systems in seafl oor, sedimentary, magmatic, and metamorphic environments. Deciphering the hydrothermal record in tourmaline also holds promise for aiding exploration programs in the search for new ore deposits.

Deciphering the Transitional Tectonics of the Southern Alaska Margin Through Gulf Sedimentology and Geophysics: IODP Expedition 341

NASA Astrophysics Data System (ADS)

Reece, R.; Gulick, S. P. S.; Jaeger, J. M.

2014-12-01

Southern Alaska is a complex amalgam of tectonic environments, centered on the subduction/collision of the Yakutat Block with North America. Along the Aleutians in the west, the Pacific Plate subducts normally beneath North America, with a gradually shallowing subduction angle towards the Yakutat Terrane to the east. The western region of the Yakutat Block undergoes nearly flat-slab subduction beneath North America, whereas it transitions to collision in the northeast, which is the primary driver for the growth of the Chugach-St. Elias orogen. Farther to the east, the collisional system transitions to a transform boundary with the Fairweather-Queen Charlotte fault system. The collisional system contributes to farfield tectonic effects in many regions, including northern Alaska and the Pacific Plate, but also combines with glaciation to drive sedimentation in the Gulf of Alaska. Glaciation has periodically increased in the St. Elias Range since the Miocene, but began dominating erosion and spurred enhanced exhumation since the intensification of Northern Hemisphere glaciation, at ~2.5 Ma. Results from IODP Expedition 341 show the first appearance of ice-rafted debris and a doubling of Gulf sedimentation at site U1417 at this age, and a major increase in sedimentation at ~1 Ma at sites U1417 and U1418. Glacigenic sediment flux into the Gulf of Alaska represents the majority of accumulation in the deepwater Surveyor Fan, and was the impetus for formation of the Surveyor Channel system. Climate events correlate to three major differentiable sequences across the Surveyor Fan that have been previously mapped using seismic reflection profiles. The change in morphology observed throughout the sequences allows us to characterize the influence that a glaciated orogen can have in shaping margin processes and the sediment pathways from source to sink. IODP Expedition 341 results allow us to now apply this method at higher resolution time scales (i.e., 100 kyr). We will explore changes in fan geomorphology observed in seismic reflection data to decipher changes in southern Alaska tectonics and climate, and to show the effect of those changes on deepwater sedimentary systems.

The Carbonates in ALH 84001 Record the Evolution of the Martian Atmosphere Through Multiple Formation Events

NASA Technical Reports Server (NTRS)

Shaheen, R.; Niles, P. B.; Corrgan, C.

2012-01-01

Current Martian conditions restrict the presence of liquid water due to low temperatures (approx 210K), a thin atmosphere (approx 7mb), and intense UV radiation. However, past conditions on Mars may have been different with the possibility that the ancient Martian climate was warm and wet with a dense CO2 atmosphere. The cycling of carbon on Mars through atmospheric CO2 and carbonate minerals is critical for deciphering its climate history. In particular stable isotopes contained in carbonates can provide information of their origin and formation environment as well as possibly hinting at the composition of global reservoirs such as atmospheric CO2. Martian meteorite ALH 84001 contains widely studied carbonate rosettes that have been dated to approx. 3.9 Ga and have been used to interpret climatic conditions present at that time. However, there is mount-ing evidence for multiple episodes of carbonate formation in ALH 84001 with potentially distinct isotopic compositions. This study seeks to tease out these different carbonate assemblages using stepped phosphoric acid dissolution and analysis of carbon and triple oxygen stable isotopes. In addition, we report SIMS analyses of the delta O-18 several petrographically unusual carbonate phases in the meteorite.

Metabolic Signaling and Therapy of Lung Cancer

DTIC Science & Technology

2013-09-01

this grant is to decipher molecular mechanisms by which glycolytic enzyme phosphoglycerate mutase 1 (PGAM1) promotes lung cancer cell metabolism and...PGAM1 in regulation of lung cancer metabolism; molecular mechanisms underlying PGAM1 activation in lung cancer; PGAM1 inhibitor as novel therapy to...leukemia cells from human patients with minimal toxicity. Therefore, the current funded proposal focuses to decipher molecular mechanisms by which

Deciphering the Molecular Mechanisms of Breast Cancer

DTIC Science & Technology

2005-03-01

2007). Nicolas E., Lee M.G., Hakimi M.A., Cam H.P., Grewal S.I., Shiekhattar R. Fussion yeast homologs of human H3 lysinee 4 demethylase regulate a...Baillat D., Hakimi M.A., Naar A., Shilatifard A., Cooch N., Shiekhattar R. Integrator, a multiprotein mediator of small nuclear RNA processing...fractionof FLAG-BARD1 using anti-FLAG antibodies from H1299 of BRCA1 and BARD1 elute at a smaller molecular masscells. Nuclear extract from native H1299

Deciphering spreading mechanisms in amyotrophic lateral sclerosis: clinical evidence and potential molecular processes.

PubMed

Pradat, Pierre-François; Kabashi, Edor; Desnuelle, Claude

2015-10-01

The aim of this review is to refer to recent arguments supporting the existence of specific propagation mechanisms associated with spreading of neuron injury in amyotrophic lateral sclerosis (ALS). Misfolded ALS-linked protein accumulation can induce aggregation of their native equivalent isoforms through a mechanism analogous to the infectious prion proteins initiation and its propagation. Although ALS is clinically heterogeneous, a shared characteristic is the focal onset and the progressive extension to all body regions. Being viewed until now as just summation of the increased number of affected neurons, dispersion is now rather considered as the result of a seeded self-propagating process. A sequential regional spreading pattern is supported by the distribution of TDP-43 aggregates in ALS autopsy cases. Electrophysiology and advanced neuroimaging methods also recently provided some evidence for propagation of lesions both in the brain and spinal cord, more longitudinal studies being still needed. Lesions are supposed to spread cell-to-cell regionally or through connected neuronal pathway. At the molecular level, the prion-like spreading is an emerging mechanism hypothesis, but other machineries such as those that are in charge of dealing with misfolded proteins and secretion of deleterious peptides may be involved in the propagation of neuron loss. Deciphering the mechanisms underlying spreading of ALS symptoms is of crucial importance to better understand this neurodegenerative disease, build new and appropriate animal models and to define novel therapeutic targets.

Optogenetic exploration and modulation of pain processing.

PubMed

Xie, Yu-Feng; Wang, Jing; Bonin, Robert P

2018-08-01

Intractable pain is the single most common cause of disability, affecting more than 20% of the population world-wide. There is accordingly a global effort to decipher how changes in nociceptive processing in the peripheral and central nervous systems contribute to the onset and maintenance of chronic pain. The past several years have brought rapid progress in the adaptation of optogenetic approaches to study and manipulate the activity of sensory afferents and spinal cord neurons in freely behaving animals, and to investigate cortical processing and modulation of pain responses. This review discusses methodological advances that underlie this recent progress, and discusses practical considerations for the optogenetic modulation of nociceptive sensory processing. Crown Copyright © 2018. Published by Elsevier Inc. All rights reserved.

Study on the curie transition of P(VDF-TrFE) copolymer

NASA Astrophysics Data System (ADS)

Eka Septiyani Arifin, Devi; Ruan, J. J.

2018-01-01

A systematic study was carried out to decipher the mechanism of Curie transition of piezoelectric crystals of poly(vinylidene fluoride trifluoroethylene) P(VDF-TrFE). The unique polarity of P(VDF-TrFE) crystalline phase below curie transition temperature is attributed to the lattice packing of all-trans molecular chains, which allocates all the substituted fluorine atoms on one side of molecular chains and hydrogen atoms on the other side. Therefore, a net dipole moment is created across the lateral packing of molecular chains. Nevertheless, due to the mutual repulsion among fluorene atoms, this all-trans conformation is not stable, and ready to change above Curie temperature, where thermal kinetic energy is sufficient to cause segmental rotation. As being illustrated by in-situ recorded X-ray diffraction and thermal analysis, the concerned curie transition is deciphered as a one-step process which is involved two process and this is different from conventional one-step solid-solid transitions. Accompanied with this one-step process during heating, the occurrence of lamellar bending is inferred for elucidating the decline of stacking regularity of crystalline lamellae, which reversibly recover during subsequent cooling. However, as the crystalline lamellae of P(VDF-TrFE) are confined in between the stacking of crystalline lamellae of PVDF, lamellar bending is restricted accordingly. As a result, a certain fraction of the piezoelectric crystalline lamellae was found to survive through the Curie transition. Thus, in addition to the suggestion of a one-step process as a new concept for understanding the Curie transition, the relationship between the lamellar stacking and transition of molecular packing is unveiled as well in this research.

Trace and minor element variations and sulfur isotopes in crystalline and colloform ZnS: Incorporation mechanisms and implications for their genesis

USGS Publications Warehouse

Pfaff, Katharina; Koenig, Alan; Wenzel, Thomas; Ridley, Ian; Hildebrandt, Ludwig H.; Leach, David L.; Markl, Gregor

2011-01-01

Various models have been proposed to explain the formation mechanism of colloform sphalerite, but the origin is still under debate. In order to decipher influences on trace element incorporation and sulfur isotope composition, crystalline and colloform sphalerite from the carbonate-hosted Mississippi-Valley Type (MVT) deposit near Wiesloch, SW Germany, were investigated and compared to sphalerite samples from 52 hydrothermal vein-type deposits in the Schwarzwald ore district, SW Germany to study the influence of different host rocks, formation mechanisms and fluid origin on trace element incorporation. Trace and minor element incorporation in sphalerite shows some correlation to their host rock and/or origin of fluid, gangue, paragenetic minerals and precipitation mechanisms (e.g., diagenetic processes, fluid cooling or fluid mixing). Furthermore, crystalline sphalerite is generally enriched in elements like Cd, Cu, Sb and Ag compared to colloform sphalerite that mainly incorporates elements like As, Pb and Tl. In addition, sulfur isotopes are characterized by positive values for crystalline and strongly negative values for colloform sphalerite. The combination of trace element contents, typical minerals associated with colloform sphalerite from Wiesloch, sulfur isotopes and thermodynamic considerations helped to evaluate the involvement of sulfate-reducing bacteria in water-filled karst cavities. Sulfate-reducing bacteria cause a sulfide-rich environment that leads in case of a metal-rich fluid supply to a sudden oversaturation of the fluid with respect to galena, sphalerite and pyrite. This, however, exactly coincides with the observed crystallization sequence of samples involving colloform sphalerite from the Wiesloch MVT deposit.

WE-E-204-02: Journal of Medical Physics and JACMP

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

Williamson, J.

Research papers authored by Medical Physicists address a large spectrum of oncologic, imaging, or basic research problems; exploit a wide range of physical and engineering methodologies; and often describe the efforts of a multidisciplinary research team. Given dozens of competing journals accepting medical physics articles, it may not be clear to an individual author which journal is the best venue for disseminating their work to the scientific community. Relevant factors usually include the Journal’s audience and scientific impact, but also such factors as perceived acceptance rate, interest in their topic, and quality of service. The purpose of this symposium ismore » to provide the medical physics community with an overview of scope, review processes, and article guidelines for the following journals: Radiology, Medical Physics, International Journal of Radiation Biology and Physics, Journal of Applied Clinical Medical Physics, and Practical Radiation Oncology. Senior members of the editorial board for each journal will provide details as to the journals review process, for example: single blind versus double blind reviews; open access policies, the hierarchy of the review process in terms of editorial board structure; the reality of acceptance, in terms of acceptance rate; and the types of research the journal prefers to publish. Other journals will be discussed as well. The goal is to provide for authors guidance before they begin to write their papers, not only for proper formatting, but also that the readership is appropriate for the particular paper, hopefully increasing the quality and impact of the paper and the likelihood of publication. Learning Objectives: To review each Journal’s submission and review process Guidance as to how to increase quality, impact and chances of acceptance To help decipher which journal is appropriate for a given work A. Karellas, Research collaboration with Koning, Corporation.« less

WE-E-204-00: Where to Send My Manuscript

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

NONE

Research papers authored by Medical Physicists address a large spectrum of oncologic, imaging, or basic research problems; exploit a wide range of physical and engineering methodologies; and often describe the efforts of a multidisciplinary research team. Given dozens of competing journals accepting medical physics articles, it may not be clear to an individual author which journal is the best venue for disseminating their work to the scientific community. Relevant factors usually include the Journal’s audience and scientific impact, but also such factors as perceived acceptance rate, interest in their topic, and quality of service. The purpose of this symposium ismore » to provide the medical physics community with an overview of scope, review processes, and article guidelines for the following journals: Radiology, Medical Physics, International Journal of Radiation Biology and Physics, Journal of Applied Clinical Medical Physics, and Practical Radiation Oncology. Senior members of the editorial board for each journal will provide details as to the journals review process, for example: single blind versus double blind reviews; open access policies, the hierarchy of the review process in terms of editorial board structure; the reality of acceptance, in terms of acceptance rate; and the types of research the journal prefers to publish. Other journals will be discussed as well. The goal is to provide for authors guidance before they begin to write their papers, not only for proper formatting, but also that the readership is appropriate for the particular paper, hopefully increasing the quality and impact of the paper and the likelihood of publication. Learning Objectives: To review each Journal’s submission and review process Guidance as to how to increase quality, impact and chances of acceptance To help decipher which journal is appropriate for a given work A. Karellas, Research collaboration with Koning, Corporation.« less

WE-E-204-01: ASTRO Based Journals

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

Klein, E.

Research papers authored by Medical Physicists address a large spectrum of oncologic, imaging, or basic research problems; exploit a wide range of physical and engineering methodologies; and often describe the efforts of a multidisciplinary research team. Given dozens of competing journals accepting medical physics articles, it may not be clear to an individual author which journal is the best venue for disseminating their work to the scientific community. Relevant factors usually include the Journal’s audience and scientific impact, but also such factors as perceived acceptance rate, interest in their topic, and quality of service. The purpose of this symposium ismore » to provide the medical physics community with an overview of scope, review processes, and article guidelines for the following journals: Radiology, Medical Physics, International Journal of Radiation Biology and Physics, Journal of Applied Clinical Medical Physics, and Practical Radiation Oncology. Senior members of the editorial board for each journal will provide details as to the journals review process, for example: single blind versus double blind reviews; open access policies, the hierarchy of the review process in terms of editorial board structure; the reality of acceptance, in terms of acceptance rate; and the types of research the journal prefers to publish. Other journals will be discussed as well. The goal is to provide for authors guidance before they begin to write their papers, not only for proper formatting, but also that the readership is appropriate for the particular paper, hopefully increasing the quality and impact of the paper and the likelihood of publication. Learning Objectives: To review each Journal’s submission and review process Guidance as to how to increase quality, impact and chances of acceptance To help decipher which journal is appropriate for a given work A. Karellas, Research collaboration with Koning, Corporation.« less

TU-B-16A-01: To Which Journal Should I Submit My Paper

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

Williamson, J; Mills, M; Klein, E

Research papers authored by Medical Physicists address a large spectrum of oncologic, imaging, or basic research problems; exploit a wide range of physical and engineering methodologies; and often describe the efforts of a multidisciplinary research team. Given the large number (about 100) competing journals accepting medical physics articles, it may not be clear to an individual author which journal is the best venue for disseminating their work to the scientific community. Relevant factors usually include the Journal’s audience and scientific impact, but also such factors as perceived acceptance rate, interest in their topic, and quality of service. The purpose ofmore » this symposium is to provide the medical physics community with an overview of scope, review processes, and article guidelines for the following journals: Medical Physics, International Journal of Radiation Biology and Physics, Journal of Applied Clinical Medical Physics, and Practical Radiation Oncology. The senior editors for each journal will provide details as to the journals review process, for example: single blind versus double blind reviews; the hierarchy of the review process in terms of editorial board structure; the reality of acceptance, in terms of acceptance rate; and the types of research the journal prefers to publish. The goal is to provide for authors guidance before they begin to write their papers, not only for proper formatting, but also that the readership is appropriate for the particular paper, hopefully increasing the likelihood of publication. Learning Objectives: To review each Journal’s submission and review process Guidance as to how to increase chances of acceptance To help decipher which journal is appropriate for a given work.« less

WE-E-204-03: Radiology and Other Imaging Journals

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

Karellas, A.

Research papers authored by Medical Physicists address a large spectrum of oncologic, imaging, or basic research problems; exploit a wide range of physical and engineering methodologies; and often describe the efforts of a multidisciplinary research team. Given dozens of competing journals accepting medical physics articles, it may not be clear to an individual author which journal is the best venue for disseminating their work to the scientific community. Relevant factors usually include the Journal’s audience and scientific impact, but also such factors as perceived acceptance rate, interest in their topic, and quality of service. The purpose of this symposium ismore » to provide the medical physics community with an overview of scope, review processes, and article guidelines for the following journals: Radiology, Medical Physics, International Journal of Radiation Biology and Physics, Journal of Applied Clinical Medical Physics, and Practical Radiation Oncology. Senior members of the editorial board for each journal will provide details as to the journals review process, for example: single blind versus double blind reviews; open access policies, the hierarchy of the review process in terms of editorial board structure; the reality of acceptance, in terms of acceptance rate; and the types of research the journal prefers to publish. Other journals will be discussed as well. The goal is to provide for authors guidance before they begin to write their papers, not only for proper formatting, but also that the readership is appropriate for the particular paper, hopefully increasing the quality and impact of the paper and the likelihood of publication. Learning Objectives: To review each Journal’s submission and review process Guidance as to how to increase quality, impact and chances of acceptance To help decipher which journal is appropriate for a given work A. Karellas, Research collaboration with Koning, Corporation.« less

Assembling the bacterial segrosome.

PubMed

Hayes, Finbarr; Barillà, Daniela

2006-05-01

Genome segregation in prokaryotes is a highly ordered process that integrates with DNA replication, cytokinesis and other fundamental facets of the bacterial cell cycle. The segrosome is the nucleoprotein complex that mediates DNA segregation in bacteria, its assembly and organization is best understood for plasmid partition. The recent elucidation of structures of the ParB plasmid segregation protein bound to centromeric DNA, and of the tertiary structures of other segregation proteins, are key milestones in the path to deciphering the molecular basis of bacterial DNA segregation.

Are delusional contents replayed during dreams?

PubMed

D'Agostino, Armando; Aletti, Giacomo; Carboni, Martina; Cavallotti, Simone; Limosani, Ivan; Manzone, Marialaura; Scarone, Silvio

2013-09-01

The relationship between dream content and waking life experiences remains difficult to decipher. However, some neurobiological findings suggest that dreaming can, at least in part, be considered epiphenomenal to ongoing memory consolidation processes in sleep. Both abnormalities in sleep architecture and impairment in memory consolidation mechanisms are thought to be involved in the development of psychosis. The objective of this study was to assess the continuity between delusional contents and dreams in acutely psychotic patients. Ten patients with a single fixed and recurring delusional content were asked to report their dreams during an acute psychotic break. Sixteen judges with four different levels of acquaintance to the specific content of the patients' delusions were asked to group the dreams, expecting that fragments of the delusional thought would guide the task. A mathematical index (f,t) was developed in order to compare correct groupings between the four groups of judges. Most judges grouped the dreams slightly above chance level and no relevant differences could be found between the four groups [F(3,12)=1.297; p=n.s.]. Scoring of dreams for specific delusional themes suggested a continuity in terms of dream and waking mentation for two contents (Grandiosity and Religion). These findings seem to suggest that at least some delusional contents recur within patients' dreams. Future studies will need to determine whether such continuity reflects ongoing consolidation processes that are relevant to current theories of delusion formation and stabilization. Copyright © 2013 Elsevier Inc. All rights reserved.

A Network Biology Approach to Decipher Stress Response in Bacteria Using Escherichia coli As a Model.

PubMed

Nagar, Shashwat Deepali; Aggarwal, Bhavye; Joon, Shikha; Bhatnagar, Rakesh; Bhatnagar, Sonika

2016-05-01

The development of drug-resistant pathogenic bacteria poses challenges to global health for their treatment and control. In this context, stress response enables bacterial populations to survive extreme perturbations in the environment but remains poorly understood. Specific modules are activated for unique stressors with few recognized global regulators. The phenomenon of cross-stress protection strongly suggests the presence of central proteins that control the diverse stress responses. In this work, Escherichia coli was used to model the bacterial stress response. A Protein-Protein Interaction Network was generated by integrating differentially expressed genes in eight stress conditions of pH, temperature, and antibiotics with relevant gene ontology terms. Topological analysis identified 24 central proteins. The well-documented role of 16 central proteins in stress indicates central control of the response, while the remaining eight proteins may have a novel role in stress response. Cluster analysis of the generated network implicated RNA binding, flagellar assembly, ABC transporters, and DNA repair as important processes during response to stress. Pathway analysis showed crosstalk of Two Component Systems with metabolic processes, oxidative phosphorylation, and ABC transporters. The results were further validated by analysis of an independent cross-stress protection dataset. This study also reports on the ways in which bacterial stress response can progress to biofilm formation. In conclusion, we suggest that drug targets or pathways disrupting bacterial stress responses can potentially be exploited to combat antibiotic tolerance and multidrug resistance in the future.

Deciphering the Genetic Programme Triggering Timely and Spatially-Regulated Chitin Deposition

PubMed Central

Rotstein, Bárbara; Casali, Andreu; Llimargas, Marta

2015-01-01

Organ and tissue formation requires a finely tuned temporal and spatial regulation of differentiation programmes. This is necessary to balance sufficient plasticity to undergo morphogenesis with the acquisition of the mature traits needed for physiological activity. Here we addressed this issue by analysing the deposition of the chitinous extracellular matrix of Drosophila, an essential element of the cuticle (skin) and respiratory system (tracheae) in this insect. Chitin deposition requires the activity of the chitin synthase Krotzkopf verkehrt (Kkv). Our data demonstrate that this process equally requires the activity of two other genes, namely expansion (exp) and rebuf (reb). We found that Exp and Reb have interchangeable functions, and in their absence no chitin is produced, in spite of the presence of Kkv. Conversely, when Kkv and Exp/Reb are co-expressed in the ectoderm, they promote chitin deposition, even in tissues normally devoid of this polysaccharide. Therefore, our results indicate that both functions are not only required but also sufficient to trigger chitin accumulation. We show that this mechanism is highly regulated in time and space, ensuring chitin accumulation in the correct tissues and developmental stages. Accordingly, we observed that unregulated chitin deposition disturbs morphogenesis, thus highlighting the need for tight regulation of this process. In summary, here we identify the genetic programme that triggers the timely and spatially regulated deposition of chitin and thus provide new insights into the extracellular matrix maturation required for physiological activity. PMID:25617778

Skeletal muscle hypertrophy and regeneration: interplay between the myogenic regulatory factors (MRFs) and insulin-like growth factors (IGFs) pathways.

PubMed

Zanou, Nadège; Gailly, Philippe

2013-11-01

Adult skeletal muscle can regenerate in response to muscle damage. This ability is conferred by the presence of myogenic stem cells called satellite cells. In response to stimuli such as injury or exercise, these cells become activated and express myogenic regulatory factors (MRFs), i.e., transcription factors of the myogenic lineage including Myf5, MyoD, myogenin, and Mrf4 to proliferate and differentiate into myofibers. The MRF family of proteins controls the transcription of important muscle-specific proteins such as myosin heavy chain and muscle creatine kinase. Different growth factors are secreted during muscle repair among which insulin-like growth factors (IGFs) are the only ones that promote both muscle cell proliferation and differentiation and that play a key role in muscle regeneration and hypertrophy. Different isoforms of IGFs are expressed during muscle repair: IGF-IEa, IGF-IEb, or IGF-IEc (also known as mechano growth factor, MGF) and IGF-II. MGF is expressed first and is observed in satellite cells and in proliferating myoblasts whereas IGF-Ia and IGF-II expression occurs at the state of muscle fiber formation. Interestingly, several studies report the induction of MRFs in response to IGFs stimulation. Inversely, IGFs expression may also be regulated by MRFs. Various mechanisms are proposed to support these interactions. In this review, we describe the general process of muscle hypertrophy and regeneration and decipher the interactions between the two groups of factors involved in the process.

Contributions of the Clementine mission to our understanding of the processes and history of the Moon

NASA Technical Reports Server (NTRS)

Spudis, Paul D.; Lucey, Paul G.

1993-01-01

The Clementine mission will provide us with an abundance of information about lunar surface morphology, topography, and composition, and it will permit us to infer the history of the Moon and the processes that have shaped that history. This information can be used to address fundamental questions in lunar science and allow us to make significant advances towards deciphering the complex story of the Moon. The Clementine mission will also permit a first-order global assessment of the resources of the Moon and provide a strategic base of knowledge upon which future robotic and human missions to the Moon can build.

High-resolution chemical composition of geothermal scalings from Hungary: Preliminary results

NASA Astrophysics Data System (ADS)

Boch, Ronny; Dietzel, Martin; Deák, József; Leis, Albrecht; Mindszenty, Andrea; Demeny, Attila

2015-04-01

Geothermal fluids originating from several hundreds to thousands meters depth mostly hold a high potential for secondary mineral precipitation (scaling) due to high total dissolved solid contents at elevated temperature and pressure conditions. The precipitation of e.g. carbonates, sulfates, sulfides, and silica has shown to cause severe problems in geothermal heat and electric power production, when clogging of drill-holes, downhole pumps, pipes and heat exchangers occurs (e.g. deep geothermal doublet systems). Ongoing scaling reduces the efficiency in energy extraction and might even question the abandonment of installations in worst cases. In an attempt to study scaling processes both temporally and spatially we collected mineral precipitates from selected sites in Hungary (Bükfürdo, Szechenyi, Szentes, Igal, Hajduszoboszlo). The samples of up to 8 cm thickness were recovered from different positions of the geothermal systems and precipitated from waters of various temperatures (40-120 °C) and variable overall chemical composition. Most of these scalings show fine lamination patterns representing mineral deposition from weeks up to 45 years at our study sites. Solid-fluid interaction over time captured in the samples are investigated applying high-resolution analytical techniques such as laser-ablation mass-spectrometry and electron microprobe, micromill-sampling for stable isotope analysis, and micro-XRD combined with hydrogeochemical modeling. A detailed investigation of the processes determining the formation and growth of precipitates can help to elucidate the short-term versus long-term geothermal performance with regard to anthropogenic and natural reservoir and production dynamics. Changes in fluid chemistry, temperature, pressure, pH, degassing rate (CO2) and flow rate are reflected by the mineralogical, chemical and isotopic composition of the precipitates. Consequently, this high-resolution approach is intended as a contribution to decipher the environmental conditions during the formation of the investigated scalings and to increase our knowledge on retarding and preventive measures of scaling for geothermal applications.

Casein phosphopeptides and CaCl2 increase penicillin production and cause an increment in microbody/peroxisome proteins in Penicillium chrysogenum.

PubMed

Domínguez-Santos, Rebeca; Kosalková, Katarina; García-Estrada, Carlos; Barreiro, Carlos; Ibáñez, Ana; Morales, Alejandro; Martín, Juan-Francisco

2017-03-06

Transport of penicillin intermediates and penicillin secretion are still poorly characterized in Penicillium chrysogenum (re-identified as Penicillium rubens). Calcium (Ca 2+ ) plays an important role in the metabolism of filamentous fungi, and casein phosphopeptides (CPP) are involved in Ca 2+ internalization. In this study we observe that the effect of CaCl 2 and CPP is additive and promotes an increase in penicillin production of up to 10-12 fold. Combination of CaCl 2 and CPP greatly promotes expression of the three penicillin biosynthetic genes. Comparative proteomic analysis by 2D-DIGE, identified 39 proteins differentially represented in P. chrysogenum Wisconsin 54-1255 after CPP/CaCl 2 addition. The most interesting group of overrepresented proteins were a peroxisomal catalase, three proteins of the methylcitrate cycle, two aminotransferases and cystationine β-synthase, which are directly or indirectly related to the formation of penicillin amino acid precursors. Importantly, two of the enzymes of the penicillin pathway (isopenicillin N synthase and isopenicillin N acyltransferase) are clearly induced after CPP/CaCl 2 addition. Most of these overrepresented proteins are either authentic peroxisomal proteins or microbody-associated proteins. This evidence suggests that addition of CPP/CaCl 2 promotes the formation of penicillin precursors and the penicillin biosynthetic enzymes in peroxisomes and vesicles, which may be involved in transport and secretion of penicillin. Penicillin biosynthesis in Penicillium chrysogenum is one of the best characterized secondary metabolism processes. However, the mechanism by which penicillin is secreted still remains to be elucidated. Taking into account the role played by Ca 2+ and CPP in the secretory pathway and considering the positive effect that Ca 2+ exerts on penicillin production, the analysis of global protein changes produced after CPP/CaCl 2 addition is very helpful to decipher the processes related to the biosynthesis and secretion of penicillin. Copyright © 2017 Elsevier B.V. All rights reserved.

Serum miRNAs Signature Plays an Important Role in Keloid Disease.

PubMed

Luan, Y; Liu, Y; Liu, C; Lin, Q; He, F; Dong, X; Xiao, Z

2016-01-01

The molecular mechanism underlying the pathogenesis of keloid is largely unknown. MicroRNA (miRNA) is a class of small regulatory RNA that has emerged as a group of posttranscriptional gene repressors, participating in diverse pathophysiological processes of skin diseases. We investigated the expression profiles of miRNAs in the sera of patients to decipher the complicated factors involved in the development of keloid disease. MiRNA expression profiling in the sera from 9 keloid patients and 7 normal controls were characterized using a miRNA microarray containing established human mature and precursor miRNA sequences. Quantitative real-time PCR was performed to confirm the expression of miRNAs. The putative targets of differentially expressed miRNAs were functionally annotated by bioinformatics. MiRNA microarray analysis identified 37 differentially expressed miRNAs (17 upregulated and 20 downregulated) in keloid patients, compared to the healthy controls. Functional annotations revealed that the targets of those differentially expressed miRNAs were enriched in signaling pathways essential for scar formation and wound healing. The expression profiling of miRNAs is altered in the keloid, providing a clue for the molecular mechanisms underlying its initiation and progression. MiRNAs may partly contribute to the etiology of keloids by affecting the critical signaling pathways relevant to keloid pathogenesis.

Women in black: challenging Israel's gender and socio-political orders.

PubMed

Helman, S; Rapoport, T

1997-12-01

The Israeli protest movement 'Women in Black' is studied by focusing on the movement's mode of protest, which is used as a prism through which to analyse the manner in which the structure, contents and goals of protest challenge the socio-political and gender orders. The article analyses the protest vigil of 'Women in Black' in Jerusalem, and characterizes it, following Handelman (1990), as a minimalist public event. After examining and analysing the sources of minimalism it was concluded that minimalism was the result of two social processes attendant at the formation of 'Women in Black' as a social movement: personal interpretation of the political field, and avoidance of ideological deliberation amongst the participants. The minimalism of the public event preserved the movement for six years and created a collective identity that emphasized the symbolic difference between those within the demonstration and those outside it. This difference was symbolized by a juxtaposition of opposites. The essence of opposites is analysed by means of 'thick description', i.e., by deciphering them in the context of Israeli society. The study concluded that the mode of protest of 'Women in Black' has created a symbolic space in which a new type of political woman is enacted. This identity challenges established socio-cultural categories Israel.

Decoding cell signalling and regulation of oligodendrocyte differentiation.

PubMed

Santos, A K; Vieira, M S; Vasconcellos, R; Goulart, V A M; Kihara, A H; Resende, R R

2018-05-22

Oligodendrocytes are fundamental for the functioning of the nervous system; they participate in several cellular processes, including axonal myelination and metabolic maintenance for astrocytes and neurons. In the mammalian nervous system, they are produced through waves of proliferation and differentiation, which occur during embryogenesis. However, oligodendrocytes and their precursors continue to be generated during adulthood from specific niches of stem cells that were not recruited during development. Deficiencies in the formation and maturation of these cells can generate pathologies mainly related to myelination. Understanding the mechanisms involved in oligodendrocyte development, from the precursor to mature cell level, will allow inferring therapies and treatments for associated pathologies and disorders. Such mechanisms include cell signalling pathways that involve many growth factors, small metabolic molecules, non-coding RNAs, and transcription factors, as well as specific elements of the extracellular matrix, which act in a coordinated temporal and spatial manner according to a given stimulus. Deciphering those aspects will allow researchers to replicate them in vitro in a controlled environment and thus mimic oligodendrocyte maturation to understand the role of oligodendrocytes in myelination in pathologies and normal conditions. In this study, we review these aspects, based on the most recent in vivo and in vitro data on oligodendrocyte generation and differentiation. Copyright © 2018 Elsevier Ltd. All rights reserved.

MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation.

PubMed

Lugli, Gabriele Andrea; Milani, Christian; Mancabelli, Leonardo; van Sinderen, Douwe; Ventura, Marco

2016-04-01

Genome annotation is one of the key actions that must be undertaken in order to decipher the genetic blueprint of organisms. Thus, a correct and reliable annotation is essential in rendering genomic data valuable. Here, we describe a bioinformatics pipeline based on freely available software programs coordinated by a multithreaded script named MEGAnnotator (Multithreaded Enhanced prokaryotic Genome Annotator). This pipeline allows the generation of multiple annotated formats fulfilling the NCBI guidelines for assembled microbial genome submission, based on DNA shotgun sequencing reads, and minimizes manual intervention, while also reducing waiting times between software program executions and improving final quality of both assembly and annotation outputs. MEGAnnotator provides an efficient way to pre-arrange the assembly and annotation work required to process NGS genome sequence data. The script improves the final quality of microbial genome annotation by reducing ambiguous annotations. Moreover, the MEGAnnotator platform allows the user to perform a partial annotation of pre-assembled genomes and includes an option to accomplish metagenomic data set assemblies. MEGAnnotator platform will be useful for microbiologists interested in genome analyses of bacteria as well as those investigating the complexity of microbial communities that do not possess the necessary skills to prepare their own bioinformatics pipeline. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A tale of two toxicities: malformed selenoproteins and oxidative stress both contribute to selenium stress in plants

PubMed Central

Van Hoewyk, Doug

2013-01-01

Background Despite selenium's toxicity in plants at higher levels, crops supply most of the essential dietary selenium in humans. In plants, inorganic selenium can be assimilated into selenocysteine, which can replace cysteine in proteins. Selenium toxicity in plants has been attributed to the formation of non-specific selenoproteins. However, this paradigm can be challenged now that there is increasingly abundant evidence suggesting that selenium-induced oxidative stress also contributes to toxicity in plants. Scope This Botanical Briefing summarizes the evidence indicating that selenium toxicity in plants is attributable to both the accumulation of non-specific selenoproteins and selenium-induced oxidative stress. Evidence is also presented to substantiate the claim that inadvertent selenocysteine replacement probably impairs or misfolds proteins, which supports the malformed selenoprotein hypothesis. The possible physiological ramifications of selenoproteins and selenium-induced oxidative stress are discussed. Conclusions Malformed selenoproteins and oxidative stress are two distinct types of stress that drive selenium toxicity in plants and could impact cellular processes in plants that have yet to be thoroughly explored. Although challenging, deciphering whether the extent of selenium toxicity in plants is imparted by selenoproteins or oxidative stress could be helpful in the development of crops with fortified levels of selenium. PMID:23904445

Antihistone Properties of C1 Esterase Inhibitor Protect against Lung Injury.

PubMed

Wygrecka, Malgorzata; Kosanovic, Djuro; Wujak, Lukasz; Reppe, Katrin; Henneke, Ingrid; Frey, Helena; Didiasova, Miroslava; Kwapiszewska, Grazyna; Marsh, Leigh M; Baal, Nelli; Hackstein, Holger; Zakrzewicz, Dariusz; Müller-Redetzky, Holger C; de Maat, Steven; Maas, Coen; Nolte, Marc W; Panousis, Con; Schermuly, Ralph T; Seeger, Werner; Witzenrath, Martin; Schaefer, Liliana; Markart, Philipp

2017-07-15

Acute respiratory distress syndrome is characterized by alveolar epithelial cell injury, edema formation, and intraalveolar contact phase activation. To explore whether C1 esterase inhibitor (C1INH), an endogenous inhibitor of the contact phase, may protect from lung injury in vivo and to decipher the possible underlying mechanisms mediating protection. The ability of C1INH to control the inflammatory processes was studied in vitro and in vivo. Here, we demonstrate that application of C1INH alleviates bleomycin-induced lung injury via direct interaction with extracellular histones. In vitro, C1INH was found to bind all histone types. Interaction with histones was independent of its protease inhibitory activity, as demonstrated by the use of reactive-center-cleaved C1INH, but dependent on its glycosylation status. C1INH sialylated-N- and -O-glycans were not only essential for its interaction with histones but also to protect against histone-induced cell death. In vivo, histone-C1INH complexes were detected in bronchoalveolar lavage fluid from patients with acute respiratory distress syndrome and multiple models of lung injury. Furthermore, reactive-center-cleaved C1INH attenuated pulmonary damage evoked by intravenous histone instillation. Collectively, C1INH administration provides a new therapeutic option for disorders associated with histone release.

Multiplexing of miniaturized planar antibody arrays for serum protein profiling--a biomarker discovery in SLE nephritis.

PubMed

Petersson, Linn; Dexlin-Mellby, Linda; Bengtsson, Anders A; Sturfelt, Gunnar; Borrebaeck, Carl A K; Wingren, Christer

2014-06-07

In the quest to decipher disease-associated biomarkers, miniaturized and multiplexed antibody arrays may play a central role in generating protein expression profiles, or protein maps, of crude serum samples. In this conceptual study, we explored a novel, 4-times larger pen design, enabling us to, in a unique manner, simultaneously print 48 different reagents (antibodies) as individual 78.5 μm(2) (10 μm in diameter) sized spots at a density of 38,000 spots cm(-2) using dip-pen nanolithography technology. The antibody array set-up was interfaced with a high-resolution fluorescent-based scanner for sensitive sensing. The performance and applicability of this novel 48-plex recombinant antibody array platform design was demonstrated in a first clinical application targeting SLE nephritis, a severe chronic autoimmune connective tissue disorder, as the model disease. To this end, crude, directly biotinylated serum samples were targeted. The results showed that the miniaturized and multiplexed array platform displayed adequate performance, and that SLE-associated serum biomarker panels reflecting the disease process could be deciphered, outlining the use of miniaturized antibody arrays for disease proteomics and biomarker discovery.

High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga Ectocarpus

PubMed Central

Avia, Komlan; Coelho, Susana M.; Montecinos, Gabriel J.; Cormier, Alexandre; Lerck, Fiona; Mauger, Stéphane; Faugeron, Sylvain; Valero, Myriam; Cock, J. Mark; Boudry, Pierre

2017-01-01

Deciphering the genetic architecture of adaptation of brown algae to environmental stresses such as temperature and salinity is of evolutionary as well as of practical interest. The filamentous brown alga Ectocarpus sp. is a model for the brown algae and its genome has been sequenced. As sessile organisms, brown algae need to be capable of resisting the various abiotic stressors that act in the intertidal zone (e.g. osmotic pressure, temperature, salinity, UV radiation) and previous studies have shown that an important proportion of the expressed genes is regulated in response to hyposaline, hypersaline or oxidative stress conditions. Using the double digest RAD sequencing method, we constructed a dense genetic map with 3,588 SNP markers and identified 39 QTLs for growth-related traits and their plasticity under different temperature and salinity conditions (tolerance to high temperature and low salinity). GO enrichment tests within QTL intervals highlighted membrane transport processes such as ion transporters. Our study represents a significant step towards deciphering the genetic basis of adaptation of Ectocarpus sp. to stress conditions and provides a substantial resource to the increasing list of tools generated for the species. PMID:28256542

Deciphering the Mechanism of Action of Wrightia tinctoria for Psoriasis Based on Systems Pharmacology Approach.

PubMed

Sundarrajan, Sudharsana; Lulu, Sajitha; Arumugam, Mohanapriya

2017-11-01

Psoriasis is a chronic immune-mediated disorder of the skin. The disease manifests itself with red or silvery scaly plaques distributing over the lower back, scalp, and extensor aspects of limbs. Several medications are available for the treatment of psoriasis; however, high rates of remission and side-effects still persist as a major concern. Siddha, one of the traditional systems of Indian medicine offers cure to many dermatological conditions, including psoriasis. The oil prepared from the leaves of Wrightia tinctoria is prescribed by many healers for the treatment of psoriasis. This work aims to decipher the mechanism of action of the W. tinctoria in curing psoriasis and its associated comorbidities. The work integrates various pharmacology approaches such as drug-likeness evaluation, oral bioavailability predictions, and network pharmacology approaches to understand the roles of various bioactive components of the herb. This work identified 67 compounds of W. tinctoria interacting with 238 protein targets. The compounds were found to act through synergistic mechanism in reviving the disrupted process in the diseased state. The results of this work not only shed light on the pharmacological action of the herb but also validate the usage of safe herbal drugs.

In vivo PET imaging of neuroinflammation in Alzheimer's disease.

PubMed

Lagarde, Julien; Sarazin, Marie; Bottlaender, Michel

2018-05-01

Increasing evidence suggests that neuroinflammation contributes to the pathophysiology of many neurodegenerative diseases, especially Alzheimer's disease (AD). Molecular imaging by PET may be a useful tool to assess neuroinflammation in vivo, thus helping to decipher the complex role of inflammatory processes in the pathophysiology of neurodegenerative diseases and providing a potential means of monitoring the effect of new therapeutic approaches. For this objective, the main target of PET studies is the 18 kDa translocator protein (TSPO), as it is overexpressed by activated microglia. In the present review, we describe the most widely used PET tracers targeting the TSPO, the methodological issues in tracer quantification and summarize the results obtained by TSPO PET imaging in AD, as well as in neurodegenerative disorders associated with AD, in psychiatric disorders and ageing. We also briefly describe alternative PET targets and imaging modalities to study neuroinflammation. Lastly, we question the meaning of PET imaging data in the context of a highly complex and multifaceted role of neuroinflammation in neurodegenerative diseases. This overview leads to the conclusion that PET imaging of neuroinflammation is a promising way of deciphering the enigma of the pathophysiology of AD and of monitoring the effect of new therapies.

Deciphering Molecular Mechanisms of Interface Buildup and Stability in Porous Si/Eumelanin Hybrids

PubMed Central

Pinna, Elisa; Melis, Claudio; Antidormi, Aleandro; Cardia, Roberto; Sechi, Elisa; Cappellini, Giancarlo; Colombo, Luciano

2017-01-01

Porous Si/eumelanin hybrids are a novel class of organic–inorganic hybrid materials that hold considerable promise for photovoltaic applications. Current progress toward device setup is, however, hindered by photocurrent stability issues, which require a detailed understanding of the mechanisms underlying the buildup and consolidation of the eumelanin–silicon interface. Herein we report an integrated experimental and computational study aimed at probing interface stability via surface modification and eumelanin manipulation, and at modeling the organic–inorganic interface via formation of a 5,6-dihydroxyindole (DHI) tetramer and its adhesion to silicon. The results indicated that mild silicon oxidation increases photocurrent stability via enhancement of the DHI–surface interaction, and that higher oxidation states in DHI oligomers create more favorable conditions for the efficient adhesion of growing eumelanin. PMID:28753933

Iberian plate kinematics: A jumping plate boundary between Eurasia and Africa

USGS Publications Warehouse

Srivastava, S.P.; Schouten, Hans; Roest, W.R.; Klitgord, Kim D.; Kovacs, L.C.; Verhoef, J.; Macnab, R.

1990-01-01

THE rotation of Iberia and its relation to the formation of the Pyrenees has been difficult to decipher because of the lack of detailed sea-floor spreading data, although several models have been proposed1-7. Here we use detailed aeromagnetic measurements from the sea floor offshore of the Grand Banks of Newfoundland to show that Iberia moved as part of the African plate from late Cretaceous to mid-Eocene time, with a plate boundary extending westward from the Bay of Biscay. When motion along this boundary ceased, a boundary linking extension in the King's Trough to compression along the Pyrenees came into existence. Finally, since the late Oligocene, Iberia has been part of the Eurasian plate, with the boundary between Eurasia and Africa situated along the Azores-Gibraltar fracture zone.

Deciphering spectral fingerprints of habitable exoplanets.

PubMed

Kaltenegger, Lisa; Selsis, Frank; Fridlund, Malcolm; Lammer, Helmut; Beichman, Charles; Danchi, William; Eiroa, Carlos; Henning, Thomas; Herbst, Tom; Léger, Alain; Liseau, René; Lunine, Jonathan; Paresce, Francesco; Penny, Alan; Quirrenbach, Andreas; Röttgering, Huub; Schneider, Jean; Stam, Daphne; Tinetti, Giovanna; White, Glenn J

2010-01-01

We discuss how to read a planet's spectrum to assess its habitability and search for the signatures of a biosphere. After a decade rich in giant exoplanet detections, observation techniques have advanced to a level where we now have the capability to find planets of less than 10 Earth masses (M(Earth)) (so-called "super Earths"), which may be habitable. How can we characterize those planets and assess whether they are habitable? This new field of exoplanet search has shown an extraordinary capacity to combine research in astrophysics, chemistry, biology, and geophysics into a new and exciting interdisciplinary approach to understanding our place in the Universe. The results of a first-generation mission will most likely generate an amazing scope of diverse planets that will set planet formation, evolution, and our planet into an overall context.

[Deciphering the argots of the names of materia medica and its dosage in the Yi lin kou pu liu zhi mi shu (A Secret Medical Book of Six Therapies in Rhymes of Medical Professionals)].

PubMed

Zhou, Jian; Lin, Shiyi; Liu, Shijue

2014-11-01

Yi lin kou pu liu zhi mi shu (A Secret Medical Book of Six Therapies in Rhymes of Medical Professionals) was additionally compiled, supplemented and annotated by Zhou Sheng, a famous doctor of the Qing Dynasty, based on Yi lin kou pu (Rhymes of Medical Professionals) which was composed by Lu Qi. The book contains four volumes in total, dealing mainly with the miscellaneous diseases of internal medicine, as well as external medicine, gynecology, and pediatrics etc. The syndrome differentiation and treatment, prescriptions and medications in this book has its own characteristic with rather high academic value and practical significance. There were 20 drug names were deciphered by the argots, for instance, "you che" was the argot of golden thread, and "wu yue (May)" was the argot of medicinal evodia fruit, etc. In addition, the argots were often used to decipher numerals and quantifiers, for example, "su, qi, zi, qi, man" referring to 1, 2, 3, 4, 5 respectively, and "huo, pu, xiang, feng, lai" referring to 6, 7, 8, 9, 10 respectively, and "qing","zhong","xi" referring to qian, liang and fen respectively. Hence, deciphering of these argots could help to understand and apply these prescriptions correctly.

Lgr5(+ve) stem/progenitor cells contribute to nephron formation during kidney development.

PubMed

Barker, Nick; Rookmaaker, Maarten B; Kujala, Pekka; Ng, Annie; Leushacke, Marc; Snippert, Hugo; van de Wetering, Marc; Tan, Shawna; Van Es, Johan H; Huch, Meritxell; Poulsom, Richard; Verhaar, Marianne C; Peters, Peter J; Clevers, Hans

2012-09-27

Multipotent stem cells and their lineage-restricted progeny drive nephron formation within the developing kidney. Here, we document expression of the adult stem cell marker Lgr5 in the developing kidney and assess the stem/progenitor identity of Lgr5(+ve) cells via in vivo lineage tracing. The appearance and localization of Lgr5(+ve) cells coincided with that of the S-shaped body around embryonic day 14. Lgr5 expression remained restricted to cell clusters within developing nephrons in the cortex until postnatal day 7, when expression was permanently silenced. In vivo lineage tracing identified Lgr5 as a marker of a stem/progenitor population within nascent nephrons dedicated to generating the thick ascending limb of Henle's loop and distal convoluted tubule. The Lgr5 surface marker and experimental models described here will be invaluable for deciphering the contribution of early nephron stem cells to developmental defects and for isolating human nephron progenitors as a prerequisite to evaluating their therapeutic potential. Copyright © 2012 The Authors. Published by Elsevier Inc. All rights reserved.

On Design and Implementation of Neural-Machine Interface for Artificial Legs

PubMed Central

Zhang, Xiaorong; Liu, Yuhong; Zhang, Fan; Ren, Jin; Sun, Yan (Lindsay); Yang, Qing

2011-01-01

The quality of life of leg amputees can be improved dramatically by using a cyber physical system (CPS) that controls artificial legs based on neural signals representing amputees’ intended movements. The key to the CPS is the neural-machine interface (NMI) that senses electromyographic (EMG) signals to make control decisions. This paper presents a design and implementation of a novel NMI using an embedded computer system to collect neural signals from a physical system - a leg amputee, provide adequate computational capability to interpret such signals, and make decisions to identify user’s intent for prostheses control in real time. A new deciphering algorithm, composed of an EMG pattern classifier and a post-processing scheme, was developed to identify the user’s intended lower limb movements. To deal with environmental uncertainty, a trust management mechanism was designed to handle unexpected sensor failures and signal disturbances. Integrating the neural deciphering algorithm with the trust management mechanism resulted in a highly accurate and reliable software system for neural control of artificial legs. The software was then embedded in a newly designed hardware platform based on an embedded microcontroller and a graphic processing unit (GPU) to form a complete NMI for real time testing. Real time experiments on a leg amputee subject and an able-bodied subject have been carried out to test the control accuracy of the new NMI. Our extensive experiments have shown promising results on both subjects, paving the way for clinical feasibility of neural controlled artificial legs. PMID:22389637

Comprehensive proteome profiling in Aedes albopictus to decipher Wolbachia-arbovirus interference phenomenon.

PubMed

Saucereau, Yoann; Valiente Moro, Claire; Dieryckx, Cindy; Dupuy, Jean-William; Tran, Florence-Hélène; Girard, Vincent; Potier, Patrick; Mavingui, Patrick

2017-08-18

Aedes albopictus is a vector of arboviruses that cause severe diseases in humans such as Chikungunya, Dengue and Zika fevers. The vector competence of Ae. albopictus varies depending on the mosquito population involved and the virus transmitted. Wolbachia infection status in believed to be among key elements that determine viral transmission efficiency. Little is known about the cellular functions mobilized in Ae. albopictus during co-infection by Wolbachia and a given arbovirus. To decipher this tripartite interaction at the molecular level, we performed a proteome analysis in Ae. albopictus C6/36 cells mono-infected by Wolbachia wAlbB strain or Chikungunya virus (CHIKV), and bi-infected. We first confirmed significant inhibition of CHIKV by Wolbachia. Using two-dimensional gel electrophoresis followed by nano liquid chromatography coupled with tandem mass spectrometry, we identified 600 unique differentially expressed proteins mostly related to glycolysis, translation and protein metabolism. Wolbachia infection had greater impact on cellular functions than CHIKV infection, inducing either up or down-regulation of proteins associated with metabolic processes such as glycolysis and ATP metabolism, or structural glycoproteins and capsid proteins in the case of bi-infection with CHIKV. CHIKV infection inhibited expression of proteins linked with the processes of transcription, translation, lipid storage and miRNA pathways. The results of our proteome profiling have provided new insights into the molecular pathways involved in tripartite Ae. albopictus-Wolbachia-CHIKV interaction and may help defining targets for the better implementation of Wolbachia-based strategies for disease transmission control.

Iron isotope fractionation during hydrothermal ore deposition and alteration

NASA Astrophysics Data System (ADS)

Markl, Gregor; von Blanckenburg, Friedhelm; Wagner, Thomas

2006-06-01

Iron isotopes fractionate during hydrothermal processes. Therefore, the Fe isotope composition of ore-forming minerals characterizes either iron sources or fluid histories. The former potentially serves to distinguish between sedimentary, magmatic or metamorphic iron sources, and the latter allows the reconstruction of precipitation and redox processes. These processes take place during ore formation or alteration. The aim of this contribution is to investigate the suitability of this new isotope method as a probe of ore-related processes. For this purpose 51 samples of iron ores and iron mineral separates from the Schwarzwald region, southwest Germany, were analyzed for their iron isotope composition using multicollector ICP-MS. Further, the ore-forming and ore-altering processes were quantitatively modeled using reaction path calculations. The Schwarzwald mining district hosts mineralizations that formed discontinuously over almost 300 Ma of hydrothermal activity. Primary hematite, siderite and sulfides formed from mixing of meteoric fluids with deeper crustal brines. Later, these minerals were partly dissolved and oxidized, and secondary hematite, goethite and iron arsenates were precipitated. Two types of alteration products formed: (1) primary and high-temperature secondary Fe minerals formed between 120 and 300 °C, and (2) low-temperature secondary Fe minerals formed under supergene conditions (<100 °C). Measured iron isotope compositions are variable and cover a range in δ56Fe between -2.3‰ and +1.3‰. Primary hematite ( δ56Fe: -0.5‰ to +0.5‰) precipitated by mixing oxidizing surface waters with a hydrothermal fluid that contained moderately light Fe ( δ56Fe: -0.5‰) leached from the crystalline basement. Occasional input of CO 2-rich waters resulted in precipitation of isotopically light siderite ( δ56Fe: -1.4 to -0.7‰). The difference between hematite and siderite is compatible with published Fe isotope fractionation factors. The observed range in isotopic compositions can be accounted for by variable fractions of Fe precipitating from the fluid. Therefore, both fluid processes and mass balance can be inferred from Fe isotopes. Supergene weathering of siderite by oxidizing surface waters led to replacement of isotopically light primary siderite by similarly light secondary hematite and goethite, respectively. Because this replacement entails quantitative transfer of iron from precursor mineral to product, no significant isotope fractionation is produced. Hence, Fe isotopes potentially serve to identify precursors in ore alteration products. Goethites from oolitic sedimentary iron ores were also analyzed. Their compositional range appears to indicate oxidative precipitation from relatively uniform Fe dissolved in coastal water. This comprehensive iron isotope study illustrates the potential of the new technique in deciphering ore formation and alteration processes. Isotope ratios are strongly dependent on and highly characteristic of fluid and precipitation histories. Therefore, they are less suitable to provide information on Fe sources. However, it will be possible to unravel the physico-chemical processes leading to the formation, dissolution and redeposition of ores in great detail.

How to Make a Neurocrystal: Modeling the developmental patterning of the fly's retina

NASA Astrophysics Data System (ADS)

Lubensky, David

2005-03-01

Animals' ability to create the complex patterns found in many organisms is an enduring source of wonder and a topic that has long drawn the interest of scientists of all stripes. Famously, it was an attempt to model developmental patterning that led to the discovery of the Turing instability. Here, we study one of the most remarkable and best-characterized examples of such pattern formation, the development of the fruit fly's compound eye. In the fly larva, a front of differentiation moves across the sheet of tissue that will become the adult retina. It leaves behind it a striking hexagonal array of cells marked by high levels of the protein Atonal. It has previously been noted that a standard activator-inhibitor model might explain this process [Meinhardt, 1992], but only recently has the basic genetic logic governing photoreceptor specification been deciphered [e.g. Frankfort and Mardon, 2002]. We build on these advances with the first model of retinal patterning based on experimentally verified interactions. Surprisingly, we conclude that a Turing-instability-based mechanism alone cannot reproduce the observed behavior. Instead, we propose that the pattern is generated primarily by a novel ``epitaxial'' process in which, as the front progresses, each newly-created row of unit cells acts as a template for the next one. A clear prediction of this model is that if the communication between successive rows is broken, even transiently, a striped pattern will appear. Preliminary experimental tests suggest that just such a phenomenon occurs in some mutants. Related patterning processes have been observed in systems as diverse as chick feather buds and vertebrate retinal ganglion cells [Pichaud, Treisman, and Desplan, 2001]; our model may thus describe an evolutionarily conserved module.

IGF-1 contributes to the expansion of melanoma-initiating cells through an epithelial-mesenchymal transition process.

PubMed

Le Coz, Vincent; Zhu, Chaobin; Devocelle, Aurore; Vazquez, Aimé; Boucheix, Claude; Azzi, Sandy; Gallerne, Cindy; Eid, Pierre; Lecourt, Séverine; Giron-Michel, Julien

2016-12-13

Melanoma is a particularly virulent human cancer, due to its resistance to conventional treatments and high frequency of metastasis. Melanomas contain a fraction of cells, the melanoma-initiating cells (MICs), responsible for tumor propagation and relapse. Identification of the molecular pathways supporting MICs is, therefore, vital for the development of targeted treatments. One factor produced by melanoma cells and their microenvironment, insulin-like growth factor-1 (IGF- 1), is linked to epithelial-mesenchymal transition (EMT) and stemness features in several cancers.We evaluated the effect of IGF-1 on the phenotype and chemoresistance of B16-F10 cells. IGF-1 inhibition in these cells prevented malignant cell proliferation, migration and invasion, and lung colony formation in immunodeficient mice. IGF-1 downregulation also markedly inhibited EMT, with low levels of ZEB1 and mesenchymal markers (N-cadherin, CD44, CD29, CD105) associated with high levels of E-cadherin and MITF, the major regulator of melanocyte differentiation. IGF-1 inhibition greatly reduced stemness features, including the expression of key stem markers (SOX2, Oct-3/4, CD24 and CD133), and the functional characteristics of MICs (melanosphere formation, aldehyde dehydrogenase activity, side population). These features were associated with a high degree of sensitivity to mitoxantrone treatment.In this study, we deciphered new connections between IGF-1 and stemness features and identified IGF-1 as instrumental for maintaining the MIC phenotype. The IGF1/IGF1-R nexus could be targeted for the development of more efficient anti-melanoma treatments. Blocking the IGF-1 pathway would improve the immune response, decrease the metastatic potential of tumor cells and sensitize melanoma cells to conventional treatments.

Restoration of Apollo Data by the NSSDC and the PDS Lunar Data Node

NASA Technical Reports Server (NTRS)

Williams, David R.; Hills, H. Kent; Lowman, Paul D.; Taylor, Patrick T.; Guinness, Edward A.

2011-01-01

The Lunar Data Node (LDN), under the auspices of the Geosciences Node of the Planetary Data System (PDS), is restoring Apollo data archived at the National Space Science Data Center. The Apollo data were arch ived on older media (7 -track tapes. microfilm, microfiche) and in ob solete digital formats, which limits use of the data. The LDN is maki ng these data accessible by restoring them to standard formats and archiving them through PDS. The restoration involves reading the older m edia, collecting supporting data (metadata), deciphering and understa nding the data, and organizing into a data set. The data undergo a pe er review before archive at PDS. We will give an update on last year' s work. We have scanned notebooks from Otto Berg, P.1. for the Lunar Ejecta and Meteorites Experiment. These notebooks contain information on the data and calibration coefficients which we hope to be able to use to restore the raw data into a usable archive. We have scanned Ap ollo 14 and 15 Dust Detector data from microfilm and are in the proce ss of archiving thc scans with PDS. We are also restoring raw dust de tector data from magnetic tape supplied by Yosio Nakamura (UT Austin) . Seiichi Nagihara (Texas Tech Univ.) and others in cooperation with NSSDC are recovering ARCSAV tapes (tapes containing raw data streams from all the ALSEP instruments). We will be preparing these data for archive with PDS. We are also in the process of recovering and archivi ng data not previously archived, from the Apollo 16 Gamma Ray Spectro meter and the Apollo 17 Infrared Spectrometer.

Chemical Probes of Histone Lysine Methyltransferases

PubMed Central

2015-01-01

Growing evidence suggests that histone methyltransferases (HMTs, also known as protein methyltransferases (PMTs)) play an important role in diverse biological processes and human diseases by regulating gene expression and the chromatin state. Therefore, HMTs have been increasingly recognized by the biomedical community as a class of potential therapeutic targets. High quality chemical probes of HMTs, as tools for deciphering their physiological functions and roles in human diseases and testing therapeutic hypotheses, are critical for advancing this promising field. In this review, we focus on the discovery, characterization, and biological applications of chemical probes for HMTs. PMID:25423077

Optical encryption interface

NASA Technical Reports Server (NTRS)

Jackson, Deborah J. (Inventor)

1998-01-01

An analog optical encryption system based on phase scrambling of two-dimensional optical images and holographic transformation for achieving large encryption keys and high encryption speed. An enciphering interface uses a spatial light modulator for converting a digital data stream into a two dimensional optical image. The optical image is further transformed into a hologram with a random phase distribution. The hologram is converted into digital form for transmission over a shared information channel. A respective deciphering interface at a receiver reverses the encrypting process by using a phase conjugate reconstruction of the phase scrambled hologram.

Trinity: Transcriptome Assembly for Genetic and Functional Analysis of Cancer | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The cancer transcriptome is shaped by genetic changes, variation in gene transcription, mRNA processing, editing and stability, and the cancer microbiome. Deciphering this variation and understanding its implications on tumorigenesis requires sophisticated computational analyses. Most RNA-Seq analyses rely on methods that first map short reads to a reference genome, and then compare them to annotated transcripts or assemble them. However, this strategy can be limited when the cancer genome is substantially different than the reference or for detecting sequences from the cancer microbiome.

Non-equilibrium chemistry in the solar nebula and early solar system: Implications for the chemistry of comets

NASA Technical Reports Server (NTRS)

Fegley, Bruce, Jr.

1989-01-01

Theoretical models of solar nebula and early solar system chemistry which take into account the interplay between chemical, physical, and dynamical processes have great utility for deciphering the origin and evolution of the abundant chemically reactive volatiles (H, O, C, N, S) observed in comets. In particular, such models are essential for attempting to distinguish between presolar and solar nebula products and for quantifying the nature and duration of nebular and early solar system processing to which the volatile constituents of comets have been subjected. The diverse processes and energy sources responsible for chemical processing in the solar nebula and early solar system are discussed. The processes considered include homogeneous and heterogeneous thermochemical and photochemical reactions, and disequilibration resulting from fluid transport, condensation, and cooling whenever they occur on timescales shorter than those for chemical reactions.

Samples from Differentiated Asteroids; Regolithic Achondrites

NASA Technical Reports Server (NTRS)

Herrin J. S.; Ross, A. J.; Cartwright, J. A.; Ross, D. K.; Zolensky, Michael E.; Jenniskens, P.

2011-01-01

Differentiated and partially differentiated asteroids preserve a glimpse of planet formation frozen in time from the early solar system and thus are attractive targets for future exploration. Samples of such asteroids arrive to Earth in the form of achondrite meteorites. Many achondrites, particularly those thought to be most representative of asteroidal regolith, contain a diverse assortment of materials both indigenous and exogenous to the original igneous parent body intermixed at microscopic scales. Remote sensing spacecraft and landers would have difficulty deciphering individual components at these spatial scales, potentially leading to confusing results. Sample return would thus be much more informative than a robotic probe. In this and a companion abstract [1] we consider two regolithic achondrite types, howardites and (polymict) ureilites, in order to evaluate what materials might occur in samples returned from surfaces of differentiated asteroids and what sampling strategies might be prudent.

Progress in the Study of Coastal Storm Deposits

NASA Astrophysics Data System (ADS)

Xiong, Haixian; Huang, Guangqing; Fu, Shuqing; Qian, Peng

2018-05-01

Numerous studies have been carried out to identify storm deposits and decipher storm-induced sedimentary processes in coastal and shallow-marine areas. This study aims to provide an in-depth review on the study of coastal storm deposits from the following five aspects. 1) The formation of storm deposits is a function of hydrodynamic and sedimentary processes under the constraints of local geological and ecological factors. Many questions remain to demonstrate the genetic links between storm-related processes and a variety of resulting deposits such as overwash deposits, underwater deposits and hummocky cross-stratification (HCS). Future research into the formation of storm deposits should combine flume experiments, field observations and numerical simulations, and make full use of sediment source tracing methods. 2) Recently there has been rapid growth in the number of studies utilizing sediment provenance analysis to investigate the source of storm deposits. The development of source tracing techniques, such as mineral composition, magnetic susceptibility, microfossil and geochemical property, has allowed for better understanding of the depositional processes and environmental changes associated with coastal storms. 3) The role of extreme storms in the sedimentation of low-lying coastal wetlands with diverse ecosystem services has also drawn a great deal of attention. Many investigations have attempted to quantify widespread land loss, vertical marsh sediment accumulation and wetland elevation change induced by major hurricanes. 4) Paleostorm reconstructions based on storm sedimentary proxies have shown many advantages over the instrumental records and historic documents as they allow for the reconstruction of storm activities on millennial or longer time scales. Storm deposits having been used to establish proxies mainly include beach ridges and shelly cheniers, coral reefs, estuary-deltaic storm sequences and overwash deposits. Particularly over the past few decades, the proxies developed from overwash deposits have successfully retrieved many records of storm activities during the mid to late Holocene worldwide. 5) Distinguishing sediments deposited by storms and tsunamis is one of the most difficult issues among the many aspects of storm deposit studies. Comparative studies have investigated numerous diagnostic evidences including hydrodynamic condition, landward extent, grain property, texture and grading, thickness, microfossil assemblage and landscape conformity. Perhaps integrating physical, biological and geochemical evidences will, in the future, allow unambiguous identification of tsunami deposits and storm deposits.

Unveiling the stimulatory effects of tartrazine on human and bovine serum albumin fibrillogenesis: Spectroscopic and microscopic study

NASA Astrophysics Data System (ADS)

Al-Shabib, Nasser Abdulatif; Khan, Javed Masood; Alsenaidy, Mohammad A.; Alsenaidy, Abdulrahman M.; Khan, Mohd Shahnawaz; Husain, Fohad Mabood; Khan, Mohammad Rashid; Naseem, Mohammad; Sen, Priyankar; Alam, Parvez; Khan, Rizwan Hasan

2018-02-01

Amyloid fibrils are playing key role in the pathogenesis of various neurodegenerative diseases. Generally anionic molecules are known to induce amyloid fibril in several proteins. In this work, we have studied the effect of anionic food additive dye i.e., tartrazine (TZ) on the amyloid fibril formation of human serum albumins (HSA) and bovine serum albumin (BSA) at pHs 7.4 and 3.5. We have employed various biophysical methods like, turbidity measurements, Rayleigh Light Scattering (RLS), Dynamic Light Scattering (DLS), intrinsic fluorescence, Congo red assay, far-UV CD, transmission electron microscopy (TEM) and atomic force microscopy (AFM) to decipher the mechanism of TZ-induce amyloid fibril formation in both the serum albumins at pHs 7.4 and 3.5. The obtained results suggest that both the albumins forms amyloid-like aggregates in the presence of 1.0 to 15.0 mM of TZ at pH 3.5, but no amyloid fibril were seen at pH 7.4. The possible cause of TZ-induced amyloid fibril formation is electrostatic and hydrophobic interaction because sulfate group of TZ may have interacted electrostatically with positively charged amino acids of the albumins at pH 3.5 and increased protein-protein and protein-TZ interactions leading to amyloid fibril formation. The TEM, RLS and DLS results are suggesting that BSA forms bigger size amyloids compared to HSA, may be due to high surface hydrophobicity of BSA.

Deciphering the Temporal Link between Pain and Sleep in a Heterogeneous Chronic Pain Patient Sample: A Multilevel Daily Process Study

PubMed Central

Tang, Nicole K.Y.; Goodchild, Claire E.; Sanborn, Adam N.; Howard, Jonathan; Salkovskis, Paul M.

2012-01-01

Objectives: Because insomnia is a common comorbidity of chronic pain, scientific and clinical interest in the relationship of pain and sleep has surged in recent years. Although experimental studies suggest a sleep-interfering property of pain and a pain-enhancing effect of sleep deprivation/fragmentation, the temporal association between pain and sleep as experienced by patients is less understood. The current study was conducted to examine the influence of presleep pain on subsequent sleep and sleep on pain reports the next day, taking into consideration other related psychophysiologic variables such as mood and arousal. Design: A daily process study, involving participants to monitor their pain, sleep, mood, and presleep arousal for 1 wk. Multilevel modeling was used to analyze the data. Setting: In the patients' natural living and sleeping environment. Patients: One hundred nineteen patients (73.9% female, mean age = 46 years) with chronic pain and concomitant insomnia. Measurement: An electronic diary was used to record patients' self-reported sleep quality/efficiency and ratings of pain, mood, and arousal at different times of the day; actigraphy was also used to provide estimates of sleep efficiency. Results: Results indicated that presleep pain was not a reliable predictor of subsequent sleep. Instead, sleep was better predicted by presleep cognitive arousal. Although sleep quality was a consistent predictor of pain the next day, the pain-relieving effect of sleep was only evident during the first half of the day. Conclusions: These findings challenge the often-assumed reciprocal relationship between pain and sleep and call for a diversification in thinking of the daily interaction of these 2 processes. Citation: Tang NKY; Goodchild CE; Sanborn AN; Howard J; Salkovskis PM. Deciphering the temporal link between pain and sleep in a heterogeneous chronic pain patient sample: a multilevel daily process study. SLEEP 2012;35(5):675-687. PMID:22547894

Cancer cells enter dormancy after cannibalizing mesenchymal stem/stromal cells (MSCs)

PubMed Central

Bartosh, Thomas J.; Ullah, Mujib; Zeitouni, Suzanne; Beaver, Joshua; Prockop, Darwin J.

2016-01-01

Patients with breast cancer often develop malignant regrowth of residual drug-resistant dormant tumor cells years after primary treatment, a process defined as cancer relapse. Deciphering the causal basis of tumor dormancy therefore has obvious therapeutic significance. Because cancer cell behavior is strongly influenced by stromal cells, particularly the mesenchymal stem/stromal cells (MSCs) that are actively recruited into tumor-associated stroma, we assessed the impact of MSCs on breast cancer cell (BCC) dormancy. Using 3D cocultures to mimic the cellular interactions of an emerging tumor niche, we observed that MSCs sequentially surrounded the BCCs, promoted formation of cancer spheroids, and then were internalized/degraded through a process resembling the well-documented yet ill-defined clinical phenomenon of cancer cell cannibalism. This suspected feeding behavior was less appreciable in the presence of a rho kinase inhibitor and in 2D monolayer cocultures. Notably, cannibalism of MSCs enhanced survival of BCCs deprived of nutrients but suppressed their tumorigenicity, together suggesting the cancer cells entered dormancy. Transcriptome profiles revealed that the resulting BCCs acquired a unique molecular signature enriched in prosurvival factors and tumor suppressors, as well as inflammatory mediators that demarcate the secretome of senescent cells, also referred to as the senescence-associated secretory phenotype. Overall, our results provide intriguing evidence that cancer cells under duress enter dormancy after cannibalizing MSCs. Importantly, our practical 3D coculture model could provide a valuable tool to understand the antitumor activity of MSCs and cell cannibalism further, and therefore open new therapeutic avenues for the prevention of cancer recurrence. PMID:27698134

The composition and function of the striatin-interacting phosphatases and kinases (STRIPAK) complex in fungi.

PubMed

Kück, Ulrich; Beier, Anna M; Teichert, Ines

2016-05-01

The striatin-interacting phosphatases and kinases (STRIPAK) complex is a highly conserved eukaryotic protein complex that was recently described for diverse animal and fungal species. Here, we summarize our current knowledge about the composition and function of the STRIPAK complex from the ascomycete Sordaria macrospora, which we discovered by investigating sexually sterile mutants (pro), having a defect in fruiting body development. Mass spectrometry and yeast two-hybrid analysis defined core subunits of the STRIPAK complex, which have structural homologs in animal and other fungal organisms. These subunits (and their mammalian homologs) are PRO11 (striatin), PRO22 (STRIP1/2), SmMOB3 (Mob3), PRO45 (SLMAP), and PP2AA, the structural, and PP2Ac, the catalytic subunits of protein phosphatase 2A (PP2A). Beside fruiting body formation, the STRIPAK complex controls vegetative growth and hyphal fusion in S. macrospora. Although the contribution of single subunits to diverse cellular and developmental processes is not yet fully understood, functional analysis has already shown that mammalian homologs are able to substitute the function of distinct fungal STRIPAK subunits. This underscores the view that fungal model organisms serve as useful tools to get a molecular insight into cellular and developmental processes of eukaryotes in general. Future work will unravel the precise localization of single subunits within the cell and decipher their STRIPAK-related and STRIPAK-independent functions. Finally, evidence is accumulating that there is a crosstalk between STRIPAK and various signaling pathways, suggesting that eukaryotic development is dependent on STRIPAK signaling. Copyright © 2015 Elsevier Inc. All rights reserved.

Cancer cells enter dormancy after cannibalizing mesenchymal stem/stromal cells (MSCs).

PubMed

Bartosh, Thomas J; Ullah, Mujib; Zeitouni, Suzanne; Beaver, Joshua; Prockop, Darwin J

2016-10-18

Patients with breast cancer often develop malignant regrowth of residual drug-resistant dormant tumor cells years after primary treatment, a process defined as cancer relapse. Deciphering the causal basis of tumor dormancy therefore has obvious therapeutic significance. Because cancer cell behavior is strongly influenced by stromal cells, particularly the mesenchymal stem/stromal cells (MSCs) that are actively recruited into tumor-associated stroma, we assessed the impact of MSCs on breast cancer cell (BCC) dormancy. Using 3D cocultures to mimic the cellular interactions of an emerging tumor niche, we observed that MSCs sequentially surrounded the BCCs, promoted formation of cancer spheroids, and then were internalized/degraded through a process resembling the well-documented yet ill-defined clinical phenomenon of cancer cell cannibalism. This suspected feeding behavior was less appreciable in the presence of a rho kinase inhibitor and in 2D monolayer cocultures. Notably, cannibalism of MSCs enhanced survival of BCCs deprived of nutrients but suppressed their tumorigenicity, together suggesting the cancer cells entered dormancy. Transcriptome profiles revealed that the resulting BCCs acquired a unique molecular signature enriched in prosurvival factors and tumor suppressors, as well as inflammatory mediators that demarcate the secretome of senescent cells, also referred to as the senescence-associated secretory phenotype. Overall, our results provide intriguing evidence that cancer cells under duress enter dormancy after cannibalizing MSCs. Importantly, our practical 3D coculture model could provide a valuable tool to understand the antitumor activity of MSCs and cell cannibalism further, and therefore open new therapeutic avenues for the prevention of cancer recurrence.

Future Lunar Sampling Missions: Big Returns on Small Samples

NASA Astrophysics Data System (ADS)

Shearer, C. K.; Borg, L.

2002-01-01

The next sampling missions to the Moon will result in the return of sample mass (100g to 1 kg) substantially smaller than those returned by the Apollo missions (380 kg). Lunar samples to be returned by these missions are vital for: (1) calibrating the late impact history of the inner solar system that can then be extended to other planetary surfaces; (2) deciphering the effects of catastrophic impacts on a planetary body (i.e. Aitken crater); (3) understanding the very late-stage thermal and magmatic evolution of a cooling planet; (4) exploring the interior of a planet; and (5) examining volatile reservoirs and transport on an airless planetary body. Can small lunar samples be used to answer these and other pressing questions concerning important solar system processes? Two potential problems with small, robotically collected samples are placing them in a geologic context and extracting robust planetary information. Although geologic context will always be a potential problem with any planetary sample, new lunar samples can be placed within the context of the important Apollo - Luna collections and the burgeoning planet-scale data sets for the lunar surface and interior. Here we illustrate the usefulness of applying both new or refined analytical approaches in deciphering information locked in small lunar samples.

Assessing grain-size correspondence between flow and deposits of controlled floods in the Colorado River, USA

USGS Publications Warehouse

Draut, Amy; Rubin, David M.

2013-01-01

Flood-deposited sediment has been used to decipher environmental parameters such as variability in watershed sediment supply, paleoflood hydrology, and channel morphology. It is not well known, however, how accurately the deposits reflect sedimentary processes within the flow, and hence what sampling intensity is needed to decipher records of recent or long-past conditions. We examine these problems using deposits from dam-regulated floods in the Colorado River corridor through Marble Canyon–Grand Canyon, Arizona, U.S.A., in which steady-peaked floods represent a simple end-member case. For these simple floods, most deposits show inverse grading that reflects coarsening suspended sediment (a result of fine-sediment-supply limitation), but there is enough eddy-scale variability that some profiles show normal grading that did not reflect grain-size evolution in the flow as a whole. To infer systemwide grain-size evolution in modern or ancient depositional systems requires sampling enough deposit profiles that the standard error of the mean of grain-size-change measurements becomes small relative to the magnitude of observed changes. For simple, steady-peaked floods, 5–10 profiles or fewer may suffice to characterize grain-size trends robustly, but many more samples may be needed from deposits with greater variability in their grain-size evolution.

Conceptual analysis of Physiology of vision in Ayurveda.

PubMed

Balakrishnan, Praveen; Ashwini, M J

2014-07-01

The process by which the world outside is seen is termed as visual process or physiology of vision. There are three phases in this visual process: phase of refraction of light, phase of conversion of light energy into electrical impulse and finally peripheral and central neurophysiology. With the advent of modern instruments step by step biochemical changes occurring at each level of the visual process has been deciphered. Many investigations have emerged to track these changes and helping to diagnose the exact nature of the disease. Ayurveda has described this physiology of vision based on the functions of vata and pitta. Philosophical textbook of ayurveda, Tarka Sangraha, gives certain basics facts of visual process. This article discusses the second and third phase of visual process. Step by step analysis of the visual process through the spectacles of ayurveda amalgamated with the basics of philosophy from Tarka Sangraha has been analyzed critically to generate a concrete idea regarding the physiology and hence thereby interpret the pathology on the grounds of ayurveda based on the investigative reports.

Small rare recurrent deletions and reciprocal duplications in 2q21.1, including brain-specific ARHGEF4 and GPR148

PubMed Central

Dharmadhikari, Avinash V.; Kang, Sung-Hae L.; Szafranski, Przemyslaw; Person, Richard E.; Sampath, Srirangan; Prakash, Siddharth K.; Bader, Patricia I.; Phillips, John A.; Hannig, Vickie; Williams, Misti; Vinson, Sherry S.; Wilfong, Angus A.; Reimschisel, Tyler E.; Craigen, William J.; Patel, Ankita; Bi, Weimin; Lupski, James R.; Belmont, John; Cheung, Sau Wai; Stankiewicz, Pawel

2012-01-01

We have identified a rare small (∼450 kb unique sequence) recurrent deletion in a previously linked attention-deficit hyperactivity disorder (ADHD) locus at 2q21.1 in five unrelated families with developmental delay (DD)/intellectual disability (ID), ADHD, epilepsy and other neurobehavioral abnormalities from 17 035 samples referred for clinical chromosomal microarray analysis. Additionally, a DECIPHER (http://decipher.sanger.ac.uk) patient 2311 was found to have the same deletion and presented with aggressive behavior. The deletion was not found in either six control groups consisting of 13 999 healthy individuals or in the DGV database. We have also identified reciprocal duplications in five unrelated families with autism, developmental delay (DD), seizures and ADHD. This genomic region is flanked by large, complex low-copy repeats (LCRs) with directly oriented subunits of ∼109 kb in size that have 97.7% DNA sequence identity. We sequenced the deletion breakpoints within the directly oriented paralogous subunits of the flanking LCR clusters, demonstrating non-allelic homologous recombination as a mechanism of formation. The rearranged segment harbors five genes: GPR148, FAM123C, ARHGEF4, FAM168B and PLEKHB2. Expression of ARHGEF4 (Rho guanine nucleotide exchange factor 4) is restricted to the brain and may regulate the actin cytoskeletal network, cell morphology and migration, and neuronal function. GPR148 encodes a G-protein-coupled receptor protein expressed in the brain and testes. We suggest that small rare recurrent deletion of 2q21.1 is pathogenic for DD/ID, ADHD, epilepsy and other neurobehavioral abnormalities and, because of its small size, low frequency and more severe phenotype might have been missed in other previous genome-wide screening studies using single-nucleotide polymorphism analyses. PMID:22543972

Sparse dynamical Boltzmann machine for reconstructing complex networks with binary dynamics

NASA Astrophysics Data System (ADS)

Chen, Yu-Zhong; Lai, Ying-Cheng

2018-03-01

Revealing the structure and dynamics of complex networked systems from observed data is a problem of current interest. Is it possible to develop a completely data-driven framework to decipher the network structure and different types of dynamical processes on complex networks? We develop a model named sparse dynamical Boltzmann machine (SDBM) as a structural estimator for complex networks that host binary dynamical processes. The SDBM attains its topology according to that of the original system and is capable of simulating the original binary dynamical process. We develop a fully automated method based on compressive sensing and a clustering algorithm to construct the SDBM. We demonstrate, for a variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and simulates its dynamical behavior with high precision.

Sparse dynamical Boltzmann machine for reconstructing complex networks with binary dynamics.

PubMed

Chen, Yu-Zhong; Lai, Ying-Cheng

2018-03-01

Revealing the structure and dynamics of complex networked systems from observed data is a problem of current interest. Is it possible to develop a completely data-driven framework to decipher the network structure and different types of dynamical processes on complex networks? We develop a model named sparse dynamical Boltzmann machine (SDBM) as a structural estimator for complex networks that host binary dynamical processes. The SDBM attains its topology according to that of the original system and is capable of simulating the original binary dynamical process. We develop a fully automated method based on compressive sensing and a clustering algorithm to construct the SDBM. We demonstrate, for a variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and simulates its dynamical behavior with high precision.

Role of mechanical factors in cortical folding development

NASA Astrophysics Data System (ADS)

Razavi, Mir Jalil; Zhang, Tuo; Li, Xiao; Liu, Tianming; Wang, Xianqiao

2015-09-01

Deciphering mysteries of the structure-function relationship in cortical folding has emerged as the cynosure of recent research on brain. Understanding the mechanism of convolution patterns can provide useful insight into the normal and pathological brain function. However, despite decades of speculation and endeavors the underlying mechanism of the brain folding process remains poorly understood. This paper focuses on the three-dimensional morphological patterns of a developing brain under different tissue specification assumptions via theoretical analyses, computational modeling, and experiment verifications. The living human brain is modeled with a soft structure having outer cortex and inner core to investigate the brain development. Analytical interpretations of differential growth of the brain model provide preliminary insight into the critical growth ratio for instability and crease formation of the developing brain followed by computational modeling as a way to offer clues for brain's postbuckling morphology. Especially, tissue geometry, growth ratio, and material properties of the cortex are explored as the most determinant parameters to control the morphogenesis of a growing brain model. As indicated in results, compressive residual stresses caused by the sufficient growth trigger instability and the brain forms highly convoluted patterns wherein its gyrification degree is specified with the cortex thickness. Morphological patterns of the developing brain predicted from the computational modeling are consistent with our neuroimaging observations, thereby clarifying, in part, the reason of some classical malformation in a developing brain.

NMR and molecular modeling of wine tannins binding to saliva proteins: revisiting astringency from molecular and colloidal prospects.

PubMed

Cala, Olivier; Pinaud, Noël; Simon, Cécile; Fouquet, Eric; Laguerre, Michel; Dufourc, Erick J; Pianet, Isabelle

2010-11-01

In organoleptic science, the association of tannins to saliva proteins leads to the poorly understood phenomenon of astringency. To decipher this interaction at molecular and colloidal levels, the binding of 4 procyanidin dimers (B1-4) and 1 trimer (C2) to a human saliva proline-rich peptide, IB7(14), was studied. Interactions have been characterized by measuring dissociation constants, sizes of complexes, number, and nature of binding sites using NMR (chemical shift variations, diffusion-ordered spectroscopy, and saturation transfer diffusion). The binding sites were identified using molecular mechanics, and the hydrophilic/hydrophobic nature of the interactions was resolved by calculating the molecular lipophilicity potential within the complexes. The following comprehensive scheme can be proposed: 1) below the tannin critical micelle concentration (CMC), interaction is specific, and the procyanidin anchorage always occurs on the same three IB7(14) sites. The tannin 3-dimensional structure plays a key role in the binding force and in the tannin's ability to act as a bidentate ligand: tannins adopting an extended conformation exhibit higher affinity toward protein and initiate the formation of a network. 2) Above the CMC, after the first specific hydrophilic interaction has taken place, a random hydrophobic stacking occurs between tannins and proteins. The whole process is discussed in the general frame of wine tannins eliciting astringency.

Deciphering the morphology of ice films on metal surfaces

NASA Astrophysics Data System (ADS)

Thürmer, Konrad

2011-03-01

Although extensive research has been aimed at the structure of ice films, questions regarding basic processes that govern film evolution remain. Recently we discovered how ice films as many as 30 molecular layers thick can be imaged with STM. The observed morphology yields new insights about water-solid interactions and how they affect the structure of ice films. This talk gives an overview of this progress for crystalline ice films on Pt(111) [2-5]. STM reveals a first molecular water layer very different from bulk ice: besides the usual hexagons it also contains pentagons and heptagons. Slightly thicker films (~ 1 nm, at T> 120 K) arecomprisedof ~ 3 nm - highcrystallites , surroundedbytheone - molecule - thickwettinglayer . Thesecrystalsdewetbynucleatinglayersontheirtopfacets [ 4 ] . Measurementsofthenucleationrateasafunctionofcrystalheightprovideestimatesoftheenergyoftheice - Ptinterface . ForT > 115 Ksurfacediffusionisfastenoughthatsurfacesmoothingand 2 D - islandripeningisobservable [ 5 ] . ByquantifyingtheT - dependentripeningofislandarrayswedeterminedtheactivationenergyforsurfaceself - diffusion . Theshapeofthese 2 Dislandsvariesstronglywithfilmthickness . Weattributethistoatransitionfrompolarizediceatthesubstratetowardsprotondisorderatlargerfilmthicknesses . Despitefastsurfacediffusionicemultilayersareoftenfarfromequilibrium . Forexample , icegrowsbetween ~ 120 and ~ 160 K in its cubic variant rather than in its equilibrium hexagonal form. We found this to be a consequence of the mismatch in the atomic Pt-step height and the ice-bilayer separation and propose a mechanism of cubic-ice formation via growth spirals around screw dislocations. Joint work with N.C. Bartelt and S. Nie, Sandia Natl. Labs, CA. This work was supported by the Office of Basic Energy Sciences, Division of Materials Sciences, U.S. DOE under Contracts No. DEAC04-94AL85000.

Chromospheric Lyman-alpha spectro-polarimeter (CLASP)

NASA Astrophysics Data System (ADS)

Kano, Ryouhei; Bando, Takamasa; Narukage, Noriyuki; Ishikawa, Ryoko; Tsuneta, Saku; Katsukawa, Yukio; Kubo, Masahito; Ishikawa, Shin-nosuke; Hara, Hirohisa; Shimizu, Toshifumi; Suematsu, Yoshinori; Ichimoto, Kiyoshi; Sakao, Taro; Goto, Motoshi; Kato, Yoshiaki; Imada, Shinsuke; Kobayashi, Ken; Holloway, Todd; Winebarger, Amy; Cirtain, Jonathan; De Pontieu, Bart; Casini, Roberto; Trujillo Bueno, Javier; Štepán, Jiří; Manso Sainz, Rafael; Belluzzi, Luca; Asensio Ramos, Andres; Auchère, Frédéric; Carlsson, Mats

2012-09-01

One of the biggest challenges in heliophysics is to decipher the magnetic structure of the solar chromosphere. The importance of measuring the chromospheric magnetic field is due to both the key role the chromosphere plays in energizing and structuring the outer solar atmosphere and the inability of extrapolation of photospheric fields to adequately describe this key boundary region. Over the last few years, significant progress has been made in the spectral line formation of UV lines as well as the MHD modeling of the solar atmosphere. It is found that the Hanle effect in the Lyman-alpha line (121.567 nm) is a most promising diagnostic tool for weaker magnetic fields in the chromosphere and transition region. Based on this groundbreaking research, we propose the Chromospheric Lyman-Alpha Spectro-Polarimeter (CLASP) to NASA as a sounding rocket experiment, for making the first measurement of the linear polarization produced by scattering processes and the Hanle effect in the Lyman-alpha line (121.567 nm), and making the first exploration of the magnetic field in the upper chromosphere and transition region of the Sun. The CLASP instrument consists of a Cassegrain telescope, a rotating 1/2-wave plate, a dual-beam spectrograph assembly with a grating working as a beam splitter, and an identical pair of reflective polarization analyzers each equipped with a CCD camera. We propose to launch CLASP in December 2014.

In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes.

PubMed

Husbands, Aman Y; Aggarwal, Vasudha; Ha, Taekjip; Timmermans, Marja C P

2016-08-01

Deciphering complex biological processes markedly benefits from approaches that directly assess the underlying biomolecular interactions. Most commonly used approaches to monitor protein-protein interactions typically provide nonquantitative readouts that lack statistical power and do not yield information on the heterogeneity or stoichiometry of protein complexes. Single-molecule pull-down (SiMPull) uses single-molecule fluorescence detection to mitigate these disadvantages and can quantitatively interrogate interactions between proteins and other compounds, such as nucleic acids, small molecule ligands, and lipids. Here, we establish SiMPull in plants using the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) and LITTLE ZIPPER (ZPR) interaction as proof-of-principle. Colocalization analysis of fluorophore-tagged HD-ZIPIII and ZPR proteins provides strong statistical evidence of complex formation. In addition, we use SiMPull to directly quantify YFP and mCherry maturation probabilities, showing these differ substantially from values obtained in mammalian systems. Leveraging these probabilities, in conjunction with fluorophore photobleaching assays on over 2000 individual complexes, we determined HD-ZIPIII:ZPR stoichiometry. Intriguingly, these complexes appear as heterotetramers, comprising two HD-ZIPIII and two ZPR molecules, rather than heterodimers as described in the current model. This surprising result raises new questions about the regulation of these key developmental factors and is illustrative of the unique contribution SiMPull is poised to make to in planta protein interaction studies. © 2016 American Society of Plant Biologists. All rights reserved.

Envirotyping for deciphering environmental impacts on crop plants.

PubMed

Xu, Yunbi

2016-04-01

Global climate change imposes increasing impacts on our environments and crop production. To decipher environmental impacts on crop plants, the concept "envirotyping" is proposed, as a third "typing" technology, complementing with genotyping and phenotyping. Environmental factors can be collected through multiple environmental trials, geographic and soil information systems, measurement of soil and canopy properties, and evaluation of companion organisms. Envirotyping contributes to crop modeling and phenotype prediction through its functional components, including genotype-by-environment interaction (GEI), genes responsive to environmental signals, biotic and abiotic stresses, and integrative phenotyping. Envirotyping, driven by information and support systems, has a wide range of applications, including environmental characterization, GEI analysis, phenotype prediction, near-iso-environment construction, agronomic genomics, precision agriculture and breeding, and development of a four-dimensional profile of crop science involving genotype (G), phenotype (P), envirotype (E) and time (T) (developmental stage). In the future, envirotyping needs to zoom into specific experimental plots and individual plants, along with the development of high-throughput and precision envirotyping platforms, to integrate genotypic, phenotypic and envirotypic information for establishing a high-efficient precision breeding and sustainable crop production system based on deciphered environmental impacts.

Proteomics and circadian rhythms: It’s all about signaling!

PubMed Central

Mauvoisin, Daniel; Dayon, Loïc; Gachon, Frédéric; Kussmann, Martin

2014-01-01

1. Abstract Proteomic technologies using mass spectrometry (MS) offer new perspectives in circadian biology, in particular the possibility to study posttranslational modifications (PTMs). To date, only very few studies have been carried out to decipher the rhythmicity of protein expression in mammals with large-scale proteomics. Although signaling has been shown to be of high relevance, comprehensive characterization studies of PTMs are even more rare. This review aims at describing the actual landscape of circadian proteomics and the opportunities and challenges appearing on the horizon. Emphasis was given to signaling processes for their role in metabolic heath as regulated by circadian clocks and environmental factors. Those signaling processes are expected to be better and more deeply characterized in the coming years with proteomics. PMID:25103677

Deciphering the Interdependence between Ecological and Evolutionary Networks.

PubMed

Melián, Carlos J; Matthews, Blake; de Andreazzi, Cecilia S; Rodríguez, Jorge P; Harmon, Luke J; Fortuna, Miguel A

2018-05-24

Biological systems consist of elements that interact within and across hierarchical levels. For example, interactions among genes determine traits of individuals, competitive and cooperative interactions among individuals influence population dynamics, and interactions among species affect the dynamics of communities and ecosystem processes. Such systems can be represented as hierarchical networks, but can have complex dynamics when interdependencies among levels of the hierarchy occur. We propose integrating ecological and evolutionary processes in hierarchical networks to explore interdependencies in biological systems. We connect gene networks underlying predator-prey trait distributions to food webs. Our approach addresses longstanding questions about how complex traits and intraspecific trait variation affect the interdependencies among biological levels and the stability of meta-ecosystems. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mechanoresponsive, omni-directional and local matrix-degrading actin protrusions in human mesenchymal stem cells microencapsulated in a 3D collagen matrix.

PubMed

Ho, Fu Chak; Zhang, Wei; Li, Yuk Yin; Chan, Barbara Pui

2015-01-01

Cells are known to respond to multiple niche signals including extracellular matrix and mechanical loading. In others and our own studies, mechanical loading has been shown to induce the formation of cell alignment in 3D collagen matrix with random meshwork, challenging our traditional understanding on the necessity of having aligned substrates as the prerequisite of alignment formation. This motivates our adventure in deciphering the mechanism of loading-induced cell alignment and hence the discovery of the novel protrusive functional structure at the cell-matrix interface. Here we report the formation of mechanoresponsive, omni-directional and local matrix-degrading actin protrusions in human mesenchymal stem cells (hMSCs) microencapsulated in collagen following a shifted actin assembly/disassembly balance. These actin protrusive structures exhibit morphological and compositional similarity to filopodia and invadopodia but differ from them in stability, abundance, signaling and function. Without ruling out the possibility that these structures may comprise special subsets of filopodia and invadopodia, we propose to name them as mechanopodia so as to reveal their mechano-inductive mechanism. We also suggest that more intensive investigations are needed to delineate the functional significance and physiological relevance of these structures. This work identifies a brand new target for cell-matrix interaction and mechanoregulation studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biofilm formation - What we can learn from recent developments.

PubMed

Bjarnsholt, Thomas; Buhlin, Kåre; Dufrêne, Yves F; Gomelsky, Mark; Moroni, Anna; Ramstedt, Madeleine; Rumbaugh, Kendra P; Schulte, Tim; Sun, Lei; Åkerlund, Börje; Römling, Ute

2018-06-01

Although biofilms have been observed early in the history of microbial research, their impact has only recently been fully recognized. Biofilm infections, which contribute to up to 80% of human microbial infections, are associated with common human disorders, such as diabetes mellitus and poor dental hygiene, but also with medical implants. The associated chronic infections such as wound infections, dental caries and periodontitis significantly enhance morbidity, affect quality of life and can result in contraction of follow-up diseases such as cancer. Biofilm infections remain challenging to treat and antibiotic monotherapy is often insufficient, although some rediscovered traditional compounds have shown surprising efficiency. Innovative anti-biofilm strategies include application of anti-biofilm small molecules, intrinsic or external stimulation of production of reactive molecules, utilization of materials with antimicrobial properties and dispersion of biofilms by digestion of the extracellular matrix, also in combination with physical biofilm breakdown. Although basic principles of biofilm formation have been deciphered, the molecular understanding of the formation and structural organization of various types of biofilms has just begun to emerge. Basic studies of biofilm physiology have also resulted in an unexpected discovery of cyclic dinucleotide second messengers that are involved in interkingdom crosstalk via specific mammalian receptors. These findings even open up new venues for exploring novel anti-biofilm strategies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Deciphering the interaction of bovine heart cystatin with ZnO nanoparticles: Spectroscopic and thermodynamic approach.

PubMed

Sohail, Aamir; Faraz, Mohd; Arif, Hussain; Bhat, Sheraz Ahmad; Siddiqui, Azad Alam; Bano, Bilqees

2017-02-01

ZnO-NPs have been widely used in biomedical fields such as therapeutics, cellular imaging, and drug delivery. However, the risk of exposure of nanoparticles to the biological system is not well understood. Nanoparticle-protein interaction is pivotal to understand their biological behavior and predict nanoparticle toxicity that is crucial for its safer applications. In the present study zinc oxide nanoparticles (ZnO-NPs) were synthesized and subjected to interact with buffalo heart cystatin (BHC), purified from buffalo heart, to assess the effect(s) of ZnO-NPs on the structure and function of BHC. In vitro toxicity assessments revealed that BHC, upon interaction with ZnO-NPs, led to the altered protein conformation and perturbed function. A decrease in the anti-papain activity of BHC was observed. Spectroscopic studies demonstrated that formation of BHC-ZnO-NPs complex accompanied by structural changes in BHC along with a significant decrease in its α-helical content. ITC determined the thermodynamic parameters of binding between ZnO-NPs and BHC quantitatively. Increased surface hydrophobicity (change in the tertiary structure) was observed by ANS fluorescence that demonstrated the formation of molten globular intermediates that were found to be stable without any signs of aggregation as depicted by ThT fluorescence. TEM images gave the physical evidence of the formation of ZnO-NPs-BHC corona. Copyright © 2016. Published by Elsevier B.V.

Using large-scale genome variation cohorts to decipher the molecular mechanism of cancer.

PubMed

Habermann, Nina; Mardin, Balca R; Yakneen, Sergei; Korbel, Jan O

2016-01-01

Characterizing genomic structural variations (SVs) in the human genome remains challenging, and there is a growing interest to understand somatic SVs occurring in cancer, a disease of the genome. A havoc-causing SV process known as chromothripsis scars the genome when localized chromosome shattering and repair occur in a one-off catastrophe. Recent efforts led to the development of a set of conceptual criteria for the inference of chromothripsis events in cancer genomes and to the development of experimental model systems for studying this striking DNA alteration process in vitro. We discuss these approaches, and additionally touch upon current "Big Data" efforts that employ hybrid cloud computing to enable studies of numerous cancer genomes in an effort to search for commonalities and differences in molecular DNA alteration processes in cancer. Copyright © 2016. Published by Elsevier SAS.

Heterogeneous vesiculation of 2011 El Hierro xeno-pumice revealed by X-ray computed microtomography

NASA Astrophysics Data System (ADS)

Berg, S. E.; Troll, V. R.; Deegan, F. M.; Burchardt, S.; Krumbholz, M.; Mancini, L.; Polacci, M.; Carracedo, J. C.; Soler, V.; Arzilli, F.; Brun, F.

2016-12-01

During the first week of the 2011 El Hierro submarine eruption, abundant light-coloured pumiceous, high-silica volcanic bombs coated in dark basanite were found floating on the sea. The composition of the light-coloured frothy material (`xeno-pumice') is akin to that of sedimentary rocks from the region, but the textures resemble felsic magmatic pumice, leaving their exact mode of formation unclear. To help decipher their origin, we investigated representative El Hierro xeno-pumice samples using X-ray computed microtomography for their internal vesicle shapes, volumes, and bulk porosity, as well as for the spatial arrangement and size distributions of vesicles in three dimensions (3D). We find a wide range of vesicle morphologies, which are especially variable around small fragments of rock contained in the xeno-pumice samples. Notably, these rock fragments are almost exclusively of sedimentary origin, and we therefore interpret them as relicts an the original sedimentary ocean crust protolith(s). The irregular vesiculation textures observed probably resulted from pulsatory release of volatiles from multiple sources during xeno-pumice formation, most likely by successive release of pore water and mineral water during incremental heating and decompression of the sedimentary protoliths.

Monitoring Healthy Metabolic Trajectories with Nutritional Metabonomics

PubMed Central

Collino, Sebastiano; Martin, François-Pierre J.; Kochhar, Sunil; Rezzi, Serge

2009-01-01

Metabonomics is a well established analytical approach for the analysis of physiological regulatory processes via the metabolic profiling of biofluids and tissues in living organisms. Its potential is fully exploited in the field of “nutrimetabonomics” that aims at assessing the metabolic effects of active ingredients and foods in individuals. Yet, one of the greatest challenges in nutrition research is to decipher the critical interactions between mammalian organisms and environmental factors, including the gut microbiota. “Nutrimetabonomics” is today foreseen as a powerful approach for future nutritional programs tailored at health maintenance and disease prevention. PMID:22253970

Deciphering the Code of the Cancer Genome: Mechanisms of Chromosome Rearrangement

PubMed Central

Willis, Nicholas A.; Rass, Emilie; Scully, Ralph

2015-01-01

Chromosome rearrangement plays a causal role in tumorigenesis by contributing to the inactivation of tumor suppressor genes, the dysregulated expression or amplification of oncogenes and the generation of novel gene fusions. Chromosome breaks are important intermediates in this process. How, when and where these breaks arise and the specific mechanisms engaged in their repair strongly influence the resulting patterns of chromosome rearrangement. Here, we review recent progress in understanding how certain distinctive features of the cancer genome, including clustered mutagenesis, tandem segmental duplications, complex breakpoints, chromothripsis, chromoplexy and chromoanasynthesis may arise. PMID:26726318

A glimpse of structural biology through X-ray crystallography.

PubMed

Shi, Yigong

2014-11-20

Since determination of the myoglobin structure in 1957, X-ray crystallography, as the anchoring tool of structural biology, has played an instrumental role in deciphering the secrets of life. Knowledge gained through X-ray crystallography has fundamentally advanced our views on cellular processes and greatly facilitated development of modern medicine. In this brief narrative, I describe my personal understanding of the evolution of structural biology through X-ray crystallography-using as examples mechanistic understanding of protein kinases and integral membrane proteins-and comment on the impact of technological development and outlook of X-ray crystallography.

How Chemical Synthesis of Ubiquitin Conjugates Helps To Understand Ubiquitin Signal Transduction.

PubMed

Hameed, Dharjath S; Sapmaz, Aysegul; Ovaa, Huib

2017-03-15

Ubiquitin (Ub) is a small post-translational modifier protein involved in a myriad of biochemical processes including DNA damage repair, proteasomal proteolysis, and cell cycle control. Ubiquitin signaling pathways have not been completely deciphered due to the complex nature of the enzymes involved in ubiquitin conjugation and deconjugation. Hence, probes and assay reagents are important to get a better understanding of this pathway. Recently, improvements have been made in synthesis procedures of Ub derivatives. In this perspective, we explain various research reagents available and how chemical synthesis has made an important contribution to Ub research.

Tectonothermal modeling of hydrocarbon maturation, Central Maracaibo Basin, Venezuela

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

Manske, M.C.

1996-08-01

The petroliferous Maracaibo Basin of northwestern Venezuela and extreme eastern Colombia has evolved through a complex geologic history. Deciphering the tectonic and thermal evolution is essential in the prediction of hydrocarbon maturation (timing) within the basin. Individual wells in two areas of the central basin, Blocks III and V, have been modeled to predict timing of hydrocarbon generation within the source Upper Cretaceous La Luna Formation, as well as within interbedded shales of the Lower-Middle Eocene Misoa Formation reservoir sandstones. Tectonic evolution, including burial and uplift (erosional) history, has been constrained with available well data. The initial extensional thermal regimemore » of the basin has been approximated with a Mackenzie-type thermal model, and the following compressional stage of basin development by applying a foreland basin model. Corrected Bottom Hole Temperature (BHT) measurements; from wells in the central basin, along with thermal conductivity measurements of rock samples from the entire sedimentary sequence, resulted in the estimation of present day heat flow. An understanding of the basin`s heat flow, then, allowed extrapolation of geothermal gradients through time. The relation of geothermal gradients and overpressure within the Upper Cretaceous hydrocarbon-generating La Luna Formation and thick Colon Formation shales was also taken into account. Maturation modeling by both the conventional Time-Temperature Index (TTI) and kinetic Transformation Ratio (TR) methods predicts the timing of hydrocarbon maturation in the potential source units of these two wells. These modeling results are constrained by vitrinite reflectance and illite/smectite clay dehydration data, and show general agreement. These results also have importance regarding the timing of structural formation and hydrocarbon migration into Misoa reservoirs.« less

Involvement of old crustal materials during formation of the Sakhalin Island (Russian Far East) and its paleogeographic implication: Constraints from detrital zircon ages of modern river sand and Miocene sandstone

NASA Astrophysics Data System (ADS)

Zhao, Pan; Li, Jia-jin; Alexandrov, Igor; Ivin, Vitaly; Jahn, Bor-ming

2017-09-01

In order to decipher crustal nature of the Sakhalin Island in Russian Far East, we carried out detrital zircon U-Pb age analyses on Miocene sandstone and river sand from the longest river (Poronay River) of the Sakhalin Island. The detrital zircon data from two river sand samples display similar age distribution patterns with a dominant Mesozoic age group, subordinate age peaks at 1.8 Ga and 2.5 Ga, and a few Paleozoic and Neoproterozoic grains. The Miocene sandstone shows age peaks at 22, 84, 260 and 497 Ma, respectively, and a few Paleo-proterozoic grains. These age groups indicate that abundant old crustal materials have been involved in the crustal formation of the Sakhalin Island. Detrital zircon result reveals two episodes of post-accretion magmatism from the Sakhalin Island in ages of 37 Ma and 22-21 Ma. They can be correlated with coeval post-accretion magmatic events in the Hokkaido Island, supporting the geological correlation between the Sakhalin Island and the Hokkaido Island. Comparison of detrital zircon dating result from the Sakhalin Island with those from surrounding blocks and cratons in eastern Asia allows us to propose two possible sources in eastern Asia: the Bureya-Jiamusi-Khanka block with the Sikhote-Alin orogenic belt to its west and the South China Craton. The detrital zircon result indicates that the formation of the Sakhalin Island should be close to the East Asia continent, rather than as an independent intro-oceanic island arc within the Pacific Ocean. Similar to formation of the Japanese islands, the South China Craton may have played an important role during formation of the Sakhalin Island.

Variability over time in the sources of South Portuguese Zone turbidites: evidence of denudation of different crustal blocks during the assembly of Pangaea

NASA Astrophysics Data System (ADS)

Pereira, M. F.; Ribeiro, C.; Vilallonga, F.; Chichorro, M.; Drost, K.; Silva, J. B.; Albardeiro, L.; Hofmann, M.; Linnemann, U.

2014-07-01

This study combines geochemical and geochronological data in order to decipher the provenance of Carboniferous turbidites from the South Portuguese Zone (SW Iberia). Major and trace elements of 25 samples of graywackes and mudstones from the Mértola (Visean), Mira (Serpukhovian), and Brejeira (Moscovian) Formations were analyzed, and 363 U-Pb ages were obtained on detrital zircons from five samples of graywackes from the Mira and Brejeira Formations using LA-ICPMS. The results indicate that turbiditic sedimentation during the Carboniferous was marked by variability in the sources, involving the denudation of different crustal blocks and a break in synorogenic volcanism. The Visean is characterized by the accumulation of immature turbidites (Mértola Formation and the base of the Mira Formation) inherited from a terrane with intermediate to mafic source rocks. These source rocks were probably formed in relation to Devonian magmatic arcs poorly influenced by sedimentary recycling, as indicated by the almost total absence of pre-Devonian zircons typical of the Gondwana and/or Laurussia basements. The presence of Carboniferous grains in Visean turbidites indicates that volcanism was active at this time. Later, Serpukhovian to Moscovian turbiditic sedimentation (Mira and Brejeira Formations) included sedimentary detritus derived from felsic mature source rocks situated far from active magmatism. The abundance of Precambrian and Paleozoic zircons reveals strong recycling of the Gondwana and/or Laurussia basements. A peri-Gondwanan provenance is indicated by zircon populations with Neoproterozoic (Cadomian-Avalonian and Pan-African zircon-forming events), Paleoproterozoic, and Archean ages. The presence of late Ordovician and Silurian detrital zircons in Brejeira turbidites, which have no correspondence in the Gondwana basement of SW Iberia, indicates Laurussia as their most probable source.

Application of ring tectonic theory to Mercury and other solar system bodies

NASA Technical Reports Server (NTRS)

Mckinnon, W. B.

1981-01-01

It is pointed out that multiringed structures, by their presence or absence, provide a powerful tool for deciphering the thermal histories of the solid planets. The theory of ring tectonics considered by Melosh and McKinnon (1978) and Melosh et al. (1980) establishes the framework of that undertaking. The present investigation has the objective to apply this conceptualization in detail to the multiringed basins on Mercury, taking into account also a brief review concerning the current state of understanding of ring tectonics on the moon, Mars, earth, Ganymede, and Callisto. The small, icy satellites of Saturn are also discussed. The mechanics of multiple ring formation are related to the collapse of the transient basin cavity when the excavation depth and lithosphere thickness are comparable. Attention is given to the Caloris Basin on Mercury, the peak ring basins on Mercury, and the Argyre Basin on Mars.

Deciphering dynamics of clathrin-mediated endocytosis in a living organism

PubMed Central

Heidotting, Spencer P.; Huber, Scott D.

2016-01-01

Current understanding of clathrin-mediated endocytosis (CME) dynamics is based on detection and tracking of fluorescently tagged clathrin coat components within cultured cells. Because of technical limitations inherent to detection and tracking of single fluorescent particles, CME dynamics is not characterized in vivo, so the effects of mechanical cues generated during development of multicellular organisms on formation and dissolution of clathrin-coated structures (CCSs) have not been directly observed. Here, we use growth rates of fluorescence signals obtained from short CCS intensity trace fragments to assess CME dynamics. This methodology does not rely on determining the complete lifespan of individual endocytic assemblies. Therefore, it allows for real-time monitoring of spatiotemporal changes in CME dynamics and is less prone to errors associated with particle detection and tracking. We validate the applicability of this approach to in vivo systems by demonstrating the reduction of CME dynamics during dorsal closure of Drosophila melanogaster embryos. PMID:27458134

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water

PubMed Central

Frank, Alexander H.; Garcia, Juan A. L.; Herndl, Gerhard J.

2016-01-01

Summary To decipher the influence of depth stratification and surface provincialism on the dark ocean prokaryotic community composition, we sampled the major deep‐water masses in the eastern North Atlantic covering three biogeographic provinces. Their diversity was evaluated using ordination and canonical analysis of 454 pyrotag sequences. Variance partitioning suggested that 16% of the variation in the bacterial community composition was based on depth stratification while 9% of the variation was due to geographic location. General linear mixed effect models showed that the community of the subsurface waters was connected to the dark ocean prokaryotic communities in different biogeographic provinces. Cluster analysis indicated that some prokaryotic taxa are specific to distinct regions in bathypelagic water masses. Taken together, our data suggest that the dark ocean prokaryotic community composition of the eastern North Atlantic is primed by the formation and the horizontal transport of water masses. PMID:26914787

NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network.

PubMed

Anderson, David J; Kaplan, David I; Bell, Katrina M; Koutsis, Katerina; Haynes, John M; Mills, Richard J; Phelan, Dean G; Qian, Elizabeth L; Leitoguinho, Ana Rita; Arasaratnam, Deevina; Labonne, Tanya; Ng, Elizabeth S; Davis, Richard P; Casini, Simona; Passier, Robert; Hudson, James E; Porrello, Enzo R; Costa, Mauro W; Rafii, Arash; Curl, Clare L; Delbridge, Lea M; Harvey, Richard P; Oshlack, Alicia; Cheung, Michael M; Mummery, Christine L; Petrou, Stephen; Elefanty, Andrew G; Stanley, Edouard G; Elliott, David A

2018-04-10

Congenital heart defects can be caused by mutations in genes that guide cardiac lineage formation. Here, we show deletion of NKX2-5, a critical component of the cardiac gene regulatory network, in human embryonic stem cells (hESCs), results in impaired cardiomyogenesis, failure to activate VCAM1 and to downregulate the progenitor marker PDGFRα. Furthermore, NKX2-5 null cardiomyocytes have abnormal physiology, with asynchronous contractions and altered action potentials. Molecular profiling and genetic rescue experiments demonstrate that the bHLH protein HEY2 is a key mediator of NKX2-5 function during human cardiomyogenesis. These findings identify HEY2 as a novel component of the NKX2-5 cardiac transcriptional network, providing tangible evidence that hESC models can decipher the complex pathways that regulate early stage human heart development. These data provide a human context for the evaluation of pathogenic mutations in congenital heart disease.

Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids.

PubMed

Nguyen, Hung D; Reddy, Vijay S; Brooks, Charles L

2007-02-01

Self-assembly of viral proteins into icosahedral capsids is an interesting yet poorly understood phenomenon of which elucidation may aid the exploration of beneficial applications of capsids in materials science and medicine. Using molecular dynamics simulations of coarse-grained models for capsid proteins, we show that the competition between the formation of full capsids and nonidealized structures is strongly dependent upon the protein concentration and temperature, occurring kinetically as a cascade of elementary reactions in which free monomers are added to the growing oligomers on a downhill free-energy landscape. However, the insertion of the final subunits is the rate-limiting, energetically unfavorable step in viral capsid assembly. A phase diagram has been constructed to show the regions where capsids or nonidealized structures are stable at each concentration and temperature. We anticipate that our findings will provide guidance in identifying suitable conditions required for in vitro viral capsid assembly experiments.

Nanoscale invaginations of the nuclear envelope: Shedding new light on wormholes with elusive function.

PubMed

Schoen, Ingmar; Aires, Lina; Ries, Jonas; Vogel, Viola

2017-09-03

Recent advances in fluorescence microscopy have opened up new possibilities to investigate chromosomal and nuclear 3D organization on the nanoscale. We here discuss their potential for elucidating topographical details of the nuclear lamina. Single molecule localization microscopy (SMLM) in combination with immunostainings of lamina proteins readily reveals tube-like invaginations with a diameter of 100-500 nm. Although these invaginations have been established as a frequent and general feature of interphase nuclei across different cell types, their formation mechanism and function have remained largely elusive. We critically review the current state of research, propose possible connections to lamina associated domains (LADs), and revisit the discussion about the potential role of these invaginations for accelerating mRNA nuclear export. Illustrative studies using 3D super-resolution imaging are shown and will be instrumental to decipher the physiological role of these nanoscale invaginations.

Sedimentary Deposits within Ius Chasma

NASA Image and Video Library

2015-07-15

Sedimentary deposits are common within Valles Marineris. Most larger chasmata contain kilometer-thick light-toned layered deposits composed of sulfates. However, some of the chasmata, like Ius Chasma shown in this image from NASA Mars Reconnaissance Orbiter, lack these deposits or have much thinner deposits. The light-toned deposits in Ius Chasma are observed both along the floor and inner wallrock materials. Some of the light-toned deposits appear to post-date formation of the chasma floor, whereas other deposits appear to lie beneath wallrock materials, indicating they are older. By examining the stratigraphy using digital terrain models and 3D images, it should be possible to decipher the relative ages of the different geologic units. CRISM data may also provide insight into the mineralogy, which will tell scientists about the aqueous conditions that emplaced the light-toned deposits. http://photojournal.jpl.nasa.gov/catalog/PIA19855

Reconstruction of limnology and microbialite formation conditions from carbonate clumped isotope thermometry.

PubMed

Petryshyn, V A; Lim, D; Laval, B L; Brady, A; Slater, G; Tripati, A K

2015-01-01

Quantitative tools for deciphering the environment of microbialite formation are relatively limited. For example, the oxygen isotope carbonate-water geothermometer requires assumptions about the isotopic composition of the water of formation. We explored the utility of using 'clumped' isotope thermometry as a tool to study the temperatures of microbialite formation. We studied microbialites recovered from water depths of 10-55 m in Pavilion Lake, and 10-25 m in Kelly Lake, spanning the thermocline in both lakes. We determined the temperature of carbonate growth and the (18)O/(16)O ratio of the waters that microbialites grew in. Results were then compared to current limnological data from the lakes to reconstruct the history of microbialite formation. Modern microbialites collected at shallow depths (11.7 m) in both lakes yield clumped isotope-based temperatures of formation that are within error of summer water temperatures, suggesting that clumped isotope analyses may be used to reconstruct past climates and to probe the environments in which microbialites formed. The deepest microbialites (21.7-55 m) were recovered from below the present-day thermoclines in both lakes and yield radioisotope ages indicating they primarily formed earlier in the Holocene. During this time, pollen data and our reconstructed water (18)O/(16)O ratios indicate a period of aridity, with lower lake levels. At present, there is a close association between both photosynthetic and heterotrophic communities, and carbonate precipitation/microbialite formation, with biosignatures of photosynthetic influences on carbonate detected in microbialites from the photic zone and above the thermocline (i.e., depths of generally <20 m). Given the deeper microbialites are receiving <1% of photosynthetically active radiation (PAR), it is likely these microbialites primarily formed when lower lake levels resulted in microbialites being located higher in the photic zone, in warm surface waters. © 2014 John Wiley & Sons Ltd.

Geophysical interpretation of the Caribbean plate and Gulf of Mexico from reprocessed potential field data

NASA Astrophysics Data System (ADS)

Garcia-Reyes, A.; Dyment, J.; Thebault, E.

2016-12-01

Despite of the Caribbean plate and Gulf of Mexico have been widely explored from the last 60 years, there is still no consensus about its nature and age of formation. The imaging of the acoustic basement which can help to better understand the composition of the upper crust, is dependent on seismic reflection and exploratory wells but both of them lack of sufficient penetration. Regarding the magnetic anomalies and possible contribution to decipher the age of the Caribbean seafloor, some authors have reported the lack of an identifiable pattern over the Caribbean Plate (Duncan and Hargraves, 1984, Pindell et al. many publications). Marine tracks widely spaced or with very short coverage, and low amplitude magnetic anomalies constitute a limitation in terms of mapping and interpretation. In this work we present a geophysical interpretation from recently reprocessed marine magnetic data (Garcia et al., 2015), satellite geomagnetic models, and new free-air gravity anomaly derived from altimetry (Sandwell et al., 2014), which is useful to better understand the structure and age of the seafloor and constrain its nature and formation. A marine magnetic anomaly map of the Caribbean region and the Gulf of Mexico to 0.18 degree spatial resolution is showed as resulting from a dedicated processing of the NGDC marine magnetic measurements over the Caribbean region, applied over 516 surveys that were acquired between epochs 1958 and 2012. The corrections applied include the main internal field using a CM4 model for epochs ranging between 1960 and 2002.5 and the IGRF-11 model outside the time range of the CM4 model, removal of outliers, correction by magnetic heading effect, analysis and improvement of the internal and external cross-overs and frequency analysis and separation. This processing allows us to integrate and to interpret the results along with the potential field data mentioned above and open the discussion about the meaning of the magnetic and gravity signatures of some of the striking structures of the area. Special emphasis is done over the Gulf of Mexico, in where a magnetic isochrons identification and plate tectonic reconstruction is in progress.

Tuning a climate model using nudging to reanalysis.

NASA Astrophysics Data System (ADS)

Cheedela, S. K.; Mapes, B. E.

2014-12-01

Tuning a atmospheric general circulation model involves a daunting task of adjusting non-observable parameters to adjust the mean climate. These parameters arise from necessity to describe unresolved flow through parametrizations. Tuning a climate model is often done with certain set of priorities, such as global mean temperature, net top of the atmosphere radiation. These priorities are hard enough to reach let alone reducing systematic biases in the models. The goal of currently study is to explore alternate ways to tune a climate model to reduce some systematic biases that can be used in synergy with existing efforts. Nudging a climate model to a known state is a poor man's inverse of tuning process described above. Our approach involves nudging the atmospheric model to state of art reanalysis fields thereby providing a balanced state with respect to the global mean temperature and winds. The tendencies derived from nudging are negative of errors from physical parametrizations as the errors from dynamical core would be small. Patterns of nudging are compared to the patterns of different physical parametrizations to decipher the cause for certain biases in relation to tuning parameters. This approach might also help in understanding certain compensating errors that arise from tuning process. ECHAM6 is a comprehensive general model, also used in recent Coupled Model Intercomparision Project(CMIP5). The approach used to tune it and effect of certain parameters that effect its mean climate are reported clearly, hence it serves as a benchmark for our approach. Our planned experiments include nudging ECHAM6 atmospheric model to European Center Reanalysis (ERA-Interim) and reanalysis from National Center for Environmental Prediction (NCEP) and decipher choice of certain parameters that lead to systematic biases in its simulations. Of particular interest are reducing long standing biases related to simulation of Asian summer monsoon.

Invoking adaptation to decipher the genetic legacy of past climate change.

PubMed

de Lafontaine, Guillaume; Napier, Joseph D; Petit, Rémy J; Hu, Feng Sheng

2018-05-05

Persistence of natural populations during periods of climate change is likely to depend on migration (range shifts) or adaptation. These responses were traditionally considered discrete processes and conceptually divided into the realms of ecology and evolution. In a milestone paper, Davis and Shaw (2001) argued that the interplay of adaptation and migration was central to biotic responses to Quaternary climate, but since then there has been no synthesis of efforts made to set up this research program. Here we review some of the salient findings from molecular genetic studies assessing ecological and evolutionary responses to Quaternary climate change. These studies have revolutionized our understanding of population processes associated with past species migration. However, knowledge remains limited about the role of natural selection for local adaptation of populations to Quaternary environmental fluctuations and associated range shifts, and for the footprints this might have left on extant populations. Next-generation sequencing technologies, high-resolution paleoclimate analyses, and advances in population genetic theory offer an unprecedented opportunity to test hypotheses about adaptation through time. Recent population genomics studies have greatly improved our understanding of the role of contemporary adaptation to local environments in shaping spatial patterns of genetic diversity across modern-day landscapes. Advances in this burgeoning field provide important conceptual and methodological bases to decipher the historical role of natural selection and assess adaptation to past environmental variation. We suggest that a process called "temporal conditional neutrality" has taken place: some alleles favored in glacial environments become selectively neutral in modern-day conditions, whereas some alleles that had been neutral during glacial periods become under selection in modern environments. Building on this view, we present a new integrative framework for addressing the interplay of demographic and adaptive evolutionary responses to Quaternary climate dynamics, the research agenda initially envisioned by Davis and Shaw (2001). This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Reconstruction of DNA sequences using genetic algorithms and cellular automata: towards mutation prediction?

PubMed

Mizas, Ch; Sirakoulis, G Ch; Mardiris, V; Karafyllidis, I; Glykos, N; Sandaltzopoulos, R

2008-04-01

Change of DNA sequence that fuels evolution is, to a certain extent, a deterministic process because mutagenesis does not occur in an absolutely random manner. So far, it has not been possible to decipher the rules that govern DNA sequence evolution due to the extreme complexity of the entire process. In our attempt to approach this issue we focus solely on the mechanisms of mutagenesis and deliberately disregard the role of natural selection. Hence, in this analysis, evolution refers to the accumulation of genetic alterations that originate from mutations and are transmitted through generations without being subjected to natural selection. We have developed a software tool that allows modelling of a DNA sequence as a one-dimensional cellular automaton (CA) with four states per cell which correspond to the four DNA bases, i.e. A, C, T and G. The four states are represented by numbers of the quaternary number system. Moreover, we have developed genetic algorithms (GAs) in order to determine the rules of CA evolution that simulate the DNA evolution process. Linear evolution rules were considered and square matrices were used to represent them. If DNA sequences of different evolution steps are available, our approach allows the determination of the underlying evolution rule(s). Conversely, once the evolution rules are deciphered, our tool may reconstruct the DNA sequence in any previous evolution step for which the exact sequence information was unknown. The developed tool may be used to test various parameters that could influence evolution. We describe a paradigm relying on the assumption that mutagenesis is governed by a near-neighbour-dependent mechanism. Based on the satisfactory performance of our system in the deliberately simplified example, we propose that our approach could offer a starting point for future attempts to understand the mechanisms that govern evolution. The developed software is open-source and has a user-friendly graphical input interface.

Formation of the Martian Polar Layered Terrains: Quantifying Polar Water Ice and Dust Surface Deposition during Current and Past Orbital Epochs with the NASA Ames GCM

NASA Astrophysics Data System (ADS)

Emmett, Jeremy; Murphy, Jim

2016-10-01

Structural and compositional variability in the layering sequences comprising Mars' polar layered terrains (PLT's) is likely explained by orbital-forced climatic variations in the sedimentary cycles of water ice and dust from which they formed [1]. The PLT's therefore contain a direct, extensive record of the recent climate history of Mars encoded in their structure and stratigraphy, but deciphering this record requires understanding the depositional history of their dust and water ice constituents. 3D Mars atmosphere modeling enables direct simulation of atmospheric dynamics, aerosol transport and quantification of surface accumulation for a range of past and present orbital configurations. By quantifying the net yearly polar deposition rates of water ice and dust under Mars' current and past orbital configurations characteristic of the last several millions of years, and integrating these into the present with a time-stepping model, the formation history of the north and south PLT's will be investigated, further constraining their age and composition, and, if reproducible, revealing the processes responsible for prominent features and stratigraphy observed within the deposits. Simulating the formation of the deposits by quantifying net deposition rates during past orbital epochs and integrating these into the present, effectively 'rebuilding' the terrains, could aid in understanding deeper stratigraphic trends, correlating between geographically-separated deposits, explaining the presence and shapes of large-scale polar features, and correlating stratigraphy with geological time. Quantification of the magnitude and geographical distribution of surface aerosol accumulation will build on the work of previous GCM-based investigations [3]. Construction and analysis of hypothetical stratigraphic sequences in the PLT's will draw from previous climate-controlled stratigraphy methodologies [2,4], but will utilize GCM-derived net deposition rates to model orbital influences on sedimentation and erosion.[1] Milkovich S.M. and Head J. W. (2005) JGR, 110. [2] Laskar J.B. and Mustard J.F. (2002) Nature, 419, 375-377 [3] Newman C.E. et al. (2005) Icarus, 174, 135-160. [4] Hvidberg C.S. et al. (2012) Icarus, 221, 405-419.

Identification of functional interactome of a key cell division regulatory protein CedA of E.coli.

PubMed

Sharma, Pankaj; Tomar, Anil Kumar; Kundu, Bishwajit

2018-01-01

Cell division is compromised in DnaAcos mutant Escherichia coli cells that results in filamentous cell morphology. This is countered by over-expression of CedA protein that induces cytokinesis and thus, regular cell morphology is regained; however via an unknown mechanism. To understand the process systematically, exact role of CedA should be deciphered. Protein interactions are crucial for functional organization of a cell and their identification helps in revealing exact function(s) of a protein and its binding partners. Thus, this study was intended to identify CedA binding proteins (CBPs) to gain more clues of CedA function. We isolated CBPs by pull down assay using purified recombinant CedA and identified nine CBPs by mass spectrometric analysis (MALDI-TOF MS and LC-MS/MS), viz. PDHA1, RL2, DNAK, LPP, RPOB, G6PD, GLMS, RL3 and YBCJ. Based on CBPs identified, we hypothesize that CedA plays a crucial and multifaceted role in cell cycle regulation and specific pathways in which CedA participates may include transcription and energy metabolism. However, further validation through in-vitro and in-vivo experiments is necessary. In conclusion, identification of CBPs may help us in deciphering mechanism of CedA mediated cell division during chromosomal DNA over-replication. Copyright © 2017 Elsevier B.V. All rights reserved.

Dancing to different tunes: heterospecific deciphering of the honeybee waggle dance

NASA Astrophysics Data System (ADS)

Tan, K.; Yang, M. X.; Radloff, S. E.; Hepburn, H. R.; Zhang, Z. Y.; Luo, L. J.; Li, H.

2008-12-01

Although the structure of the dance language is very similar among species of honeybees, communication of the distance component of the message varies both intraspecifically and interspecifically. However, it is not known whether different honeybee species would attend interspecific waggle dances and, if so, whether they can decipher such dances. Using mixed-species colonies of Apis cerana and Apis mellifera, we show that, despite internal differences in the structure of the waggle dances of foragers, both species attend, and act on the information encoded in each other’s waggle dances but with limited accuracy. These observations indicate that direction and distance communication pre-date speciation in honeybees.

Deciphering the evolutionary history of open and closed mitosis

PubMed Central

Sazer, Shelley; Lynch, Michael; Needleman, Daniel

2014-01-01

Summary The origin of the nucleus at the prokaryote to eukaryote transition represents one of the most important events in the evolution of cellular organization. The nuclear envelope encircles the chromosomes in interphase and is a selectively permeable barrier between the nucleoplasm and cytoplasm and an organizational scaffold for the nucleus. It remains intact in the "closed" mitosis of some yeast but loses its integrity in the "open" mitosis of mammals. Instances of both types of mitosis within two evolutionary clades indicate multiple evolutionary transitions between open and closed mitosis, although the underlying genetic changes that influenced these transitions remain unknown. A survey of the diversity of mitotic nuclei that fall between these extremes is the starting point from which to determine the physiologically relevant characteristics distinguishing open from closed mitosis and to understand how they evolved and why they are retained in present-day organisms. The field is now poised to begin addressing these issues by defining and document patterns of mitotic nuclear variation within and among species and map them onto a phylogenic tree. Deciphering the evolutionary history of open and closed mitosis will complement cell biological and genetic approaches aimed at deciphering the fundamental organizational principles of the nucleus. PMID:25458223

Come one, come all.

PubMed

Lee, Siu Sylvia

2004-05-05

Aging is a complex process that involves the gradual functional decline of many different tissues and cells. Gene expression microarray analysis provides a comprehensive view of the gene expression signature associated with age and is particularly valuable for understanding the molecular mechanisms that contribute to the aging process. However, because of the stochastic nature of the aging process, animals of the same chronological age often manifest great physiological differences. Therefore, profiling the gene expression pattern of a large population of aging animals risks either exaggerating or masking the changes in gene expression that correspond to physiological aging. In a recent paper, Golden and Melov surveyed the gene expression profiles of individual aging Caenorhabditis elegans, hoping to circumvent the problem of variability among worms of the same chronological age. This initial analysis of age-dependent gene expression in individual aging worms is an important step toward deciphering the molecular basis of physiological aging.

Emerging Imaging and Genomic Tools for Developmental Systems Biology.

PubMed

Liu, Zhe; Keller, Philipp J

2016-03-21

Animal development is a complex and dynamic process orchestrated by exquisitely timed cell lineage commitment, divisions, migration, and morphological changes at the single-cell level. In the past decade, extensive genetic, stem cell, and genomic studies provided crucial insights into molecular underpinnings and the functional importance of genetic pathways governing various cellular differentiation processes. However, it is still largely unknown how the precise coordination of these pathways is achieved at the whole-organism level and how the highly regulated spatiotemporal choreography of development is established in turn. Here, we discuss the latest technological advances in imaging and single-cell genomics that hold great promise for advancing our understanding of this intricate process. We propose an integrated approach that combines such methods to quantitatively decipher in vivo cellular dynamic behaviors and their underlying molecular mechanisms at the systems level with single-cell, single-molecule resolution. Copyright © 2016 Elsevier Inc. All rights reserved.

Deciphering the post-cratonization history of the Kaapvaal craton, South Africa from titanite and zircon (U-Th)/He thermochronology

NASA Astrophysics Data System (ADS)

Baughman, J. S.; Flowers, R. M.

2017-12-01

Cratons are the most stable portions of continents, but the degree to which they are affected by post-cratonization tectonic and magmatic processes is unclear. Complete time-temperature (t-T) histories are necessary to understand the timing, extent, and characteristics of post-cratonization events that disrupted these regions. However, deciphering extended cratonic t-T records is difficult owing to the incomplete stratigraphic records of continental interior settings, and the challenge of accessing the appropriate thermal history range with conventional thermochronometers. The Kaapvaal craton in South Africa is an archetypal craton that initially stabilized in the Archean and was subsequently affected by magmatic and marginal accretionary events. Here we exploit titanite and zircon (U-Th)/He (THe, ZHe) thermochronology to better decipher the somewhat cryptic Proterozoic through early Paleozoic history of the craton. Radiation damage effects on the He diffusivity of these two minerals provides the potential to access a wide temperature window from 200°C to near surface conditions. Existing low-temperature apatite (U-Th)/He and fission-track results constrain Late Paleozoic to Mesozoic burial of the Karoo basin and subsequent Cretaceous unroofing, while 40Ar/39Ar and Rb-Sr data document cooling through temperatures of 300°C by 2 Ga. We obtained THe and ZHe dates from across the northern Kaapvaal craton to fill in the thermal history gap between these constraints. THe and ZHe dates range from 1200 to 200 Ma, and 1000 to 30 Ma, respectively. Both sets of dates are negatively correlated with effective uranium concentration (eU), manifesting the effect of radiation damage on the He retentivity, and therefore closure temperature, of these minerals. The results allow us to assess the Mesoproterozoic through present day thermal history of the northern Kaapvaal craton. The THe data suggest that Mesoproterozoic exhumation and large-scale reheating associated with Namaqua-Natal orogenesis affected the region. While, the ZHe data constrain maximum burial temperatures during Mesozoic Karoo burial. Together the results show the power of exploiting thermochronologic advances to access new information about long-term continental evolution.

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.

PubMed

Wang, Julia; Al-Ouran, Rami; Hu, Yanhui; Kim, Seon-Young; Wan, Ying-Wooi; Wangler, Michael F; Yamamoto, Shinya; Chao, Hsiao-Tuan; Comjean, Aram; Mohr, Stephanie E; Perrimon, Norbert; Liu, Zhandong; Bellen, Hugo J

2017-06-01

One major challenge encountered with interpreting human genetic variants is the limited understanding of the functional impact of genetic alterations on biological processes. Furthermore, there remains an unmet demand for an efficient survey of the wealth of information on human homologs in model organisms across numerous databases. To efficiently assess the large volume of publically available information, it is important to provide a concise summary of the most relevant information in a rapid user-friendly format. To this end, we created MARRVEL (model organism aggregated resources for rare variant exploration). MARRVEL is a publicly available website that integrates information from six human genetic databases and seven model organism databases. For any given variant or gene, MARRVEL displays information from OMIM, ExAC, ClinVar, Geno2MP, DGV, and DECIPHER. Importantly, it curates model organism-specific databases to concurrently display a concise summary regarding the human gene homologs in budding and fission yeast, worm, fly, fish, mouse, and rat on a single webpage. Experiment-based information on tissue expression, protein subcellular localization, biological process, and molecular function for the human gene and homologs in the seven model organisms are arranged into a concise output. Hence, rather than visiting multiple separate databases for variant and gene analysis, users can obtain important information by searching once through MARRVEL. Altogether, MARRVEL dramatically improves efficiency and accessibility to data collection and facilitates analysis of human genes and variants by cross-disciplinary integration of 18 million records available in public databases to facilitate clinical diagnosis and basic research. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Pore Characterization of Shale Rock and Shale Interaction with Fluids at Reservoir Pressure-Temperature Conditions Using Small-Angle Neutron Scattering

NASA Astrophysics Data System (ADS)

Ding, M.; Hjelm, R.; Watkins, E.; Xu, H.; Pawar, R.

2015-12-01

Oil/gas produced from unconventional reservoirs has become strategically important for the US domestic energy independence. In unconventional realm, hydrocarbons are generated and stored in nanopores media ranging from a few to hundreds of nanometers. Fundamental knowledge of coupled thermo-hydro-mechanical-chemical (THMC) processes that control fluid flow and propagation within nano-pore confinement is critical for maximizing unconventional oil/gas production. The size and confinement of the nanometer pores creates many complex rock-fluid interface interactions. It is imperative to promote innovative experimental studies to decipher physical and chemical processes at the nanopore scale that govern hydrocarbon generation and mass transport of hydrocarbon mixtures in tight shale and other low permeability formations at reservoir pressure-temperature conditions. We have carried out laboratory investigations exploring quantitative relationship between pore characteristics of the Wolfcamp shale from Western Texas and the shale interaction with fluids at reservoir P-T conditions using small-angle neutron scattering (SANS). We have performed SANS measurements of the shale rock in single fluid (e.g., H2O and D2O) and multifluid (CH4/(30% H2O+70% D2O)) systems at various pressures up to 20000 psi and temperature up to 150 oF. Figure 1 shows our SANS data at different pressures with H2O as the pressure medium. Our data analysis using IRENA software suggests that the principal changes of pore volume in the shale occurred on smaller than 50 nm pores and pressure at 5000 psi (Figure 2). Our results also suggest that with increasing P, more water flows into pores; with decreasing P, water is retained in the pores.

Conceptual analysis of Physiology of vision in Ayurveda

PubMed Central

Balakrishnan, Praveen; Ashwini, M. J.

2014-01-01

The process by which the world outside is seen is termed as visual process or physiology of vision. There are three phases in this visual process: phase of refraction of light, phase of conversion of light energy into electrical impulse and finally peripheral and central neurophysiology. With the advent of modern instruments step by step biochemical changes occurring at each level of the visual process has been deciphered. Many investigations have emerged to track these changes and helping to diagnose the exact nature of the disease. Ayurveda has described this physiology of vision based on the functions of vata and pitta. Philosophical textbook of ayurveda, Tarka Sangraha, gives certain basics facts of visual process. This article discusses the second and third phase of visual process. Step by step analysis of the visual process through the spectacles of ayurveda amalgamated with the basics of philosophy from Tarka Sangraha has been analyzed critically to generate a concrete idea regarding the physiology and hence thereby interpret the pathology on the grounds of ayurveda based on the investigative reports. PMID:25336853

Documentation of Old Turkic Runic Inscriptions of the Altai Mountains Using Photogrammetric Technology

NASA Astrophysics Data System (ADS)

Vavulin, M. V.

2017-11-01

Old Turkic runic inscriptions of the Altai Mountains (8th-9th centuries AD) were digitized in the course of this project to be preserved in the current state on the Web and deciphered by linguistic experts. The ways the inscriptions were made as well as their location in hardly accessible areas required finding an inexpensive solution that would provide detailed 3D documentation of rock faces, while at the same time mobility and autonomy. Digital photogrammetry came as a quite affordable and optimal choice for getting high-quality outcomes using inexpensive software and further data processing using free software.

Characterization of metabolic network of oxalic acid biosynthesis through RNA seq data analysis of developing spikes of finger millet (Eleusine coracana): Deciphering the role of key genes involved in oxalate formation in relation to grain calcium accumulation.

PubMed

Akbar, Naved; Gupta, Supriya; Tiwari, Apoorv; Singh, K P; Kumar, Anil

2018-04-05

In the present study, we identified seven major genes of oxalic acid biosynthesis pathway (SGAT, GGAT, ICL, GLO, MHAR, APO and OXO) from developing spike transcriptome of finger millet using rice as a reference. Sequence alignment of identified genes showed high similarity with their respective homolog in rice except for OXO and GLO. Transcript abundance (FPKM) reflects the higher accumulation of identified genes in GP-1 (low calcium genotype) as compared to GP-45 (high calcium genotype) which was further confirmed by qRT-PCR analysis, indicating differential oxalate formation in both genotypes. Determination of oxalic acid and tartaric acid content in developing spikes explain that higher oxalic acid content in GP-1 however, tartaric acid content was more in GP-45. Higher calcium content in GP-45 and lower oxalate accumulation may be due to the diversion of more ascorbic acid into tartaric acid and may correspond to less formation of calcium oxalate. Our results suggest that more than one pathway for oxalic acid biosynthesis might be present in finger millet with probable predominance of ascorbate-tartarate pathway rather than glyoxalate-oxalate conversion. Thus, finger millet can be use as an excellent model system for understanding more specific role of nutrients-antinutrients interactions, as evident from the present study. Copyright © 2018 Elsevier B.V. All rights reserved.

iTRAQ-based protein profiling provides insights into the central metabolism changes driving grape berry development and ripening

PubMed Central

2013-01-01

Background Grapevine (Vitis vinifera L.) is an economically important fruit crop. Quality-determining grape components such as sugars, acids, flavors, anthocyanins, tannins, etc., accumulate in the different grape berry development stages. Thus, correlating the proteomic profiles with the biochemical and physiological changes occurring in grape is of paramount importance to advance in our understanding of berry development and ripening processes. Results We report the developmental analysis of Vitis vinifera cv. Muscat Hamburg berries at the protein level from fruit set to full ripening. An iTRAQ-based bottom-up proteomic approach followed by tandem mass spectrometry led to the identification and quantitation of 411 and 630 proteins in the green and ripening phases, respectively. Two key points in development relating to changes in protein level were detected: end of the first growth period (7 mm-to-15 mm) and onset of ripening (15 mm-to-V100, V100-to-110). A functional analysis was performed using the Blast2GO software based on the enrichment of GO terms during berry growth. Conclusions The study of the proteome contributes to decipher the biological processes and metabolic pathways involved in the development and quality traits of fruit and its derived products. These findings lie mainly in metabolism and storage of sugars and malate, energy-related pathways such as respiration, photosynthesis and fermentation, and the synthesis of polyphenolics as major secondary metabolites in grape berry. In addition, some key steps in carbohydrate and malate metabolism have been identified in this study, i.e., PFP-PFK or SuSy-INV switches among others, which may influence the final sugar and acid balance in ripe fruit. In conclusion, some proteins not reported to date have been detected to be deregulated in specific tissues and developmental stages, leading to formulate new hypotheses on the metabolic processes underlying grape berry development. These results open up new lines to decipher the processes controlling grape berry development and ripening. PMID:24152288

Effects of Drake Passage on a strongly eddying global ocean

NASA Astrophysics Data System (ADS)

Viebahn, Jan P.; von der Heydt, Anna S.; Le Bars, Dewi; Dijkstra, Henk A.

2016-05-01

The climate impact of ocean gateway openings during the Eocene-Oligocene transition is still under debate. Previous model studies employed grid resolutions at which the impact of mesoscale eddies has to be parameterized. We present results of a state-of-the-art eddy-resolving global ocean model with a closed Drake Passage and compare with results of the same model at noneddying resolution. An analysis of the pathways of heat by decomposing the meridional heat transport into eddy, horizontal, and overturning circulation components indicates that the model behavior on the large scale is qualitatively similar at both resolutions. Closing Drake Passage induces (i) sea surface warming around Antarctica due to equatorward expansion of the subpolar gyres, (ii) the collapse of the overturning circulation related to North Atlantic Deep Water formation leading to surface cooling in the North Atlantic, and (iii) significant equatorward eddy heat transport near Antarctica. However, quantitative details significantly depend on the chosen resolution. The warming around Antarctica is substantially larger for the noneddying configuration (˜5.5°C) than for the eddying configuration (˜2.5°C). This is a consequence of the subpolar mean flow which partitions differently into gyres and circumpolar current at different resolutions. We conclude that for a deciphering of the different mechanisms active in Eocene-Oligocene climate change detailed analyses of the pathways of heat in the different climate subsystems are crucial in order to clearly identify the physical processes actually at work.

Transgenesis of the Wolffian duct visualizes dynamic behavior of cells undergoing tubulogenesis in vivo.

PubMed

Atsuta, Yuji; Tadokoro, Ryosuke; Saito, Daisuke; Takahashi, Yoshiko

2013-05-01

Deciphering how the tubulogenesis is regulated is an essential but unsolved issue in developmental biology. Here, using Wolffian duct (WD) formation in chicken embryos, we have developed a novel method that enables gene manipulation during tubulogenesis in vivo. Exploiting that WD arises from a defined site located anteriorly in the embryo (pronephric region), we targeted this region with the enhanced green fluorescent protein (EGFP) gene by the in ovo electroporation technique. EGFP-positive signals were detected in a wide area of elongating WD, where transgenic cells formed an epithelial component in a mosaic manner. Time-lapse live imaging analyses further revealed dynamic behavior of cells during WD elongation: some cells possessed numerous filopodia, and others exhibited cellular tails that repeated elongation and retraction. The retraction of the tail was precisely regulated by Rho activity via actin dynamics. When electroporated with the C3 gene, encoding Rho inhibitor, WD cells failed to contract their tails, resulting in an aberrantly elongated process. We further combined with the Tol2 transposon-mediated gene transfer technique, and could trace EGFP-positive cells at later stages in the ureteric bud sprouting from WD. This is the first demonstration that exogenous gene(s) can directly be introduced into elongating tubular structures in living amniote embryos. This method has opened a way to investigate how a complex tubulogenesis proceeds in higher vertebrates. © 2013 The Authors Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

Ras GTPases Modulate Morphogenesis, Sporulation and Cellulase Gene Expression in the Cellulolytic Fungus Trichoderma reesei

PubMed Central

Zhang, Jiwei; Zhang, Yanmei; Zhong, Yaohua; Qu, Yinbo; Wang, Tianhong

2012-01-01

Background The model cellulolytic fungus Trichoderma reesei (teleomorph Hypocrea jecorina) is capable of responding to environmental cues to compete for nutrients in its natural saprophytic habitat despite its genome encodes fewer degradative enzymes. Efficient signalling pathways in perception and interpretation of environmental signals are indispensable in this process. Ras GTPases represent a kind of critical signal proteins involved in signal transduction and regulation of gene expression. In T. reesei the genome contains two Ras subfamily small GTPases TrRas1 and TrRas2 homologous to Ras1 and Ras2 from S. cerevisiae, but their functions remain unknown. Methodology/Principal Findings Here, we have investigated the roles of GTPases TrRas1 and TrRas2 during fungal morphogenesis and cellulase gene expression. We show that both TrRas1 and TrRas2 play important roles in some cellular processes such as polarized apical growth, hyphal branch formation, sporulation and cAMP level adjustment, while TrRas1 is more dominant in these processes. Strikingly, we find that TrRas2 is involved in modulation of cellulase gene expression. Deletion of TrRas2 results in considerably decreased transcription of cellulolytic genes upon growth on cellulose. Although the strain carrying a constitutively activated TrRas2G16V allele exhibits increased cellulase gene transcription, the cbh1 and cbh2 expression in this mutant still strictly depends on cellulose, indicating TrRas2 does not directly mediate the transmission of the cellulose signal. In addition, our data suggest that the effect of TrRas2 on cellulase gene is exerted through regulation of transcript abundance of cellulase transcription factors such as Xyr1, but the influence is independent of cAMP signalling pathway. Conclusions/Significance Together, these findings elucidate the functions for Ras signalling of T. reesei in cellular morphogenesis, especially in cellulase gene expression, which contribute to deciphering the powerful competitive ability of plant cell wall degrading fungi in nature. PMID:23152805

Deciphering the Landauer-Büttiker Transmission Function from Single Molecule Break Junction Experiments

NASA Astrophysics Data System (ADS)

Reuter, Matthew; Tschudi, Stephen

When investigating the electrical response properties of molecules, experiments often measure conductance whereas computation predicts transmission probabilities. Although the Landauer-Büttiker theory relates the two in the limit of coherent scattering through the molecule, a direct comparison between experiment and computation can still be difficult. Experimental data (specifically that from break junctions) is statistical and computational results are deterministic. Many studies compare the most probable experimental conductance with computation, but such an analysis discards almost all of the experimental statistics. In this work we develop tools to decipher the Landauer-Büttiker transmission function directly from experimental statistics and then apply them to enable a fairer comparison between experimental and computational results.

Stages of weathering mantle formation from carbonate rocks in the light of rare earth elements (REE) and Sr-Nd-Pb isotopes

NASA Astrophysics Data System (ADS)

Hissler, Christophe; Stille, Peter

2015-04-01

Weathering mantles are widespread and include lateritic, sandy and kaolinite-rich saprolites and residuals of partially dissolved rocks. These old regolith systems have a complex history of formation and may present a polycyclic evolution due to successive geological and pedogenetic processes that affected the profile. Until now, only few studies highlighted the unusual high content of associated trace elements in weathering mantles originating from carbonate rocks, which have been poorly studied, compared to those developing on magmatic bedrocks. For instance, these enrichments can be up to five times the content of the underlying carbonate rocks. However, these studies also showed that the carbonate bedrock content only partially explains the soil enrichment for all the considered major and trace elements. Up to now, neither soil, nor saprolite formation has to our knowledge been geochemically elucidated. Therefore, the aim of this study was to examine more closely the soil forming dynamics and the relationship of the chemical soil composition to potential sources. REE distribution patterns and Sr-Nd-Pb isotope ratios have been used because they are particularly well suited to identify trace element migration, to recognize origin and mixing processes and, in addition, to decipher possible anthropogenic and/or "natural" atmosphere-derived contributions to the soil. Moreover, leaching experiments have been applied to identify mobile phases in the soil system and to yield information on the stability of trace elements and especially on their behaviour in these Fe-enriched carbonate systems. All these geochemical informations indicate that the cambisol developing on such a typical weathering mantle ("terra fusca") has been formed through weathering of a condensed Bajocian limestone-marl facies. This facies shows compared to average world carbonates important trace element enrichments. Their trace element distribution patterns are similar to those of the soil suggesting their close genetic relationships. Sr-Nd-Pb isotope data allow to identify four principal components in the soil: a silicate-rich pool at close to the surface, a leachable REE enriched pool at the bottom of the soil profile, the limestone facies on which the weathering profile developed and an anthropogenic, atmosphere-derived component detected in the soil leachates of the uppermost soil horizon. The leachable phases are mainly secondary carbonate-bearing REE phases such as bastnaesite. The isotope data and trace element distribution patterns indicate that at least four geological and environmental events impacted the chemical and isotopical compositions of the soil system since the Cretaceous.

Study of Polymer Crystallization by Physical Vapor Deposition

NASA Astrophysics Data System (ADS)

Jeong, Hyuncheol

When a polymer is confined under the submicron length scale, confinement size and interfaces can significantly impact the crystallization kinetics and resulting morphology. The ability to tune the morphology of confined polymer systems is of critical importance for the development of high-performance polymer microelectronics. The wisdom from the research on confined crystallization suggests that it would be beneficial to have a processing route in which the crystallization of polymers is driven by interface and temperature effects at a nanometer-scale confinement. In practice, for atomic and small-molecular systems, physical vapor deposition (PVD) has been recognized as the most successful processing route for the precise control of the film structure at surface utilizing confinement effects. While standard PVD technologies are not generally applicable to the deposition of the chemically fragile macromolecules, the development of matrix-assisted pulsed laser evaporation (MAPLE) now enables the non-destructive PVD of high-molecular weight polymers. In this thesis work, we investigated the use of MAPLE for the precise control of the crystallization of polymer films at a molecular level. We also sought to decipher the rules governing the crystallization of confined polymers, by using MAPLE as a tool to form confined polymer systems onto substrates with a controlled temperature. We first explored the early stages of film growth and crystallization of poly(ethylene oxide) (PEO) at the substrate surface formed by MAPLE. The unique mechanism of film formation in MAPLE, the deposition of submicron-sized polymer droplets, allowed for the manifestation of confinement and substrate effects in the crystallization of MAPLE-deposited PEO. Furthermore, we also focused on the property of the amorphous PEO film formed by MAPLE, showing the dependence of polymer crystallization kinetics on the thermal history of the amorphous phase. Lastly, we probed how MAPLE processing affected the semi-crystalline structure in MAPLE-deposited polyethylene (PE) films. Depositing PE at various temperatures remarkably allowed for the tunability of the melting temperature and crystallinity of the PE films, thus manipulating the semi-crystalline structure. By comparing the structure of PE formed by different processing routes, i.e., MAPLE and melt-crystallization, we discussed how processing routes affect the development of semi-crystalline phase in polymer films.

Discriminating sediment archives and sedimentary processes in the arid endorheic Ejina Basin, NW China using a robust geochemical approach

NASA Astrophysics Data System (ADS)

Yu, Kaifeng; Hartmann, Kai; Nottebaum, Veit; Stauch, Georg; Lu, Huayu; Zeeden, Christian; Yi, Shuangwen; Wünnemann, Bernd; Lehmkuhl, Frank

2016-04-01

Geochemical characteristics have been intensively used to assign sediment properties to paleoclimate and provenance. Nonetheless, in particular concerning the arid context, bulk geochemistry of different sediment archives and corresponding process interpretations are hitherto elusive. The Ejina Basin, with its suite of different sediment archives, is known as one of the main sources for the loess accumulation on the Chinese Loess Plateau. In order to understand mechanisms along this supra-regional sediment cascade, it is crucial to decipher the archive characteristics and formation processes. To address these issues, five profiles in different geomorphological contexts were selected. Analyses of X-ray fluorescence and diffraction, grain size, optically stimulated luminescence and radiocarbon dating were performed. Robust factor analysis was applied to reduce the attribute space to the process space of sedimentation history. Five sediment archives from three lithologic units exhibit geochemical characteristics as follows: (i) aeolian sands have high contents of Zr and Hf, whereas only Hf can be regarded as a valuable indicator to discriminate the coarse sand proportion; (ii) sandy loess has high Ca and Sr contents which both exhibit broad correlations with the medium to coarse silt proportions; (iii) lacustrine clays have high contents of felsic, ferromagnesian and mica source elements e.g., K, Fe, Ti, V, and Ni; (iv) fluvial sands have high contents of Mg, Cl and Na which may be enriched in evaporite minerals; (v) alluvial gravels have high contents of Cr which may originate from nearby Cr-rich bedrock. Temporal variations can be illustrated by four robust factors: weathering intensity, silicate-bearing mineral abundance, saline/alkaline magnitude and quasi-constant aeolian input. In summary, the bulk-composition of the late Quaternary sediments in this arid context is governed by the nature of the source terrain, weak chemical weathering, authigenic minerals, aeolian sand input, whereas pedogenesis and diagenesis exert only limited influences. Hence, this study demonstrates a practical geochemical strategy supplemented by grain size and mineralogical data, to discriminate sediment archives and thereafter enhance our ability to offer more intriguing information about the sedimentary processes in the arid central Asia.

High cytokinin levels induce a hypersensitive-like response in tobacco.

PubMed

Novák, Jan; Pavlů, Jaroslav; Novák, Ondřej; Nožková-Hlaváčková, Vladimíra; Špundová, Martina; Hlavinka, Jan; Koukalová, Šárka; Skalák, Jan; Černý, Martin; Brzobohatý, Břetislav

2013-07-01

Cytokinins are positive regulators of shoot development. However, it has previously been demonstrated that efficient activation of the cytokinin biosynthesis gene ipt can cause necrotic lesions and wilting in tobacco leaves. Some plant pathogens reportedly use their ability to produce cytokinins in disease development. In response to pathogen attacks, plants can trigger a hypersensitive response that rapidly kills cells near the infection site, depriving the pathogen of nutrients and preventing its spread. In this study, a diverse set of processes that link ipt activation to necrotic lesion formation were investigated in order to evaluate the potential of cytokinins as signals and/or mediators in plant defence against pathogens. The binary pOp-ipt/LhGR system for dexamethasone-inducible ipt expression was used to increase endogenous cytokinin levels in transgenic tobacco. Changes in the levels of cytokinins and the stress hormones salicylic, jasmonic and abscisic acid following ipt activation were determined by ultra-performance liquid chromatography-electrospray tandem mass spectrometry (UPLC-MS/MS). Trends in hydrogen peroxide content and lipid peroxidation were monitored using the potassium iodide and malondialdehyde assays. The subcellular distribution of hydrogen peroxide was investigated using 3,3'-diaminobenzidine staining. The dynamics of transcripts related to photosynthesis and pathogen response were analysed by reverse transcription followed by quantitative PCR. The effects of cytokinins on photosynthesis were deciphered by analysing changes in chlorophyll fluorescence and leaf gas exchange. Plants can produce sufficiently high levels of cytokinins to trigger fast cell death without any intervening chlorosis - a hallmark of the hypersensitive response. The results suggest that chloroplastic hydrogen peroxide orchestrates the molecular responses underpinning the hypersensitive-like response, including the inhibition of photosynthesis, elevated levels of stress hormones, oxidative membrane damage and stomatal closure. Necrotic lesion formation triggered by ipt activation closely resembles the hypersensitive response. Cytokinins may thus act as signals and/or mediators in plant defence against pathogen attack.

Conformational Equilibria in Monomeric α-Synuclein at the Single-Molecule Level

PubMed Central

Tessari, Isabella; Mammi, Stefano; Bergantino, Elisabetta; Musiani, Francesco; Brucale, Marco; Bubacco, Luigi; Samorì, Bruno

2008-01-01

Human α-Synuclein (αSyn) is a natively unfolded protein whose aggregation into amyloid fibrils is involved in the pathology of Parkinson disease. A full comprehension of the structure and dynamics of early intermediates leading to the aggregated states is an unsolved problem of essential importance to researchers attempting to decipher the molecular mechanisms of αSyn aggregation and formation of fibrils. Traditional bulk techniques used so far to solve this problem point to a direct correlation between αSyn's unique conformational properties and its propensity to aggregate, but these techniques can only provide ensemble-averaged information for monomers and oligomers alike. They therefore cannot characterize the full complexity of the conformational equilibria that trigger the aggregation process. We applied atomic force microscopy–based single-molecule mechanical unfolding methodology to study the conformational equilibrium of human wild-type and mutant αSyn. The conformational heterogeneity of monomeric αSyn was characterized at the single-molecule level. Three main classes of conformations, including disordered and “β-like” structures, were directly observed and quantified without any interference from oligomeric soluble forms. The relative abundance of the “β-like” structures significantly increased in different conditions promoting the aggregation of αSyn: the presence of Cu2+, the pathogenic A30P mutation, and high ionic strength. This methodology can explore the full conformational space of a protein at the single-molecule level, detecting even poorly populated conformers and measuring their distribution in a variety of biologically important conditions. To the best of our knowledge, we present for the first time evidence of a conformational equilibrium that controls the population of a specific class of monomeric αSyn conformers, positively correlated with conditions known to promote the formation of aggregates. A new tool is thus made available to test directly the influence of mutations and pharmacological strategies on the conformational equilibrium of monomeric αSyn. PMID:18198943

Effects of Trophic Status on Mercury Methylation Pathways in Peatlands

NASA Astrophysics Data System (ADS)

Hines, M. E.; Zhang, L.; Sampath, S.; Hu, R.; Barkay, T.

2014-12-01

Methyl mercury (MeHg) is a bioaccumulative toxicant. It was believed to be produced by sulfate (SO4)- and iron- reducing bacteria (SRB and FeRB), but recent studies suggest that organisms that possess the gene cluster (hgcAB) can methylate Hg, which includes other microbial groups besides SRB and FeRB. Many areas known to accumulate high levels of MeHg are freshwater wetlands that lack sufficient electron acceptors to support the production of MeHg. To test the hypothesis that oligotrophic wetlands are able to methylate Hg by pathways that are not respiratory, peat was collected from three wetland sites in Alaska and three in Massachusetts that represented a trophic gradient. We determined rates of gas (CH4, CO2, H2) and LMW organic acid (formate, acetate, propionate, butyrate) formation, and rates of Hg methylation using the short-lived radioisotope 197Hg (half life 2.67 days). Two temperate sites exhibited strong terminal respiration (methanogenesis) and syntrophy, while the Alaskan sites and an oligotrophic temperate site exhibited low rates of both. Primary fermentation was an important process in the latter sites. Hg methylation was most active at the minerotrophic sites that exhibited active syntrophy and methanogenesis. Methylation decreased greatly in the presence of a methanogenic inhibitor and was stimulated by H2 indicating that methanogens and perhaps syntrophs were primary methylators. In the oligotrophic sites, the addition of SO4 stimulated methylation while a SO4 reduction inhibitor decreased methylation. There was no evidence of SO4 reduction in these samples suggesting that methylation was conducted by SRB that were metabolizing via fermentation and not SO4 reduction. While further studies are required to decipher the role of syntrophs including SRB varieties such as Syntrophobacter sp., these results indicate that fermentative bacteria may be able to significantly methylate Hg in wetlands that do not support anaerobic respiration.

Compressional reactivation of hyperextended domains on a rifted margin: a requirement for a reappraisal of traditional restoration procedures?

NASA Astrophysics Data System (ADS)

Cadenas Martínez, P.; Fernandez Viejo, G.; Pulgar, J. A.

2017-12-01

The North Iberian margin is an inverted hyperextended rifted margin that preserves the initial stages of compressional reactivation. Rift inheritance conditioned in a determinant way the contractional reactivation. The underthrusting of the hyperextended distal domains beneath the platform and the formation of an accretionary wedge at the toe of the slope focused most of the compression. The underthrusting gave place to the formation of a crustal root and the uplifting of the Cantabrian Mountains onshore. Meanwhile, the main rift basins within the continental platform were slightly inverted. Plate kinematic reconstructions and palinspatic restorations have provided different shortening values. Thereby, the amount of shortening linked with the Cenozoic compression is still unclear and a matter of debate on this area.In this work, we present a full cross-section at the central part of the North Iberian margin developed from the restoration of a high quality depth migrated seismic profile running from the continental platform to the Biscay abyssal plain. A shortening calculation gives an estimate of about 1 km within the Asturian Basin, in the continental platform, while in the accretionary wedge at the bottom of the slope, shortening values ranges between 12 km and 15 km. The limited values estimated within the Asturian Basin support the mild inversion observed within this basin, which preserves most of the extensional imprint. Within the abyssal plain, shortening values differ from previous estimations and cannot account for a high amount of compression in the upper crust. Deformation of the hyperextended crust and the exhumed mantle domains inherited from the rifting processes would have accommodated most of the compression. Restoration of these domains seems to be the key to decipher the structure and the tectonic evolution of the reactivated rifted margin but cannot be solved accurately using traditional restoration methods. This leads to a reappraisal of the traditional way of restoring compressional belt transects and particularly, when previous hyperextended domains within the rifted margins are involved.

Morphotectonic analysis and 10Be dating of the Kyngarga river terraces (southwestern flank of the Baikal rift system, South Siberia)

NASA Astrophysics Data System (ADS)

Arzhannikova, A.; Arzhannikov, S.; Braucher, R.; Jolivet, M.; Aumaître, G.; Bourlès, D.; Keddadouche, K.

2018-02-01

The formation of the Baikal rift system basins is controlled by active faults separating each basin from the adjacent horsts. The kinematics of these faults is mainly explored through investigation of complex sequences of the fault-intersecting river terraces that record both tectonic and climatic events. This study focuses on the northern margin of the major Tunka basin that develops south-west of Lake Baikal. The development of the basin is controlled by the segmented Tunka fault. We performed a detailed mapping of the Kyngarga river terraces, the best preserved terraces staircase in Baikal rift system, at their intersection with the Tunka fault. In order to decipher the chronology of seismic events and the slip rates along that segment of the fault, key terraces were dated using in situ produced cosmogenic 10Be. We demonstrate that the formation of the terrace staircase occurred entirely during MIS1-MIS2. The obtained data allowed us to estimate the rate of incision at different stages of the terrace staircase formation and the relationship between the vertical and horizontal slip rates along this sub-latitudinal segment of the Tunka fault making respectively 0.8 and 1.12 mm yr- 1 over the past 12.5 ka. Analysis of the paleoseismology and paleoclimate data together with terrace dating provided the possibility to estimate the influence of tectonic and climatic factors on the terrace formation. Our proposed model of the Kyngarga river terrace development shows that the incisions into terraces T3 and T6 were induced by the abrupt climatic warming episodes GI-1 and GI-2, respectively, whereas terraces T5, T4 and T2 were abandoned due to the vertical tectonic displacement along the Tunka fault caused by coseismic ruptures.

The Oligocene-Miocene stratigraphic evolution of the Majella carbonate platform (Central Apennines, Italy)

NASA Astrophysics Data System (ADS)

Brandano, Marco; Cornacchia, Irene; Raffi, Isabella; Tomassetti, Laura

2016-03-01

The stratigraphic architecture of the Bolognano Formation documents the evolution of the Majella carbonate platform in response to global and local changes that affected the Mediterranean area during the Oligocene-Miocene interval. The Bolognano Formation consists of a homoclinal ramp that developed in a warm, subtropical environment. Five different lithofacies associations have been identified: Lepidocyclina calcarenites, cherty marly limestones, bryozon calcarenites, hemipelagic marls and marly limestones, and Lithothamnion limestones. Each association corresponds to a single lithostratigraphic unit except for the Lepidocyclina calcarenites that form two distinct lithostratigraphic units (Lepidocyclina calcarenites 1 and 2). These six units reflect alternation of shallow-water carbonate production and drowning. Specifically, two of the three stages of shallow-water carbonate production regard the development of wide dune fields within the middle ramp, one stage dominated by red algae and a sea-grass carbonate factory, whereas the two drowning phases are represented by marly cherty limestones and calcareous marls. A new biostratigraphic framework for Bolognano Formation is presented, based on high-resolution analysis of calcareous nannofossil assemblages, which proved to be very useful for biostratigraphic constraints also in shallow-water settings. Using this approach, we have linked the first drowning phase, late Chattian-Aquitanian p.p. in age, to western Mediterranean volcanism and the Mi-1 event, and the second drowning phase, late Burdigalian-Serravallian in age, to the closure of the Indo-Pacific passage and the occurrence of the global Monterey event. These results permit a new deciphering, in terms of sequence stratigraphy, of the Bolognano Formation that is interpreted as a 2nd-order super-sequence that can be subdivided into 3 transgressive-regressive sequences.

Improvements in cloning efficiencies may be possible by increasing uniformity in recipient oocytes and donor cells.

PubMed

Miyoshi, Kazuchika; Rzucidlo, S Jacek; Pratt, Scott L; Stice, Steven L

2003-04-01

The low efficiency of somatic cell cloning is the major obstacle to widespread use of this technology. Incomplete nuclear reprogramming following the transfer of donor nuclei into recipient oocytes has been implicated as a primary reason for the low efficiency of the cloning procedure. The mechanisms and factors that affect the progression of the nuclear reprogramming process have not been completely elucidated, but the identification of these factors and their subsequent manipulation would increase cloning efficiency. At present, many groups are studying donor nucleus reprogramming. Here, we present an approach in which the efficiency of producing viable offspring is improved by selecting recipient oocytes and donor cells that will produce cloned embryos with functionally reprogrammed nuclei. This approach will produce information useful in future studies aimed at further deciphering the nuclear reprogramming process.

Guiding bioprocess design by microbial ecology.

PubMed

Volmer, Jan; Schmid, Andreas; Bühler, Bruno

2015-06-01

Industrial bioprocess development is driven by profitability and eco-efficiency. It profits from an early stage definition of process and biocatalyst design objectives. Microbial bioprocess environments can be considered as synthetic technical microbial ecosystems. Natural systems follow Darwinian evolution principles aiming at survival and reproduction. Technical systems objectives are eco-efficiency, productivity, and profitable production. Deciphering technical microbial ecology reveals differences and similarities of natural and technical systems objectives, which are discussed in this review in view of biocatalyst and process design and engineering strategies. Strategies for handling opposing objectives of natural and technical systems and for exploiting and engineering natural properties of microorganisms for technical systems are reviewed based on examples. This illustrates the relevance of considering microbial ecology for bioprocess design and the potential for exploitation by synthetic biology strategies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Adult stem cell lineage tracing and deep tissue imaging

PubMed Central

Fink, Juergen; Andersson-Rolf, Amanda; Koo, Bon-Kyoung

2015-01-01

Lineage tracing is a widely used method for understanding cellular dynamics in multicellular organisms during processes such as development, adult tissue maintenance, injury repair and tumorigenesis. Advances in tracing or tracking methods, from light microscopy-based live cell tracking to fluorescent label-tracing with two-photon microscopy, together with emerging tissue clearing strategies and intravital imaging approaches have enabled scientists to decipher adult stem and progenitor cell properties in various tissues and in a wide variety of biological processes. Although technical advances have enabled time-controlled genetic labeling and simultaneous live imaging, a number of obstacles still need to be overcome. In this review, we aim to provide an in-depth description of the traditional use of lineage tracing as well as current strategies and upcoming new methods of labeling and imaging. [BMB Reports 2015; 48(12): 655-667] PMID:26634741

Deciphering the evolutionary history of open and closed mitosis.

PubMed

Sazer, Shelley; Lynch, Michael; Needleman, Daniel

2014-11-17

The origin of the nucleus at the prokaryote-to-eukaryote transition represents one of the most important events in the evolution of cellular organization. The nuclear envelope encircles the chromosomes in interphase and is a selectively permeable barrier between the nucleoplasm and cytoplasm and an organizational scaffold for the nucleus. It remains intact in the 'closed' mitosis of some yeasts, but loses its integrity in the 'open' mitosis of mammals. Instances of both types of mitosis within two evolutionary clades indicate multiple evolutionary transitions between open and closed mitosis, although the underlying genetic changes that influenced these transitions remain unknown. A survey of the diversity of mitotic nuclei that fall between these extremes is the starting point from which to determine the physiologically relevant characteristics distinguishing open from closed mitosis and to understand how they evolved and why they are retained in present-day organisms. The field is now poised to begin addressing these issues by defining and documenting patterns of mitotic nuclear variation within and among species and mapping them onto a phylogenic tree. Deciphering the evolutionary history of open and closed mitosis will complement cell biological and genetic approaches aimed at deciphering the fundamental organizational principles of the nucleus. Copyright © 2014 Elsevier Ltd. All rights reserved.

Deciphering of ADP-induced, phosphotyrosine-dependent signaling networks in human platelets by Src-homology 2 region (SH2)-profiling.

PubMed

Schweigel, Hardy; Geiger, Jörg; Beck, Florian; Buhs, Sophia; Gerull, Helwe; Walter, Ulrich; Sickmann, Albert; Nollau, Peter

2013-03-01

Tyrosine phosphorylation plays a central role in signal transduction controlling many important biological processes. In platelets, the activity of several signaling proteins is controlled by tyrosine phosphorylation ensuring proper platelet activation and aggregation essential for regulation of the delicate balance between bleeding and hemostasis. Here, we applied Src-homology 2 region (SH2)-profiling for deciphering of the phosphotyrosine state of human platelets activated by adenosine diphosphate (ADP). Applying a panel of 31 SH2-domains, rapid and complex regulation of the phosphotyrosine state of platelets was observed after ADP stimulation. Specific inhibition of platelet P2Y receptors by synthetic drugs revealed a major role for the P2Y1 receptor in tyrosine phosphorylation. Concomitant activation of protein kinase A (PKA) abolished ADP-induced tyrosine phosphorylation in a time and concentration-dependent manner. Given the fact that PKA activity is negatively regulated by the P2Y12 receptor, our data provide evidence for a novel link of synergistic control of the state of tyrosine phosphorylation by both P2Y receptors. By SH2 domain pull down and MS/MS analysis, we identified distinct tyrosine phosphorylation sites in cell adhesion molecules, intracellular adapter proteins and phosphatases suggesting a major, functional role of tyrosine phosphorylation of theses candidate proteins in ADP-dependent signaling in human platelets. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Deciphering Periodic Methanol Masers

NASA Astrophysics Data System (ADS)

Stecklum, Bringfried; Caratti o Garatti, Alessio; Henning, Thomas; Hodapp, Klaus; Hopp, Ulrich; Kraus, Alex; Linz, Hendrik; Sanna, Alberto; Sobolev, Andrej; Wolf, Verena

2018-05-01

Impressive progress has been made in recent years on massive star formation, yet the involved high optical depths even at submm/mm wavelengths make it difficult to reveal its details. Recently, accretion bursts of massive YSOs have been identified to cause flares of Class II methanol masers (methanol masers for short) due to enhanced mid-IR pumping. This opens a new window to protostellar accretion variability, and implies that periodic methanol masers hint at cyclic accretion. Pinning down the cause of the periodicity requires joint IR and radio monitoring. We derived the first IR light curve of a periodic maser host from NEOWISE data. The source, G107.298+5.639, is an intermediate-mass YSO hosting methanol and water masers which flare every 34.5 days. Our recent joint K-band and radio observations yielded first but marginal evidence for a phase lag between the rise of IR and maser emission, respectively, and revealed that both NEOWISE and K-band light curves are strongly affected by the light echo from the ambient dust. Both the superior resolution of IRAC over NEOWISE and the longer wavelengths compared to our ground-based imaging are required to inhibit the distractive contamination by the light echo. Thus, we ask for IRAC monitoring of G107 to cover one flare cycle, in tandem with 100-m Effelsberg and 2-m Wendelstein radio and NIR observations to obtain the first high-quality synoptic measurements of this kind of sources. The IR-maser phase lag, the intrinsic shape of the IR light curves and their possible color variation during the cycle allow us to constrain models for the periodic maser excitation. Since methanol masers are signposts of intermediate-mass and massive YSOs, deciphering their variability offers a clue to the dynamics of the accretion-mediated growth of massive stars and their feedback onto the immediate natal environment. The Spitzer light curve of such a maser-hosting YSO would be a legacy science product of the mission.

Deciphering mineralogical changes and carbonation development during hydration and ageing of a consolidated ternary blended cement paste

PubMed Central

Grangeon, Sylvain; De Nolf, Wout; Harker, Nicholas; Boulahya, Faiza; Bourbon, Xavier

2018-01-01

To understand the main properties of cement, a ubiquitous material, a sound description of its chemistry and mineralogy, including its reactivity in aggressive environments and its mechanical properties, is vital. In particular, the porosity distribution and associated sample carbonation, both of which affect cement’s properties and durability, should be quantified accurately, and their kinetics and mechanisms of formation known both in detail and in situ. However, traditional methods of cement mineralogy analysis (e.g. chemical mapping) involve sample preparation (e.g. slicing) that can be destructive and/or expose cement to the atmosphere, leading to preparation artefacts (e.g. dehydration). In addition, the kinetics of mineralogical development during hydration, and associated porosity development, cannot be examined. To circumvent these issues, X-ray diffraction computed tomography (XRD-CT) has been used. This allowed the mineralogy of ternary blended cement composed of clinker, fly ash and blast furnace slag to be deciphered. Consistent with previous results obtained for both powdered samples and dilute systems, it was possible, using a consolidated cement paste (with a water-to-solid ratio akin to that used in civil engineering), to determine that the mineralogy consists of alite (only detected in the in situ hydration experiment), calcite, calcium silicate hydrates (C-S-H), ettringite, mullite, portlandite, and an amorphous fraction of unreacted slag and fly ash. Mineralogical evolution during the first hydration steps indicated fast ferrite reactivity. Insights were also gained into how the cement porosity evolves over time and into associated spatially and time-resolved carbonation mechanisms. It was observed that macroporosity developed in less than 30 h of hydration, with pore sizes reaching about 100–150 µm in width. Carbonation was not observed for this time scale, but was found to affect the first 100 µm of cement located around macropores in a sample cured for six months. Regarding this carbonation, the only mineral detected was calcite. PMID:29765604

Ants regulate colony spatial organization using multiple chemical road-signs

PubMed Central

Heyman, Yael; Shental, Noam; Brandis, Alexander; Hefetz, Abraham; Feinerman, Ofer

2017-01-01

Communication provides the basis for social life. In ant colonies, the prevalence of local, often chemically mediated, interactions introduces strong links between communication networks and the spatial distribution of ants. It is, however, unknown how ants identify and maintain nest chambers with distinct functions. Here, we combine individual tracking, chemical analysis and machine learning to decipher the chemical signatures present on multiple nest surfaces. We present evidence for several distinct chemical ‘road-signs' that guide the ants' movements within the dark nest. These chemical signatures can be used to classify nest chambers with different functional roles. Using behavioural manipulations, we demonstrate that at least three of these chemical signatures are functionally meaningful and allow ants from different task groups to identify their specific nest destinations, thus facilitating colony coordination and stabilization. The use of multiple chemicals that assist spatiotemporal guidance, segregation and pattern formation is abundant in multi-cellular organisms. Here, we provide a rare example for the use of these principles in the ant colony. PMID:28569746

A new Miocene baleen whale from Peru deciphers the dawn of cetotheriids

PubMed Central

2017-01-01

Cetotheriidae are an iconic, nearly extinct family of baleen whales (Mysticeti) with a highly distinct cranial morphology. Their origins remain a mystery, with even the most archaic species showing a variety of characteristic features. Here, we describe a new species of archaic cetotheriid, Tiucetus rosae, from the Miocene of Peru. The new material represents the first mysticete from the poorly explored lowest portion of the highly fossiliferous Pisco Formation (allomember P0), and appears to form part of a more archaic assemblage than observed at the well-known localities of Cerro Colorado, Cerro los Quesos, Sud-Sacaco and Aguada de Lomas. Tiucetus resembles basal plicogulans (crown Mysticeti excluding right whales), such as Diorocetus and Parietobalaena, but shares with cetotheriids a distinct morphology of the auditory region, including the presence of an enlarged paroccipital concavity. The distinctive morphology of Tiucetus firmly places Cetotheriidae in the context of the poorly understood ‘cetotheres’ sensu lato, and helps to resolve basal relationships within crown Mysticeti. PMID:28989761

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water.

PubMed

Frank, Alexander H; Garcia, Juan A L; Herndl, Gerhard J; Reinthaler, Thomas

2016-06-01

To decipher the influence of depth stratification and surface provincialism on the dark ocean prokaryotic community composition, we sampled the major deep-water masses in the eastern North Atlantic covering three biogeographic provinces. Their diversity was evaluated using ordination and canonical analysis of 454 pyrotag sequences. Variance partitioning suggested that 16% of the variation in the bacterial community composition was based on depth stratification while 9% of the variation was due to geographic location. General linear mixed effect models showed that the community of the subsurface waters was connected to the dark ocean prokaryotic communities in different biogeographic provinces. Cluster analysis indicated that some prokaryotic taxa are specific to distinct regions in bathypelagic water masses. Taken together, our data suggest that the dark ocean prokaryotic community composition of the eastern North Atlantic is primed by the formation and the horizontal transport of water masses. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Holokinetic centromeres and efficient telomere healing enable rapid karyotype evolution.

PubMed

Jankowska, Maja; Fuchs, Jörg; Klocke, Evelyn; Fojtová, Miloslava; Polanská, Pavla; Fajkus, Jiří; Schubert, Veit; Houben, Andreas

2015-12-01

Species with holocentric chromosomes are often characterized by a rapid karyotype evolution. In contrast to species with monocentric chromosomes where acentric fragments are lost during cell division, breakage of holocentric chromosomes creates fragments with normal centromere activity. To decipher the mechanism that allows holocentric species an accelerated karyotype evolution via chromosome breakage, we analyzed the chromosome complements of irradiated Luzula elegans plants. The resulting chromosomal fragments and rearranged chromosomes revealed holocentromere-typical CENH3 and histone H2AThr120ph signals as well as the same mitotic mobility like unfragmented chromosomes. Newly synthesized telomeres at break points become detectable 3 weeks after irradiation. The presence of active telomerase suggests a telomerase-based mechanism of chromosome healing. A successful transmission of holocentric chromosome fragments across different generations was found for most offspring of irradiated plants. Hence, a combination of holokinetic centromere activity and the fast formation of new telomeres at break points enables holocentric species a rapid karyotype evolution involving chromosome fissions and rearrangements.

Education and personalized genomics: deciphering the public's genetic health report

PubMed Central

Lamb, Neil E; Myers, Richard M; Gunter, Chris

2010-01-01

Where do members of the public turn to understand what genetic tests mean in terms of their own health? Now that genome-wide association studies and complete genome sequencing are widely available, the importance of education in personalized genomics cannot be overstated. Although some media have introduced the concept of genetic testing to better understand health and disease, the public's understanding of the scope and impact of genetic variation has not kept up with the pace of the science or technology. Unfortunately, the likely sources to which the public turn to for guidance – their physician and the media – are often no better prepared. We examine several venues for information, including print and online guides for both lay and health-oriented audiences, and summarize selected resources in multiple formats. We also note on the roadblocks to progress and discuss ways to remove them, as urgent action is needed to connect people with their genomes in a meaningful way. PMID:20161675

Deciphering Halogen Competition in Organometallic Halide Perovskite Growth

DOE PAGES

Keum, Jong Kahk; Ovchinnikova, Olga S.; Chen, Shiyou; ...

2016-03-01

Organometallic halide perovskites (OHPs) hold great promise for next-generation, low-cost optoelectronic devices. During the chemical synthesis and crystallization of OHP thin films a major unresolved question is the competition between multiple halide species (e.g. I-, Cl-, Br-) in the formation of the mixed halide perovskite crystals. Whether Cl- ions are successfully incorporated into the perovskite crystal structure or alternatively, where they are located, is not yet fully understood. Here, in situ X-ray diffraction measurements of crystallization dynamics are combined with ex situ TOF-SIMS chemical analysis to reveal that Br- or Cl- ions can promote crystal growth, yet reactive I- ionsmore » prevent them from incorporating into the lattice of the final perovskite crystal structure. The Cl- ions are located in the grain boundaries of the perovskite films. These findings significantly advance our understanding of the role of halogens during synthesis of hybrid perovskites, and provide an insightful guidance to the engineering of high-quality perovskite films, essential for exploring superior-performance and cost-effective optoelectronic devices.« less

Hardening mechanisms in olivine single crystal deformed at 1090 °C: an electron tomography study

NASA Astrophysics Data System (ADS)

Mussi, Alexandre; Cordier, Patrick; Demouchy, Sylvie; Hue, Benoit

2017-11-01

The dislocation microstructures in a single crystal of olivine deformed experimentally in uniaxial compression at 1090 °C and under a confining pressure of 300 MPa, have been investigated by transmission electron tomography in order to better understand deformation mechanisms at the microscale relevant for lithospheric mantle deformations. Investigation by electron tomography reveals microstructures, which are more complex than previously described, composed of ? and ? dislocations commonly exhibiting 3D configurations. Numerous mechanisms such as climb, cross-slip, double cross-slip as well as interactions like junction formations and collinear annihilations are the source of this complexity. The diversity observed advocates for microscale deformation of olivine significantly less simple than classic dislocation creep reported in metals or ice close to melting temperature. Deciphering mechanism of hardening in olivine at temperatures where ionic diffusion is slow and is then expected to play very little role is crucial to better understand and thus model deformation at larger scale and at temperatures (900-1100 °C) highly relevant for the lithospheric mantle.

Deciphering Halogen Competition in Organometallic Halide Perovskite Growth

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

Keum, Jong Kahk; Ovchinnikova, Olga S.; Chen, Shiyou

Organometallic halide perovskites (OHPs) hold great promise for next-generation, low-cost optoelectronic devices. During the chemical synthesis and crystallization of OHP thin films a major unresolved question is the competition between multiple halide species (e.g. I-, Cl-, Br-) in the formation of the mixed halide perovskite crystals. Whether Cl- ions are successfully incorporated into the perovskite crystal structure or alternatively, where they are located, is not yet fully understood. Here, in situ X-ray diffraction measurements of crystallization dynamics are combined with ex situ TOF-SIMS chemical analysis to reveal that Br- or Cl- ions can promote crystal growth, yet reactive I- ionsmore » prevent them from incorporating into the lattice of the final perovskite crystal structure. The Cl- ions are located in the grain boundaries of the perovskite films. These findings significantly advance our understanding of the role of halogens during synthesis of hybrid perovskites, and provide an insightful guidance to the engineering of high-quality perovskite films, essential for exploring superior-performance and cost-effective optoelectronic devices.« less

Ants regulate colony spatial organization using multiple chemical road-signs.

PubMed

Heyman, Yael; Shental, Noam; Brandis, Alexander; Hefetz, Abraham; Feinerman, Ofer

2017-06-01

Communication provides the basis for social life. In ant colonies, the prevalence of local, often chemically mediated, interactions introduces strong links between communication networks and the spatial distribution of ants. It is, however, unknown how ants identify and maintain nest chambers with distinct functions. Here, we combine individual tracking, chemical analysis and machine learning to decipher the chemical signatures present on multiple nest surfaces. We present evidence for several distinct chemical 'road-signs' that guide the ants' movements within the dark nest. These chemical signatures can be used to classify nest chambers with different functional roles. Using behavioural manipulations, we demonstrate that at least three of these chemical signatures are functionally meaningful and allow ants from different task groups to identify their specific nest destinations, thus facilitating colony coordination and stabilization. The use of multiple chemicals that assist spatiotemporal guidance, segregation and pattern formation is abundant in multi-cellular organisms. Here, we provide a rare example for the use of these principles in the ant colony.

The journey of integrins and partners in a complex interactions landscape studied by super-resolution microscopy and single protein tracking

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

Rossier, Olivier; Giannone, Grégory; CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000 Bordeaux

Cells adjust their adhesive and cytoskeletal organizations according to changes in the biochemical and physical nature of their surroundings. In return, by adhering and generating forces on the extracellular matrix (ECM) cells organize their microenvironment. Integrin-dependent focal adhesions (FAs) are the converging zones integrating biochemical and biomechanical signals arising from the ECM and the actin cytoskeleton. Thus, integrin-mediated adhesion and mechanotransduction, the conversion of mechanical forces into biochemical signals, are involved in critical cellular functions such as migration, proliferation and differentiation, and their deregulation contributes to pathologies including cancer. A challenging problem is to decipher how stochastic protein movements andmore » interactions lead to formation of dynamic architecture such as integrin-dependent adhesive structures. In this review, we will describe recent advances made possible by super-resolution microscopies and single molecule tracking approaches that provided new understanding on the organization and the dynamics of integrins and intracellular regulators at the nanoscale in living cells.« less

A new Miocene baleen whale from Peru deciphers the dawn of cetotheriids

NASA Astrophysics Data System (ADS)

Marx, Felix G.; Lambert, Olivier; de Muizon, Christian

2017-09-01

Cetotheriidae are an iconic, nearly extinct family of baleen whales (Mysticeti) with a highly distinct cranial morphology. Their origins remain a mystery, with even the most archaic species showing a variety of characteristic features. Here, we describe a new species of archaic cetotheriid, Tiucetus rosae, from the Miocene of Peru. The new material represents the first mysticete from the poorly explored lowest portion of the highly fossiliferous Pisco Formation (allomember P0), and appears to form part of a more archaic assemblage than observed at the well-known localities of Cerro Colorado, Cerro los Quesos, Sud-Sacaco and Aguada de Lomas. Tiucetus resembles basal plicogulans (crown Mysticeti excluding right whales), such as Diorocetus and Parietobalaena, but shares with cetotheriids a distinct morphology of the auditory region, including the presence of an enlarged paroccipital concavity. The distinctive morphology of Tiucetus firmly places Cetotheriidae in the context of the poorly understood `cetotheres' sensu lato, and helps to resolve basal relationships within crown Mysticeti.

An insight into the exploration of druggable genome of Streptococcus gordonii for the identification of novel therapeutic candidates.

PubMed

Azam, Syed Sikander; Shamim, Amen

2014-09-01

The discovery of novel drug targets of a genome that can bind with high affinity to drug-like compounds is a significant challenge in drug development. Streptococcus gordonii initiates dental plaque formation and endocarditis by entering into the blood stream, usually after oral trauma. The prolonged use of antibiotics is raising a problem of multi-drug resistance and lack of an optimal therapeutic regime that necessitates the drug discovery of vital importance in curing various infections. To overcome this dilemma, the in silico approach paves the way for identification and qualitative characterization of promising drug targets for S. gordonii that encompass three phases of analyses. The present study deciphers drug target genomes of S. gordonii in which 93 proteins were identified as potential drug targets and 16 proteins were found to be involved in unique metabolic pathways. Highlighted information will convincingly render to facilitate selection of S. gordonii proteins for successful entry into drug design pipelines. Copyright © 2014 Elsevier Inc. All rights reserved.

The journey of integrins and partners in a complex interactions landscape studied by super-resolution microscopy and single protein tracking.

PubMed

Rossier, Olivier; Giannone, Grégory

2016-04-10

Cells adjust their adhesive and cytoskeletal organizations according to changes in the biochemical and physical nature of their surroundings. In return, by adhering and generating forces on the extracellular matrix (ECM) cells organize their microenvironment. Integrin-dependent focal adhesions (FAs) are the converging zones integrating biochemical and biomechanical signals arising from the ECM and the actin cytoskeleton. Thus, integrin-mediated adhesion and mechanotransduction, the conversion of mechanical forces into biochemical signals, are involved in critical cellular functions such as migration, proliferation and differentiation, and their deregulation contributes to pathologies including cancer. A challenging problem is to decipher how stochastic protein movements and interactions lead to formation of dynamic architecture such as integrin-dependent adhesive structures. In this review, we will describe recent advances made possible by super-resolution microscopies and single molecule tracking approaches that provided new understanding on the organization and the dynamics of integrins and intracellular regulators at the nanoscale in living cells. Copyright © 2015. Published by Elsevier Inc.

reCAPTCHA: human-based character recognition via Web security measures.

PubMed

von Ahn, Luis; Maurer, Benjamin; McMillen, Colin; Abraham, David; Blum, Manuel

2008-09-12

CAPTCHAs (Completely Automated Public Turing test to tell Computers and Humans Apart) are widespread security measures on the World Wide Web that prevent automated programs from abusing online services. They do so by asking humans to perform a task that computers cannot yet perform, such as deciphering distorted characters. Our research explored whether such human effort can be channeled into a useful purpose: helping to digitize old printed material by asking users to decipher scanned words from books that computerized optical character recognition failed to recognize. We showed that this method can transcribe text with a word accuracy exceeding 99%, matching the guarantee of professional human transcribers. Our apparatus is deployed in more than 40,000 Web sites and has transcribed over 440 million words.

From crustal thinning to mantle exhumation: what the Pyrenean breccia formations tell us.

NASA Astrophysics Data System (ADS)

Clerc, C.; Chauvet, A.; Lagabrielle, Y.; Reynaud, J.-Y.; Boulvais, P.; Bousquet, R.; Lahfid, A.; Vauchez, A.; Mahé, S.

2012-04-01

Several formations with various breccia types occur in Mesozoic basins disseminated along the North Pyrenean fault, on the northern flank of the French Pyrenees. Due to their location along the Iberia-Europa plate boundary, the North Pyrenean breccia formations represent complex archives documenting the tectonic and sedimentary evolution of the Pyrenean realm during the Aptian-Albian period. In particular, the North Pyrenean breccia formations have recorded the main stages of crustal thinning, continental break-up and mantle exhumation, which occurred along the North Pyrenean Zone (NPZ). We will review the main sedimentary, structural, metamorphic and geochemical characters of these breccias, based on new field investigations conducted in both the Western and Eastern Pyrenées (Agly, Aulus, Moncaup-St Béas and Urdach localities). Based on our new founding, we re-intrepret the significance of the breccia formations in the light of the most recent models developed for the pre-orogenic evolution of the Pyrenees. In several places and mostly close to the contact between Paleozoic basement and Mesozoic cover, we systematically recognized the following three types of breccias: i) Semi-ductile syn-metamorphic breccias resulting from the boudinage of silicic or dolomitic beddings in ductily deformed marbles. ii) Cataclastic breccias disturbing the neighbouring host rocks and displaying a relatively monogenetic character. These tectonic breccias result from the disruption of the Mesozoic metamorphic platform under cooling conditions. They are dominated by cataclastic levels mainly located in the Triassic and Liassic weaker levels, iii) Polymictic sedimentary breccias, which composition is dominated by clasts of Mesozoic metasediments. Locally, close to subcontinental mantle bodies, the sedimentary breccias include numerous clasts of ultramafic and/or crustal basement rocks. Such breccias are the witness of the disruption of the sedimentary cover of the North Pyrenean Zone massifs followed by clastic sedimentation in a context of hyper-extended crust and mantle exhumation. Improving the knowledge of the formation of the different types of breccia exposed all along the Northern Pyrenees brings important hints to decipher the tectonic history responsible for the formation of the metamorphic basins and the exhumation (and reworking) of deep crustal and mantle rocks in the NPZ.

The dental identification of victims of an aircraft accident in Malaysia.

PubMed

Nambiar, P; Jalil, N; Singh, B

1997-02-01

On 15 September 1995 a Malaysian Airlines (MAS) Fokker 50 plane plunged while descending and crashed, killing thirty-four passengers aboard. The dental disaster victim identification team comprising dental surgeons from the Dental faculty, University of Malaya; Ministry of Health, Sabah; and the Malaysian Defence Forces played an active role in the identification process. Most of the bodies were badly mutilated, disfigured and severely incinerated. Problems were encountered due to inadequate facilities and space at the mortuary. Difficulties were also encountered during the procurement and deciphering of information from dental records. This disaster has however created greater awareness amongst Malaysians of the important role of forensic odontology in mass disasters.

Deciphering the role of interleukin-22 in metabolic alterations.

PubMed

Sabat, Robert; Wolk, Kerstin

2015-01-01

Inflammatory processes and metabolic alterations are supposed to substantially interact. Recently, cumulating reports describe a profound role of interleukin(IL)-22 in this relationship. IL-22 is a particular kind of immune mediator that is produced by certain lymphocyte populations and regulates the function of several tissue cells but not immune cells. So far, IL-22 was known to plays a fundamental role in the elimination of bacterial infections at border surfaces of the body and to protect tissues from damage. This research highlight article arranges the facts regarding the effects of IL-22 in the context of adiposity and metabolic alterations and postulates a new function of the immune system.

Perspective: Materials informatics and big data: Realization of the "fourth paradigm" of science in materials science

NASA Astrophysics Data System (ADS)

Agrawal, Ankit; Choudhary, Alok

2016-05-01

Our ability to collect "big data" has greatly surpassed our capability to analyze it, underscoring the emergence of the fourth paradigm of science, which is data-driven discovery. The need for data informatics is also emphasized by the Materials Genome Initiative (MGI), further boosting the emerging field of materials informatics. In this article, we look at how data-driven techniques are playing a big role in deciphering processing-structure-property-performance relationships in materials, with illustrative examples of both forward models (property prediction) and inverse models (materials discovery). Such analytics can significantly reduce time-to-insight and accelerate cost-effective materials discovery, which is the goal of MGI.

The Language of the Protein Universe

PubMed Central

Scaiewicz, Andrea; Levitt, Michael

2015-01-01

Proteins, the main cell machinery which play a major roll in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the “Rosetta Stone” of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins. PMID:26451980

Landform Erosion and Volatile Redistribution on Ganymede and Callisto

NASA Technical Reports Server (NTRS)

Moore, Jeffrey Morgan; Howard, Alan D.; McKinnon, William B.; Schenk, Paul M.; Wood, Stephen E.

2009-01-01

We have been modeling landscape evolution on the Galilean satellites driven by volatile transport. Our work directly addresses some of the most fundamental issues pertinent to deciphering icy Galilean satellite geologic histories by employing techniques currently at the forefront of terrestrial, martian, and icy satellite landscape evolution studies [e.g., 1-6], including modeling of surface and subsurface energy and volatile exchanges, and computer simulation of long-term landform evolution by a variety of processes. A quantitative understanding of the expression and rates of landform erosion, and of volatile redistribution on landforms, is especially essential in interpreting endogenic landforms that have, in many cases, been significantly modified by erosion [e.g., 7-9].

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning.

PubMed

Teng, Haotian; Cao, Minh Duc; Hall, Michael B; Duarte, Tania; Wang, Sheng; Coin, Lachlan J M

2018-05-01

Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.

Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase.

PubMed

Wang, Wen-Juan; Wei, Wen-Jie; Liao, Rong-Zhen

2018-06-13

The reaction mechanism and chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase (2,4-QueD) have been investigated using the QM/MM approach. The protonation state of the Glu74 residue, a first-shell ligand of Ni, has been considered to be either neutral or deprotonated. QM/MM calculations predict that Glu74 must be deprotonated to rationalize the chemoselectivity and steer the 2,4-dioxygenolytic cleavage of quercetin, which harvests the experimentally-observed product, 2-protocatechuoylphloroglucinol carboxylic acid, coupled with the release of carbon monoxide. If the enzyme has a neutral Glu74 residue, the undesired 2,3-dioxygenolytic cleavage of quercetin becomes the dominant pathway, leading to the formation of α-keto acid. The calculations suggest that the reaction takes place via three major steps: (1) attack of the superoxide on the C2 of the substrate pyrone ring to generate a NiII-peroxide intermediate; (2) formation of the second C-O bond between C4 and the peroxide to produce a peroxide bridge; (3) simultaneous cleavage of the C2-C3, C3-C4, and O1-O2 bonds with the formation of 2-protocatechuoylphloroglucinol carboxylic acid and carbon monoxide. The third step was found to be rate-limiting, with a barrier of 17.4 kcal mol-1, which is in very good agreement with the experimental kinetic data. For the second C-O bond formation, an alternative pathway is that the peroxide attacks the C3 of the substrate pyrone ring, leading to the formation of a four-membered ring intermediate, which then undergoes concerted C2-C3 and O1-O2 bond cleavages to produce an α-keto acid. This pathway is associated with a barrier of 30.6 kcal mol-1, which is much higher than the major pathway. When Glu74 is protonated, the 2,3-dioxygenolytic pathway, however, has a lower barrier (21.8 kcal mol-1) than the 2,4-dioxygenolytic pathway.

Deciphering Epithelial–Mesenchymal Transition Regulatory Networks in Cancer through Computational Approaches

PubMed Central

Burger, Gerhard A.; Danen, Erik H. J.; Beltman, Joost B.

2017-01-01

Epithelial–mesenchymal transition (EMT), the process by which epithelial cells can convert into motile mesenchymal cells, plays an important role in development and wound healing but is also involved in cancer progression. It is increasingly recognized that EMT is a dynamic process involving multiple intermediate or “hybrid” phenotypes rather than an “all-or-none” process. However, the role of EMT in various cancer hallmarks, including metastasis, is debated. Given the complexity of EMT regulation, computational modeling has proven to be an invaluable tool for cancer research, i.e., to resolve apparent conflicts in experimental data and to guide experiments by generating testable hypotheses. In this review, we provide an overview of computational modeling efforts that have been applied to regulation of EMT in the context of cancer progression and its associated tumor characteristics. Moreover, we identify possibilities to bridge different modeling approaches and point out outstanding questions in which computational modeling can contribute to advance our understanding of pathological EMT. PMID:28824874

Leishmania parasites: could we consider them as living organisms per se?

PubMed

Milon, Geneviève

2008-07-01

Over the last 10 years - in Microbes and Infection - the publications dealing with protozoan parasites were mainly providing insights on the pathogenic processes leading to the local or systemic damages in the mammals, these parasitic organisms exploit/subvert as hosts. As a result, many investigators introduced the objectives of their analysis by referring to "host-pathogen" interactions. Though we, as investigators, are all determined to decipher the pathogenic processes which can indeed be coupled to the parasite uncontrolled development, I think that the parasites - alike the living organisms they subvert as hosts - need to be considered as living organisms per se, instead of being considered as "pathogens". Such a conceptual frame will promote research on the processes on which relies their perpetuation whatever the level under investigations - individual and/or population level. Only the unicellular protozoan parasites of the genus Leishmania known to be hosted by blood-feeding insects and mammals will be further considered in this brief contribution.

The Hubble Deep UV Legacy Survey (HDUV): Survey Overview and First Results

NASA Astrophysics Data System (ADS)

Oesch, Pascal; Montes, Mireia; HDUV Survey Team

2015-08-01

Deep HST imaging has shown that the overall star formation density and UV light density at z>3 is dominated by faint, blue galaxies. Remarkably, very little is known about the equivalent galaxy population at lower redshifts. Understanding how these galaxies evolve across the epoch of peak cosmic star-formation is key to a complete picture of galaxy evolution. Here, we present a new HST WFC3/UVIS program, the Hubble Deep UV (HDUV) legacy survey. The HDUV is a 132 orbit program to obtain deep imaging in two filters (F275W and F336W) over the two CANDELS Deep fields. We will cover ~100 arcmin2, reaching down to 27.5-28.0 mag at 5 sigma. By directly sampling the rest-frame far-UV at z>~0.5, this will provide a unique legacy dataset with exquisite HST multi-wavelength imaging as well as ancillary HST grism NIR spectroscopy for a detailed study of faint, star-forming galaxies at z~0.5-2. The HDUV will enable a wealth of research by the community, which includes tracing the evolution of the FUV luminosity function over the peak of the star formation rate density from z~3 down to z~0.5, measuring the physical properties of sub-L* galaxies, and characterizing resolved stellar populations to decipher the build-up of the Hubble sequence from sub-galactic clumps. This poster provides an overview of the HDUV survey and presents the reduced data products and catalogs which will be released to the community.

Identification and paleoclimatic significance of magnetite nanoparticles in soils

NASA Astrophysics Data System (ADS)

Ahmed, Imad A. M.; Maher, Barbara A.

2018-02-01

In the world-famous sediments of the Chinese Loess Plateau, fossil soils alternate with windblown dust layers to record monsoonal variations over the last ˜3 My. The less-weathered, weakly magnetic dust layers reflect drier, colder glaciations. The fossil soils (paleosols) contain variable concentrations of nanoscale, strongly magnetic iron oxides, formed in situ during the wetter, warmer interglaciations. Mineralogical identification of the magnetic soil oxides is essential for deciphering these key paleoclimatic records. Formation of magnetite, a mixed Fe2+/Fe3+ ferrimagnet, has been linked to soil redox oscillations, and thence to paleorainfall. An opposite hypothesis states that magnetite can only form if the soil is water saturated for significant periods in order for Fe3+ to be reduced to Fe2+, and suggests instead the temperature-dependent formation of maghemite, an Fe3+-oxide, much of which ages subsequently into hematite, typically aluminum substituted. This latter, oxidizing pathway would have been temperature, but not rainfall dependent. Here, through structural fingerprinting and scanning transmission electron microscopy and electron energy loss spectroscopy analysis, we prove that magnetite is the dominant soil-formed ferrite. Maghemite is present in lower concentrations, and shows no evidence of aluminum substitution, negating its proposed precursor role for the aluminum-substituted hematite prevalent in the paleosols. Magnetite dominance demonstrates that magnetite formation occurs in well-drained, generally oxidizing soils, and that soil wetting/drying oscillations drive the degree of soil magnetic enhancement. The magnetic variations of the Chinese Loess Plateau paleosols thus record changes in monsoonal rainfall, over timescales of millions of years.

The Interactions between the Long Non-coding RNA NERDL and Its Target Gene Affect Wood Formation in Populus tomentosa

PubMed Central

Shi, Wan; Quan, Mingyang; Du, Qingzhang; Zhang, Deqiang

2017-01-01

Long non-coding RNAs (lncRNAs) are important regulatory factors for plant growth and development, but little is known about the allelic interactions of lncRNAs with mRNA in perennial plants. Here, we analyzed the interaction of the NERD (Needed for RDR2-independent DNA methylation) Populus tomentosa gene PtoNERD with its putative regulator, the lncRNA NERDL (NERD-related lncRNA), which partially overlaps with the promoter region of this gene. Expression analysis in eight tissues showed a positive correlation between NERDL and PtoNERD (r = 0.62), suggesting that the interaction of NERDL with its putative target might be involved in wood formation. We conducted association mapping in a natural population of P. tomentosa (435 unrelated individuals) to evaluate genetic variation and the interaction of the lncRNA NERDL with PtoNERD. Using additive and dominant models, we identified 30 SNPs (P < 0.01) associated with five tree growth and wood property traits. Each SNP explained 3.90–8.57% of phenotypic variance, suggesting that NERDL and its putative target play a common role in wood formation. Epistasis analysis uncovered nine SNP-SNP association pairs between NERDL and PtoNERD, with an information gain of -7.55 to 2.16%, reflecting the strong interactions between NERDL and its putative target. This analysis provides a powerful method for deciphering the genetic interactions of lncRNAs with mRNA and dissecting the complex genetic network of quantitative traits in trees. PMID:28674544

Modified Vaccinia Virus Ankara-Infected Dendritic Cells Present CD4+ T-Cell Epitopes by Endogenous Major Histocompatibility Complex Class II Presentation Pathways

PubMed Central

Thiele, Frank; Tao, Sha; Zhang, Yi; Muschaweckh, Andreas; Zollmann, Tina; Protzer, Ulrike; Abele, Rubert

2014-01-01

ABSTRACT CD4+ T lymphocytes play a central role in the immune system and mediate their function after recognition of their respective antigens presented on major histocompatibility complex II (MHCII) molecules on antigen-presenting cells (APCs). Conventionally, phagocytosed antigens are loaded on MHCII for stimulation of CD4+ T cells. Certain epitopes, however, can be processed directly from intracellular antigens and are presented on MHCII (endogenous MHCII presentation). Here we characterized the MHCII antigen presentation pathways that are possibly involved in the immune response upon vaccination with modified vaccinia virus Ankara (MVA), a promising live viral vaccine vector. We established CD4+ T-cell lines specific for MVA-derived epitopes as tools for in vitro analysis of MHCII antigen processing and presentation in MVA-infected APCs. We provide evidence that infected APCs are able to directly transfer endogenous viral proteins into the MHCII pathway to efficiently activate CD4+ T cells. By using knockout mice and chemical inhibitory compounds, we further elucidated the molecular basis, showing that among the various subcellular pathways investigated, proteasomes and autophagy are key players in the endogenous MHCII presentation during MVA infection. Interestingly, although proteasomal processing plays an important role, neither TAP nor LAMP-2 was found to be involved in the peptide transport. Defining the molecular mechanism of MHCII presentation during MVA infection provides a basis for improving MVA-based vaccination strategies by aiming for enhanced CD4+ T-cell activation by directing antigens into the responsible pathways. IMPORTANCE This work contributes significantly to our understanding of the immunogenic properties of pathogens by deciphering antigen processing pathways contributing to efficient activation of antigen-specific CD4+ T cells. We identified autophagosome formation, proteasomal activity, and lysosomal integrity as being crucial for endogenous CD4+ T-cell activation. Since poxvirus vectors such as MVA are already used in clinical trials as recombinant vaccines, the data provide important information for the future design of optimized poxviral vaccines for the study of advanced immunotherapy options. PMID:25520512

Role of calcium permeable channels in dendritic cell migration.

PubMed

Sáez, Pablo J; Sáez, Juan C; Lennon-Duménil, Ana-María; Vargas, Pablo

2018-06-01

Calcium ion (Ca 2+ ) is an essential second messenger involved in multiple cellular and subcellular processes. Ca 2+ can be released and sensed globally or locally within cells, providing complex signals of variable amplitudes and time-scales. The key function of Ca 2+ in the regulation of acto-myosin contractility has provided a simple explanation for its role in the regulation of immune cell migration. However, many questions remain, including the identity of the Ca 2+ stores, channels and upstream signals involved in this process. Here, we focus on dendritic cells (DCs), because their immune sentinel function heavily relies on their capacity to migrate within tissues and later on between tissues and lymphoid organs. Deciphering the mechanisms by which cytoplasmic Ca 2+ regulate DC migration should shed light on their role in initiating and tuning immune responses. Copyright © 2018 Elsevier Ltd. All rights reserved.

Multiple functions of BCL-2 family proteins.

PubMed

Hardwick, J Marie; Soane, Lucian

2013-02-01

BCL-2 family proteins are the regulators of apoptosis, but also have other functions. This family of interacting partners includes inhibitors and inducers of cell death. Together they regulate and mediate the process by which mitochondria contribute to cell death known as the intrinsic apoptosis pathway. This pathway is required for normal embryonic development and for preventing cancer. However, before apoptosis is induced, BCL-2 proteins have critical roles in normal cell physiology related to neuronal activity, autophagy, calcium handling, mitochondrial dynamics and energetics, and other processes of normal healthy cells. The relative importance of these physiological functions compared to their apoptosis functions in overall organismal physiology is difficult to decipher. Apoptotic and noncanonical functions of these proteins may be intertwined to link cell growth to cell death. Disentanglement of these functions may require delineation of biochemical activities inherent to the characteristic three-dimensional shape shared by distantly related viral and cellular BCL-2 family members.

Insights into the mechanisms and the emergence of sex-differences in pain.

PubMed

Melchior, Meggane; Poisbeau, Pierrick; Gaumond, Isabelle; Marchand, Serge

2016-12-03

Recent studies describe sex and gender as critical factors conditioning the experience of pain and the strategies to respond to it. It is now clear that men and women have different physiological and behavioral responses to pain. Some pathological pain states are also highly sex-specific. This clinical observation has been often verified with animal studies which helped to decipher the mechanisms underlying the observed female hyper-reactivity and hyper-sensitivity to pain states. The role of gonadal hormones in the modulation of pain responses has been a straightforward hypothesis but, if pertinent in many cases, cannot fully account for this complex sensation, which includes an important cognitive component. Clinical and fundamental data are reviewed here with a special emphasis on possible developmental processes giving rise to sex-differences in pain processing. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

The changing nature of the Brucella-containing vacuole.

PubMed

Celli, Jean

2015-07-01

Bacteria of the genus Brucella are intracellular vacuolar pathogens of mammals that cause the worldwide zoonosis brucellosis, and reside within phagocytes of infected hosts to promote their survival, persistence and proliferation. These traits are essential to the bacterium's ability to cause disease and have been the subject of much investigation to gain an understanding of Brucella pathogenic mechanisms. Although the endoplasmic reticulum-derived nature of the Brucella replicative niche has been long known, major strides have recently been made in deciphering the molecular mechanisms of its biogenesis, including the identification of bacterial determinants and host cellular pathways involved in this process. Here I will review and discuss the most recent advances in our knowledge of Brucella intracellular pathogenesis, with an emphasis on bacterial exploitation of the host endoplasmic reticulum-associated functions, and how autophagy-related processes contribute to the bacterium's intracellular cycle. © 2015 John Wiley & Sons Ltd.

Neural mechanisms of movement planning: motor cortex and beyond.

PubMed

Svoboda, Karel; Li, Nuo

2018-04-01

Neurons in motor cortex and connected brain regions fire in anticipation of specific movements, long before movement occurs. This neural activity reflects internal processes by which the brain plans and executes volitional movements. The study of motor planning offers an opportunity to understand how the structure and dynamics of neural circuits support persistent internal states and how these states influence behavior. Recent advances in large-scale neural recordings are beginning to decipher the relationship of the dynamics of populations of neurons during motor planning and movements. New behavioral tasks in rodents, together with quantified perturbations, link dynamics in specific nodes of neural circuits to behavior. These studies reveal a neural network distributed across multiple brain regions that collectively supports motor planning. We review recent advances and highlight areas where further work is needed to achieve a deeper understanding of the mechanisms underlying motor planning and related cognitive processes. Copyright © 2017. Published by Elsevier Ltd.

Using face validity to recognize empirical community observations.

PubMed

Gaber, John; Gaber, Sharon L

2010-05-01

There is a growing interest among international planning scholars to explore community participation in the plan making process from a qualitative research approach. In this paper the research assessment tool "face validity" is discussed as one way to help planners decipher when the community is sharing empirically grounded observations that can advance the applicability of the plan making process. Face validity provides a common sense assessment of research conclusions. It allows the assessor to look at an entire research project and ask: "on the face of things, does this research make sense?" With planners listening to citizen comments with an ear for face validity observations, holds open the opportunity for government to empirically learn from the community to see if they "got it right." And if not, to chart out a course on how they can get it right. Copyright 2009 Elsevier Ltd. All rights reserved.

Deciphering the sugar biosynthetic pathway and tailoring steps of nucleoside antibiotic A201A unveils a GDP-l-galactose mutase

PubMed Central

Zhu, Qinghua; Chen, Qi; Song, Yongxiang; Huang, Hongbo; Li, Jun; Ma, Junying; Li, Qinglian; Ju, Jianhua

2017-01-01

Galactose, a monosaccharide capable of assuming two possible configurational isomers (d-/l-), can exist as a six-membered ring, galactopyranose (Galp), or as a five-membered ring, galactofuranose (Galf). UDP-galactopyranose mutase (UGM) mediates the conversion of pyranose to furanose thereby providing a precursor for d-Galf. Moreover, UGM is critical to the virulence of numerous eukaryotic and prokaryotic human pathogens and thus represents an excellent antimicrobial drug target. However, the biosynthetic mechanism and relevant enzymes that drive l-Galf production have not yet been characterized. Herein we report that efforts to decipher the sugar biosynthetic pathway and tailoring steps en route to nucleoside antibiotic A201A led to the discovery of a GDP-l-galactose mutase, MtdL. Systematic inactivation of 18 of the 33 biosynthetic genes in the A201A cluster and elucidation of 10 congeners, coupled with feeding and in vitro biochemical experiments, enabled us to: (i) decipher the unique enzyme, GDP-l-galactose mutase associated with production of two unique d-mannose-derived sugars, and (ii) assign two glycosyltransferases, four methyltransferases, and one desaturase that regiospecifically tailor the A201A scaffold and display relaxed substrate specificities. Taken together, these data provide important insight into the origin of l-Galf-containing natural product biosynthetic pathways with likely ramifications in other organisms and possible antimicrobial drug targeting strategies. PMID:28438999

Provenance and tectonic setting of the Neoproterozoic clastic rocks hosting the Banana Zone Cu-Ag mineralisation, northwest Botswana

NASA Astrophysics Data System (ADS)

Kelepile, Tebogo; Bineli Betsi, Thierry; Franchi, Fulvio; Shemang, Elisha; Suh, Cheo Emmanuel

2017-05-01

Petrographic and geochemical data were combined in order to decipher the petrogenesis of the Neoproterozoic sedimentary succession associated with the Banana Zone Cu-Ag mineralisation (northwest Botswana), in the Kalahari Copperbelt. The investigated Neoproterozoic sedimentary succession is composed of two formations including the Ngwako Pan and the D'kar Formations. The Ngwako Pan Formation is made up of continental siliciclastic sediments, mainly sandstones interbedded with siltstones and mudstones, whereas the D'kar Formation is comprised of shallow marine laminated siltstones, sandstones and mudstones, with subordinate limestone. Copper-Ag mineralisation is essentially confined at the base of the D'kar Formation, which bears reduced organic components, likely to have controlled Cu-Ag precipitation. Sandstones of both the Ngwako Pan and the D'kar Formations are arkoses and subarkoses, composed of quartz (Q), feldspars (F) and lithic fragments (L). Moreover, geochemically the sandstones are considered as potassic and classified as arkoses. On the other hand, mudrocks of the D'kar Formation are finely laminated and are dominated by muscovite, sericite, chlorite and quartz. The modified chemical index of weathering (CIW‧) values indicated an intense chemical weathering of the source rock. The dominance of detrital quartz and feldspar grains coupled with Al2O3/TiO2 ratios (average 29.67 and 24.52 for Ngwako Pan and D'kar Formations, respectively) and Ni and Cr depletion in the sandstones, suggest a dominant felsic source. However, high concentrations of Ni and Cr and a low Al2O3/TiO2 ratio (<20) in the mudrocks of the D'kar Formation indicate a mixed source. Provenance of the investigated sandstones and mudrocks samples is further supported by the REE patterns, the size of Eu anomaly as well as La/Co, Th/Co, Th/Cr and Cr/Th ratios, which show a felsic source for the sandstones of both the Ngwako Pan and D'kar Formations and an intermediate source for the mudrocks of the D'kar Formation. Detrital modes (QFL diagrams) and geochemical characteristics of the sandstones of both the Ngwako Pan and D'kar Formations indicate that the detritus were probably supplied from a heavily weathered felsic continental block and deposited in a continental rift setting (passive margin) in a humid environment. The source rocks might have been the Palaeoproterozoic basement rocks (granitoids and granitic gneiss) and the Mesoproterozoic Kgwebe volcanic rocks exposed north of the study area.

Chemical and U-Sr isotopic variations of stream and source waters at a small catchment scale (the Strengbach case; Vosges mountains; France)

NASA Astrophysics Data System (ADS)

Pierret, M. C.; Stille, P.; Prunier, J.; Viville, D.; Chabaux, F.

2014-03-01

This is the first comprehensive study dealing with major and trace element data as well as 87Sr/86Sr isotope and (234U/238U) activity ratios (AR) determined on the totality of springs and brooks of the Strengbach catchment. It shows that the small and more or less monolithic catchment drains different sources and streamlets with very different isotopic and geochemical signatures. Different parameters control the diversity of the source characteristics. Of importance is especially the hydrothermal overprint of the granitic bedrock, which was stronger for the granite from the northern than from the southern slope; also significant are the different meteoric alteration processes of the bedrock causing the formation of 0.5 to 9 m thick saprolite and above the formation of an up to 1 m thick soil system. These processes mainly account for springs and brooks from the northern slope having higher Ca/Na, Mg/Na, Sr/Na ratios but lower 87Sr/86Sr isotopic ratios than those from the southern slope. The chemical compositions of the source waters in the Strengbach catchment are only to a small extent the result of alteration of primary bedrock minerals and rather reflect dissolution/precipitation processes of secondary mineral phases like clay minerals. The (234U/238U) AR, however, are decoupled from the 87Sr/86Sr isotope system and reflect to some extent the level of altitude of the source and, thus, the degree of alteration of the bedrock. The sources emerging at high altitudes have circulated through already weathered materials (saprolite and fractured rock depleted in 234U) implying (234U/238U) AR < 1, which is uncommon for surface waters. Preferential flow paths along constant fractures in the bedrocks might explain the over time homogeneous U AR of the different spring waters. However, the geochemical and isotopic variations of stream waters at the outlet of the catchment are controlled by variable contributions of different springs depending on the hydrological conditions. It appears that the (234U/238U) AR is an appropriate very important tracer for studying and deciphering the contribution of the different source fluxes at the catchment scale because this unique geochemical parameter is different for each individual spring and at the same time remains unchanged for each of the springs with changing discharge and fluctuating hydrological conditions. This study further highlights the important impact of different and independent water pathways in fractured granite controlling the different geochemical and isotopic signatures of the waters.

Understanding triggers and dynamics of wood-laden flash floods in mountain catchments: examples from the Zulg River (Switzerland)

NASA Astrophysics Data System (ADS)

Ruiz-Villanueva, Virginia; Galatiotto, Niccolo; Bürkli, Livia; Stoffel, Markus

2017-04-01

Mountain rivers are prone to flash floods, and in forested basins, large quantities of wood can be moved and transported long distances downstream during such events. Under certain circumstances, congested transport of wood may result in wood-laden flows in which a large number of logs form a mass moving together with the flow and thus alter its dynamics. This process could significantly increase the flood hazard and risk, however, the knowledge about the formation of these wood-laden flows is still very limited. The Zulg River (23 km long and 89 km2 drainage area) is located in the Swiss Prealps in the canton of Bern (Switzerland). In the Zulg catchment, heavy local precipitation usually leads to a fast reaction of the water level downstream and very often flash floods are transporting significant volume of wood. There are several bridges crossing the river at the area of Steffisburg and downstream of this town the Zulg flows into the Aare River that crosses the city of Bern few kilometres downstream. Therefore, a better understanding of these processes will help to improve the flood risk management of the region. In this work we are analysing four recent floods (i.e., 2012, 2013, 2015 and 2016) with significant wood transport and the goal is to decipher the triggering and formation of the wood-laden flash floods. We collected aerial pictures from before and after each flood to map the pre- and post-flood conditions and mapped riverscape units, landslides and the wood logs and jams already deposited along the river channel. The forest stand volumes recruited during the events is analysed based on the land use maps available and provided by the Cantonal Forest Service. We also analysed movies taken by witnesses during these flash flood events, which may potentially provide highly valuable information (i.e., the amount and type of wood in motion or what was roughly the velocity and direction of the water) to quantify wood fluxes. However, the usage of these home movies is challenging and we are applying different techniques to extract as much information as possible from these kind of videos. Results will shed light into the dynamics of the wood-laden flows estimating wood fluxes and volumes in the Zulg River, but they will also contribute to better understand these processes in mountain rivers in general. This study is performed within the scope of the Research Project WoodFlow founded by the Swiss Federal Office for the Environment (FOEN).

A coupled model between mechanical deformation and chemical diffusion: An explanation for the preservation of chemical zonation in plagioclase at high temperatures

NASA Astrophysics Data System (ADS)

Zhong, Xin; Vrijmoed, Johannes; Moulas, Evangelos; Tajcmanová, Lucie

2016-04-01

Compositional zoning in metamorphic minerals have been generally recognized as an important geological feature to decipher the metamorphic history of rocks. The observed chemical zoning of, e.g. garnet, is commonly interpreted as disequilibrium between the fractionated inner core and the surrounding matrix. However, chemically zoned minerals were also observed in high grade rocks (T>800 degree C) where the duration of metamorphic processes was independently dated to take several Ma. This implies that temperature may not be the only factor that controls diffusion timescales, and grain scale pressure variation was proposed to be a complementary factor that may significantly contribute to the formation and preservation of chemical zoning in high temperature metamorphic minerals [Tajcmanová 2013, 2015]. Here, a coupled model is developed to simulate viscous deformation and chemical diffusion. The numerical approach considers the conservation of mass, momentum, and a constitutive relation developed from equilibrium thermodynamics. A compressible viscoelastic rheology is applied, which associates the volumetric change triggered by deformation and diffusion to a change of pressure. The numerical model is applied to the chemically zoned plagioclase rim described by [Tajcmanová 2014]. The diffusion process operating during the plagioclase rim formation can lead to a development of a pressure gradient. Such a pressure gradient, if maintained during ongoing viscous relaxation, can lead to the preservation of the observed chemical zonation in minerals. An important dimensionless number, the Deborah number, is defined as the ratio between the Maxwell viscoelastic relaxation time and the characteristic diffusion time. It characterizes the relative influence between the maintenance of grain scale pressure variation and chemical diffusion. Two extreme regimes are shown: the mechanically-controlled regime (high Deborah number) and diffusion-controlled regime (low Deborah number). In the mechanically-controlled regime, the grain scale pressure variation and thus the chemical zonation can be maintained due to slow viscous relaxation. Furthermore, by utilizing experimental flow laws and diffusion coefficients, the Deborah number is estimated in a variety of physical conditions. References Tajcmanová, L., Y. Podladchikov, R. Powell, E. Moulas, J.C. Vrijmoed, and J.A.D. Connolly, 2014. Journal of Metamorphic Geology, 32(2):195-207. Tajcmanová, L., J.C. Vrijmoed, and E. Moulas, 2015. Lithos, 216-217:338-351.

Mapping Ionic Currents and Reactivity on the Nanoscale: Electrochemical Strain Microscopy

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

Kalinin, S.V.

2010-10-19

Solid-state electrochemical processes in oxides underpin a broad spectrum of energy and information storage devices, ranging from Li-ion and Li-air batteries, to solid oxide fuel cells (SOFC) to electroresistive and memristive systems. These functionalities are controlled by the bias-driven diffusive and electromigration transport of mobile ionic species, as well as intricate a set of electrochemical and defect-controlled reactions at interfaces and in bulk. Despite the wealth of device-level and atomistic studies, little is known on the mesoscopic mechanisms of ion diffusion and electronic transport on the level of grain clusters, individual grains, and extended defects. The development of the capabilitymore » for probing ion transport on the nanometer scale is a key to deciphering complex interplay between structure, functionality, and performance in these systems. Here we introduce Electrochemical Strain Microscopy, a scanning probe microscopy technique based on strong strain-bias coupling in the systems in which local ion concentrations are changed by electrical fields. The imaging capability, as well as time- and voltage spectroscopies analogous to traditional current based electrochemical characterization methods are developed. The reversible intercalation of Li and mapping electrochemical activity in LiCoO2 is demonstrated, illustrating higher Li diffusivity at non-basal planes and grain boundaries. In Si-anode device structure, the direct mapping of Li diffusion at extended defects and evolution of Li-activity with charge state is explored. The electrical field-dependence of Li mobility is studied to determine the critical bias required for the onset of electrochemical transformation, allowing reaction and diffusion processes in the battery system to be separated at each location. Finally, the applicability of ESM for probing oxygen vacancy diffusion and oxygen reduction/evolution reactions is illustrated, and the high resolution ESM maps are correlated with aberration corrected scanning transmission electron microscopy imaging. The future potential for deciphering mechanisms of electrochemical transformations on an atomically-defined single-defect level is discussed.« less

Salty Six

MedlinePlus

... Simple Cooking and Recipes Dining Out Choosing a Restaurant Deciphering the Menu Ordering Your Meal Eating Fast ... A sandwich or burger from a fast food restaurant can contain more than 100 percent of you ...

Langevin Dynamics Deciphers the Motility Pattern of Swimming Parasites

NASA Astrophysics Data System (ADS)

Zaburdaev, Vasily; Uppaluri, Sravanti; Pfohl, Thomas; Engstler, Markus; Friedrich, Rudolf; Stark, Holger

2011-05-01

The parasite African trypanosome swims in the bloodstream of mammals and causes the highly dangerous human sleeping sickness. Cell motility is essential for the parasite’s survival within the mammalian host. We present an analysis of the random-walk pattern of a swimming trypanosome. From experimental time-autocorrelation functions for the direction of motion we identify two relaxation times that differ by an order of magnitude. They originate from the rapid deformations of the cell body and a slower rotational diffusion of the average swimming direction. Velocity fluctuations are athermal and increase for faster cells whose trajectories are also straighter. We demonstrate that such a complex dynamics is captured by two decoupled Langevin equations that decipher the complex trajectory pattern by referring it to the microscopic details of cell behavior.

Stereoselectivity in Polyphenol Biosynthesis

NASA Technical Reports Server (NTRS)

Lewis, Norman G.; Davin, Laurence B.

1992-01-01

Stereoselectivity plays an important role in the late stages of phenyl-propanoid metabolism, affording lignins, lignans, and neolignans. Stereoselectivity is manifested during monolignol (glucoside) synthesis, e.g., where the geometry (E or Z) of the pendant double bond affects the specificity of UDPG:coniferyl alcohol glucosyltransferases in different species. Such findings are viewed to have important ramifications in monolignol transport and storage processes, with roles for both E- and Z-monolignols and their glucosides in lignin/lignan biosynthesis being envisaged. Stereoselectivity is also of great importance in enantiose-lective enzymatic processes affording optically active lignans. Thus, cell-free extracts from Forsythia species were demonstrated to synthesize the enantiomerically pure lignans, (-)-secoisolariciresinol, and (-)-pinoresinol, when NAD(P)H, H2O2 and E-coniferyl alcohol were added. Progress toward elucidating the enzymatic steps involved in such highly stereoselective processes is discussed. Also described are preliminary studies aimed at developing methodologies to determine the subcellular location of late-stage phenylpropanoid metabolites (e.g., coniferyl alcohol) and key enzymes thereof, in intact tissue or cells. This knowledge is essential if questions regarding lignin and lignan tissue specificity and regulation of these processes are to be deciphered.

Exploring the diversity of Listeria monocytogenes biofilm architecture by high-throughput confocal laser scanning microscopy and the predominance of the honeycomb-like morphotype.

PubMed

Guilbaud, Morgan; Piveteau, Pascal; Desvaux, Mickaël; Brisse, Sylvain; Briandet, Romain

2015-03-01

Listeria monocytogenes is involved in food-borne illness with a high mortality rate. The persistence of the pathogen along the food chain can be associated with its ability to form biofilms on inert surfaces. While most of the phenotypes associated with biofilms are related to their spatial organization, most published data comparing biofilm formation by L. monocytogenes isolates are based on the quantitative crystal violet assay, which does not give access to structural information. Using a high-throughput confocal-imaging approach, the aim of this work was to decipher the structural diversity of biofilms formed by 96 L. monocytogenes strains isolated from various environments. Prior to large-scale analysis, an experimental design was created to improve L. monocytogenes biofilm formation in microscopic-grade microplates, with special emphasis on the growth medium composition. Microscopic analysis of biofilms formed under the selected conditions by the 96 isolates revealed only weak correlation between the genetic lineages of the isolates and the structural properties of the biofilms. However, a gradient in their geometric descriptors (biovolume, mean thickness, and roughness), ranging from flat multilayers to complex honeycomb-like structures, was shown. The dominant honeycomb-like morphotype was characterized by hollow voids hosting free-swimming cells and localized pockets containing mixtures of dead cells and extracellular DNA (eDNA). Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Analysis of the [RNQ+] Prion Reveals Stability of Amyloid Fibers as the Key Determinant of Yeast Prion Variant Propagation*

PubMed Central

Kalastavadi, Tejas; True, Heather L.

2010-01-01

Variation in pathology of human prion disease is believed to be caused, in part, by distinct conformations of aggregated protein resulting in different prion strains. Several prions also exist in yeast and maintain different self-propagating structures, referred to as prion variants. Investigation of the yeast prion [PSI+] has been instrumental in deciphering properties of prion variants and modeling the physical basis of their formation. Here, we describe the generation of specific variants of the [RNQ+] prion in yeast transformed with fibers formed in vitro in different conditions. The fibers of the Rnq1p prion-forming domain (PFD) that induce different variants in vivo have distinct biochemical properties. The physical basis of propagation of prion variants has been previously correlated to rates of aggregation and disaggregation. With [RNQ+] prion variants, we found that the prion variant does not correlate with the rate of aggregation as anticipated but does correlate with stability. Interestingly, we found that there are differences in the ability of the [RNQ+] prion variants to faithfully propagate themselves and to template the aggregation of other proteins. Incorporating the mechanism of variant formation elucidated in this study with that previously proposed for [PSI+] variants has provided a framework to separate general characteristics of prion variant properties from those specific to individual prion proteins. PMID:20442412

Synchrotron x-ray microdiffraction reveals intrinsic structural features of amyloid deposits in situ.

PubMed

Briki, Fatma; Vérine, Jérôme; Doucet, Jean; Bénas, Philippe; Fayard, Barbara; Delpech, Marc; Grateau, Gilles; Riès-Kautt, Madeleine

2011-07-20

Amyloidoses are increasingly recognized as a major public health concern in Western countries. All amyloidoses share common morphological, structural, and tinctorial properties. These consist of staining by specific dyes, a fibrillar aspect in electron microscopy and a typical cross-β folding in x-ray diffraction patterns. Most studies that aim at deciphering the amyloid structure rely on fibers generated in vitro or extracted from tissues using protocols that may modify their intrinsic structure. Therefore, the fine details of the in situ architecture of the deposits remain unknown. Here, we present to our knowledge the first data obtained on ex vivo human renal tissue sections using x-ray microdiffraction. The typical cross-β features from fixed paraffin-embedded samples are similar to those formed in vitro or extracted from tissues. Moreover, the fiber orientation maps obtained across glomerular sections reveal an intrinsic texture that is correlated with the glomerulus morphology. These results are of the highest importance to understanding the formation of amyloid deposits and are thus expected to trigger new incentives for tissue investigation. Moreover, the access to intrinsic structural parameters such as fiber size and orientation using synchrotron x-ray microdiffraction, could provide valuable information concerning in situ mechanisms and deposit formation with potential benefits for diagnostic and therapeutic purposes. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

Lu, S; Chourey, Karuna; REICHE, M

Metaproteomics combined with total nucleic acid-based methods aided in deciphering the roles of microorganisms in the formation and transformation of iron-rich macroscopic aggregates (iron snow) formed in the redoxcline of an acidic lignite mine lake. Iron snow had high total bacterial 16S rRNA gene copies, with 2 x 109 copies g (dry wt)-1 in the acidic (pH 3.5) central lake basin and 4 x 1010 copies g (dry wt)-1 in the less acidic (pH 5.5) northern lake basin. Active microbial communities in the central basin were dominated by Alphaproteobacteria (36.6%) and Actinobacteria (21.4%), and by Betaproteobacteria (36.2%) in the northernmore » basin. Microbial Fe-cycling appeared to be the dominant metabolism in the schwertmannite-rich iron snow, because cloning and qPCR assigned up to 61% of active bacteria as Fe-cycling bacteria (FeB). Metaproteomics revealed 70 unique proteins from central basin iron snow and 283 unique proteins from 43 genera from northern basin. Protein identification provided a glimpse into in situ processes, such as primary production, motility, metabolism of acidophilic FeB, and survival strategies of neutrophilic FeB. Expression of carboxysome shell proteins and RubisCO indicated active CO2 fixation by Fe(II) oxidizers. Flagellar proteins from heterotrophs indicated their activity to reach and attach surfaces. Gas vesicle proteins related to CO2-fixing Chlorobium suggested that microbes could influence iron snow sinking. We suggest that iron snow formed by autotrophs in the redoxcline acts as a microbial parachute, since it is colonized by motile heterotrophs during sinking which start to dissolve schwertmannite.« less

A causal framework for integrating contemporary and Vedic holism.

PubMed

Kineman, John J

2017-12-01

Whereas the last Century of science was characterized by epistemological uncertainty; the current Century will likely be characterized by ontological complexity (Gorban and Yablonsky, 2013). Advances in Systems Theory by mathematical biologist Robert Rosen suggest an elegant way forward (Rosen, 2013). "R-theory" (Kineman, 2012) is a synthesis of Rosen's theories explaining complexity and life in terms of a meta-model for 'whole' systems (and their fractions) in terms of "5 th -order holons". Such holons are Rosen "modeling relations" relating system-dependent processes with their formative contexts via closed cycles of four archetypal (Aristotelian) causes. This approach has post-predicted the three most basic taxa of life, plus a quasi-organismic form that may describe proto, component, and ecosystemic life. R-theory thus suggests a fundamentally complex ontology of existence inverting the current view that complexity arises from simple mechanisms. This model of cyclical causality corresponds to the ancient meta-model described in the Vedas and Upanishads of India. Part I of this discussion (Kineman, 2016a) presented a case for associating Vedic philosophy with Harappan civilization, allowing interpretation of ancient concepts of "cosmic order" (Rta) in the Rig Veda, nonduality (advaita), seven-fold beingness (saptanna) and other forms of holism appearing later in the Upanishads. By deciphering the model of wholeness that was applied and tested in ancient times, it is possible to compare, test, and confirm the holon model as a mathematical definition of life, systemic wholeness, and sustainability that may be applied today in modern terms, even as a foundation for holistic science. Copyright © 2017 Elsevier Ltd. All rights reserved.

Determination of the Prebomb Southern (Antartic) Ocean Radiocarbon in Organic Matter

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

Guilderson, T P

2001-02-26

The Southern Hemisphere is an important and unique region of the world's oceans for water-mass formation and mixing, upwelling, nutrient utilization, and carbon export. In fact, one of the primary interests of the oceanographic community is to decipher the climatic record of these processes in the source or sink terms for Southern Ocean surface waters in the CO{sub 2} balance of the atmosphere. Current coupled ocean-atmosphere modeling efforts to trace the input of CO{sub 2} into the ocean imply a strong sink of anthropogenic CO{sub 2} in the southern ocean. However, because of its relative inaccessibility and the difficulty inmore » directly measuring CO{sub 2} fluxes in the Southern Ocean, these results are controversial at best. An accepted diagnostic of the exchange of CO{sub 2} between the atmosphere and ocean is the prebomb distribution of radiocarbon in the ocean and its time-history since atmospheric nuclear testing. Such histories of {sup 14}C in the surface waters of the Southern Ocean do not currently exist, primarily because there are few continuous biological archives (e.g., in corals) such as those that have been used to monitor the {sup 14}C history of the tropics and subtropics. One of the possible long-term archives is the scallop Adamussium collbecki. Although not independently confirmed, relatively crude growth rate estimates of A. collbecki indicate that it has the potential to provide continuous 100 year time-series. We are exploring the suitability of this potential archive.« less

Disassembly and reassembly of amyloid fibrils in water-ethanol mixtures.

PubMed

Jordens, Sophia; Adamcik, Jozef; Amar-Yuli, Idit; Mezzenga, Raffaele

2011-01-10

This work presents the structural analysis of amyloid-like β-lactoglobulin fibrils incubated in ethanol-water mixtures after their formation in water. We observe for the first time the disassembly of semiflexible heat-denatured β-lactoglobulin fibrils and reassembly into highly flexible wormlike fibrils in ethanol-water solutions. Tapping mode atomic force microscopy is performed to follow structural changes. Our results show that in addition to their growth in length, there is a continuous nucleation process of new wormlike objects with time at the expense of the original β-lactoglobulin fibrils. The persistence length of wormlike fibrils (29.43 nm in the presence of 50% ethanol), indicative of their degree of flexibility, differs by 2 orders of magnitude from that of untreated β-lactoglobulin fibrils (2368.75 nm in pure water). Interestingly, wormlike fibrils do not exhibit a multiple strands nature like the pristine fibrils, as revealed by the lower maximum height and the lack of clear height periodicity along their contour length profile. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) demonstrates that the set of polypeptides obtained by ethanol degradation differs in some fractions from that present in pristine β-lactoglobulin fibrils. ATR-FTIR (attenuated total reflectance-Fourier transform infrared) spectroscopy also supports a different composition of the secondary structure of wormlike fibrils with a decreased amount of α-helix and increased random coils and turns content. These findings can contribute to deciphering the molecular mechanisms of protein aggregation into amyloid fibrils and their disassembly as well as enabling tailor-made production of protein fibrils.

Deciphering fluid sources of hydrothermal systems: A combined Sr- and S-isotope study on barite (Schwarzwald, SW Germany)

USGS Publications Warehouse

Staude, S.; Gob, S.; Pfaff, K.; Strobele, F.; Premo, W.R.; Markl, G.

2011-01-01

Primary and secondary barites from hydrothermal mineralizations in SW Germany were investigated, for the first time, by a combination of strontium (Sr) isotope systematics (87Sr/86Sr), Sr contents and δ34S values to distinguish fluid sources and precipitation mechanisms responsible for their formation. Barite of Permian age derived its Sr solely from crystalline basement rocks, whereas all younger barite also incorporate Sr from formation waters of the overlying sediments. In fact, most of the Sr in younger barite is leached from Lower and Middle Triassic sediments. In contrast, most of the sulfur (S) of Permian, Jurassic and northern Schwarzwald Miocene barite originated from basement rocks. The S source of Upper Rhinegraben (URG)-related Paleogene barite differs depending on geographic position: for veins of the southern URG, it is the Oligocene evaporitic sequence, while central URG mineralizations derived its S from Middle Triassic evaporites. Using Sr isotopes of barite of known age combined with estimates on the Sr contents and Sr isotopic ratios of the fluids' source rocks, we were able to quantify mixing ratios of basement-derived fluids and sedimentary formation waters for the first time. These calculations show that Jurassic barite formed by mixing of 75–95% ascending basement-derived fluids with 5–25% sedimentary formation water, but that only 20–55% of the Sr was brought by the basement-derived fluid to the depositional site. Miocene barite formed by mixing of an ascending basement-derived brine (60–70%) with 30–40% sedimentary formation waters. In this case, only 8–15% of the Sr was derived from the deep brine. This fluid-mixing calculation is an example for deposits in which the fluid source is known. This method applied to a greater number of deposits formed at different times and in various geological settings may shed light on more general causes of fluid movement in the Earth's crust and on the formation of hydrothermal ore deposits.

Coupling effect analysis between landslides, river channel changes and sediment budgets - extreme climate events in Laishe River, southern Taiwan

NASA Astrophysics Data System (ADS)

Chang, Kuo-Jen; Huang, Mei-Jen; Tseng, Chih-Ming

2016-04-01

Taiwan, due to the high seismicity and high annual rainfall, numerous landslides triggered every year and severe impacts affect the island. Concerning to the catastrophic landslides, the key information of landslide, including range of landslide, volume estimation and the subsequent evolution are important when analyzing the triggering mechanism, hazard assessment and mitigation. Thus, the morphological analysis gives a general overview for the landslides and been considered as one of the most fundamental information. Typhoon Morakot brought extreme and long-time rainfall for Taiwan in August 2009, and caused severe disasters. In this study we integrate several technologies, especially by Unmanned Aerial Vehicle (UAV) and multi-spectral camera, to decipher the consequence and the potential hazard, and the social impact. In recent years, the remote sensing technology improves rapidly, providing a wide range of image, essential and precise information. This study integrates several methods, including, 1) Remote-sensing images gathered by Unmanned Aerial Vehicle (UAV) and by aerial photos taken in different periods; 2) field in-situ geologic investigation; 3) Differential GPS, RTK GPS geomatic measurements. The methods allow to constructing the DTMs before and after landslide, as well as the subsequent periods by using aerial photos and UAV derived images. The data sets permits to analysis the morphological changes. In the past, the study of sediment budgets usually relies on field investigation, but due to inconvenient transportation, topographical barriers, or located in remote areas, etc. the survey is hardly to be completed sometimes. In recent years, the rapid development of remote sensing technology improves image resolution and quality significantly. Remote sensing technology can provide a wide range of image data, and provide essential and precious information. The purpose of this study is to investigate the phenomenon of river migration and to evaluate the amount of migration along Laishe River by analyzing the 3D DEM before and after the typhoon Morakot. The DEMs are built by using the aerial images taken by digital mapping camera (DMC) and by airborne digital scanner 40 (ADS40) before and after typhoon event. Recently, this research integrates Unmanned Aerial Vehicle (UAV) and oblique photogrammetric technologies for image acquisition by 5-10cm GSD photos. This approach permits to construct true 3D model so as to decipher ground information more realistically. 10-20cm DSM and DEM, and field GPS, were compiled together to decipher the morphologic changes. All the information, especially by means of true 3D model, the datasets provides detail ground information that may use to evaluate the landslide triggering mechanism and river channel evolution. The goals of this study is to integrates the UAS system and to decipher the sliding process and morphologic changes of large landslide areas, sediment transport and budgets, and to investigate the phenomenon of river migration. The results of this study provides not only geomatics and GIS dataset of the hazards, but also for essential geomorphologic information for other study, and for hazard mitigation and planning, as well.

Micro-Paleontology

ERIC Educational Resources Information Center

Lipps, Jere H.

1978-01-01

In the past year micropaleontology has added new understandings of early protistan history as well as contributed to the deciphering of the history of the world's oceans. Studies of formaminifer a have been especially important. (MA)

Psychiatry's Catch 22, Need For Precision, And Placing Schools In Perspective

PubMed Central

Singh, Ajai R.

2013-01-01

The catch 22 situation in psychiatry is that for precise diagnostic categories/criteria, we need precise investigative tests, and for precise investigative tests, we need precise diagnostic criteria/categories; and precision in both diagnostics and investigative tests is nonexistent at present. The effort to establish clarity often results in a fresh maze of evidence. In finding the way forward, it is tempting to abandon the scientific method, but that is not possible, since we deal with real human psychopathology, not just concepts to speculate over. Search for clear-cut definitions/diagnostic criteria in psychiatry must be relentless. There is a greater need to be ruthless and blunt in this, rather than being accommodative of diverse opinions. Investigative tests – psychological, serum, CSF, or neuroimaging - are only corroborative at present; they need to become definitive. Medicalisation appears most prominent in psychiatry; so, diagnostic proliferation and fuzziness appear inevitable. And yet, the established diagnostic entities need to forward greater and conclusive precision. Also, the need for clarity and precision must outweigh pandering to and mollifying diverse interests, moreso in the upcoming revision of diagnostic manuals. This is specially because the DSM-5, being an Association manual, may need to accommodate powerful member lobbies; and ICD-11 may similarly need to cater to diverse country lobbies. Finding precise biological correlates of psychiatric phenomena, whether through neuroimaging, molecular neurobiology and/or neurogenomics, is the right way forward. It is in the 1.5-kg structure in the cranium that all secrets of psychiatric conditions lie. Social forces, behavioural modification, psychosocial restructuring, study of intrapsychic processes, and philosophical insights are not to be discounted, but they are supplementary to the primary goal – studying and deciphering those brain processes that result in psychiatric malfunction. Experimental breakthroughs, both in psychiatric aetiology and therapeutics, will come mainly from biology and its adjunct, psychopharmacology; while supplementary and complementary breakthroughs will come from the psychosocial, cognitive and behavioural approaches; the support base will come from phenomenology, epidemiology, nosology and diagnostics; while insights and leads can hopefully come from many fields, especially the psychosocial, the behavioural, the cognitive and the philosophical. Major energies must now be marshalled towards finding biomarkers and deciphering the precise phenotype–genotype–endophenotype axis of psychiatric disorders. Energies also need to be focussed on unravelling those critical processes in the brain that tip the scale towards psychiatric disorders. At how those critical processes are set into motion by forces de novo, in utero, in the genes and their expression, by the environment's psychopathological social forces – stress, peer pressure, poverty, deprivation, alienation, malnutrition, discrimination of various types (caste, gender, race, etc.), mass conflicts (war, terror attacks, etc.), disasters (natural and man-made), religious/ideological fascism – or social institutions like marriage, family, work place, political governance, etc. Ultimately, we must decipher how the brain goes into malfunction when such varied forces impinge on it, which precise cortical areas and neuronal cellular and molecular processes are involved in such malfunction and its manifestation, as also which of these are involved when malfunction ceases and health is restored, and the psychosocial processes and institutions which aid such health restoration, as also those which promote well-being and help in primary prevention. Emphasis on the brain and its intimate neurological and molecular mechanisms will not impinge on, or nullify, importance of the ‘mind,’ wherein subtle and gross brain functions in the form of behaviour, thought and emotions in all their ramifications will continue to be the focus of psychological, cognitive, sociological, psychopharmacological, behavioural and philosophical research. Progress in brain research must move in tandem with progress in ‘mind’ research. PMID:23678237

Psychiatry's Catch 22, Need For Precision, And Placing Schools In Perspective.

PubMed

Singh, Ajai R

2013-01-01

The catch 22 situation in psychiatry is that for precise diagnostic categories/criteria, we need precise investigative tests, and for precise investigative tests, we need precise diagnostic criteria/categories; and precision in both diagnostics and investigative tests is nonexistent at present. The effort to establish clarity often results in a fresh maze of evidence. In finding the way forward, it is tempting to abandon the scientific method, but that is not possible, since we deal with real human psychopathology, not just concepts to speculate over. Search for clear-cut definitions/diagnostic criteria in psychiatry must be relentless. There is a greater need to be ruthless and blunt in this, rather than being accommodative of diverse opinions. Investigative tests - psychological, serum, CSF, or neuroimaging - are only corroborative at present; they need to become definitive. Medicalisation appears most prominent in psychiatry; so, diagnostic proliferation and fuzziness appear inevitable. And yet, the established diagnostic entities need to forward greater and conclusive precision. Also, the need for clarity and precision must outweigh pandering to and mollifying diverse interests, moreso in the upcoming revision of diagnostic manuals. This is specially because the DSM-5, being an Association manual, may need to accommodate powerful member lobbies; and ICD-11 may similarly need to cater to diverse country lobbies. Finding precise biological correlates of psychiatric phenomena, whether through neuroimaging, molecular neurobiology and/or neurogenomics, is the right way forward. It is in the 1.5-kg structure in the cranium that all secrets of psychiatric conditions lie. Social forces, behavioural modification, psychosocial restructuring, study of intrapsychic processes, and philosophical insights are not to be discounted, but they are supplementary to the primary goal - studying and deciphering those brain processes that result in psychiatric malfunction. Experimental breakthroughs, both in psychiatric aetiology and therapeutics, will come mainly from biology and its adjunct, psychopharmacology; while supplementary and complementary breakthroughs will come from the psychosocial, cognitive and behavioural approaches; the support base will come from phenomenology, epidemiology, nosology and diagnostics; while insights and leads can hopefully come from many fields, especially the psychosocial, the behavioural, the cognitive and the philosophical. Major energies must now be marshalled towards finding biomarkers and deciphering the precise phenotype-genotype-endophenotype axis of psychiatric disorders. Energies also need to be focussed on unravelling those critical processes in the brain that tip the scale towards psychiatric disorders. At how those critical processes are set into motion by forces de novo, in utero, in the genes and their expression, by the environment's psychopathological social forces - stress, peer pressure, poverty, deprivation, alienation, malnutrition, discrimination of various types (caste, gender, race, etc.), mass conflicts (war, terror attacks, etc.), disasters (natural and man-made), religious/ideological fascism - or social institutions like marriage, family, work place, political governance, etc. Ultimately, we must decipher how the brain goes into malfunction when such varied forces impinge on it, which precise cortical areas and neuronal cellular and molecular processes are involved in such malfunction and its manifestation, as also which of these are involved when malfunction ceases and health is restored, and the psychosocial processes and institutions which aid such health restoration, as also those which promote well-being and help in primary prevention. Emphasis on the brain and its intimate neurological and molecular mechanisms will not impinge on, or nullify, importance of the 'mind,' wherein subtle and gross brain functions in the form of behaviour, thought and emotions in all their ramifications will continue to be the focus of psychological, cognitive, sociological, psychopharmacological, behavioural and philosophical research. Progress in brain research must move in tandem with progress in 'mind' research.

The language of the protein universe.

PubMed

Scaiewicz, Andrea; Levitt, Michael

2015-12-01

Proteins, the main cell machinery which play a major role in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the 'Rosetta Stone' of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genetic and genomic glimpses of the elusive arbuscular mycorrhizal fungi.

PubMed

Lanfranco, Luisa; Young, J Peter W

2012-08-01

Arbuscular mycorrhizal fungi (AMF), which form an ancient and widespread mutualistic symbiosis with plants, are a crucial but still enigmatic component of the plant microbiome. Nowadays, their obligate biotrophy is no longer an obstacle to deciphering the role played by AMF in this fascinating symbiosis. The first genome-wide transcriptomic analysis of an AMF showed a metabolic complexity with no sign of massive gene loss, and the presence of genes for meiotic recombination suggests that AMF are not simple clonal organisms, as originally thought. New findings on suppression of host defenses and nutrient exchange processes have shed light on the mechanisms that contribute to such an intimate and long-lasting integration between living plant and fungal cells. Copyright © 2012 Elsevier Ltd. All rights reserved.

Systems biology of seeds: deciphering the molecular mechanisms of seed storage, dormancy and onset of germination.

PubMed

Sreenivasulu, Nese

2017-05-01

Seeds are heterogeneous storage reserves with wide array of storage compounds that include various soluble carbohydrates, starch polymer, storage proteins and lipids. These stored reserves comprise 70% of the world's caloric intake in the form of food and animal feed produced through sustainable agriculture, which contributes to food and nutritional security. Seed systems biology remains an enigmatic subject in understanding seed storage processes, maturation and pre-germinative metabolism. The reviews and research articles covered in this special issue of Plant Cell Reports highlight recent advances made in the area of seed biology that cover various systems biology applications such as gene regulatory networks, metabolomics, epigenetics and the role of micro-RNA in seed development.

Deciphering Neural Codes of Memory during Sleep

PubMed Central

Chen, Zhe; Wilson, Matthew A.

2017-01-01

Memories of experiences are stored in the cerebral cortex. Sleep is critical for consolidating hippocampal memory of wake experiences into the neocortex. Understanding representations of neural codes of hippocampal-neocortical networks during sleep would reveal important circuit mechanisms on memory consolidation, and provide novel insights into memory and dreams. Although sleep-associated ensemble spike activity has been investigated, identifying the content of memory in sleep remains challenging. Here, we revisit important experimental findings on sleep-associated memory (i.e., neural activity patterns in sleep that reflect memory processing) and review computational approaches for analyzing sleep-associated neural codes (SANC). We focus on two analysis paradigms for sleep-associated memory, and propose a new unsupervised learning framework (“memory first, meaning later”) for unbiased assessment of SANC. PMID:28390699

Rivers of the Andes and the Amazon Basin: Deciphering global change from the hydroclimatic variability in the critical zone

NASA Astrophysics Data System (ADS)

Moreira-Turcq, Patricia; Carlo Espinoza, Jhan; Filizola, Naziano; Martinez, Jean-Michel

2018-01-01

The Critical Zone has been defined as the thin layer of the continental surfaces extending from fresh bedrock and the bottom of groundwater up to vegetation canopy, where soil, rock, water, air, and living organisms interact (Banwart et al., 2012; Lin et al., 2011). Despite the Critical Zone's importance to terrestrial life, it remains poorly understood. In this context, understanding the complex interactions between physical, chemical, and biological processes of the Critical Zone requires long-term observations (Anderson et al., 2012; Brantley et al., 2017), not only because different mechanisms have varying time frames, but also because it is necessary to monitor its natural and anthropogenic evolution in response to global climate and environmental changes.

Light-Toned Layering in a Labyrinthus Noctis Pit

NASA Image and Video Library

2017-01-03

Understanding both the spatial and temporal distribution of hydrated (water-bearing) minerals on Mars is essential for deciphering the aqueous history of the planet. Over 300 meters of layered beds are exposed in this trough of Noctis Labyrinthus, at the western edge of Valles Marineris. The beds are mixtures of light- and dark-toned materials, and include units that contain hydrated minerals, like sulfates and clays. Mapping these minerals and their stratigraphic relationships indicates numerous hydrologic and/or depositional events in localized environments spread over time. The diversity of materials within the trough implies active hydrologic processes and/or changing chemical conditions, perhaps due to influxes of groundwater from nearby Tharsis volcanism. http://photojournal.jpl.nasa.gov/catalog/PIA14455

Overview of Drosophila immunity: a historical perspective.

PubMed

Imler, Jean-Luc

2014-01-01

The functional analysis of genes from the model organism Drosophila melanogaster has provided invaluable information for many cellular and developmental or physiological processes, including immunity. The best-understood aspect of Drosophila immunity is the inducible humoral response, first recognized in 1972. This pioneering work led to a remarkable series of findings over the next 30 years, ranging from the identification and characterization of the antimicrobial peptides produced, to the deciphering of the signalling pathways activating the genes that encode them and, ultimately, to the discovery of the receptors sensing infection. These studies on an insect model coincided with a revival of the field of innate immunity, and had an unanticipated impact on the biomedical field. Copyright © 2013 Elsevier Ltd. All rights reserved.

Portion Size Versus Serving Size

MedlinePlus

... Simple Cooking and Recipes Dining Out Choosing a Restaurant Deciphering the Menu Ordering Your Meal Eating Fast ... don’t know what a healthy portion is. Restaurants offer extras like breads, chips and other appetizers ...

Frequency Domain Analysis of Sensor Data for Event Classification in Real-Time Robot Assisted Deburring

PubMed Central

Pappachan, Bobby K; Caesarendra, Wahyu; Tjahjowidodo, Tegoeh; Wijaya, Tomi

2017-01-01

Process monitoring using indirect methods relies on the usage of sensors. Using sensors to acquire vital process related information also presents itself with the problem of big data management and analysis. Due to uncertainty in the frequency of events occurring, a higher sampling rate is often used in real-time monitoring applications to increase the chances of capturing and understanding all possible events related to the process. Advanced signal processing methods are used to further decipher meaningful information from the acquired data. In this research work, power spectrum density (PSD) of sensor data acquired at sampling rates between 40–51.2 kHz was calculated and the corelation between PSD and completed number of cycles/passes is presented. Here, the progress in number of cycles/passes is the event this research work intends to classify and the algorithm used to compute PSD is Welch’s estimate method. A comparison between Welch’s estimate method and statistical methods is also discussed. A clear co-relation was observed using Welch’s estimate to classify the number of cycles/passes. The paper also succeeds in classifying vibration signal generated by the spindle from the vibration signal acquired during finishing process. PMID:28556809

Genetics Home Reference: periventricular heterotopia

MedlinePlus

... Metcalfe KA, Isidor B, Louvier UW, Poduri A, Taylor JC, Tilly P, Poirier K, Saillour Y, Lebrun N, Stemmelen T, Rudolf G, Muraca G, Saintpierre B, Elmorjani A; Deciphering Developmental Disorders study, Moïse M, ...

Public Key Cryptography.

ERIC Educational Resources Information Center

Tapson, Frank

1996-01-01

Describes public key cryptography, also known as RSA, which is a system using two keys, one used to put a message into cipher and another used to decipher the message. Presents examples using small prime numbers. (MKR)

Information security system based on virtual-optics imaging methodology and public key infrastructure

NASA Astrophysics Data System (ADS)

Peng, Xiang; Zhang, Peng; Cai, Lilong

In this paper, we present a virtual-optical based information security system model with the aid of public-key-infrastructure (PKI) techniques. The proposed model employs a hybrid architecture in which our previously published encryption algorithm based on virtual-optics imaging methodology (VOIM) can be used to encipher and decipher data while an asymmetric algorithm, for example RSA, is applied for enciphering and deciphering the session key(s). For an asymmetric system, given an encryption key, it is computationally infeasible to determine the decryption key and vice versa. The whole information security model is run under the framework of PKI, which is on basis of public-key cryptography and digital signatures. This PKI-based VOIM security approach has additional features like confidentiality, authentication, and integrity for the purpose of data encryption under the environment of network.

Deciphering the sugar biosynthetic pathway and tailoring steps of nucleoside antibiotic A201A unveils a GDP-l-galactose mutase.

PubMed

Zhu, Qinghua; Chen, Qi; Song, Yongxiang; Huang, Hongbo; Li, Jun; Ma, Junying; Li, Qinglian; Ju, Jianhua

2017-05-09

Galactose, a monosaccharide capable of assuming two possible configurational isomers (d-/l-), can exist as a six-membered ring, galactopyranose (Gal p ), or as a five-membered ring, galactofuranose (Gal f ). UDP-galactopyranose mutase (UGM) mediates the conversion of pyranose to furanose thereby providing a precursor for d-Gal f Moreover, UGM is critical to the virulence of numerous eukaryotic and prokaryotic human pathogens and thus represents an excellent antimicrobial drug target. However, the biosynthetic mechanism and relevant enzymes that drive l-Gal f production have not yet been characterized. Herein we report that efforts to decipher the sugar biosynthetic pathway and tailoring steps en route to nucleoside antibiotic A201A led to the discovery of a GDP-l-galactose mutase, MtdL. Systematic inactivation of 18 of the 33 biosynthetic genes in the A201A cluster and elucidation of 10 congeners, coupled with feeding and in vitro biochemical experiments, enabled us to: ( i ) decipher the unique enzyme, GDP-l-galactose mutase associated with production of two unique d-mannose-derived sugars, and ( ii ) assign two glycosyltransferases, four methyltransferases, and one desaturase that regiospecifically tailor the A201A scaffold and display relaxed substrate specificities. Taken together, these data provide important insight into the origin of l-Gal f -containing natural product biosynthetic pathways with likely ramifications in other organisms and possible antimicrobial drug targeting strategies.

­­­­High-Resolution Mapping of Kick`em Jenny Submarine Volcano and Associated Landslides

NASA Astrophysics Data System (ADS)

Ruchala, T. L.; Carey, S.; Hart, L.; Chen, M.; Scott, C.; Tominaga, M.; Dondin, F. J. Y.; Fujii, M.

2016-02-01

To understand the physical and geological processes that drive the volcanism and control the morphology of Kick`em Jenny (KEJ) volcano, the only active submarine volcano in the in the Lesser Antilles volcanic arc, we conducted near-source, high-resolution mapping of KEJ and its subsurface using the Remotely Operated Vehicle (ROV) Hercules during cruise NA054 of the E/V Nautilus (Sept.-Oct. 2014). Shipboard bathymetric data (EM302 system) and slope analysis maps were used to decipher the detailed seafloor morphology surrounding KEJ. Multiple generations of submarine landslides and canyons were observed, suggesting the area has been hosting dynamic sediment transport systems at multiple scales over time. Some of them might have been associated by past eruptions. Clear contacts between partially lithified carbonate sediments and volcanic formations were identified from ROV videos at the middle of the landslide slope face. Detailed observations of facies on these exposures provide constraints on the time intervals between landslide events along the western slope of KEJ. ROV video imagery also identified outcrops of columnar basalts located in the middle of the landslide deposits. These are similar in appearance to those observed in the KEJ crater during previous ROV dives, indicating a possible travel distance of volcanic materials from the crater region along landslide path. High-resolution photo mosaics, bathymetry, and magnetic data acquired by ROV Hercules were used to investigate geological processes and the possible volcanic source of landslide material within the KEJ crater. Mapping in the northwestern part of the crater floor revealed distinctive regions, including (i) microbial mats, (ii) active hydrothermal vent sites; (iii) landforms curved by channelized bottom current where seafloor is outcropped; and (iv) coarse scree the distribution of which may correlate with the distance from the crater rim. Near-bottom magnetic profiles show coherent magnetic signatures with correlatable high amplitude anomalies located in the middle of the KEJ crater.

Impact of Oxidative Dissolution on Black Shale Fracturing: Implication for Shale Fracturing Treatment Design

NASA Astrophysics Data System (ADS)

You, L.; Chen, Q.; Kang, Y.; Cheng, Q.; Sheng, J.

2017-12-01

Black shales contain a large amount of environment-sensitive compositions, e.g., clay minerals, carbonate, siderite, pyrite, and organic matter. There have been numerous studies on the black shales compositional and pore structure changes caused by oxic environments. However, most of the studies did not focus on their ability to facilitate shale fracturing. To test the redox-sensitive aspects of shale fracturing and its potentially favorable effects on hydraulic fracturing in shale gas reservoirs, the induced microfractures of Longmaxi black shales exposed to deionized water, hydrochloric acid, and hydrogen peroxide at room-temperature for 240 hours were imaged by scanning electron microscopy (SEM) and CT-scanning in this paper. Mineral composition, acoustic emission, swelling, and zeta potential of the untreated and oxidative treatment shale samples were also recorded to decipher the coupled physical and chemical effects of oxidizing environments on shale fracturing processes. Results show that pervasive microfractures (Fig.1) with apertures ranging from tens of nanometers to tens of microns formed in response to oxidative dissolution by hydrogen peroxide, whereas no new microfracture was observed after the exposure to deionized water and hydrochloric acid. The trajectory of these oxidation-induced microfractures was controlled by the distribution of phyllosilicate framework and flaky or stringy organic matter in shale. The experiments reported in this paper indicate that black shales present the least resistance to crack initiation and subcritical slow propagation in hydrogen peroxide, a process we refer to as oxidation-sensitive fracturing, which are closely related to the expansive stress of clay minerals, dissolution of redox-sensitive compositions, destruction of phyllosilicate framework, and the much lower zeta potential of hydrogen peroxide solution-shale system. It could mean that the injection of fracturing water with strong oxidizing aqueous solution may play an important role in improving hydraulic fracturing of shale formation by reducing the energy requirements for crack growth. However, additional work is needed to the selection of highly-effective, economical, and environmentally friendly oxidants.

Metabolic Engineering of Poly(3-Hydroxyalkanoates): From DNA to Plastic

PubMed Central

Madison, Lara L.; Huisman, Gjalt W.

1999-01-01

Poly(3-hydroxyalkanoates) (PHAs) are a class of microbially produced polyesters that have potential applications as conventional plastics, specifically thermoplastic elastomers. A wealth of biological diversity in PHA formation exists, with at least 100 different PHA constituents and at least five different dedicated PHA biosynthetic pathways. This diversity, in combination with classical microbial physiology and modern molecular biology, has now opened up this area for genetic and metabolic engineering to develop optimal PHA-producing organisms. Commercial processes for PHA production were initially developed by W. R. Grace in the 1960s and later developed by Imperial Chemical Industries, Ltd., in the United Kingdom in the 1970s and 1980s. Since the early 1990s, Metabolix Inc. and Monsanto have been the driving forces behind the commercial exploitation of PHA polymers in the United States. The gram-negative bacterium Ralstonia eutropha, formerly known as Alcaligenes eutrophus, has generally been used as the production organism of choice, and intracellular accumulation of PHA of over 90% of the cell dry weight have been reported. The advent of molecular biological techniques and a developing environmental awareness initiated a renewed scientific interest in PHAs, and the biosynthetic machinery for PHA metabolism has been studied in great detail over the last two decades. Because the structure and monomeric composition of PHAs determine the applications for each type of polymer, a variety of polymers have been synthesized by cofeeding of various substrates or by metabolic engineering of the production organism. Classical microbiology and modern molecular bacterial physiology have been brought together to decipher the intricacies of PHA metabolism both for production purposes and for the unraveling of the natural role of PHAs. This review provides an overview of the different PHA biosynthetic systems and their genetic background, followed by a detailed summation of how this natural diversity is being used to develop commercially attractive, recombinant processes for the large-scale production of PHAs. PMID:10066830

Mercury Methylation in Alaskan Peatlands Spanning a Large Range of Trophic Structure

NASA Astrophysics Data System (ADS)

Krabbenhoft, D. P.; Zhang, L.; Hines, M. E.; Barkay, T.; Schaefer, J.; Aiken, G.

2015-12-01

The process of mercury (Hg) methylation has long been recognized as a key area of research in order to understand spatial and temporal variability of toxic methylmercury (MeHg) on the landscape. Numerous factors affect MeHg production, the most important generally falling into those that affect inorganic Hg(II) bioavailability (e.g., Hg(II) concentration and ligand composition), and those that affect microbial community composition and activity. The principal goal of this project is to decipher the details of MeHg production in Alaskan peatlands exhibiting a range of trophic status, including those lacking in electron acceptors that support the traditional respiratory pathway of MeHg production (e.g., sulfate reduction). MeHg production is carried out by a diverse group of microorganisms that possess the gene cluster (hgcAB), including the well-studied sulfate and iron- reducing bacteria (SRB and FeRB). However, less well known bacteria also possess the hgcAB genes, including: syntrophs, methanogens, acetogens, and fermenters. Methylation and demethylation activities were determined by injecting trace levels of the stable isotope (198Hg and Me204Hg) into intact peat cores. In addition, the short-lived radioisotope 197Hg was used in laboratory incubations. Laboratory studies also included assays for changes in diagnostic gas concentrations (CH4, CO2, H2) and LMW organic acids (formate, acetate, propionate, butyrate) to infer specific microbial processes, and the use of genomics to confirm microbial assemblages and the presence/absence of hgcAB genes. Overall, we observed Hg methylation rates were greatest at minerotrophic sites with active syntrophy and methanogenesis. Methylation and demethylation rates corresponded significantly across sites. There was no evidence of SO4- reduction in these samples, and addition of SO4- did not stimulate methylation suggesting that methylation was conducted by SRB that were metabolizing syntrophically and/or by fermentation.

Metabolic engineering of poly(3-hydroxyalkanoates): from DNA to plastic.

PubMed

Madison, L L; Huisman, G W

1999-03-01

Poly(3-hydroxyalkanoates) (PHAs) are a class of microbially produced polyesters that have potential applications as conventional plastics, specifically thermoplastic elastomers. A wealth of biological diversity in PHA formation exists, with at least 100 different PHA constituents and at least five different dedicated PHA biosynthetic pathways. This diversity, in combination with classical microbial physiology and modern molecular biology, has now opened up this area for genetic and metabolic engineering to develop optimal PHA-producing organisms. Commercial processes for PHA production were initially developed by W. R. Grace in the 1960s and later developed by Imperial Chemical Industries, Ltd., in the United Kingdom in the 1970s and 1980s. Since the early 1990s, Metabolix Inc. and Monsanto have been the driving forces behind the commercial exploitation of PHA polymers in the United States. The gram-negative bacterium Ralstonia eutropha, formerly known as Alcaligenes eutrophus, has generally been used as the production organism of choice, and intracellular accumulation of PHA of over 90% of the cell dry weight have been reported. The advent of molecular biological techniques and a developing environmental awareness initiated a renewed scientific interest in PHAs, and the biosynthetic machinery for PHA metabolism has been studied in great detail over the last two decades. Because the structure and monomeric composition of PHAs determine the applications for each type of polymer, a variety of polymers have been synthesized by cofeeding of various substrates or by metabolic engineering of the production organism. Classical microbiology and modern molecular bacterial physiology have been brought together to decipher the intricacies of PHA metabolism both for production purposes and for the unraveling of the natural role of PHAs. This review provides an overview of the different PHA biosynthetic systems and their genetic background, followed by a detailed summation of how this natural diversity is being used to develop commercially attractive, recombinant processes for the large-scale production of PHAs.

Application of remote sensing data to monitoring of oil pollution as part of the environmental expert system

NASA Astrophysics Data System (ADS)

Shagarova, Lyudmila; Muratova, Mira; Abuova, Sholpan

2016-07-01

The impact of oil-producing facilities on the environment is caused by toxicity of hydrocarbons and by-products, a variety of chemicals used in industrial processes, as well as specificity of production, treatment, transportation and storage of oil and oil products. To predict the state of the geological environment, scientists carry out investigations, which help to choose the optimal strategy for creation of the expert system taking into account simulations and to provide efficient use of available environmentally relevant information related to the current state of the geological environment. The expert system is a complex of interconnected blocks, one of which is the information on the presence of oil pollution, which can be identified using satellite imagery. The satellite imagery has practical application in monitoring of oil pollution, as it allows specialists to identify oil spills remotely and to determine their characteristics based on the differentiation of the surface reflectance spectra. Snapshots are used to estimate the area of oil-contamination and location of spills. To detect contaminants it is necessary to perform the following steps in processing of the remote sensing data: - Identify and isolate all the dark deformations in the satellite images, as a result of processing of segmentation and threshold processing; - Calculate statistical parameters of dark deformations, i.e., signs similar to areas prone to contamination. These signs are related to the geometry of formation, their physical changes (backscattering value) and the image context; - Classify the selected spectral anomalies as oil pollution and oil sludge. On the basis of classification of satellite imagery, the objects of oil pollution are detected and deciphering signs are analyzed in order to refer classified objects to implicit or explicit contaminations. To detect oil pollution, pixels are classified into categories with learning on the given areas with creation of the corresponding signature for each of them, i.e. the area with a given class, which is used to determine centers of classes in further supervised classification. The classification process compares the luminance of pixels with the training sample, as a result, each pixel is referred to the most appropriate class of objects. The development of an expert system using digital space information will extend the circle of problems solved in the environmental protection, creation of complex schemes of intensive development of hydrocarbon production regions in view of environmental risks.

Noncanonical Gβ Gib2 is a scaffolding protein promoting cAMP signaling through functions of Ras1 and Cac1 proteins in Cryptococcus neoformans.

PubMed

Wang, Yanli; Shen, Gui; Gong, Jinjun; Shen, Danyu; Whittington, Amy; Qing, Jiang; Treloar, Joshua; Boisvert, Scott; Zhang, Zhengguang; Yang, Cai; Wang, Ping

2014-05-02

Gβ-like/RACK1 functions as a key mediator of various pathways and contributes to numerous cellular functions in eukaryotic organisms. In the pathogenic fungus Cryptococcus neoformans, noncanonical Gβ Gib2 promotes cAMP signaling in cells lacking normal Gpa1 function while displaying versatility in interactions with Gα Gpa1, protein kinase Pkc1, and endocytic intersectin Cin1. To elucidate the Gib2 functional mechanism(s), we demonstrate that Gib2 is required for normal growth and virulence. We show that Gib2 directly binds to Gpa1 and Gγ Gpg1/Gpg2 and that it interacts with phosphodiesterase Pde2 and monomeric GTPase Ras1. Pde2 remains functionally dispensable, but Ras1 is found to associate with adenylyl cyclase Cac1 through the conserved Ras association domain. In addition, the ras1 mutant exhibits normal capsule formation, whereas the ras1 gpa1 mutant displays enhanced capsule formation, and the ras1 gpa1 cac1 mutant is acapsular. Collectively, these findings suggest that Gib2 promotes cAMP levels by relieving an inhibitory function of Ras1 on Cac1 in the absence of Gpa1. In addition, using GST affinity purification combined with mass spectrometry, we identified 47 additional proteins that interact with Gib2. These proteins have putative functions ranging from signal transduction, energy generation, metabolism, and stress response to ribosomal function. After establishing and validating a protein-protein interactive network, we believe Gib2 to be a key adaptor/scaffolding protein that drives the formation of various protein complexes required for growth and virulence. Our study reveals Gib2 as an essential component in deciphering the complexity of regulatory networks that control growth and virulence in C. neoformans.

Root-Knot and Cyst Nematodes Activate Procambium-Associated Genes in Arabidopsis Roots.

PubMed

Yamaguchi, Yasuka L; Suzuki, Reira; Cabrera, Javier; Nakagami, Satoru; Sagara, Tomomi; Ejima, Chika; Sano, Ryosuke; Aoki, Yuichi; Olmo, Rocio; Kurata, Tetsuya; Obayashi, Takeshi; Demura, Taku; Ishida, Takashi; Escobar, Carolina; Sawa, Shinichiro

2017-01-01

Developmental plasticity is one of the most striking features of plant morphogenesis, as plants are able to vary their shapes in response to environmental cues. Biotic or abiotic stimuli often promote organogenesis events in plants not observed under normal growth conditions. Root-knot nematodes (RKNs) are known to parasitize multiple species of rooting plants and to induce characteristic tissue expansion called galls or root-knots on the roots of their hosts by perturbing the plant cellular machinery. Galls contain giant cells (GCs) and neighboring cells, and the GCs are a source of nutrients for the parasitizing nematode. Highly active cell proliferation was observed in galls. However, the underlying mechanisms that regulate the symptoms triggered by the plant-nematode interaction have not yet been elucidated. In this study, we deciphered the molecular mechanism of gall formation with an in vitro infection assay system using RKN Meloidogyne incognita , and the model plant Arabidopsis thaliana. By taking advantages of this system, we performed next-generation sequencing-based transcriptome profiling, and found that the expression of procambium identity-associated genes were enriched during gall formation. Clustering analyses with artificial xylogenic systems, together with the results of expression analyses of the candidate genes, showed a significant correlation between the induction of gall cells and procambium-associated cells. Furthermore, the promoters of several procambial marker genes such as ATHB8 , TDR and WOX4 were activated not only in M. incognita -induced galls, but similarly in M. javanica induced-galls and Heterodera schachtii -induced syncytia. Our findings suggest that phytoparasitic nematodes modulate the host's developmental regulation of the vascular stem cells during gall formation.

Fuzzy inference system for identification of geological stratigraphy off Prydz Bay, East Antarctica

NASA Astrophysics Data System (ADS)

Singh, Upendra K.

2011-12-01

The analysis of well logging data plays key role in the exploration and development of hydrocarbon reservoirs. Various well log parameters such as porosity, gamma ray, density, transit time and resistivity, help in classification of strata and estimation of the physical, electrical and acoustical properties of the subsurface lithology. Strong and conspicuous changes in some of the log parameters associated with any particular geological stratigraphy formation are function of its composition, physical properties that help in classification. However some substrata show moderate values in respective log parameters and make difficult to identify the kind of strata, if we go by the standard variability ranges of any log parameters and visual inspection. The complexity increases further with more number of sensors involved. An attempt is made to identify the kinds of stratigraphy from well logs over Prydz bay basin, East Antarctica using fuzzy inference system. A model is built based on few data sets of known stratigraphy and further the network model is used as test model to infer the lithology of a borehole from their geophysical logs, not used in simulation. Initially the fuzzy based algorithm is trained, validated and tested on well log data and finally identifies the formation lithology of a hydrocarbon reservoir system of study area. The effectiveness of this technique is demonstrated by the analysis of the results for actual lithologs and coring data of ODP Leg 188. The fuzzy results show that the training performance equals to 82.95% while the prediction ability is 87.69%. The fuzzy results are very encouraging and the model is able to decipher even thin layer seams and other strata from geophysical logs. The result provides the significant sand formation of depth range 316.0- 341.0 m, where core recovery is incomplete.

Thermal history of volcanic debris flow deposits on the eastern flanks of Mt. Taranaki, New Zealand: Implications for future hazards

NASA Astrophysics Data System (ADS)

Turner, Gillian M.; Alloway, Brent V.; Dixon, Benjamin J.; Atkins, Cliff B.

2018-03-01

We use palaeomagnetic methods to decipher the thermal histories of a succession of massive to weakly stratified debris flow deposits (Ngatoro and Te Popo formations) of late Holocene age located on the eastern lower flanks of Mt. Taranaki/Egmont Volcano, western North Island, New Zealand. Results from two sites, Vickers Quarry and Surrey Road Quarry, both c. 9.6 km from the present-day summit, enable us to distinguish between clast incorporation temperatures of about 400 °C and emplacement temperatures between 150 and 200 °C, consistent with observation of superficial charring and desiccation of outer podocarp-hardwood tree trunks at Vickers Quarry. Analysis of palaeomagnetic directions and lithofacies architecture suggest that these deposits were likely initiated as a closely-spaced succession of block-and-ash flows (BAFs) that rapidly cooled as they descended the volcano flanks. Radiocarbon chronology and the widespread occurrence of a palaeosol between the products of the preceding Inglewood eruptive phase, c. 3.4 cal. ka B.P., and the overlying Ngatoro Formation suggest that these two events are temporally unrelated. Certainly, there is no field evidence of contemporaneous explosive volcanic activity that might be related to the emplacement of Ngatoro Formation. However, we suggest that these low-temperature deposits might either relate to collapse of a small emergent lava dome or a cooling dome remnant, possibly emplaced in the aftermath of the Inglewood eruption. How collapse was initiated remains uncertain: the remnant dome may have been rendered unstable by volcano-tectonic or tectonic seismic events and/or by adverse meteorological events. Nevertheless, this study demonstrates that edifice collapse events generating potentially hazardous debris flows can occur independent of specific eruptive activity.

Endothelium as a Potential Target for Treatment of Abdominal Aortic Aneurysm

PubMed Central

Sun, Jingyuan; Deng, Hongping; Zhou, Zhen

2018-01-01

Abdominal aortic aneurysm (AAA) was previously ascribed to weaken defective medial arterial/adventitial layers, for example, smooth muscle/fibroblast cells. Therefore, besides surgical repair, medications targeting the medial layer to strengthen the aortic wall are the most feasible treatment strategy for AAA. However, so far, it is unclear whether such drugs have any beneficial effect on AAA prognosis, rate of aneurysm growth, rupture, or survival. Notably, clinical studies have shown that AAA is highly associated with endothelial dysfunction in the aged population. Additionally, animal models of endothelial dysfunction and endothelial nitric oxide synthase (eNOS) uncoupling had a very high rate of AAA formation, indicating there is crucial involvement of the endothelium and a possible pharmacological solution targeting the endothelium in AAA treatment. Endothelial cells have been found to trigger vascular wall remodeling by releasing proteases, or recruiting macrophages along with other neutrophils, into the medial layer. Moreover, inflammation and oxidative stress of the arterial wall were induced by endothelial dysfunction. Interestingly, there is a paradoxical differential correlation between diabetes and aneurysm formation in retinal capillaries and the aorta. Deciphering the significance of such a difference may explain current unsuccessful AAA medications and offer a solution to this treatment challenge. It is now believed that AAA and atherosclerosis are two separate but related diseases, based on their different clinical patterns which have further complicated the puzzle. Therefore, a thorough investigation of the interaction between endothelium and medial/adventitial layer may provide us a better understanding and new perspective on AAA formation, especially after taking into account the importance of endothelium in the development of AAA. Moreover, a novel medication strategy replacing the currently used, but suboptimal treatments for AAA, could be informed with this analysis. PMID:29849906

Deciphering the Ubiquitin Code.

PubMed

Dittmar, Gunnar; Selbach, Matthias

2017-03-02

In this issue of Molecular Cell, Zhang et al. (2017) systematically identify proteins interacting with all possible di-ubiquitin linkages, thus providing a catalog of readers of the ubiquitin code. Copyright © 2017 Elsevier Inc. All rights reserved.

Dead Sea Scrolls

NASA Technical Reports Server (NTRS)

1994-01-01

A consortium of researchers from Jet Propulsion Laboratory and three other organizations used charged coupled devices (CCDs) and other imaging enhancement technology to decipher previously unreadable portions of the Dead Sea Scrolls. The technique has potentially important implications for archeology.

The Human Genome Project: An Imperative for International Collaboration.

ERIC Educational Resources Information Center

Allende, J. E.

1989-01-01

Discussed is the Human Genome Project which aims to decipher the totality of the human genetic information. The historical background, the objectives, international cooperation, ethical discussion, and the role of UNESCO are included. (KR)

Passive Signals from Aggressive Methods: The Origin and Implications of Organic Material in a Carbonate Stromatolite

NASA Astrophysics Data System (ADS)

Petryshyn, V.; Bailey, J.; Stamps, B. W.; Stevenson, B. S.; Corsetti, F. A.

2017-12-01

Microbial activity can play a role in the construction of carbonate features like stromatolites and thrombolites, but determining whether microbes were directly or indirectly involved in the formation can be difficult—an endeavor that becomes more difficult as geologic time passes and organic signals degrade. In order to assess our ability to decipher the role of microbes in stromatolite formation, DNA (geologically short-lived) and alkanes (potentially geologically long-lived) were extracted and analyzed from finely-laminated Holocene carbonate stromatolites of Walker Lake, Nevada. The stromatolitic laminations were typically between 50 and 100 microns thick. The surrounding sediment and lake water was also sampled, for comparison. SSU rRNA gene sequencing suggests that a large percentage (25-40 % relative abundance) of the microbial community found within the stromatolite is comprised of ambient lake algae, not known to form stromatolite-building mats given their size vs. stromatolite lamination thickness, rather than the usual taxa associated with the formation of stromatolites. Other minor taxa were identified, including the bacterial families Cyanobacteria, Flavobacteriaceae, and Rhodobacteraceae. Mirroring the DNA results, the carbon isotopic compositions of the alkanes were largely indistinguishable from the limnic biomass dominated by lake algae. The results suggest that organic matter was passively incorporated into the carbonate structure from the lake as it accreted. Although evidence of life was abundant in the stromatolite, a direct role (builders) or even an indirect role (tenants) is difficult to establish, as the 16S/18S and lipid biomarkers appear to simply originate from the water column (squatters) and not from a unique microbial mat. In the absence of in situ analyses during the formation of the stromatolite, it may be difficult to disentangle the builders from the tenants and/or squatters based solely on molecular or organic geochemical data collected after the fact, or to determine if the stromatolite was indeed biogenic at all based on such techniques.

Stratigraphic units overlying the Zambales Ophiolite Complex (ZOC) in Luzon, (Philippines): Tectonostratigraphic significance and regional implications

NASA Astrophysics Data System (ADS)

Queaño, Karlo L.; Dimalanta, Carla B.; Yumul, Graciano P.; Marquez, Edanjarlo J.; Faustino-Eslava, Decibel V.; Suzuki, Shigeyuki; Ishida, Keisuke

2017-07-01

The Zambales Ophiolite Complex (ZOC) on the island of Luzon, Philippines is one of the most well-studied crust-mantle sequences in the region. Several massifs comprise the ZOC, one of which is the Coto Block overlain by clastic sedimentary units previously dated as Eocene. Geochronologic studies from diabase, granodiorites and other late-stage magmatic products similarly yielded the same age. Succeeding tectonic models have therefore all been grounded on the assumption that the entire ZOC is Eocene. Recent investigations, however, revealed the presence of chert blocks within the Early to Middle Miocene clastic formation overlying the Acoje Block in the northern part of the ophiolite complex. Radiolarians extracted from the cherts yielded a stratigraphic range that suggests a Late Jurassic to Early Cretaceous age. The recognition of a much older age than previously reported of the ZOC warrants a re-examination of its actual distribution and genesis. Correlating with other similarly-aged ophiolites, we suggest defining a western Mesozoic ophiolite belt, largely extending from the west-central portion of the archipelago to the northeastern tip of Luzon island. Tentatively, we attribute the Mesozoic ophiolitic and associated rocks in western Luzon to an arc-continent collision involving the Philippine Mobile Belt and the Palawan Microcontinental Block. In addition, differences in the clastic compositions of the Cenozoic sedimentary formations provide material not only for deciphering the ZOC's unroofing history but also for constraining the timing of province linkage. The intermittent appearance of lithic fragments and detrital minerals from the ophiolite in the units of the Middle Miocene Candelaria Limestone and the Late Miocene to Early Pliocene Sta. Cruz Formation indicates significant but geographically variable contributions from the ophiolite complex. In the northern Zambales Range, the Sta. Cruz Formation caps the Coto Block and the Acoje Block of the ZOC, providing a minimum age for their amalgamation.

Deciphering the mid-Carboniferous eustatic event in the central Appalachian foreland basin, southern West Virginia, USA

USGS Publications Warehouse

Blake, B.M.; Beuthin, J.D.

2008-01-01

A prominent unconformity, present across shallow shelf areas of the Euramerican paleoequatorial basins, is used to demark the boundary between the Mississippian and Pennsylvanian subsystems. This unconformity, the mid-Carboniferous eustatic event, is generally attributed to a major glacio-eustatic sea-level fall. Although a Mississippian-Pennsylvanian unconformity is recognized throughout most of the Appalachian region, the record of the mid-Carboniferous eustatic event in the structurally deepest part of the basin has been controversial. Based on early reports that suggested the most complete Pennsylvanian section was present in southern West Virginia, various conceptual depositional models postulated continuous sedimentation between the youngest Mississippian Bluestone Formation and the oldest Penn-sylvanian Pocahontas Formation. In contrast, tabular-erosion models envisioned axial drainage systems that evolved in response to changing basin dynamics. These models predicted a Mississippian-Pennsylvanian unconformity. All these models suffered from a lack of biostratigraphic control. The presence of a sub-Pocahontas paleovalley, herein named the Lashmeet paleovalley, has been confirmed in southern West Virginia. The Lashmeet paleovalley was incised over 35 m into Bluestone strata and filled by lithic sands derived from the Appalachian orogen to the northeast and east. The polygenetic Green Valley paleosol complex marks the Bluestone-Pocahontas contact on associated interfluves. Together, these features indicate a substantial period of subaerial exposure and argue strongly in favor of a Mississippian-Pennsylvanian unconformity. Paleontologic data from the Bluestone Formation, including marine invertebrates and conodonts from the marine Bramwell Member and paleofloral data, support a late, but not latest, Arnsbergian age assignment. Marine fossils are not known from the Pocahontas Formation, but macrofloral and palynomorph taxa support a Langsettian age for most of the Poca-hontas. The biostratigraphic, sedimentologic, and paleogeographic data support the presence of an early Pennsylvanian (middle to late Namurian) disconformity in the Appalachian Basin that corresponds to the mid-Carboniferous eustatic event. ?? 2008 Geological Society of America.

Looking For a Needle in the Haystack: Deciphering Indigenous 1.79 km Deep Subsurface Microbial Communities from Drilling Mud Contaminants Using 454 Pyrotag Sequencing

NASA Astrophysics Data System (ADS)

Dong, Y.; Cann, I.; Mackie, R.; Price, N.; Flynn, T. M.; Sanford, R.; Miller, P.; Chia, N.; Kumar, C. G.; Kim, P.; Sivaguru, M.; Fouke, B. W.

2010-12-01

Knowledge of the composition, structure and activity of microbial communities that live in deeply buried sedimentary rocks is fundamental to the future of subsurface biosphere stewardship as it relates to hydrocarbon exploration and extraction, carbon sequestration, gas storage and groundwater management. However, the study of indigenous subsurface microorganisms has been limited by the technical challenges of collecting deep formation water samples that have not been heavily contaminated by the mud used to drill the wells. To address this issue, a “clean-sampling method” deploying the newly developed Schlumberger Quicksilver MDT probe was used to collect a subsurface sample at a depth of 1.79 km (5872 ft) from an exploratory well within Cambrian-age sandstones in the Illinois Basin. This yielded a formation water sample that was determined to have less than 4% drilling mud contamination based on tracking changes in the aqueous geochemistry of the formation water during ~3 hours of pumping at depth prior to sample collection. A suite of microscopy and culture-independent molecular analyses were completed using the DNA extracted from microbial cells in the formation water, which included 454 amplicon pyrosequencing that targeted the V1-V3 hypervariable region of bacterial 16S rRNA gene sequences. Results demonstrated an extremely low diversity microbial community living in formation water at 1.79 km-depth. More than 95 % of the total V1-V3 pyrosequencing reads (n=11574) obtained from the formation water were affiliated with a halophilic γ-proteobacterium and most closely related to the genus Halomonas. In contrast, about 3 % of the V1-V3 sequences in the drilling mud library (n=13044) were classified as genus Halomonas but were distinctly different and distantly related to the formation water Halomonas detected at 1.79 km-depth. These results were consistent with those obtained using a suite of other molecular screens (e.g., Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and the initial full length 16S rRNA amplicon libraries) and bioinformatic analyses (e.g., 16S rRNA and Open Reading Frame (ORF) calls established from the 454 metagenomic community analyses). Functional pathway modeling is underway to evaluate the adaptation of this indigenous microbial community to the hydrologic and geologic history of the deep subsurface environment of the Illinois Basin.

The basal part of the Oman ophiolitic mantle: a fossil Mantle Wedge?

NASA Astrophysics Data System (ADS)

Prigent, Cécile; Guillot, Stéphane; Agard, Philippe; Godard, Marguerite; Chauvet, Alain; Dubacq, Benoit; Monié, Patrick; Yamato, Philippe

2014-05-01

Although the Oman ophiolite is classically regarded as being the direct analog of oceanic lithosphere created at fast spreading ridges, the geodynamic context of its formation is still highly debated. The other alternative end-member model suggests that this ophiolite entirely formed in a supra-subduction zone setting. Fluids involved in the hydration of the oceanic lithosphere and in the presence of a secondary boninitic and andesitic volcanism may provide a way to discriminate between these two interpretations: are they descending near-axis hydrothermal fluxes (first model) or ascending from a subducting slab (second model)? We herein focus on the base of the ophiolitic mantle in order to characterize the origin of fluids and decipher hydration processes. Samples were taken along hecto- to kilometre-long sections across the basal banded unit directly overlying the amphibolitic/granulitic metamorphic sole. We carried out a petrological, structural and geochemical study on these rocks and their constitutive minerals. Our results show that, unlike the generally refractory character of Oman harzburgites, all the basal mantle rocks display secondary crystallization of clinopyroxene and amphibole through metasomatic processes. The microstructures and the chronology of these secondary mineralizations (clinopyroxene, pargasitic amphibole, antigorite and then lizardite/chrysotile) suggest that these basal rocks have been affected by cooling from mantle temperatures (<1200°C) to low-T serpentinisation (<300°C). Furthermore, major elements required to crystallize these minerals and the observed fluid-mobile elements (FMEs) enrichments in the clinopyroxenes and in the amphiboles (B, Pb, Sr), as well as in the serpentines (B, Sr, Rb, Ba, As), are consistent with amphibolite-derived fluids (Ishikawa et al., 2005) and cannot be easily explained by other sources. Based on these observations, we propose a geodynamic model in which intense and continuous metasomatism of the cooling base of the ophiolitic mantle is due to the release of fluids coming from the progressive dehydration of underlying amphibolitic rocks. This process is compatible with the progressive subduction of the Arabian margin during the Upper Cretaceous (e.g., HP-LT units history, and tectonic structures observed on top of it). The basal part of the Oman ophiolite would thus represent a fossil incipient mantle wedge.

Intracellular delivery of universal proteins using a lysine headgroup containing cationic liposomes: deciphering the uptake mechanism.

PubMed

Sarker, Satya Ranjan; Hokama, Ryosuke; Takeoka, Shinji

2014-01-06

An amino acid-based cationic lipid having a TFA counterion (trifluoroacetic acid counterion) in the lysine headgroup was used to deliver functional proteins into human cervical cancer cells, HeLa, in the presence of serum. Proteins used in the study were fluorescein isothiocyanate (FITC) labeled bovine serum albumin, mouse anti-F actin antibody [NH3], and goat anti mouse IgG conjugated with FITC. The formation of liposome/protein complexes was confirmed using native polyacrylamide gel electrophoresis. Furthermore, the complexes were characterized in terms of their size and zeta potential at different pH values and found to be responsive to changes in pH. The highest delivery efficiency of the liposome/albumin complexes was 99% at 37 °C. The liposomes effectively delivered albumin and antibodies as confirmed by confocal laser scanning microscopy (CLSM). Inhibition studies showed that the cellular uptake mechanism of the complexes was via caveolae-mediated endocytosis, and the proteins were subsequently released from either the early endosomes or the caveosomes as suggested by CLSM. Thus, lysine-based cationic liposomes can be a useful tool for intracellular protein delivery.

multiplierz v2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data.

PubMed

Alexander, William M; Ficarro, Scott B; Adelmant, Guillaume; Marto, Jarrod A

2017-08-01

The continued evolution of modern mass spectrometry instrumentation and associated methods represents a critical component in efforts to decipher the molecular mechanisms which underlie normal physiology and understand how dysregulation of biological pathways contributes to human disease. The increasing scale of these experiments combined with the technological diversity of mass spectrometers presents several challenges for community-wide data access, analysis, and distribution. Here we detail a redesigned version of multiplierz, our Python software library which leverages our common application programming interface (mzAPI) for analysis and distribution of proteomic data. New features include support for a wider range of native mass spectrometry file types, interfaces to additional database search engines, compatibility with new reporting formats, and high-level tools to perform post-search proteomic analyses. A GUI desktop environment, mzDesktop, provides access to multiplierz functionality through a user friendly interface. multiplierz is available for download from: https://github.com/BlaisProteomics/multiplierz; and mzDesktop is available for download from: https://sourceforge.net/projects/multiplierz/. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transcriptomic and epigenomic characterization of the developing bat wing

PubMed Central

Eckalbar, Walter L.; Schlebusch, Stephen A.; Mason, Mandy K.; Gill, Zoe; Parker, Ash V.; Booker, Betty M.; Nishizaki, Sierra; Muswamba-Nday, Christiane; Terhune, Elizabeth; Nevonen, Kimberly; Makki, Nadja; Friedrich, Tara; VanderMeer, Julia E.; Pollard, Katherine S.; Carbone, Lucia; Wall, Jeff D.; Illing, Nicola; Ahituv, Nadav

2016-01-01

Bats are the only mammals capable of powered flight, but little is known about the genetic determinants that shape their wings. Here, we generated a genome for Miniopterus natalensis and performed RNA-seq and ChIP-seq (H3K27ac, H3K27me3) on its developing forelimb and hindlimb autopods at sequential embryonic stages to decipher the molecular events that underlie bat wing development. Over 7,000 genes and several lncRNAs, including Tbx5-as1 and Hottip, were differentially expressed between forelimb, hindlimb and different stages. ChIP-seq identified thousands of regions that are differentially modified in forelimb versus hindlimb. Comparative genomics found 2,796 bat-accelerated regions within H3K27ac peaks, several of which cluster near limb-associated genes. Pathway analyses revealed multiple ribosomal proteins and known limb patterning signaling pathways as differentially regulated, and implicated increased forelimb mesenchymal condensations with differential growth. Combined, our work outlines multiple genetic components that contribute to bat wing formation, providing a genomic blueprint for this morphological innovation. PMID:27019111

Constitutive expression and silencing of a novel seed specific calcium dependent protein kinase gene in rice reveals its role in grain filling.

PubMed

Manimaran, P; Mangrauthia, Satendra K; Sundaram, R M; Balachandran, S M

2015-02-01

Ca(2+) sensor protein kinases are prevalent in most plant species including rice. They play diverse roles in plant signaling mechanism. Thirty one CDPK genes have been identified in rice and some are functionally characterized. In the present study, the newly identified rice CDPK gene OsCPK31 was functionally validated by overexpression and silencing in Taipei 309 rice cultivar. Spikelets of overexpressing plants showed hard dough stage within 15d after pollination (DAP) with rapid grain filling and early maturation. Scanning electron microscopy of endosperm during starch granule formation confirmed early grain filling. Further, seeds of overexpressing transgenic lines matured early (20-22 DAP) and the average number of maturity days reduced significantly. On the other hand, silencing lines showed more number of unfilled spikelet without any difference in maturity duration. It will be interesting to further decipher the role of OsCPK31 in biological pathways associated with distribution of photosynthetic assimilates during grain filling stage. Copyright © 2014 Elsevier GmbH. All rights reserved.

Femtosecond UV-laser pulses to unveil protein-protein interactions in living cells.

PubMed

Itri, Francesco; Monti, Daria M; Della Ventura, Bartolomeo; Vinciguerra, Roberto; Chino, Marco; Gesuele, Felice; Lombardi, Angelina; Velotta, Raffaele; Altucci, Carlo; Birolo, Leila; Piccoli, Renata; Arciello, Angela

2016-02-01

A hallmark to decipher bioprocesses is to characterize protein-protein interactions in living cells. To do this, the development of innovative methodologies, which do not alter proteins and their natural environment, is particularly needed. Here, we report a method (LUCK, Laser UV Cross-linKing) to in vivo cross-link proteins by UV-laser irradiation of living cells. Upon irradiation of HeLa cells under controlled conditions, cross-linked products of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were detected, whose yield was found to be a linear function of the total irradiation energy. We demonstrated that stable dimers of GAPDH were formed through intersubunit cross-linking, as also observed when the pure protein was irradiated by UV-laser in vitro. We proposed a defined patch of aromatic residues located at the enzyme subunit interface as the cross-linking sites involved in dimer formation. Hence, by this technique, UV-laser is able to photofix protein surfaces that come in direct contact. Due to the ultra-short time scale of UV-laser-induced cross-linking, this technique could be extended to weld even transient protein interactions in their native context.

A genomic window into the virulence of Histophilus somni.

PubMed

Sandal, Indra; Inzana, Thomas J

2010-02-01

Histophilus somni is an obligate inhabitant of the respiratory and genital mucosal surfaces of bovines and ovines. An individual strain can be a primary pathogen, an opportunistic pathogen, or a commensal, but can also move between these classifications if introduced into an appropriate site (e.g. the lungs) under conditions that favor bacterial persistence. H. somni is one of the bacterial agents responsible for bovine respiratory disease complex and can also cause a variety of systemic diseases in cattle and sheep. Isolates from disease sites, such as the lungs, heart, and brain, express a wide array of virulence factors (including biofilm formation) designed to evade host defense mechanisms. By contrast, some isolates from the healthy genital tract often lack many of these virulence factors. The genomic sequences of two bovine isolates, one from pneumonic lung and the other from healthy prepuce, have aided in deciphering the differences in phenotype and virulence between the two strains, and reveal their striking genetic similarity to Haemophilus influenzae and other members of the Pasteurellaceae. (c) 2009 Elsevier Ltd. All rights reserved.

Structure-function analysis of myomaker domains required for myoblast fusion.

PubMed

Millay, Douglas P; Gamage, Dilani G; Quinn, Malgorzata E; Min, Yi-Li; Mitani, Yasuyuki; Bassel-Duby, Rhonda; Olson, Eric N

2016-02-23

During skeletal muscle development, myoblasts fuse to form multinucleated myofibers. Myomaker [Transmembrane protein 8c (TMEM8c)] is a muscle-specific protein that is essential for myoblast fusion and sufficient to promote fusion of fibroblasts with muscle cells; however, the structure and biochemical properties of this membrane protein have not been explored. Here, we used CRISPR/Cas9 mutagenesis to disrupt myomaker expression in the C2C12 muscle cell line, which resulted in complete blockade to fusion. To define the functional domains of myomaker required to direct fusion, we established a heterologous cell-cell fusion system, in which fibroblasts expressing mutant versions of myomaker were mixed with WT myoblasts. Our data indicate that the majority of myomaker is embedded in the plasma membrane with seven membrane-spanning regions and a required intracellular C-terminal tail. We show that myomaker function is conserved in other mammalian orthologs; however, related family members (TMEM8a and TMEM8b) do not exhibit fusogenic activity. These findings represent an important step toward deciphering the cellular components and mechanisms that control myoblast fusion and muscle formation.

Mutation of the Na+/K+-ATPase Atp1a1a.1 causes QT interval prolongation and bradycardia in zebrafish.

PubMed

Pott, Alexander; Bock, Sarah; Berger, Ina M; Frese, Karen; Dahme, Tillman; Keßler, Mirjam; Rinné, Susanne; Decher, Niels; Just, Steffen; Rottbauer, Wolfgang

2018-05-08

The genetic underpinnings that orchestrate the vertebrate heart rate are not fully understood yet, but of high clinical importance, since diseases of cardiac impulse formation and propagation are common and severe human arrhythmias. To identify novel regulators of the vertebrate heart rate, we deciphered the pathogenesis of the bradycardia in the homozygous zebrafish mutant hiphop (hip) and identified a missense-mutation (N851K) in Na + /K + -ATPase α1-subunit (atp1a1a.1). N851K affects zebrafish Na + /K + -ATPase ion transport capacity, as revealed by in vitro pump current measurements. Inhibition of the Na + /K + -ATPase in vivo indicates that hip rather acts as a hypomorph than being a null allele. Consequently, reduced Na + /K + -ATPase function leads to prolonged QT interval and refractoriness in the hip mutant heart, as shown by electrocardiogram and in vivo electrical stimulation experiments. We here demonstrate for the first time that Na + /K + -ATPase plays an essential role in heart rate regulation by prolonging myocardial repolarization. Copyright © 2018. Published by Elsevier Ltd.

Zebrafish Craniofacial Development: A Window into Early Patterning

PubMed Central

Mork, Lindsey; Crump, Gage

2016-01-01

The formation of the face and skull involves a complex series of developmental events mediated by cells derived from the neural crest, endoderm, mesoderm, and ectoderm. Although vertebrates boast an enormous diversity of adult facial morphologies, the fundamental signaling pathways and cellular events that sculpt the nascent craniofacial skeleton in the embryo have proven to be highly conserved from fish to man. The zebrafish Danio rerio, a small freshwater cyprinid fish from eastern India, has served as a popular model of craniofacial development since the 1990s. Unique strengths of the zebrafish model include a simplified skeleton during larval stages, access to rapidly developing embryos for live imaging, and amenability to transgenesis and complex genetics. In this chapter, we describe the anatomy of the zebrafish craniofacial skeleton; its applications as models for the mammalian jaw, middle ear, palate, and cranial sutures; the superior imaging technology available in fish that has provided unprecedented insights into the dynamics of facial morphogenesis; the use of the zebrafish to decipher the genetic underpinnings of craniofacial biology; and finally a glimpse into the most promising future applications of zebrafish craniofacial research. PMID:26589928

Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells.

PubMed

Gao, Yan; Ni, Xiaohui; Guo, Hua; Su, Zhe; Ba, Yi; Tong, Zhongsheng; Guo, Zhi; Yao, Xin; Chen, Xixi; Yin, Jian; Yan, Zhao; Guo, Lin; Liu, Ying; Bai, Fan; Xie, X Sunney; Zhang, Ning

2017-08-01

Copy number alteration (CNA) is a major contributor to genome instability, a hallmark of cancer. Here, we studied genomic alterations in single primary tumor cells and circulating tumor cells (CTCs) from the same patient. Single-nucleotide variants (SNVs) in single cells from both samples occurred sporadically, whereas CNAs among primary tumor cells emerged accumulatively rather than abruptly, converging toward the CNA in CTCs. Focal CNAs affecting the MYC gene and the PTEN gene were observed only in a minor portion of primary tumor cells but were present in all CTCs, suggesting a strong selection toward metastasis. Single-cell structural variant (SV) analyses revealed a two-step mechanism, a complex rearrangement followed by gene amplification, for the simultaneous formation of anomalous CNAs in multiple chromosome regions. Integrative CNA analyses of 97 CTCs from 23 patients confirmed the convergence of CNAs and revealed single, concurrent, and mutually exclusive CNAs that could be the driving events in cancer metastasis. © 2017 Gao et al.; Published by Cold Spring Harbor Laboratory Press.

Analysis of Ribosome Stalling and Translation Elongation Dynamics by Deep Learning.

PubMed

Zhang, Sai; Hu, Hailin; Zhou, Jingtian; He, Xuan; Jiang, Tao; Zeng, Jianyang

2017-09-27

Ribosome stalling is manifested by the local accumulation of ribosomes at specific codon positions of mRNAs. Here, we present ROSE, a deep learning framework to analyze high-throughput ribosome profiling data and estimate the probability of a ribosome stalling event occurring at each genomic location. Extensive validation tests on independent data demonstrated that ROSE possessed higher prediction accuracy than conventional prediction models, with an increase in the area under the receiver operating characteristic curve by up to 18.4%. In addition, genome-wide statistical analyses showed that ROSE predictions can be well correlated with diverse putative regulatory factors of ribosome stalling. Moreover, the genome-wide ribosome stalling landscapes of both human and yeast computed by ROSE recovered the functional interplays between ribosome stalling and cotranslational events in protein biogenesis, including protein targeting by the signal recognition particles and protein secondary structure formation. Overall, our study provides a novel method to complement the ribosome profiling techniques and further decipher the complex regulatory mechanisms underlying translation elongation dynamics encoded in the mRNA sequence. Copyright © 2017 Elsevier Inc. All rights reserved.

Ca cycling and isotopic fluxes in forested ecosystems in Hawaii

USGS Publications Warehouse

Wiegand, B.A.; Chadwick, O.A.; Vitousek, P.M.; Wooden, J.L.

2005-01-01

Biogeochemical processes fractionate Ca isotopes in plants and soils along a 4 million year developmental sequence in the Hawaiian Islands. We observed that plants preferentially take up 40Ca relative to 44Ca, and that biological fractionation and changes in the relative contributions from volcanic and marine sources produce a significant increase in 44Ca in soil exchangeable pools. Our results imply moderate fluxes enriched in 44Ca from strongly nutrient-depleted old soils, in contrast with high 40Ca fluxes in young and little weathered environments. In addition, biological fractionation controls divergent geochemical pathways of Ca and Sr in the plant-soil system. While Ca depletes progressively with increasing soil age, Sr/Ca ratios increase systematically. Sr isotope ratios provide a valuable tracer for provenance studies of alkaline earth elements in forested ecosystems, but its usefulness is limited when deciphering biogeochemical processes involved in the terrestrial Ca cycle. Ca isotopes in combination with Sr/ Ca ratios reveal more complex processes involved in the biogeochemistry of Ca and Sr. Copyright 2005 by the American Geophysical Union.

An integrative discourse perspective on positive leadership in public health care.

PubMed

Pietiläinen, Ville; Salmi, Ilkka

2017-02-06

Purpose This study aims to take a discursive view on positive leadership (PL). A positive approach has gained momentum in recent years as appropriate leadership practices are implemented in organizations. Despite the turn toward discursive approaches in organization studies, there is insufficient evidence supporting PL as a socially constructed experience. Design/methodology/approach The present study addresses an integrative discourse perspective for capturing the PL concept as a social process within the public health-care context. Findings Four meanings of PL are highlighted: role-taking, servicing, balancing and deciphering. Research limitations/implications The meanings shift the emphasis of certain PL definitions to a contextual interpretation. For scholars, the perspective demonstrates a multidimensional process approach in the desired organizational context as a counterbalance to one unanimously agreed-upon PL definition. Practical implications For leaders, an integrative discourse perspective offers tools for comprehending PL as a process: how to identify, negotiate and reconcile various PL meanings. Originality/value An integrative discourse perspective provides a novel perspective capturing the PL concept within the public health-care field.

hh+ {Jet} production at 100 TeV

NASA Astrophysics Data System (ADS)

Banerjee, Shankha; Englert, Christoph; Mangano, Michelangelo L.; Selvaggi, Michele; Spannowsky, Michael

2018-04-01

Higgs pair production is a crucial phenomenological process in deciphering the nature of the TeV scale and the mechanism underlying electroweak symmetry breaking. At the Large Hadron Collider, this process is statistically limited. Pushing the energy frontier beyond the LHC's reach will create new opportunities to exploit the rich phenomenology at higher centre-of-mass energies and luminosities. In this work, we perform a comparative analysis of the hh+ {jet} channel at a future 100 TeV hadron collider. We focus on the hh→ b\\bar{b} b\\bar{b} and hh → b\\bar{b} τ ^+τ ^- channels and employ a range of analysis techniques to estimate the sensitivity potential that can be gained by including this jet-associated Higgs pair production to the list of sensitive collider processes in such an environment. In particular, we observe that hh → b\\bar{b} τ ^+τ ^- in the boosted regime exhibits a large sensitivity to the Higgs boson self-coupling and the Higgs self-coupling could be constrained at the 8% level in this channel alone.

The role of impact cratering for Mars sample return

NASA Technical Reports Server (NTRS)

Schultz, P. H.

1988-01-01

The preserved cratering record of Mars indicates that impacts play an important role in deciphering Martian geologic history, whether as a mechanism to modify the lithosphere and atmosphere or as a tool to sample the planet. The various roles of impact cratering in adding a broader understanding of Mars through returned samples are examined. Five broad roles include impact craters as: (1) a process in response to a different planetary localizer environment; (2) a probe for excavating crustal/mantle materials; (3) a possible localizer of magmatic and hydrothermal processes; (4) a chronicle of changes in the volcanic, sedimentary, atmospheric, and cosmic flux history; and (5) a chronometer for extending the geologic time scale to unsampled regions. The evidence for Earth-like processes and very nonlunar styles of volcanism and tectonism may shift the emphasis of a sampling strategy away from equally fundamental issues including crustal composition, unit ages, and climate history. Impact cratering not only played an important active role in the early Martian geologic history, it also provides an important tool for addressing such issues.

Inclusions in Minerals: the Importance of Host Mineral Composition, Pressure and Temperature for Potential Inclusion Alteration

NASA Astrophysics Data System (ADS)

Marquardt, K.; Markl, G.

2017-12-01

Inclusions in minerals are used to decipher details of the host mineral/rock history. They frequently originate from the time of mineral formation; be it diamond, garnet or `common' feldspar. Thus protected they survive changing pressure and temperature for different durations compared to their non-enclosed counterparts. Inclusions may (partially) equilibrate at a later point in history, and thus provide complementary information on past processes and alteration pathways less commonly discussed. The study investigates partially altered pyroxene inclusions in feldspars indicative of high-p-T fluid transport during granulite facies metamorphism in charnockites from the Lofoten Islands in Northern Norway. The protoliths formed about 1750 Ma ago, at about 800 - 900°C and 4 kbar. During crustal thickening, they reached high-pressure granulite-facies conditions of about 8-11 kbar at 700°C (1). While this event caused large magmatic pyroxenes to react with an infiltrating fluid to form corona textures of amphibole; pyroxenes inside feldspars behaved very differently. Pyroxenes enclosed in orthoclase-rich feldspar were partially hydrated to amphiboles. Contrastingly, feldspar with lower orthoclase content protected the magmatic pyroxenes efficiently. Transport and transformation mechanisms recorded in these µm to nm textures were studied by EMPA and TEM. Focused Ion Beam (FIB) prepared TEM-foils revealed that pyroxenes, when spatially connected to albite exsolution lamellae, show dissolution features. Based on composition, nanostructures and the known p-T-history, we propose the following succession of events. Ternary feldspar containing small magmatic pyroxenes began to exsolve between about 800 and 700°C. The exsolution changed from coherent to incoherent and a fluid infiltrated the feldspar accompanied by a formation of nanotunnels. Gradually the tunnels grew larger so that finally whole film perthites acted as pathways. When the fluid had access to pyroxene, reaction took place and amphibole formed. nm-scale observations need to be considered in studies on fluid mobility and for total reaction rates. Ref: Fitz Gerald, J. D., Parsons, I., & Cayzer, N. (2006). American Mineralogist, 91, 772-783. Markl, G., & Bucher, K. (1998). Nature, 391, 781-783.

Deciphering sub-micron ice particles on Enceladus surface

NASA Astrophysics Data System (ADS)

Scipioni, F.; Schenk, P.; Tosi, F.; D'Aversa, E.; Clark, R.; Combe, J.-Ph.; Ore, C. M. Dalle

2017-07-01

The surface of Saturn's moon Enceladus is composed primarily by pure water ice. The Cassini spacecraft has observed present-day geologic activity at the moon's South Polar Region, related with the formation and feeding of Saturn's E-ring. Plumes of micron-sized particles, composed of water ice and other non-ice contaminants (e.g., CO2, NH3, CH4), erupt from four terrain's fractures named Tiger Stripes. Some of this material falls back on Enceladus' surface to form deposits that extend to the North at ∼40°W and ∼220°W, with the highest concentration found at the South Pole. In this work we analyzed VIMS-IR data to identify plumes deposits across Enceladus' surface through the variation in band depth of the main water ice spectral features. To characterize the global variation of water ice band depths across Enceladus, the entire surface was sampled with an angular resolution of 1° in both latitude and longitude, and for each angular bin we averaged the value of all spectral indices as retrieved by VIMS. The position of the plumes' deposits predicted by theoretical models display a good match with water ice band depths' maps on the trailing hemisphere, whereas they diverge significantly on the leading side. Space weathering processes acting on Enceladus' surface ionize and break up water ice molecules, resulting in the formation of particles smaller than one micron. We also mapped the spectral indices for sub-micron particles and we compared the results with the plumes deposits models. Again, a satisfactory match is observed on the trailing hemisphere only. Finally, we investigated the variation of the depth of the water ice absorption bands as a function of the phase angle. In the visible range, some terrains surrounding the Tiger Stripes show a decrease in albedo when the phase angle is smaller than 10°. This unusual effect cannot be confirmed by near infrared data, since observations with a phase angle lower than 10° are not available. For phase angle values greater than 10°, the depth of the water ice features remains quite constant within a broad range of phase angle values.

How Precisely Can Prostate Cancer Be Managed?

PubMed Central

2016-01-01

Progress has been made in applying genetic information to disease management in the postgenomic era, and precision medicine is emerging in prostate cancer management. The prostate health index, the 4-kallikrein (4K) score, and the PCA3, TMPRSS2-ERG, and Prostarix tests have potential for refining prostate cancer screening in conjunction with traditional prostate-specific antigen testing. The Confirm MDx and PCA3 tests have shown promise in identifying men who need be rebiopsied after a primary negative biopsy. Oncotype DX, Prolaris, the biopsy-based Decipher prostate cancer test, and ProMark may improve predictive risk stratification in addition to the traditional Gleason score and tumor stage. Decipher and Prolaris may predict biochemical recurrence and metastasis after radical prostatectomy and possibly help identify patients who need adjuvant therapy. Androgen receptor splice variant 7 appears effective in guiding the selection of second hormonal manipulation with abiraterone or enzalutamide versus chemotherapy when treating metastatic castration-resistant prostate cancer. PMID:27915475

Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli

PubMed Central

Gat-Viks, Irit; Chevrier, Nicolas; Wilentzik, Roni; Eisenhaure, Thomas; Raychowdhury, Raktima; Steuerman, Yael; Shalek, Alex; Hacohen, Nir; Amit, Ido; Regev, Aviv

2013-01-01

Individual genetic variation affects gene expression in response to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness QTLs; reQTLs) and to position these variants in molecular circuit diagrams. We apply this approach to study variation in transcriptional responsiveness to pathogen components in dendritic cells from recombinant inbred mouse strains. We identify reQTLs that correlate with particular stimuli and position them in known pathways. For example, in response to a virus-like stimulus, a trans-acting variant acts as an activator of the antiviral response; using RNAi, we identify Rgs16 as the likely causal gene. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in circuits that control responses to stimuli. PMID:23503680

Virtual-optical information security system based on public key infrastructure

NASA Astrophysics Data System (ADS)

Peng, Xiang; Zhang, Peng; Cai, Lilong; Niu, Hanben

2005-01-01

A virtual-optical based encryption model with the aid of public key infrastructure (PKI) is presented in this paper. The proposed model employs a hybrid architecture in which our previously published encryption method based on virtual-optics scheme (VOS) can be used to encipher and decipher data while an asymmetric algorithm, for example RSA, is applied for enciphering and deciphering the session key(s). The whole information security model is run under the framework of international standard ITU-T X.509 PKI, which is on basis of public-key cryptography and digital signatures. This PKI-based VOS security approach has additional features like confidentiality, authentication, and integrity for the purpose of data encryption under the environment of network. Numerical experiments prove the effectiveness of the method. The security of proposed model is briefly analyzed by examining some possible attacks from the viewpoint of a cryptanalysis.

Metabolomics to Decipher the Chemical Defense of Cereals against Fusarium graminearum and Deoxynivalenol Accumulation

PubMed Central

Gauthier, Léa; Atanasova-Penichon, Vessela; Chéreau, Sylvain; Richard-Forget, Florence

2015-01-01

Fusarium graminearum is the causal agent of Fusarium head blight (FHB) and Gibberella ear rot (GER), two devastating diseases of wheat, barley, and maize. Furthermore, F. graminearum species can produce type B trichothecene mycotoxins that accumulate in grains. Use of FHB and GER resistant cultivars is one of the most promising strategies to reduce damage induced by F. graminearum. Combined with genetic approaches, metabolomic ones can provide powerful opportunities for plant breeding through the identification of resistant biomarker metabolites which have the advantage of integrating the genetic background and the influence of the environment. In the past decade, several metabolomics attempts have been made to decipher the chemical defense that cereals employ to counteract F. graminearum. By covering the major classes of metabolites that have been highlighted and addressing their potential role, this review demonstrates the complex and integrated network of events that cereals can orchestrate to resist to F. graminearum. PMID:26492237

Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.

PubMed

Gat-Viks, Irit; Chevrier, Nicolas; Wilentzik, Roni; Eisenhaure, Thomas; Raychowdhury, Raktima; Steuerman, Yael; Shalek, Alex K; Hacohen, Nir; Amit, Ido; Regev, Aviv

2013-04-01

Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness quantitative trait loci or reQTLs) and to position these variants in molecular circuit diagrams. We apply this approach to study variation in transcriptional responsiveness to pathogen components in dendritic cells from recombinant inbred mouse strains. We identify reQTLs that correlate with particular stimuli and position them in known pathways. For example, in response to a virus-like stimulus, a trans-acting variant responds as an activator of the antiviral response; using RNA interference, we identify Rgs16 as the likely causal gene. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in circuits that control responses to stimuli.

Synthesis and use of deuterated palmitic acids to decipher the cryptoregiochemistry of a Delta13 desaturation.

PubMed

Abad, José-Luis; Serra, Montserrat; Camps, Francisco; Fabriàs, Gemma

2007-02-02

The synthesis of two hexadeuterated palmitic acids differing in the position of the diagnostic labels, and their use to decipher the cryptoregiochemistry of a Delta13 desaturation are described. A dithiane and a triple bond functionalities were used to introduce the diagnostic (C13 or C14) and tagging (C8 and C9) labels, respectively, in the palmitic acid skeleton. Using these probes, the cryptoregiochemistry of the Delta13 desaturation involved in the biosynthesis of Thaumetopoea pityocampa sex pheromone was studied by means of kinetic isotope effect determinations. Transformation of both (Z)-11-hexadecenoic and 11-hexadecynoic acids into (Z, Z)-11,13-hexadecadienoic and (Z)-13-hexadecen-11-ynoic acids, respectively, is initiated by abstraction of the hydrogen atom at the C13 position, followed by the fast elimination of the C14 hydrogen to give the double bond.

Responses on a lateralized lexical decision task relate to both reading times and comprehension.

PubMed

Michael, Mary

2009-12-01

Research over the last few years has shown that the dominance of the left hemisphere in language processing is less complete than previously thought [Beeman, M. (1993). Semantic processing in the right hemisphere may contribute to drawing inferences from discourse. Brain and Language, 44, 80-120; Faust, M., & Chiarello, C. (1998). Sentence context and lexical ambiguity resolution by the two hemispheres. Neuropsychologia, 36(9), 827-835; Weems, S. A., & Zaidel, E. (2004). The relationship between reading ability and lateralized lexical decision. Brain and Cognition, 55(3), 507-515]. Engaging the right brain in language processing is required for processing speaker/writer intention, particularly in those subtle interpretive processes that help in deciphering humor, irony, and emotional inference. In two experiments employing a divided field or lateralized lexical decision task (LLDT), accuracy and reaction times (RTs) were related to reading times and comprehension on sentence reading. Differences seen in RTs and error rates by visual fields were found to relate to performance. Smaller differences in performance between fields tended to be related to better performance on the LLDT in both experiments and, in Experiment 1, to reading measures. Readers who can exploit both hemispheres for language processing equally appear to be at an advantage in lexical access and possibly also in reading performance.

Fluid-chemical evidence for one billion years of fluid flow through Mesoproterozoic deep-water carbonate mounds (Nanisivik zinc district, Nunavut)

NASA Astrophysics Data System (ADS)

Hahn, K. E.; Turner, E. C.; Kontak, D. J.; Fayek, M.

2018-02-01

Ancient carbonate rocks commonly contain numerous post-depositional phases (carbonate minerals; quartz) recording successive diagenetic events that can be deciphered and tied to known or inferred geological events using a multi-pronged in situ analytical protocol. The framework voids of large, deep-water microbial carbonate seep-mounds in Arctic Canada (Mesoproterozoic Ikpiarjuk Formation) contain multiple generations of synsedimentary and late cement. An in situ analytical study of the post-seafloor cements used optical and cathodoluminescence petrography, SEM-EDS analysis, fluid inclusion (FI) microthermometry and evaporate mound analysis, LA-ICP-MS analysis, and SIMS δ18O to decipher the mounds' long-term diagenetic history. The six void-filling late cements include, in paragenetic order: inclusion-rich euhedral dolomite (ED), finely crystalline clear dolomite (FCD), hematite-bearing dolomite (HD), coarsely crystalline clear dolomite (CCD), quartz (Q), replacive calcite (RC) and late calcite (LC). Based on the combined analytical results, the following fluid-flow history is defined: (1) ED precipitation by autocementation during shallow burial (fluid 1; Mesoproterozoic); (2) progressive mixing of Ca-rich hydrothermal fluid with the connate fluid, resulting in precipitation of FCD followed by HD (fluid 2; also Mesoproterozoic); (3) precipitation of hydrothermal dolomite (CCD) from high-Ca and K-rich fluids (fluid 3; possibly Mesoproterozoic, but timing unclear); (4) hydrothermal Q precipitation (fluid 4; timing unclear), and (5) RC and LC precipitation from a meteoric-derived water (fluid 5) in or since the Mesozoic. Fluids associated with FCD, HD, and CCD may have been mobilised during deposition of the upper Bylot Supergroup; this time interval was the most tectonically active episode in the region's Mesoproterozoic to Recent history. The entire history of intermittent fluid migration and cement precipitation recorded in seemingly unimportant void-filling mineral phases spans over 1 billion years, and was decipherable only because of the in situ protocol used. The multiple-method in situ analytical protocol employed in this study substantially augments the knowledge of an area's geological history, parts of which cannot be discerned by means other than meticulous study of diagenetic phases, and should become routine in similar studies.

Experimental Alteration of Basalt to Support Interpretation of Remote Sensing and In Situ Meausrements from Mars

NASA Technical Reports Server (NTRS)

Bell, M. S.

2014-01-01

Major occurrences of hydrous alteration minerals on Mars have been found in Noachian impact craters formed in basaltic targets and detected using visible/near infrared (VNIR) spectroscopy. Until recently phyllosilicates were detected only in craters in the southern hemisphere [1, 2]. However, it has been reported that at least nine craters in the northern plains apparently excavated thick layers of lava and sediment to expose phyllosilicates [3] as well. The MER (Mars Exploration Rovers) rovers previously reported results of in situ measurement indicating the presence of alteration minerals on Mars [4,5] and it was recently reported that the Mars Curiosity rover has detected alteration phases in situ at Yellowknife Bay in Gale crater as well [6,7]. An important discovery for Mars geochronology is that the Chemistry and Mineralogy (CheMin) x-ray diffraction (XRD) instrument on Curiosity detected phyllosilicates indicating that phyllosilicate formation on Mars extended beyond the Noachian Epoch [8]. These discoveries indicate that Mars was globally altered by water in the past but does not constrain formation conditions for alteration phase occurrences, which have important implications for the evolution of the surface and the biological potential on Mars. Understanding the alteration assemblages produced by a range of conditions is vital for the interpretation of phyllosilicate spectral signatures as well as in situ measurements and to decipher the environment and evolution of early Mars. The martian surface has been intensely altered by meteorite impacts whose effects include brecciation and melting of target materials as well as the initiation of hydrothermal circulation in a hydrous target [9,10,11,12]. Impact effects may facilitate aqueous alteration of a basaltic target because the rate of silicate dissolution is a function of the degree of crystallinity, surface area, and temperature. The resultant alteration mineralogies from shocked basaltic target material are a function of the original mineral assemblage in the parent rocks, the chemistry of fluids that interacted with the rocks, and physico-chemical conditions (pH, temperatures, and pressure) during the time of mineral formation. Understanding the alteration assemblages produced by a range of conditions is vital for the interpretation of phyllosilicate spectral signatures and to decipher the environment and evolution of early Mars, and especially for identifying habitable niches in which life could be initiated and sustained. No experimentally controlled and well characterized analog materials that simulate martian shock metamorphism and alteration conditions currently exist for calibrating either remote sensing or in situ measurements of Mars. A series of experiments was initiated to assess the effects of systematic changes in the physico-chemical conditions on Mars analog materials thereby providing samples to ground-truth Mars remote sensing observations from CRISM (Compact Reconnaissance Imaging Spectrometer for Mars) and in situ measurements from Opportunity's Mössbauer and Curiosity's CHEMIN (Chemistry and Mineralogy X-Ray Diffraction/XRay Fluorescence) instruments. Results of initial experimental runs as analysed by SEM-EDS (Secondary Electron Microscopy -Energy Dispersive Spectroscopy) and X-ray Diffraction (XRD) analysis are reported here and lay the foundation for comparison with shocked and altered samples that will be characterized in the next phase of this work.

Syn-Rift Systems of East Godavari Sub Basin: Its Evolution and Hydrocarbon Prospectivity

NASA Astrophysics Data System (ADS)

Dash, J., Jr.; Zaman, B.

2014-12-01

Krishna Godavari (K.G.) basin is a passive margin basin developed along the Eastern coast of India. This basin has a polyhistoric evolution with multiple rift systems. Rift basin exploration has provided the oil and gas industry with almost one third of discovered global hydrocarbon resources. Understanding synrift sequences, their evolution, depositional styles and hydrocarbon prospectivity has become important with recent discovery of the wells, G-4-6,YS-AF and KG-8 in the K.G. offshore basin. The East Godavari subbasin is a hydrocarbon producing basin from synrift and pre-rift sediments, and hence this was selected as the study area for this research. The study has been carried out by utilizing data of around 58 wells (w1-w58) drilled in the study area 25 of which are hydrocarbon bearing with organic thickness varying from 200 m to 600 m. Age data generated by palaentology and palynology studies have been utilized for calibration of key well logs to differentiate between formations within prerift and synrift sediments. The electrologs of wells like resistivity, gamma ray, neutron, density and sonic logs have been utilized for correlation of different formations in all the drilled wells. The individual thicknesses of sand, shale and coal in the formations have been calculated and tabulated. For Golapalli formation, the isopach and isolith maps were generated which revealed that there were four depocentres with input from the north direction. Schematic geological cross sections were prepared using the well data and seismic data to understand the facies variation across the basin. The sedimentological and petrophysical analysis reports and electro log suites were referred to decipher the environment of deposition, the reservoir characteristics, and play types. The geochemical reports [w4 (Tmax)= 455-468 °C; w1 (Tmax) = 467-514 °C; w4(VRO)= 0.65-0.85; w1(VRO)= 0.83-1.13] revealed the source facies, its maturation and migration timings i.e. the petroleum systems. It was concluded these fluvial channel systems constitute the main hydrocarbon play for the Mandapeta and Gollapalli formations and these channel systems if found at a structurally advantageous positions should prove to be good hydrocarbon targets.

Calcium-mediated shaping of naive CD4 T-cell phenotype and function

PubMed Central

Guichard, Vincent; Bonilla, Nelly; Durand, Aurélie; Audemard-Verger, Alexandra; Guilbert, Thomas; Martin, Bruno

2017-01-01

Continuous contact with self-major histocompatibility complex ligands is essential for the survival of naive CD4 T cells. We have previously shown that the resulting tonic TCR signaling also influences their fate upon activation by increasing their ability to differentiate into induced/peripheral regulatory T cells. To decipher the molecular mechanisms governing this process, we here focus on the TCR signaling cascade and demonstrate that a rise in intracellular calcium levels is sufficient to modulate the phenotype of mouse naive CD4 T cells and to increase their sensitivity to regulatory T-cell polarization signals, both processes relying on calcineurin activation. Accordingly, in vivo calcineurin inhibition leads the most self-reactive naive CD4 T cells to adopt the phenotype of their less self-reactive cell-counterparts. Collectively, our findings demonstrate that calcium-mediated activation of the calcineurin pathway acts as a rheostat to shape both the phenotype and effector potential of naive CD4 T cells in the steady-state. PMID:29239722

Contact chemosensation of phytochemicals by insect herbivores

PubMed Central

Burse, Antje

2017-01-01

Contact chemosensation, or tasting, is a complex process governed by nonvolatile phytochemicals that tell host-seeking insects whether they should accept or reject a plant. During this process, insect gustatory receptors (GRs) contribute to deciphering a host plant's metabolic code. GRs recognise many different classes of nonvolatile compounds; some GRs are likely to be narrowly tuned and others, broadly tuned. Although primary and/or secondary plant metabolites influence the insect's feeding choice, their decoding by GRs is challenging, because metabolites in planta occur in complex mixtures that have additive or inhibitory effects; in diverse forms composed of structurally unrelated molecules; and at different concentrations depending on the plant species, its tissue and developmental stage. Future studies of the mechanism of insect herbivore GRs will benefit from functional characterisation taking into account the spatio-temporal dynamics and diversity of the plant's metabolome. Metabolic information, in turn, will help to elucidate the impact of single ligands and complex natural mixtures on the insect's feeding choice. PMID:28485430

Pathophysiological significance and therapeutic applications of snake venom protease inhibitors.

PubMed

Thakur, Rupamoni; Mukherjee, Ashis K

2017-06-01

Protease inhibitors are important constituents of snake venom and play important roles in the pathophysiology of snakebite. Recently, research on snake venom protease inhibitors has provided valuable information to decipher the molecular details of various biological processes and offer insight for the development of some therapeutically important molecules from snake venom. The process of blood coagulation and fibrinolysis, in addition to affecting platelet function, are well known as the major targets of several snake venom protease inhibitors. This review summarizes the structure-functional aspects of snake venom protease inhibitors that have been described to date. Because diverse biological functions have been demonstrated by protease inhibitors, a comparative overview of their pharmacological and pathophysiological properties is also highlighted. In addition, since most snake venom protease inhibitors are non-toxic on their own, this review evaluates the different roles of individual protease inhibitors that could lead to the identification of drug candidates and diagnostic molecules. Copyright © 2017 Elsevier Ltd. All rights reserved.

Deciphering the language of nature: cryptography, secrecy, and alterity in Francis Bacon.

PubMed

Clody, Michael C

2011-01-01

The essay argues that Francis Bacon's considerations of parables and cryptography reflect larger interpretative concerns of his natural philosophic project. Bacon describes nature as having a language distinct from those of God and man, and, in so doing, establishes a central problem of his natural philosophy—namely, how can the language of nature be accessed through scientific representation? Ultimately, Bacon's solution relies on a theory of differential and duplicitous signs that conceal within them the hidden voice of nature, which is best recognized in the natural forms of efficient causality. The "alphabet of nature"—those tables of natural occurrences—consequently plays a central role in his program, as it renders nature's language susceptible to a process and decryption that mirrors the model of the bilateral cipher. It is argued that while the writing of Bacon's natural philosophy strives for literality, its investigative process preserves a space for alterity within scientific representation, that is made accessible to those with the interpretative key.

Transport characteristics of mammalian Rh and Rh glycoproteins expressed in heterologous systems.

PubMed

Westhoff, C M; Wylie, D E

2006-01-01

The development and use of heterologous expression systems is critical for deciphering the function of mammalian Rh and Rh-glycoproteins. The studies here use Xenopus oocytes, well known for their ability to readily traffic and express difficult membrane proteins, and S. cerevisiae wild-type strains and mutants that are defective in ammonium transport. Data obtained in both of these expression systems revealed that mammalian Rh-glycoprotein-mediated transport (RhAG, RhBG, and RhCG) is an electroneutral process that is driven by the NH4+ concentration and the transmembrane H+ gradient, effectively exchanging NH4+ for H+ in a process that results in transport of net NH3. Homology modeling and functional studies suggest that the more recently evolved erythrocyte blood group proteins, RhCE and RhD, may not function directly in ammonia transport and may be evolving a new function in the RBC membrane. The relationship of Rh and Rh-glycoproteins to the Amt/Mep ammonium transporters is substantiated with functional transport data and structural modeling.

Extrusion of amyloid fibrils to the extracellular space in experimental mesangial AL-amyloidosis: transmission and scanning electron microscopy studies and correlation with renal biopsy observations.

PubMed

Teng, Jiamin; Turbat-Herrera, Elba A; Herrera, Guillermo A

2014-04-01

In vitro studies have provided much information regarding the process of glomerular AL-amyloidogenesis. Research efforts have been successful in deciphering how glomerulopathic light chains interact with mesangial cells. The sequential steps involved in the genesis of amyloid fibrils include interactions with surface caveolae in mesangial cells and internalization of the monoclonal light chains through a clathrin-mediated process followed by trafficking in the mesangial cells to the mature lysosomal compartment where fibrils are formed. This manuscript focuses on how mesangial cells, once amyloid has been formed, deliver the fibrils to the extracellular matrix. The delivery of amyloid fibrils to the outside of the cells is carried out by lysosomes, which abut the mesangial cell membranes and extrude their contents into the extracellular space. This final step responsible for the fibrils to be present predominantly in the extracellular space is well demonstrated with scanning electron microscopy.

In between: gypsy in Drosophila melanogaster reveals new insights into endogenous retrovirus evolution.

PubMed

Touret, Franck; Guiguen, François; Greenland, Timothy; Terzian, Christophe

2014-12-09

Retroviruses are RNA viruses that are able to synthesize a DNA copy of their genome and insert it into a chromosome of the host cell. Sequencing of different eukaryote genomes has revealed the presence of many such endogenous retroviral sequences. The mechanisms by which these retroviral sequences have colonized the genome are still unknown, and the endogenous retrovirus gypsy of Drosophila melanogaster is a powerful experimental model for deciphering this process in vivo. Gypsy is expressed in a layer of somatic cells, and then transferred into the oocyte by an unknown mechanism. This critical step is the start of the endogenization process. Moreover gypsy has been shown to have infectious properties, probably due to its envelope gene acquired from a baculovirus. Recently we have also shown that gypsy maternal transmission is reduced in the presence of the endosymbiotic bacterium Wolbachia. These studies demonstrate that gypsy is a unique and powerful model for understanding the endogenization of retroviruses.

In between: Gypsy in Drosophila melanogaster Reveals New Insights into Endogenous Retrovirus Evolution

PubMed Central

Touret, Franck; Guiguen, François; Greenland, Timothy; Terzian, Christophe

2014-01-01

Retroviruses are RNA viruses that are able to synthesize a DNA copy of their genome and insert it into a chromosome of the host cell. Sequencing of different eukaryote genomes has revealed the presence of many such endogenous retroviral sequences. The mechanisms by which these retroviral sequences have colonized the genome are still unknown, and the endogenous retrovirus gypsy of Drosophila melanogaster is a powerful experimental model for deciphering this process in vivo. Gypsy is expressed in a layer of somatic cells, and then transferred into the oocyte by an unknown mechanism. This critical step is the start of the endogenization process. Moreover gypsy has been shown to have infectious properties, probably due to its envelope gene acquired from a baculovirus. Recently we have also shown that gypsy maternal transmission is reduced in the presence of the endosymbiotic bacterium Wolbachia. These studies demonstrate that gypsy is a unique and powerful model for understanding the endogenization of retroviruses. PMID:25502325

The Long and Arduous Road to CRAC

PubMed Central

Vig, Monika; Kinet, Jean-Pierre

2007-01-01

Store-operated calcium (SOC) entry is the major route of calcium influx in non-excitable cells, especially immune cells. The best characterized store operated current, ICRAC, is carried by calcium release activated calcium (CRAC) channels. The existence of the phenomenon of store-operated calcium influx was proposed almost two decades ago. However, in spite of rigorous research by many laboratories, the identity of the key molecules participating in the process has remained a mystery. In all these years, multiple different approaches have been adopted by countless researchers to identify the molecular players in this fundamental process. Along the way many crucial discoveries have been made, some of which have been summarized here. The last couple of years have seen significant breakthroughs in the field–identification of STIM1 as the store Ca2+ sensor and CRACM1 (Orai1) as the pore forming subunit of the CRAC channel. The field is now actively engaged in deciphering the gating mechanism of CRAC channels. We summarize here the latest progress in this direction. PMID:17517435

Unconventional Protein Secretion in Animal Cells.

PubMed

Ng, Fanny; Tang, Bor Luen

2016-01-01

All eukaryotic cells secrete a range of proteins in a constitutive or regulated manner through the conventional or canonical exocytic/secretory pathway characterized by vesicular traffic from the endoplasmic reticulum, through the Golgi apparatus, and towards the plasma membrane. However, a number of proteins are secreted in an unconventional manner, which are insensitive to inhibitors of conventional exocytosis and use a route that bypasses the Golgi apparatus. These include cytosolic proteins such as fibroblast growth factor 2 (FGF2) and interleukin-1β (IL-1β), and membrane proteins that are known to also traverse to the plasma membrane by a conventional process of exocytosis, such as α integrin and the cystic fibrosis transmembrane conductor (CFTR). Mechanisms underlying unconventional protein secretion (UPS) are actively being analyzed and deciphered, and these range from an unusual form of plasma membrane translocation to vesicular processes involving the generation of exosomes and other extracellular microvesicles. In this chapter, we provide an overview on what is currently known about UPS in animal cells.

Targeting the Metabolic Reprogramming That Controls Epithelial-to-Mesenchymal Transition in Aggressive Tumors

PubMed Central

Morandi, Andrea; Taddei, Maria Letizia; Chiarugi, Paola; Giannoni, Elisa

2017-01-01

The epithelial-to-mesenchymal transition (EMT) process allows the trans-differentiation of a cell with epithelial features into a cell with mesenchymal characteristics. This process has been reported to be a key priming event for tumor development and therefore EMT activation is now considered an established trait of malignancy. The transcriptional and epigenetic reprogramming that governs EMT has been extensively characterized and reviewed in the last decade. However, increasing evidence demonstrates a correlation between metabolic reprogramming and EMT execution. The aim of the current review is to gather the recent findings that illustrate this correlation to help deciphering whether metabolic changes are causative or just a bystander effect of EMT activation. The review is divided accordingly to the catabolic and anabolic pathways that characterize carbohydrate, aminoacid, and lipid metabolism. Moreover, at the end of each part, we have discussed a series of potential metabolic targets involved in EMT promotion and execution for which drugs are either available or that could be further investigated for therapeutic intervention. PMID:28352611

Interaction of Mitochondria with the Endoplasmic Reticulum and Plasma Membrane in Calcium Homeostasis, Lipid Trafficking and Mitochondrial Structure.

PubMed

Szymański, Jędrzej; Janikiewicz, Justyna; Michalska, Bernadeta; Patalas-Krawczyk, Paulina; Perrone, Mariasole; Ziółkowski, Wiesław; Duszyński, Jerzy; Pinton, Paolo; Dobrzyń, Agnieszka; Więckowski, Mariusz R

2017-07-20

Studying organelles in isolation has been proven to be indispensable for deciphering the underlying mechanisms of molecular cell biology. However, observing organelles in intact cells with the use of microscopic techniques reveals a new set of different junctions and contact sites between them that contribute to the control and regulation of various cellular processes, such as calcium and lipid exchange or structural reorganization of the mitochondrial network. In recent years, many studies focused their attention on the structure and function of contacts between mitochondria and other organelles. From these studies, findings emerged showing that these contacts are involved in various processes, such as lipid synthesis and trafficking, modulation of mitochondrial morphology, endoplasmic reticulum (ER) stress, apoptosis, autophagy, inflammation and Ca 2 + handling. In this review, we focused on the physical interactions of mitochondria with the endoplasmic reticulum and plasma membrane and summarized present knowledge regarding the role of mitochondria-associated membranes in calcium homeostasis and lipid metabolism.

Artificial Intelligence in Medical Practice: The Question to the Answer?

PubMed

Miller, D Douglas; Brown, Eric W

2018-02-01

Computer science advances and ultra-fast computing speeds find artificial intelligence (AI) broadly benefitting modern society-forecasting weather, recognizing faces, detecting fraud, and deciphering genomics. AI's future role in medical practice remains an unanswered question. Machines (computers) learn to detect patterns not decipherable using biostatistics by processing massive datasets (big data) through layered mathematical models (algorithms). Correcting algorithm mistakes (training) adds to AI predictive model confidence. AI is being successfully applied for image analysis in radiology, pathology, and dermatology, with diagnostic speed exceeding, and accuracy paralleling, medical experts. While diagnostic confidence never reaches 100%, combining machines plus physicians reliably enhances system performance. Cognitive programs are impacting medical practice by applying natural language processing to read the rapidly expanding scientific literature and collate years of diverse electronic medical records. In this and other ways, AI may optimize the care trajectory of chronic disease patients, suggest precision therapies for complex illnesses, reduce medical errors, and improve subject enrollment into clinical trials. Copyright © 2018 Elsevier Inc. All rights reserved.

Integrating biodiversity distribution knowledge: toward a global map of life.

PubMed

Jetz, Walter; McPherson, Jana M; Guralnick, Robert P

2012-03-01

Global knowledge about the spatial distribution of species is orders of magnitude coarser in resolution than other geographically-structured environmental datasets such as topography or land cover. Yet such knowledge is crucial in deciphering ecological and evolutionary processes and in managing global change. In this review, we propose a conceptual and cyber-infrastructure framework for refining species distributional knowledge that is novel in its ability to mobilize and integrate diverse types of data such that their collective strengths overcome individual weaknesses. The ultimate aim is a public, online, quality-vetted 'Map of Life' that for every species integrates and visualizes available distributional knowledge, while also facilitating user feedback and dynamic biodiversity analyses. First milestones toward such an infrastructure have now been implemented. Copyright © 2011 Elsevier Ltd. All rights reserved.

Deciphering the BAR code of membrane modulators.

PubMed

Salzer, Ulrich; Kostan, Julius; Djinović-Carugo, Kristina

2017-07-01

The BAR domain is the eponymous domain of the "BAR-domain protein superfamily", a large and diverse set of mostly multi-domain proteins that play eminent roles at the membrane cytoskeleton interface. BAR domain homodimers are the functional units that peripherally associate with lipid membranes and are involved in membrane sculpting activities. Differences in their intrinsic curvatures and lipid-binding properties account for a large variety in membrane modulating properties. Membrane activities of BAR domains are further modified and regulated by intramolecular or inter-subunit domains, by intermolecular protein interactions, and by posttranslational modifications. Rather than providing detailed cell biological information on single members of this superfamily, this review focuses on biochemical, biophysical, and structural aspects and on recent findings that paradigmatically promote our understanding of processes driven and modulated by BAR domains.

Identification of Tyrosine Phosphorylated Proteins by SH2 Domain Affinity Purification and Mass Spectrometry.

PubMed

Buhs, Sophia; Gerull, Helwe; Nollau, Peter

2017-01-01

Phosphotyrosine signaling plays a major role in the control of many important biological functions such as cell proliferation and apoptosis. Deciphering of phosphotyrosine-dependent signaling is therefore of great interest paving the way for the understanding of physiological and pathological processes of signal transduction. On the basis of the specific binding of SH2 domains to phosphotyrosine residues, we here present an experimental workflow for affinity purification and subsequent identification of tyrosine phosphorylated proteins by mass spectrometry. In combination with SH2 profiling, a broadly applicable platform for the characterization of phosphotyrosine profiles in cell extracts, our pull down strategy enables researchers by now to identify proteins in signaling cascades which are differentially phosphorylated and selectively recognized by distinct SH2 domains.

Unwitting self-disclosures in psychodynamic psychotherapy: deciphering their meaning and accessing the pain within.

PubMed

Gans, Jerome S

2011-04-01

Unwitting self-disclosures (USDs), unconscious yet observable parts of personality, are often behavioral relics of past suffering and, as such, constitute valuable though frequently underutilized clinical information. While ego-syntonic aspects of personality can be commented on with impunity, dealing therapeutically with patients' USDs--manifestations of their blind spots--requires sensitivity, empathy, and timing. Providing many clinical examples of patient and therapist USDs from individual and group psychotherapy, this report discusses the origins, possible meanings, and the countertransference and empathic challenges encountered in the handling of these blind spots. The importance of establishing a narcissistic alliance and of employing the methods of the existential school of psychotherapy in processing USDs is described. Self-aware therapists can minimize the clinical impasse that may result when therapist-patient blind spots overlap.

A primer on thermodynamic-based models for deciphering transcriptional regulatory logic.

PubMed

Dresch, Jacqueline M; Richards, Megan; Ay, Ahmet

2013-09-01

A rigorous analysis of transcriptional regulation at the DNA level is crucial to the understanding of many biological systems. Mathematical modeling has offered researchers a new approach to understanding this central process. In particular, thermodynamic-based modeling represents the most biophysically informed approach aimed at connecting DNA level regulatory sequences to the expression of specific genes. The goal of this review is to give biologists a thorough description of the steps involved in building, analyzing, and implementing a thermodynamic-based model of transcriptional regulation. The data requirements for this modeling approach are described, the derivation for a specific regulatory region is shown, and the challenges and future directions for the quantitative modeling of gene regulation are discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

Shared issues of wavefield inversion and illustrations in 3-D diffusive electromagnetics

NASA Astrophysics Data System (ADS)

Lesselier, Dominique; Lambert, Marc; Perrusson, Gaële

2005-07-01

Electromagnetic non-destructive evaluation of complex objects means that one has to decipher data which result from their interaction with imposed sources. This task is crucial in civil, environmental and medical engineering, to quote obvious fields, as well as for safety and reliability of industrial processes of various kinds in key energy and transportation sectors, for example. This short contribution does not attempt to review the huge variety of themes and the many applications of the science of inversion, but aims at emphasizing a number of points that seem common enough to this science to be worthwhile to be reviewed. Two illustrations and a few main references thought of good interest among the ever increasing literature are given. To cite this article: D. Lesselier et al., C. R. Physique 6 (2005).

Deciphering neuronal population codes for acute thermal pain

NASA Astrophysics Data System (ADS)

Chen, Zhe; Zhang, Qiaosheng; Phuong Sieu Tong, Ai; Manders, Toby R.; Wang, Jing

2017-06-01

Objective. Pain is defined as an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage. Current pain research mostly focuses on molecular and synaptic changes at the spinal and peripheral levels. However, a complete understanding of pain mechanisms requires the physiological study of the neocortex. Our goal is to apply a neural decoding approach to read out the onset of acute thermal pain signals, which can be used for brain-machine interface. Approach. We used micro wire arrays to record ensemble neuronal activities from the primary somatosensory cortex (S1) and anterior cingulate cortex (ACC) in freely behaving rats. We further investigated neural codes for acute thermal pain at both single-cell and population levels. To detect the onset of acute thermal pain signals, we developed a novel latent state-space framework to decipher the sorted or unsorted S1 and ACC ensemble spike activities, which reveal information about the onset of pain signals. Main results. The state space analysis allows us to uncover a latent state process that drives the observed ensemble spike activity, and to further detect the ‘neuronal threshold’ for acute thermal pain on a single-trial basis. Our method achieved good detection performance in sensitivity and specificity. In addition, our results suggested that an optimal strategy for detecting the onset of acute thermal pain signals may be based on combined evidence from S1 and ACC population codes. Significance. Our study is the first to detect the onset of acute pain signals based on neuronal ensemble spike activity. It is important from a mechanistic viewpoint as it relates to the significance of S1 and ACC activities in the regulation of the acute pain onset.

Shelfal sediment transport by undercurrents forces turbidity current activity during high sea level, Chile continental margin

NASA Astrophysics Data System (ADS)

Bernhardt, Anne; Hebbeln, Dierk; Regenberg, Marcus; Lückge, Andreas; Strecker, Manfred. R.

2016-04-01

Understanding the links between terrigenous sediment supply and marine transport and depositional processes along tectonically active margins is essential to decipher turbidite successions as potential archives of climatic and seismic forcings and to comprehend timing and quantity of marine clastic deposition. Sequence stratigraphic models predict coarse-grained terrigenous sediment delivery to deep-marine sites mainly during sea-level fall and lowstand. Marine clastic deposition during periods of transgression and highstand has been attributed to the continued geomorphic connectivity between terrestrial sediment sources and marine sinks (e.g., rivers connected to submarine canyons) often facilitated by narrow shelves, high sediment supply causing delta migration to the shelf edge, and/or abrupt increases in sediment supply due to climatic variability or catastrophic events. To decipher the controls on Holocene highstand turbidite deposition, we analyzed twelve sediment cores of spatially disparate, coeval Holocene turbidite systems along the Chile margin (29-40°S) with changing climatic and geomorphic characteristics but uniform changes of sea level. Intraslope basins in north-central Chile (29-33°S) offshore a narrow to absent shelf record a shut-off of turbidite activity during the Holocene. In contrast, core sites in south-central Chile (36-40°S) offshore a wide continental shelf have repeatedly experienced turbidite deposition during sea-level highstand conditions, even though most of the depocenters are not connected via canyons to sediment sources. The interplay of stable high sediment supply related to strong onshore precipitation in combination with a wide shelf, over which undercurrents move sediment towards the shelf edge, appears to control Holocene turbidite sedimentation and sediment export to the deep sea.

Molecular profiling of the Phytophthora plurivora secretome: a step towards understanding the cross-talk between plant pathogenic oomycetes and their hosts.

PubMed

Severino, Valeria; Farina, Annarita; Fleischmann, Frank; Dalio, Ronaldo J D; Di Maro, Antimo; Scognamiglio, Monica; Fiorentino, Antonio; Parente, Augusto; Osswald, Wolfgang; Chambery, Angela

2014-01-01

The understanding of molecular mechanisms underlying host-pathogen interactions in plant diseases is of crucial importance to gain insights on different virulence strategies of pathogens and unravel their role in plant immunity. Among plant pathogens, Phytophthora species are eliciting a growing interest for their considerable economical and environmental impact. Plant infection by Phytophthora phytopathogens is a complex process coordinated by a plethora of extracellular signals secreted by both host plants and pathogens. The characterization of the repertoire of effectors secreted by oomycetes has become an active area of research for deciphering molecular mechanisms responsible for host plants colonization and infection. Putative secreted proteins by Phytophthora species have been catalogued by applying high-throughput genome-based strategies and bioinformatic approaches. However, a comprehensive analysis of the effective secretome profile of Phytophthora is still lacking. Here, we report the first large-scale profiling of P. plurivora secretome using a shotgun LC-MS/MS strategy. To gain insight on the molecular signals underlying the cross-talk between plant pathogenic oomycetes and their host plants, we also investigate the quantitative changes of secreted protein following interaction of P. plurivora with the root exudate of Fagus sylvatica which is highly susceptible to the root pathogen. We show that besides known effectors, the expression and/or secretion levels of cell-wall-degrading enzymes were altered following the interaction with the host plant root exudate. In addition, a characterization of the F. sylvatica root exudate was performed by NMR and amino acid analysis, allowing the identification of the main released low-molecular weight components, including organic acids and free amino acids. This study provides important insights for deciphering the extracellular network involved in the highly susceptible P. plurivora-F. sylvatica interaction.

Tiny giants of gene regulation: experimental strategies for microRNA functional studies

PubMed Central

Steinkraus, Bruno R.; Toegel, Markus

2016-01-01

The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA–target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high‐throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA–target binding events in vivo drove the emergence of a slew of high‐throughput multiplex strategies, which now provide a viable prospect for elucidating genome‐wide miRNA–target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post‐transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high‐precision interference with their direct, endogenous targets. WIREs Dev Biol 2016, 5:311–362. doi: 10.1002/wdev.223 For further resources related to this article, please visit the WIREs website. PMID:26950183

Interneurons in the Honeybee Primary Auditory Center Responding to Waggle Dance-Like Vibration Pulses.

PubMed

Ai, Hiroyuki; Kai, Kazuki; Kumaraswamy, Ajayrama; Ikeno, Hidetoshi; Wachtler, Thomas

2017-11-01

Female honeybees use the "waggle dance" to communicate the location of nectar sources to their hive mates. Distance information is encoded in the duration of the waggle phase (von Frisch, 1967). During the waggle phase, the dancer produces trains of vibration pulses, which are detected by the follower bees via Johnston's organ located on the antennae. To uncover the neural mechanisms underlying the encoding of distance information in the waggle dance follower, we investigated morphology, physiology, and immunohistochemistry of interneurons arborizing in the primary auditory center of the honeybee ( Apis mellifera ). We identified major interneuron types, named DL-Int-1, DL-Int-2, and bilateral DL-dSEG-LP, that responded with different spiking patterns to vibration pulses applied to the antennae. Experimental and computational analyses suggest that inhibitory connection plays a role in encoding and processing the duration of vibration pulse trains in the primary auditory center of the honeybee. SIGNIFICANCE STATEMENT The waggle dance represents a form of symbolic communication used by honeybees to convey the location of food sources via species-specific sound. The brain mechanisms used to decipher this symbolic information are unknown. We examined interneurons in the honeybee primary auditory center and identified different neuron types with specific properties. The results of our computational analyses suggest that inhibitory connection plays a role in encoding waggle dance signals. Our results are critical for understanding how the honeybee deciphers information from the sound produced by the waggle dance and provide new insights regarding how common neural mechanisms are used by different species to achieve communication. Copyright © 2017 the authors 0270-6474/17/3710624-12$15.00/0.

Perspectives on deciphering mechanisms underlying plant heat stress response and thermotolerance

PubMed Central

Bokszczanin, Kamila L.; Fragkostefanakis, Sotirios

2013-01-01

Global warming is a major threat for agriculture and food safety and in many cases the negative effects are already apparent. The current challenge of basic and applied plant science is to decipher the molecular mechanisms of heat stress response (HSR) and thermotolerance in detail and use this information to identify genotypes that will withstand unfavorable environmental conditions. Nowadays X-omics approaches complement the findings of previous targeted studies and highlight the complexity of HSR mechanisms giving information for so far unrecognized genes, proteins and metabolites as potential key players of thermotolerance. Even more, roles of epigenetic mechanisms and the involvement of small RNAs in thermotolerance are currently emerging and thus open new directions of yet unexplored areas of plant HSR. In parallel it is emerging that although the whole plant is vulnerable to heat, specific organs are particularly sensitive to elevated temperatures. This has redirected research from the vegetative to generative tissues. The sexual reproduction phase is considered as the most sensitive to heat and specifically pollen exhibits the highest sensitivity and frequently an elevation of the temperature just a few degrees above the optimum during pollen development can have detrimental effects for crop production. Compared to our knowledge on HSR of vegetative tissues, the information on pollen is still scarce. Nowadays, several techniques for high-throughput X-omics approaches provide major tools to explore the principles of pollen HSR and thermotolerance mechanisms in specific genotypes. The collection of such information will provide an excellent support for improvement of breeding programs to facilitate the development of tolerant cultivars. The review aims at describing the current knowledge of thermotolerance mechanisms and the technical advances which will foster new insights into this process. PMID:23986766

Deciphering Egyptian Hieroglyphs: Towards a New Strategy for Navigation in Museums.

PubMed

Duque-Domingo, Jaime; Herrera, Pedro Javier; Valero, Enrique; Cerrada, Carlos

2017-03-14

This work presents a novel strategy to decipher fragments of Egyptian cartouches identifying the hieroglyphs of which they are composed. A cartouche is a drawing, usually inside an oval, that encloses a group of hieroglyphs representing the name of a monarch. Aiming to identify these drawings, the proposed method is based on several techniques frequently used in computer vision and consists of three main stages: first, a picture of the cartouche is taken as input and its contour is localized. In the second stage, each hieroglyph is individually extracted and identified. Finally, the cartouche is interpreted: the sequence of the hieroglyphs is established according to a previously generated benchmark. This sequence corresponds to the name of the king. Although this method was initially conceived to deal with both high and low relief writing in stone, it can be also applied to painted hieroglyphs. This approach is not affected by variable lighting conditions, or the intensity and the completeness of the objects. This proposal has been tested on images obtained from the Abydos King List and other Egyptian monuments and archaeological excavations. The promising results give new possibilities to recognize hieroglyphs, opening a new way to decipher longer texts and inscriptions, being particularly useful in museums and Egyptian environments. Additionally, devices used for acquiring visual information from cartouches (i.e., smartphones), can be part of a navigation system for museums where users are located in indoor environments by means of the combination of WiFi Positioning Systems (WPS) and depth cameras, as unveiled at the end of the document.

Deciphering Egyptian Hieroglyphs: Towards a New Strategy for Navigation in Museums

PubMed Central

Duque-Domingo, Jaime; Herrera, Pedro Javier; Valero, Enrique; Cerrada, Carlos

2017-01-01

This work presents a novel strategy to decipher fragments of Egyptian cartouches identifying the hieroglyphs of which they are composed. A cartouche is a drawing, usually inside an oval, that encloses a group of hieroglyphs representing the name of a monarch. Aiming to identify these drawings, the proposed method is based on several techniques frequently used in computer vision and consists of three main stages: first, a picture of the cartouche is taken as input and its contour is localized. In the second stage, each hieroglyph is individually extracted and identified. Finally, the cartouche is interpreted: the sequence of the hieroglyphs is established according to a previously generated benchmark. This sequence corresponds to the name of the king. Although this method was initially conceived to deal with both high and low relief writing in stone, it can be also applied to painted hieroglyphs. This approach is not affected by variable lighting conditions, or the intensity and the completeness of the objects. This proposal has been tested on images obtained from the Abydos King List and other Egyptian monuments and archaeological excavations. The promising results give new possibilities to recognize hieroglyphs, opening a new way to decipher longer texts and inscriptions, being particularly useful in museums and Egyptian environments. Additionally, devices used for acquiring visual information from cartouches (i.e., smartphones), can be part of a navigation system for museums where users are located in indoor environments by means of the combination of WiFi Positioning Systems (WPS) and depth cameras, as unveiled at the end of the document. PMID:28335445

Early Events in the Amyloid Formation of the A546T Mutant of Transforming Growth Factor β-Induced Protein in Corneal Dystrophies Compared to the Nonfibrillating R555W and R555Q Mutants.

PubMed

Koldsø, Heidi; Andersen, Ole Juul; Nikolajsen, Camilla Lund; Scavenius, Carsten; Sørensen, Charlotte S; Underhaug, Jarl; Runager, Kasper; Nielsen, Niels Chr; Enghild, Jan J; Schiøtt, Birgit

2015-09-15

The human transforming growth factor β-induced protein (TGFBIp) is involved in several types of corneal dystrophies where protein aggregation and amyloid fibril formation severely impair vision. Most disease-causing mutations are located in the last of four homologous fasciclin-1 (FAS1) domains of the protein, and it has been shown that when isolated, the fourth FAS1 domain (FAS1-4) mimics the behavior of full-length TGFBIp. In this study, we use molecular dynamics simulations and principal component analysis to study the wild-type FAS1-4 domain along with three disease-causing mutations (R555W, R555Q, and A546T) to decipher any internal difference in dynamical properties of the domains that may explain their varied stabilities and aggregation properties. In addition, we use a protein-protein docking method in combination with chemical cross-linking experiments and mass spectrometry of the cross-linked species to obtain information about interaction faces between identical FAS1-4 domains. The results show that the pathogenic mutations A546T and R555W affect the packing in the hydrophobic core of FAS1-4 in different directions. We further show that the FAS1-4 monomers associate using their β-rich regions, consistent with peptides observed to be part of the amyloid fibril core in lattice corneal dystrophy patients.

Therapeutic Activity of Anti-AXL Antibody against Triple-Negative Breast Cancer Patient-Derived Xenografts and Metastasis.

PubMed

Leconet, Wilhem; Chentouf, Myriam; du Manoir, Stanislas; Chevalier, Clément; Sirvent, Audrey; Aït-Arsa, Imade; Busson, Muriel; Jarlier, Marta; Radosevic-Robin, Nina; Theillet, Charles; Chalbos, Dany; Pasquet, Jean-Max; Pèlegrin, André; Larbouret, Christel; Robert, Bruno

2017-06-01

Purpose: AXL receptor tyrosine kinase has been described as a relevant molecular marker and a key player in invasiveness, especially in triple-negative breast cancer (TNBC). Experimental Design: We evaluate the antitumor efficacy of the anti-AXL monoclonal antibody 20G7-D9 in several TNBC cell xenografts or patient-derived xenograft (PDX) models and decipher the underlying mechanisms. In a dataset of 254 basal-like breast cancer samples, genes correlated with AXL expression are enriched in EMT, migration, and invasion signaling pathways. Results: Treatment with 20G7-D9 inhibited tumor growth and bone metastasis formation in AXL-positive TNBC cell xenografts or PDX, but not in AXL-negative PDX, highlighting AXL role in cancer growth and invasion. In vitro stimulation of AXL-positive cancer cells by its ligand GAS6 induced the expression of several EMT-associated genes ( SNAIL, SLUG , and VIM ) through an intracellular signaling implicating the transcription factor FRA-1, important in cell invasion and plasticity, and increased their migration/invasion capacity. 20G7-D9 induced AXL degradation and inhibited all AXL/GAS6-dependent cell signaling implicated in EMT and in cell migration/invasion. Conclusions: The anti-AXL antibody 20G7-D9 represents a promising therapeutic strategy in TNBC with mesenchymal features by inhibiting AXL-dependent EMT, tumor growth, and metastasis formation. Clin Cancer Res; 23(11); 2806-16. ©2016 AACR . ©2016 American Association for Cancer Research.

Cracking the code: a decode strategy for the international business machines punch cards of Korean war soldiers.

PubMed

Mitsunaga, Erin M

2006-05-01

During the Korean War, International Business Machines (IBM) punch cards were created for every individual involved in military combat. Each card contained all pertinent personal information about the individual and was utilized to keep track of all soldiers involved. However, at present, all of the information known about these punch cards reveals only their format and their significance; there is little to no information on how these cards were created or how to interpret the information contained without the aid of the computer system used during the war. Today, it is believed there is no one available to explain this computerized system, nor do the original computers exist. This decode strategy is the result of an attempt to decipher the information on these cards through the use of all available medical and dental records for each individual examined. By cross-referencing the relevant personal information with the known format of the cards, a basic guess-and-check method was utilized. After examining hundreds of IBM punch cards, however, it has become clear that the punch card method of recording information was not infallible. In some cases, there are gaps of information on cards where there are data recorded on personal records; in others, information is punched incorrectly onto the cards, perhaps as the result of a transcription error. Taken all together, it is clear that the information contained on each individual's card should be taken solely as another form of personal documentation.

Cryptanalysis in World War II--and Mathematics Education.

ERIC Educational Resources Information Center

Hilton, Peter

1984-01-01

Hilton describes the team of cryptanalysts who tried to decipher German and Japanese codes during the Second World War. The work of Turing, essentially developing the computer, is reported, as well as inferences about pure and applied mathematics. (MNS)

Deciphering Scavenging Propensity Among Arthropod Predators.

USDA-ARS?s Scientific Manuscript database

Scavenging is a well documented feeding behavior among many arthrop predators. However, quantifying scavenging feeding activity is not well understood because many predators are small elusive. This makes directly observing predation events in nature almost impossible. If predators prefer dead prey ...

Public Understanding of Science through Evaluations

NASA Astrophysics Data System (ADS)

Dusenbery, P.; Koke, J.

Evaluation is an integral part of exhibition development. It is usually a 3-phase process: front end, formative and summative. This report will compare science misconception studies of students with a number of front-end museum studies in order to elucidate the similarities and differences between student and general public understanding of science. The Space Science Institute (SSI) has recently conducted a major front-end evaluation of its Alien Earths exhibition. Alien Earths has four interrelated exhibit areas: Our Place in Space, Star Birth, PlanetQuest, and Search for Life. Exhibit visitors will explore the awesome events surrounding the birth of stars and planets; they will join scientists in the hunt for planets outside our solar system including those that may be in ``habitable zones'' around other stars; and finally they will be able to learn about the wide range of conditions for life on Earth and how scientists are looking for signs of life beyond Earth. The front-end evaluation elicited visitors' beliefs about the origins of life, what life is dominant on Earth, and the role indirect evidence plays in science. The front-end evaluation also examined visitors' understanding of the tools used in origins research from grand telescopes to microscopes, their ability to decipher and interpret images of star forming regions, and their fluency with the specific terminology likely to be used in the Alien Earths scripts. Front-end evaluation worked to support concept design and development by developing the visitors' entrance narrative -- their pre-existing knowledge, commonly held misconceptions, and their attitudes and interests towards the topic. This served to identify potential points of access and barriers to efficient communication.

Immune Modulation of Cardiac Repair and Regeneration: The Art of Mending Broken Hearts

PubMed Central

Zlatanova, Ivana; Pinto, Cristina; Silvestre, Jean-Sébastien

2016-01-01

The accumulation of immune cells is among the earliest responses that manifest in the cardiac tissue after injury. Both innate and adaptive immunity coordinate distinct and mutually non-exclusive events governing cardiac repair, including elimination of the cellular debris, compensatory growth of the remaining cardiac tissue, activation of resident or circulating precursor cells, quantitative and qualitative modifications of the vascular network, and formation of a fibrotic scar. The present review summarizes the mounting evidence suggesting that the inflammatory response also guides the regenerative process following cardiac damage. In particular, recent literature has reinforced the central role of monocytes/macrophages in poising the refreshment of cardiomyocytes in myocardial infarction- or apical resection-induced cardiac insult. Macrophages dictate cardiac myocyte renewal through stimulation of preexisting cardiomyocyte proliferation and/or neovascularization. Nevertheless, substantial efforts are required to identify the nature of these macrophage-derived factors as well as the molecular mechanisms engendered by the distinct subsets of macrophages pertaining in the cardiac tissue. Among the growing inflammatory intermediaries that have been recognized as essential player in heart regeneration, we will focus on the role of interleukin (IL)-6 and IL-13. Finally, it is likely that within the mayhem of the injured cardiac tissue, additional types of inflammatory cells, such as neutrophils, will enter the dance to ignite and refresh the broken heart. However, the protective and detrimental inflammatory pathways have been mainly deciphered in animal models. Future research should be focused on understanding the cellular effectors and molecular signals regulating inflammation in human heart to pave the way for the development of factual therapies targeting the inflammatory compartment in cardiac diseases. PMID:27790620

Immune Modulation of Cardiac Repair and Regeneration: The Art of Mending Broken Hearts.

PubMed

Zlatanova, Ivana; Pinto, Cristina; Silvestre, Jean-Sébastien

2016-01-01

The accumulation of immune cells is among the earliest responses that manifest in the cardiac tissue after injury. Both innate and adaptive immunity coordinate distinct and mutually non-exclusive events governing cardiac repair, including elimination of the cellular debris, compensatory growth of the remaining cardiac tissue, activation of resident or circulating precursor cells, quantitative and qualitative modifications of the vascular network, and formation of a fibrotic scar. The present review summarizes the mounting evidence suggesting that the inflammatory response also guides the regenerative process following cardiac damage. In particular, recent literature has reinforced the central role of monocytes/macrophages in poising the refreshment of cardiomyocytes in myocardial infarction- or apical resection-induced cardiac insult. Macrophages dictate cardiac myocyte renewal through stimulation of preexisting cardiomyocyte proliferation and/or neovascularization. Nevertheless, substantial efforts are required to identify the nature of these macrophage-derived factors as well as the molecular mechanisms engendered by the distinct subsets of macrophages pertaining in the cardiac tissue. Among the growing inflammatory intermediaries that have been recognized as essential player in heart regeneration, we will focus on the role of interleukin (IL)-6 and IL-13. Finally, it is likely that within the mayhem of the injured cardiac tissue, additional types of inflammatory cells, such as neutrophils, will enter the dance to ignite and refresh the broken heart. However, the protective and detrimental inflammatory pathways have been mainly deciphered in animal models. Future research should be focused on understanding the cellular effectors and molecular signals regulating inflammation in human heart to pave the way for the development of factual therapies targeting the inflammatory compartment in cardiac diseases.

How to make stripes: deciphering the transition from non-periodic to periodic patterns in Drosophila segmentation

PubMed Central

Schroeder, Mark D.; Greer, Christina; Gaul, Ulrike

2011-01-01

The generation of metameric body plans is a key process in development. In Drosophila segmentation, periodicity is established rapidly through the complex transcriptional regulation of the pair-rule genes. The ‘primary’ pair-rule genes generate their 7-stripe expression through stripe-specific cis-regulatory elements controlled by the preceding non-periodic maternal and gap gene patterns, whereas ‘secondary’ pair-rule genes are thought to rely on 7-stripe elements that read off the already periodic primary pair-rule patterns. Using a combination of computational and experimental approaches, we have conducted a comprehensive systems-level examination of the regulatory architecture underlying pair-rule stripe formation. We find that runt (run), fushi tarazu (ftz) and odd skipped (odd) establish most of their pattern through stripe-specific elements, arguing for a reclassification of ftz and odd as primary pair-rule genes. In the case of run, we observe long-range cis-regulation across multiple intervening genes. The 7-stripe elements of run, ftz and odd are active concurrently with the stripe-specific elements, indicating that maternal/gap-mediated control and pair-rule gene cross-regulation are closely integrated. Stripe-specific elements fall into three distinct classes based on their principal repressive gap factor input; stripe positions along the gap gradients correlate with the strength of predicted input. The prevalence of cis-elements that generate two stripes and their genomic organization suggest that single-stripe elements arose by splitting and subfunctionalization of ancestral dual-stripe elements. Overall, our study provides a greatly improved understanding of how periodic patterns are established in the Drosophila embryo. PMID:21693522

Neutrino-Driven Explosions

NASA Astrophysics Data System (ADS)

Janka, Hans-Thomas

The question why and how core-collapse supernovae (SNe) explode is one of the central and most long-standing riddles of stellar astrophysics. Solving this problem is crucial for deciphering the supernova (SN) phenomenon; for predicting its observable signals such as light curves and spectra, nucleosynthesis yields, neutrinos, and gravitational waves; for defining the role of SNe in the dynamical and chemo-dynamical evolution of galaxies; and for explaining the birth conditions and properties of neutron stars (NSs) and stellar-mass black holes. Since the formation of such compact remnants releases over hundred times more energy in neutrinos than the kinetic energy of the SN explosion, neutrinos can be the decisive agents for powering the SN outburst. According to the standard paradigm of the neutrino-driven mechanism, the energy transfer by the intense neutrino flux to the medium behind the stagnating core bounce shock, assisted by violent hydrodynamic mass motions (sometimes subsumed by the term "turbulence"), revives the outward shock motion and thus initiates the SN explosion. Because of the weak coupling of neutrinos in the region of this energy deposition, detailed, multidimensional hydrodynamic models including neutrino transport and a wide variety of physics are needed to assess the viability of the mechanism. Owing to advanced numerical codes and increasing supercomputer power, considerable progress has been achieved in our understanding of the physical processes that have to act in concert for the success of neutrino-driven explosions. First studies begin to reveal observational implications and avenues to test the theoretical picture by data from individual SNe and SN remnants but also from population-integrated observables. While models will be further refined, a real breakthrough is expected through the next galactic core-collapse SN, when neutrinos and gravitational waves can be used to probe the conditions deep inside the dying star.

Geoarchaeological research on Bronze Age settlement mounds in the Kolkheti lowlands at the Black Sea coast of Georgia

NASA Astrophysics Data System (ADS)

Laermanns, Hannes; Heisterkamp, Arne; Kirkitadze, Giorgi; Elashvili, Mikheil; Verheul, Jan; Kelterbaum, Daniel; Helmut, Brückner

2016-04-01

0.0.1 Situated between the Rivers Enguri in the north and Khobistsqali in the south, more than 20 settlement mounds (local name Dikhagudzuba), identified by field survey and remote sensing techniques, give evidence of a densely populated landscape in the coastal lowlands of eastern Georgia during the Bronze Age. While the existing chronology of these mounds is based on ceramic evidence obtained during a previous archaeological research, only limited information is available on their internal architecture and their palaeoenvironmental context, and the chronology of the different layers is as yet lacking. 0.0.2 Within the framework of a geoarchaeological research project, we carried out eleven vibracores on and in direct vicinity of three of the most prominent mounds, situated close to the villages of Orulu and Ergeta. Based on these sediment cores, our study aims at (i) establishing a chronostratigraphical framework for the settlements based on radiocarbon dating; (ii) reconstructing possible phases and gaps of occupation; and (iii) identifying the environmental conditions during the time of their existence. Geochemical and sedimentological analyses were carried out to decipher element contents (XRF), granulometry, and organic contents (LOI, C/N) of sediment samples, supporting the interpretation of the mounds' stratigraphical evolution and related human occupation. The three investigated settlement mounds are similar in dimension and stratigraphy, and different settlement layers could be identified in each of them. The 14C age estimates indicate that their formation occurred during the second half of the 3rd and the first half of the 2nd millennium BC, thus confirming the archaeological interpretation of their Bronze Age origin. Based on the granulometric and geochemical data, palaeoenvironmental conditions in the vicinity of the settlements were dominated by fluvial processes.

Neogene paleoelevation of intermontane basins in a narrow, compressional mountain range, southern Central Andes of Argentina

NASA Astrophysics Data System (ADS)

Hoke, Gregory D.; Giambiagi, Laura B.; Garzione, Carmala N.; Mahoney, J. Brian; Strecker, Manfred R.

2014-11-01

The topographic growth of mountain ranges at convergent margins results from the complex interaction between the motion of lithospheric plates, crustal shortening, rock uplift and exhumation. Constraints on the timing and magnitude of elevation change gleaned from isotopic archives preserved in sedimentary sequences provide insight into how these processes interact over different timescales to create topography and potentially decipher the impact of topography on atmospheric circulation and superposed exhumation. This study uses stable isotope data from pedogenic carbonates collected from seven different stratigraphic sections spanning different tectonic and topographic positions in the range today, to examine the middle to late Miocene history of elevation change in the central Andes thrust belt, which is located immediately to the south of the Altiplano-Puna Plateau, the world's second largest orogenic plateau. Paleoelevations are calculated using previously published local isotope-elevation gradients observed in modern rainfall and carbonate-formation temperatures determined from clumped isotope studies in modern soils. Calculated Neogene basin paleoelevations are between 1 km and 1.9 km for basins that today are located between 1500 and 3400 m elevation. Considering the modern elevation and δ18O values of precipitation at the sampling sites, three of the intermontane basins experienced surface uplift between the end of deposition during the late Miocene and present. The timing of elevation change cannot be linked to any documented episodes of large-magnitude crustal shortening. Paradoxically, the maximum inferred surface uplift in the core of the range is greatest where the crust is thinnest. The spatial pattern of surface uplift is best explained by eastward migration of a crustal root via ductile deformation in the lower crust and is not related to flat-slab subduction.

Influence of Extreme Storm Events on West Florida Shelf CDOM Distributions.

EPA Science Inventory

Colored Dissolved Organic Matter (CDOM) distribution and signatures provide vital information about the amount and composition of organic material in aquatic environments. This information is critical for deciphering the sources and biogeochemical pathways of organic carbon, and...

Poe and Prolixity.

ERIC Educational Resources Information Center

Powers, John

1990-01-01

Describes a method of teaching Edgar Allan Poe's writings which uses writing as a tool to decipher the story and to teach a valuable lesson in creative writing and style, and which shows students how a text changes when it is either abridged or adapted. (SR)

Brain response during the M170 time interval is sensitive to socially relevant information.

PubMed

Arviv, Oshrit; Goldstein, Abraham; Weeting, Janine C; Becker, Eni S; Lange, Wolf-Gero; Gilboa-Schechtman, Eva

2015-11-01

Deciphering the social meaning of facial displays is a highly complex neurological process. The M170, an event related field component of MEG recording, like its EEG counterpart N170, was repeatedly shown to be associated with structural encoding of faces. However, the scope of information encoded during the M170 time window is still being debated. We investigated the neuronal origin of facial processing of integrated social rank cues (SRCs) and emotional facial expressions (EFEs) during the M170 time interval. Participants viewed integrated facial displays of emotion (happy, angry, neutral) and SRCs (indicated by upward, downward, or straight head tilts). We found that the activity during the M170 time window is sensitive to both EFEs and SRCs. Specifically, highly prominent activation was observed in response to SRC connoting dominance as compared to submissive or egalitarian head cues. Interestingly, the processing of EFEs and SRCs appeared to rely on different circuitry. Our findings suggest that vertical head tilts are processed not only for their sheer structural variance, but as social information. Exploring the temporal unfolding and brain localization of non-verbal cues processing may assist in understanding the functioning of the social rank biobehavioral system. Copyright © 2015 Elsevier Ltd. All rights reserved.

Search and Coherence-Building in Intuition and Insight Problem Solving.

PubMed

Öllinger, Michael; von Müller, Albrecht

2017-01-01

Coherence-building is a key concept for a better understanding of the underlying mechanisms of intuition and insight problem solving. There are several accounts that address certain aspects of coherence-building. However, there is still no proper framework defining the general principles of coherence-building. We propose a four-stage model of coherence-building. The first stage starts with spreading activation restricted by constraints. This dynamic is a well-defined rule based process. The second stage is characterized by detecting a coherent state. We adopted a fluency account assuming that the ease of information processing indicates the realization of a coherent state. The third stage is designated to evaluate the result of the coherence-building process and assess whether the given problem is solved or not. If the coherent state does not fit the requirements of the task, the process re-enters at stage 1. These three stages characterize intuition. For insight problem solving a fourth stage is necessary, which restructures the given representation after repeated failure, so that a new search space results. The new search space enables new coherent states. We provide a review of the most important findings, outline our model, present a large number of examples, deduce potential new paradigms and measures that might help to decipher the underlying cognitive processes.

Search and Coherence-Building in Intuition and Insight Problem Solving

PubMed Central

Öllinger, Michael; von Müller, Albrecht

2017-01-01

Coherence-building is a key concept for a better understanding of the underlying mechanisms of intuition and insight problem solving. There are several accounts that address certain aspects of coherence-building. However, there is still no proper framework defining the general principles of coherence-building. We propose a four-stage model of coherence-building. The first stage starts with spreading activation restricted by constraints. This dynamic is a well-defined rule based process. The second stage is characterized by detecting a coherent state. We adopted a fluency account assuming that the ease of information processing indicates the realization of a coherent state. The third stage is designated to evaluate the result of the coherence-building process and assess whether the given problem is solved or not. If the coherent state does not fit the requirements of the task, the process re-enters at stage 1. These three stages characterize intuition. For insight problem solving a fourth stage is necessary, which restructures the given representation after repeated failure, so that a new search space results. The new search space enables new coherent states. We provide a review of the most important findings, outline our model, present a large number of examples, deduce potential new paradigms and measures that might help to decipher the underlying cognitive processes. PMID:28611702

Geochemistry and the understanding of ground-water systems

USGS Publications Warehouse

Glynn, Pierre D.; Plummer, Niel

2005-01-01

Geochemistry has contributed significantly to the understanding of ground-water systems over the last 50 years. Historic advances include development of the hydrochemical facies concept, application of equilibrium theory, investigation of redox processes, and radiocarbon dating. Other hydrochemical concepts, tools, and techniques have helped elucidate mechanisms of flow and transport in ground-water systems, and have helped unlock an archive of paleoenvironmental information. Hydrochemical and isotopic information can be used to interpret the origin and mode of ground-water recharge, refine estimates of time scales of recharge and ground-water flow, decipher reactive processes, provide paleohydrological information, and calibrate ground-water flow models. Progress needs to be made in obtaining representative samples. Improvements are needed in the interpretation of the information obtained, and in the construction and interpretation of numerical models utilizing hydrochemical data. The best approach will ensure an optimized iterative process between field data collection and analysis, interpretation, and the application of forward, inverse, and statistical modeling tools. Advances are anticipated from microbiological investigations, the characterization of natural organics, isotopic fingerprinting, applications of dissolved gas measurements, and the fields of reaction kinetics and coupled processes. A thermodynamic perspective is offered that could facilitate the comparison and understanding of the multiple physical, chemical, and biological processes affecting ground-water systems.

Using Stable Isotope Geochemistry to Determine Changing Paleohydrology and Diagenetic Alteration in the Late Cretaceous Kaiparowits Formation, UT USA

NASA Astrophysics Data System (ADS)

Yamamura, Daigo

The Western Interior Basin of the North America preserves one of the best sedimentary and paleontological records of the Cretaceous in the world. The Upper Cretaceous Kaiparowits Formation is a rapidly deposited fluvial sequence and preserves one of the most complete terrestrial fossil record of the North America. Such a unique deposit provides an opportunity to investigate the interaction between the physical environment and ecology. In an effort to decipher such interaction, stable isotope composition of cements in sedimentary rocks, concretions and vertebrate fossils were analyzed. Despite the difference in facies and sedimentary architecture, the isotope composition does not change significantly at 110 m from the base of the formation. Among the well-preserved cement samples, stable isotope composition indicates a significant hydrologic change within the informal Middle unit; a 6.37‰ depletion in delta13C and 3.30‰ enrichment in delta 18O occurs at 300 m above the base of the formation. The isotope values indicate that the sandstone cements below 300 m were precipitated in a mixing zone between marine and terrestrial groundwater, whereas the cements in upper units were precipitated in a terrestrial groundwater. Despite the difference in physical appearance (i.e. color and shape), the isotopic compositions of cements in concretions are similar to well-cemented sandstone bodies in similar stratigraphic positions. Isotope compositions of the host rock are similar to that of mudrock and weathered sandstone, suggesting the origin of cementing fluids for the sandstone and concretions were the same indicating that: 1) the concretions were formed in shallow groundwater and not related to the groundwater migration, or 2) all cements in upper Kaiparowits Formation are precipitated or altered during later stage groundwater migration. Average delta18Oc from each taxon show the same trend as the delta18Op stratigraphic change, suggesting delta18Oc is still useful as a paleoclimatic proxy. Compared to other Campanian formations, fossil delta18O p are depleted for their paleolatitude, suggesting the Kaiparowits Plateau had higher input from high-elevation runoff, consistent with other paleoclimatic studies. Estimated delta18Ow ranged between vadose influenced dry season values of -8.88‰ to high elevation runoff values of -13.76‰ suggesting dynamic hydrologic interactions.

Chemical and U-Sr isotopic variations in stream and source waters of the Strengbach watershed (Vosges mountains, France)

NASA Astrophysics Data System (ADS)

Pierret, M. C.; Stille, P.; Prunier, J.; Viville, D.; Chabaux, F.

2014-10-01

This is the first comprehensive study dealing with major and trace element data as well as 87Sr/86Sr isotope and (234U/238U) activity ratios (AR) determined on the totality of springs and brooks of the Strengbach catchment. It shows that the small and more or less monolithic catchment drains different sources and streamlets with very different isotopic and geochemical signatures. Different parameters control the diversity of the source characteristics. Of importance is especially the hydrothermal overprint of the granitic bedrock, which was stronger for the granite from the northern slope; also significant are the different meteoric alteration processes of the bedrock causing the formation of 0.5 to 9 m thick saprolite and above the formation of an up to 1m thick soil system. These processes mainly account for springs and brooks from the northern slope having higher Ca / Na, Mg / Na, and Sr / Na ratios, but lower 87Sr/86Sr isotopic ratios than those from the southern slope. The chemical compositions of the source waters in the Strengbach catchment are only to a small extent the result of alteration of primary bedrock minerals, and rather reflect dissolution/precipitation processes of secondary mineral phases like clay minerals. The (234U/238U) AR, however, are decoupled from the 87Sr/86Sr isotope system, and reflect to some extent the level of altitude of the source and, thus, the degree of alteration of the bedrock. The sources emerging at high altitudes have circulated through already weathered materials (saprolite and fractured bedrock depleted in 234U), implying (234U/238U) AR below 1, which is uncommon for surface waters. Preferential flow paths along constant fractures in the bedrocks might explain the - over time - homogeneous U AR of the different spring waters. However, the geochemical and isotopic variations of stream waters at the outlet of the catchment are controlled by variable contributions of different springs, depending on the hydrological conditions. It appears that the (234U/238U) AR are a very appropriate, important tracer for studying and deciphering the contribution of the different source fluxes at the catchment scale, because this unique geochemical parameter is different for each individual spring and at the same time remains unchanged for each of the springs with changing discharge and fluctuating hydrological conditions. This study further highlights the important impact of different and independent water pathways on fractured granite controlling the different geochemical and isotopic signatures of the waters. Despite the fact that soils and vegetation cover have a great influence on the water cycle balance (evapotranspiration, drainage, runoff), the chemical compositions of waters are strongly modified by processes occurring in deep saprolite and bedrock rather than in soils along the specific water pathways.

Microanalyzes of remarkable microfossils of the Late Mesoproterozoic-Early Neoproterozoic

NASA Astrophysics Data System (ADS)

Cornet, Yohan; Beghin, Jérémie; Baludikay, Blaise; François, Camille; Storme, Jean-Yves; Compère, Philippe; Javaux, Emanuelle

2016-04-01

The Late Mesoproterozoic-Early Neoproterozoic is an important period to investigate the diversification of early eukaryotes [1]. Following the first appearance of red algae in the Late Mesoproterozoic, other (morphological or molecular) fossils of crown groups are recorded during the Early Neoproterozoic, including green algae, sponges, amoebozoa and possibly fungi. Other microfossils also includes unambiguous eukaryotes, including several distinctive forms for that time period, such as the acritarchs Cerebrosphaera buickii (˜820-720 Ma), Trachyhystrichosphaera aimika and T . botula (1100-720 Ma), and the multicellular eukaryotic problematicum taxon Jacutianema solubila (1100-?720 Ma). To further characterize the taxonomy of these microfossils and to test hypotheses about their possible relationships to crown groups, we combine analyzes of their morphology, wall ultrastructure and microchemistry, using optical microscopy, Scanning and Transmission Electron microscopy (SEM and TEM), as well as Raman and FTIR microspectroscopy respectively. Cerebrosphaera populations from the Svanbergfjellet formation, Spitsbergen, and from the Kanpa Formation, Officer Basin, Australia, include organic vesicles with dark and robust walls ornamented by cerebroid folds [2]. Our study shows the occurrence of complex tri- or bi-layered wall ultrastructures and a highly aromatic composition [3]. The genus Trachyhystrichosphaera includes various species characterized by the presence of a variable number of hollow heteromorphic processes [2]. Preliminary infrared microspectroscopy analyzes performed on two species, T. aimika and T. botula, from the 1.1 Ga Taoudeni Basin, Mauritania, and from the ˜1.1 - 0.8 Ga Mbuji-Mayi Supergroup, RDC, indicate a strong aliphatic and carbonyl composition of the wall biopolymer, with some differences linked to thermal maturity between the two locations. TEM is also performed to characterize the wall ultrastructure of these two species. Various morphotypes of the species Jacutianema solubila from the Svanbergfjellet Formation, Spitsbergen and from the Taoudeni Basin, Mauritania, are also characterized with infrared and Raman microspectroscopy as well as with TEM, permitting to test a previous hypothesis proposing that Jacutianema represents part of the life cycle of a Vaucherian alga [4]. Deciphering the identity of these distinctive microfossils will improve our understanding of the timing and pattern of eukaryote stem and crown group diversification in the mid-Proterozoic, prior to large "snowball Earth" glaciations and during time of changing ocean chemistry. [1] Knoll et al. (2006) Philos. Trans. R. Soc. B 361 1023-1038 [2] Butterfield et al. (1994) Fossils and Strata 34 82p [3] Cornet et al. (in preparation) [4] Butterfield (2004) Paleobiology 30 (2), 231-25

Deciphering Community and Race Effects on Adolescent Premarital Childbearing.

ERIC Educational Resources Information Center

South, Scott J.; Baumer, Eric P.

2000-01-01

Racial differences in adolescent premarital childbearing were largely explained by racial differences in neighborhood quality. These neighborhood effects were attributed to peer attitudes and behaviors, adolescents' more tolerant attitudes toward unmarried parenthood, and greater residential mobility in distressed communities. Neighborhood effects…

Genetic structure of the fungal grapevine pathogen Eutypa lata from four continents

USDA-ARS?s Scientific Manuscript database

Deciphering the geographic origins of pathogens and elucidating the population biology of these microscopic organisms are necessary steps to establish effective disease-control strategies. The generalist ascomycete fungus Eutypa lata causes Eutypa dieback of grapevine (Vitis vinifera) worldwide. To ...

Genetic structure of the fungal grapevine pathogen Eutypa lata from four continents

USDA-ARS?s Scientific Manuscript database

The generalist ascomycete fungus Eutypa lata causes Eutypa dieback of grapevine (Vitis vinifera) worldwide. To decipher the cosmopolitan distribution of this fungus, the population genetic structure of 17 geographic samples was investigated from four continental regions (Australia, California, Europ...

Stephen Baylin, M.D., Explains Genetics and Epigenetics - TCGA

Cancer.gov

Stephen Baylin, M.D., at the Johns Hopkins Kimmel Cancer Center discusses the how alterations in the DNA code are deciphered in a combined effort with The Cancer Genome Atlas at the National Cancer Institute to decode the brain cancer genome.

Cost-effectiveness of the Decipher Genomic Classifier to Guide Individualized Decisions for Early Radiation Therapy After Prostatectomy for Prostate Cancer.

PubMed

Lobo, Jennifer M; Trifiletti, Daniel M; Sturz, Vanessa N; Dicker, Adam P; Buerki, Christine; Davicioni, Elai; Cooperberg, Matthew R; Karnes, R Jeffrey; Jenkins, Robert B; Den, Robert B; Showalter, Timothy N

2017-06-01

Controversy exists regarding the effectiveness of early adjuvant versus salvage radiation therapy after prostatectomy for prostate cancer. Estimates of prostate cancer progression from the Decipher genomic classifier (GC) could guide informed decision-making and improve the outcomes for patients. We developed a Markov model to compare the costs and quality-adjusted life years (QALYs) associated with GC-based treatment decisions regarding adjuvant therapy after prostatectomy with those of 2 control strategies: usual care (determined from patterns of care studies) and the alternative of 100% adjuvant radiation therapy. Using the bootstrapping method of sampling with replacement, the cases of 10,000 patients were simulated during a 10-year time horizon, with each subject having individual estimates for cancer progression (according to GC findings) and noncancer mortality (according to age). GC-based care was more effective and less costly than 100% adjuvant radiation therapy and resulted in cost savings up to an assay cost of $11,402. Compared with usual care, GC-based care resulted in more QALYs. Assuming a $4000 assay cost, the incremental cost-effectiveness ratio was $90,833 per QALY, assuming a 7% usage rate of adjuvant radiation therapy. GC-based care was also associated with a 16% reduction in the percentage of patients with distant metastasis at 5 years compared with usual care. The Decipher GC could be a cost-effective approach for genomics-driven cancer treatment decisions after prostatectomy, with improvements in estimated clinical outcomes compared with usual care. The individualized decision analytic framework applied in the present study offers a flexible approach to estimate the potential utility of genomic assays for personalized cancer medicine. Copyright © 2016 Elsevier Inc. All rights reserved.

HIPAA compliance and patient privacy protection.

PubMed

Grandison, Tyrone; Bhatti, Rafae

2010-01-01

Recent prosecution of violations of the Health Insurance Portability and Accountability Act (HIPAA), and the amendments currently in process to strengthen the Act of 1996, has led many companies to take serious notice of the measures they must take to be a compliance. A company's privacy policy states the business' privacy practices and embodies the firm's commitments to its users and is normally mandatory step in reaching legislative compliance. in the face of this, the patient has to decipher if the company's privacy practices are congruent with their thoughts on the level of privacy protection they should be receiving. This is the core of our investigation. In this paper, we explore the question "Is a healthcare entity's compliance with regulation sufficient to provide the patient with adequate privacy protection?" in the context of the United States of America.

Astrobites: Blogging Astrophysics Research, Bringing it to the Classroom, and beyond

NASA Astrophysics Data System (ADS)

Tsang, Benny Tsz Ho; Kohler, Susanna; Astrobites Team

2017-06-01

Transitioning from undergraduate studies to a career in scientific research is not without its difficulties. Astrobites (astrobites.com) is a graduate student-organized website that aims to decipher the research process in astrophysics and present the latest discoveries in form of daily digestible blog posts. Astrobites posts paint vivid mental pictures of diverse research topics without jargon or extensive presumed knowledge, helping readers to make the connections between topics. Besides summarizing research papers, our posts feature reviews on selected subjects, sharing in career development, live-blogging in conferences, and keynote speakers’ personal encounters with science! The accessibility of Astrobites attracts readers beyond undergraduate students, from professional astrophysicists exploring unfamiliar territory outside of their research to science educators looking for exciting and topical ideas for lesson plans. We will present our goals, readership, latest endeavors, and future initiatives.

Histone modifications controlling native and induced neural stem cell identity.

PubMed

Broccoli, Vania; Colasante, Gaia; Sessa, Alessandro; Rubio, Alicia

2015-10-01

During development, neural progenitor cells (NPCs) that are capable of self-renewing maintain a proliferative cellular pool while generating all differentiated neural cell components. Although the genetic network of transcription factors (TFs) required for neural specification has been well characterized, the unique set of histone modifications that accompanies this process has only recently started to be investigated. In vitro neural differentiation of pluripotent stem cells is emerging as a powerful system to examine epigenetic programs. Deciphering the histone code and how it shapes the chromatin environment will reveal the intimate link between epigenetic changes and mechanisms for neural fate determination in the developing nervous system. Furthermore, it will offer a molecular framework for a stringent comparison between native and induced neural stem cells (iNSCs) generated by direct neural cell conversion. Copyright © 2015 Elsevier Ltd. All rights reserved.

Deciphering mRNA Sequence Determinants of Protein Production Rate

NASA Astrophysics Data System (ADS)

Szavits-Nossan, Juraj; Ciandrini, Luca; Romano, M. Carmen

2018-03-01

One of the greatest challenges in biophysical models of translation is to identify coding sequence features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to solve a translation model based on the inhomogeneous totally asymmetric simple exclusion process, which allows us to unveil simple design principles of nucleotide sequences determining protein production rates. Our solution shows an excellent agreement when compared to numerical genome-wide simulations of S. cerevisiae transcript sequences and predicts that the first 10 codons, which is the ribosome footprint length on the mRNA, together with the value of the initiation rate, are the main determinants of protein production rate under physiological conditions. Finally, we interpret the obtained analytic results based on the evolutionary role of the codons' choice for regulating translation rates and ribosome densities.

Walk like me, talk like me

PubMed Central

Saffin, Jillian M.; Tohid, Hassaan

2016-01-01

Understanding social cognition has become a hallmark in deciphering autism spectrum disorder. Neurobiological theories are taking precedence in causation studies as researchers look to abnormalities in brain development as the cause of deficits in social behavior, cognitive processes, and language. Following their discovery in the 1990s, mirror neurons have become a dominant theory for that the mirror neuron system may play a critical role in the pathophysiology of various symptoms of autism. Over the decades, the theory has evolved from the suggestion of a broken mirror neuron system to impairments in mirror neuron circuitry. The mirror neuron system has not gained total support due to inconsistent findings; a comprehensive analysis of the growing body of research could shed light on the benefits, or the disadvantage of continuing to study mirror neurons and their connection to autism. PMID:27094520

Faith in floods: Field and theory in landscape evolution before geomorphology

NASA Astrophysics Data System (ADS)

Montgomery, David R.

2013-10-01

Opinions about the origin of topography have long marked the frontier between science and religion. The creation of the world we know is central to religious and secular world views; and until recently the power to shape landscapes lay beyond the reach of mortals, inviting speculation as to a role for divine intervention. For centuries, Christians framed rational inquiry into the origin of topography around theories for how Noah's Flood shaped mountains and carved valleys. Only as geologists learned how to decipher Earth history and read the signature of Earth surface processes did naturalists come to understand the forces that shaped the world. In this sense, the historical roots of geomorphology lie in the tension between faith in theories and the compelling power of field observations—issues that remain relevant to the practice of geomorphology today.

Deciphering the Functional Composition of Fusogenic Liposomes

PubMed Central

Kolašinac, Rejhana; Kleusch, Christian; Braun, Tobias; Merkel, Rudolf; Csiszár, Agnes

2018-01-01

Cationic liposomes are frequently used as carrier particles for nucleic acid delivery. The most popular formulation is the equimolar mixture of two components, a cationic lipid and a neutral phosphoethanolamine. Its uptake pathway has been described as endocytosis. The presence of an aromatic molecule as a third component strongly influences the cellular uptake process and results in complete membrane fusion instead of endocytosis. Here, we systematically varied all three components of this lipid mixture and determined how efficiently the resulting particles fused with the plasma membrane of living mammalian cells. Our results show that an aromatic molecule and a cationic lipid component with conical molecular shape are essential for efficient fusion induction. While a neutral lipid is not mandatory, it can be used to control fusion efficiency and, in the most extreme case, to revert the uptake mechanism back to endocytosis. PMID:29364187

Deciphering Neural Codes of Memory during Sleep.

PubMed

Chen, Zhe; Wilson, Matthew A

2017-05-01

Memories of experiences are stored in the cerebral cortex. Sleep is critical for the consolidation of hippocampal memory of wake experiences into the neocortex. Understanding representations of neural codes of hippocampal-neocortical networks during sleep would reveal important circuit mechanisms in memory consolidation and provide novel insights into memory and dreams. Although sleep-associated ensemble spike activity has been investigated, identifying the content of memory in sleep remains challenging. Here we revisit important experimental findings on sleep-associated memory (i.e., neural activity patterns in sleep that reflect memory processing) and review computational approaches to the analysis of sleep-associated neural codes (SANCs). We focus on two analysis paradigms for sleep-associated memory and propose a new unsupervised learning framework ('memory first, meaning later') for unbiased assessment of SANCs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations.

PubMed

Kuzmanic, Antonija; Sutto, Ludovico; Saladino, Giorgio; Nebreda, Angel R; Gervasio, Francesco L; Orozco, Modesto

2017-04-26

p38α is a Ser/Thr protein kinase involved in a variety of cellular processes and pathological conditions, which makes it a promising pharmacological target. Although the activity of the enzyme is highly regulated, its molecular mechanism of activation remains largely unexplained, even after decades of research. By using state-of-the-art molecular dynamics simulations, we decipher the key elements of the complex molecular mechanism refined by evolution to allow for a fine tuning of p38α kinase activity. Our study describes for the first time the molecular effects of different regulators of the enzymatic activity, and provides an integrative picture of the activation mechanism that explains the seemingly contradictory X-ray and NMR data.

Deciphering Past and Present Tectonics of the Rio Grande Rift in New Mexico Utilizing Apatite Fission Track Thermochronology, Geochronology, Quaternary Faulting, and Cross-Section Restoration

NASA Astrophysics Data System (ADS)

Ricketts, J. W.; Karlstrom, K. E.; Kelley, S. A.; Priewisch, A.; Crossey, L. J.; Asmerom, Y.; Polyak, V.; Selmi, M.

2011-12-01

The Rio Grande rift provides an excellent laboratory for understanding styles and processes of extensional tectonics, and their driving forces. We apply apatite fission track (AFT) thermochronology, geochronology, fracture analysis, and cross-section restoration to decipher past and present tectonics of the Rio Grande rift. AFT data has been compiled from rift flank uplifts along the Rio Grande rift in an attempt to recognize long wavelength spatial and temporal patterns. AFT ages record time of cooling of rocks below ~110°C and, when cooling is due to exhumation, age elevation traverses can record upward advection of rocks through paleo 110°C isotherms. The relatively passive sides of half-grabens (e.g. Manzanos and Santa Fe Range) preserve Laramide AFT ages ranging from 45-70 Ma, indicating they were cooled during the Laramide Orogeny and have remained cooler than 110°C since then. Rift flanks on the tectonically active sides of half-grabens, (e.g. Sierra Ladrones, Sandias, Taos Range, and Sierra Blanca) have AFT ages that range from 35 Ma to <10 Ma, and record cooling that initiated with the Oligocene ignimbrite flare-up and continues through the Neogene. Our analysis tracks the approximate elevation of paleo 110°C isotherms in 10 Ma intervals from the Laramide to the present and shows that reconstructed paleoisotherms have been differentially uplifted, warped, and faulted since their time of formation, and hence serve as markers of uplift history and its mechanisms. AFT data at Ladron Peak, an active rift flank along the western margin of the Rio Grande rift in central New Mexico, indicates that it was rapidly unroofed between 20-10 Ma. Preliminary apatite helium data gives a similar age vs. elevation trend, but apatites have highly radiogenically damaged lattices and hence have corrected closure temperatures tens of degrees higher than AFT ages. The style of faulting at Ladron Peak is unusual because it is bounded by the anomalously low-angle (~15°) Jeter fault. In order to understand the evolution of faulting in this region, a balanced cross-section was constructed and restored to its pre-rift geometry. Our working hypothesis is that the low angle of the Jeter fault is most adequately explained by a rolling hinge model, where isostatic uplift causes progressive rotation of an initially steep (~60°) normal fault to shallower dips. Thirty km north of Ladron along the west side of the rift, Quaternary extensional faulting is evident in large travertine deposits at the Belen Quarry. Extensional fractures and cm-scale displacement normal faults at 4 locations give average paleostress orientations of 087, 112, 116, 127. A U-series age of 312 ka on faulted upper layers in one quarry indicates post-312 ka slip that we interpret to reflect surface manifestations of microseismicity above the Socorro magma body.

77 FR 3393 - Atlantic Highly Migratory Species; 2012 Atlantic Shark Commercial Fishing Season

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-24

... for the public to decipher, as the wording is not clear and/or the math seems not to be accurate. NMFS... stated that if ``overharvest continues to occur and the level reaches 60 percent or more of the 2012 base...

Deciphering microbial landscapes of fish eggs to mitigate emerging disease

USDA-ARS?s Scientific Manuscript database

Animals and plants are increasingly suffering from diseases caused by fungi and oomycetes. These emerging pathogens are now recognised as a global threat to biodiversity and food security. Amongst oomycetes, Saprolegnia species cause significant declines in fish and amphibian populations. Fish eggs ...

Life-style transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

USDA-ARS?s Scientific Manuscript database

Colletotrichum species are devastating fungal pathogens of major crop plants worldwide. Infection involves differentiation of specialized cell-types associated with host surface penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). Here we report genome and t...

Wide-field time-resolved luminescence imaging and spectroscopy to decipher obliterated documents in forensic science

NASA Astrophysics Data System (ADS)

Suzuki, Mototsugu; Akiba, Norimitsu; Kurosawa, Kenji; Kuroki, Kenro; Akao, Yoshinori; Higashikawa, Yoshiyasu

2016-01-01

We applied a wide-field time-resolved luminescence (TRL) method with a pulsed laser and a gated intensified charge coupled device (ICCD) for deciphering obliterated documents for use in forensic science. The TRL method can nondestructively measure the dynamics of luminescence, including fluorescence and phosphorescence lifetimes, which prove to be useful parameters for image detection. First, we measured the TRL spectra of four brands of black porous-tip pen inks on paper to estimate their luminescence lifetimes. Next, we acquired the TRL images of 12 obliterated documents at various delay times and gate times of the ICCD. The obliterated contents were revealed in the TRL images because of the difference in the luminescence lifetimes of the inks. This method requires no pretreatment, is nondestructive, and has the advantage of wide-field imaging, which makes it is easy to control the gate timing. This demonstration proves that TRL imaging and spectroscopy are powerful tools for forensic document examination.

Deciphering the mechanisms of developmental disorders: phenotype analysis of embryos from mutant mouse lines

PubMed Central

Wilson, Robert; McGuire, Christina; Mohun, Timothy

2016-01-01

The Deciphering the Mechanisms of Developmental Disorders (DMDD) consortium is a research programme set up to identify genes in the mouse, which if mutated (or knocked-out) result in embryonic lethality when homozygous, and initiate the study of why disruption of their function has such profound effects on embryo development and survival. The project uses a combination of comprehensive high resolution 3D imaging and tissue histology to identify abnormalities in embryo and placental structures of embryonic lethal lines. The image data we have collected and the phenotypes scored are freely available through the project website (http://dmdd.org.uk). In this article we describe the web interface to the images that allows the embryo data to be viewed at full resolution in different planes, discuss how to search the database for a phenotype, and our approach to organising the data for an embryo and a mutant line so it is easy to comprehend and intuitive to navigate. PMID:26519470

Bridging the gap between supernovae and their remnants through multi-dimensional hydrodynamic modeling

NASA Astrophysics Data System (ADS)

Orlando, S.; Miceli, M.; Petruk, O.

2017-02-01

Supernova remnants (SNRs) are diffuse extended sources characterized by a complex morphology and a non-uniform distribution of ejecta. Such a morphology reflects pristine structures and features of the progenitor supernova (SN) and the early interaction of the SN blast wave with the inhomogeneous circumstellar medium (CSM). Deciphering the observations of SNRs might open the possibility to investigate the physical properties of both the interacting ejecta and the shocked CSM. This requires accurate numerical models which describe the evolution from the SN explosion to the remnant development and which connect the emission properties of the remnants to the progenitor SNe. Here we show how multi-dimensional SN-SNR hydrodynamic models have been very effective in deciphering observations of SNR Cassiopeia A and SN 1987A, thus unveiling the structure of ejecta in the immediate aftermath of the SN explosion and constraining the 3D pre-supernova structure and geometry of the environment surrounding the progenitor SN.

Multielement analysis of Canadian wines by inductively coupled plasma mass spectrometry (ICP-MS) and multivariate statistics.

PubMed

Taylor, Vivien F; Longerich, Henry P; Greenough, John D

2003-02-12

Trace element fingerprints were deciphered for wines from Canada's two major wine-producing regions, the Okanagan Valley and the Niagara Peninsula, for the purpose of examining differences in wine element composition with region of origin and identifying elements important to determining provenance. Analysis by ICP-MS allowed simultaneous determination of 34 trace elements in wine (Li, Be, Mg, Al, P, Cl, Ca, Ti, V, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br, Rb, Sr, Mo, Ag, Cd, Sb, I, Cs, Ba, La, Ce, Tl, Pb, Bi, Th, and U) at low levels of detection, and patterns in trace element concentrations were deciphered by multivariate statistical analysis. The two regions were discriminated with 100% accuracy using 10 of these elements. Differences in soil chemistry between the Niagara and Okanagan vineyards were evident, without a good correlation between soil and wine composition. The element Sr was found to be a good indicator of provenance and has been reported in fingerprinting studies of other regions.

Processes Modifying Cratered Terrains on Pluto

NASA Technical Reports Server (NTRS)

Moore, J. M.

2015-01-01

The July encounter with Pluto by the New Horizons spacecraft permitted imaging of its cratered terrains with scales as high as approximately 100 m/pixel, and in stereo. In the initial download of images, acquired at 2.2 km/pixel, widely distributed impact craters up to 260 km diameter are seen in the near-encounter hemisphere. Many of the craters appear to be significantly degraded or infilled. Some craters appear partially destroyed, perhaps by erosion such as associated with the retreat of scarps. Bright ice-rich deposits highlight some crater rims and/or floors. While the cratered terrains identified in the initial downloaded images are generally seen on high-to-intermediate albedo surfaces, the dark equatorial terrain informally known as Cthulhu Regio is also densely cratered. We will explore the range of possible processes that might have operated (or still be operating) to modify the landscape from that of an ancient pristinely cratered state to the present terrains revealed in New Horizons images. The sequence, intensity, and type of processes that have modified ancient landscapes are, among other things, the record of climate and volatile evolution throughout much of the Pluto's existence. The deciphering of this record will be discussed. This work was supported by NASA's New Horizons project.

Neuron-Like Networks Between Ribosomal Proteins Within the Ribosome

NASA Astrophysics Data System (ADS)

Poirot, Olivier; Timsit, Youri

2016-05-01

From brain to the World Wide Web, information-processing networks share common scale invariant properties. Here, we reveal the existence of neural-like networks at a molecular scale within the ribosome. We show that with their extensions, ribosomal proteins form complex assortative interaction networks through which they communicate through tiny interfaces. The analysis of the crystal structures of 50S eubacterial particles reveals that most of these interfaces involve key phylogenetically conserved residues. The systematic observation of interactions between basic and aromatic amino acids at the interfaces and along the extension provides new structural insights that may contribute to decipher the molecular mechanisms of signal transmission within or between the ribosomal proteins. Similar to neurons interacting through “molecular synapses”, ribosomal proteins form a network that suggest an analogy with a simple molecular brain in which the “sensory-proteins” innervate the functional ribosomal sites, while the “inter-proteins” interconnect them into circuits suitable to process the information flow that circulates during protein synthesis. It is likely that these circuits have evolved to coordinate both the complex macromolecular motions and the binding of the multiple factors during translation. This opens new perspectives on nanoscale information transfer and processing.

Novel insights into an old disease: recent developments in scabies mite biology.

PubMed

Holt, Deborah C; Fischer, Katja

2013-04-01

Scabies is a serious disease of both humans and other animals caused by infestation of the skin with the ectoparasitic mite Sarcoptes scabiei. Our current understanding of scabies mite biology and disease processes is far outweighed by the significant, worldwide impact of the disease. This review summarizes the recent data which furthers our knowledge of mite biology, host specificity and parasite host evasion mechanisms. Recent data concords with the previous work demonstrating limited gene flow between different host-associated populations of scabies mites. This evidence of the host specificity of scabies mites has important implications for disease control programmes. Other studies have begun to decipher the molecular basis of the complex host-parasite interactions underlying scabies infestations. Scabies mites have developed complex mechanisms to interfere with the host defence processes that may also enhance the survival of the associated skin microbiome, consistent with the epidemiological evidence. Recently developed natural host models of scabies are valuable tools to further study the disease processes and to trial novel therapeutic agents. Although significant progress has been made, further research is needed to understand the biology, host-parasite interactions and pathogenesis of this ubiquitous parasite.

Bioprospecting of functional cellulases from metagenome for second generation biofuel production: a review.

PubMed

Tiwari, Rameshwar; Nain, Lata; Labrou, Nikolaos E; Shukla, Pratyoosh

2018-03-01

Second generation biofuel production has been appeared as a sustainable and alternative energy option. The ultimate aim is the development of an industrially feasible and economic conversion process of lignocellulosic biomass into biofuel molecules. Since, cellulose is the most abundant biopolymer and also represented as the photosynthetically fixed form of carbon, the efficient hydrolysis of cellulose is the most important step towards the development of a sustainable biofuel production process. The enzymatic hydrolysis of cellulose by suites of hydrolytic enzymes underlines the importance of cellulase enzyme system in whole hydrolysis process. However, the selection of the suitable cellulolytic enzymes with enhanced activities remains a challenge for the biorefinery industry to obtain efficient enzymatic hydrolysis of biomass. The present review focuses on deciphering the novel and effective cellulases from different environmental niches by unculturable metagenomic approaches. Furthermore, a comprehensive functional aspect of cellulases is also presented and evaluated by assessing the structural and catalytic properties as well as sequence identities and expression patterns. This review summarizes the recent development in metagenomics based approaches for identifying and exploring novel cellulases which open new avenues for their successful application in biorefineries.

Direct imaging of APP proteolysis in living cells.

PubMed

Parenti, Niccoló; Del Grosso, Ambra; Antoni, Claudia; Cecchini, Marco; Corradetti, Renato; Pavone, Francesco S; Calamai, Martino

2017-01-01

Alzheimer's disease is a multifactorial disorder caused by the interaction of genetic, epigenetic and environmental factors. The formation of cytotoxic oligomers consisting of A β peptide is widely accepted as being one of the main key events triggering the development of Alzheimer's disease. A β peptide production results from the specific proteolytic processing of the amyloid precursor protein (APP). Deciphering the factors governing the activity of the secretases responsible for the cleavage of APP is still a critical issue. Kits available commercially measure the enzymatic activity of the secretases from cells lysates, in vitro . By contrast, we have developed a prototypal rapid bioassay that provides visible information on the proteolytic processing of APP directly in living cells. APP was fused to a monomeric variant of the green fluorescent protein and a monomeric variant of the red fluorescent protein at the C-terminal and N-terminal (mChAPPmGFP), respectively. Changes in the proteolytic processing rate in transfected human neuroblastoma and rat neuronal cells were imaged with confocal microscopy as changes in the red/green fluorescence intensity ratio. The significant decrease in the mean red/green ratio observed in cells over-expressing the β -secretase BACE1, or the α -secretase ADAM10, fused to a monomeric blue fluorescent protein confirms that the proteolytic site is still accessible. Specific siRNA was used to evaluate the contribution of endogenous BACE1. Interestingly, we found that the degree of proteolytic processing of APP is not completely homogeneous within the same single cell, and that there is a high degree of variability between cells of the same type. We were also able to follow with a fluorescence spectrometer the changes in the red emission intensity of the extracellular medium when BACE1 was overexpressed. This represents a complementary approach to fluorescence microscopy for rapidly detecting changes in the proteolytic processing of APP in real time. In order to allow the discrimination between the α - and the β -secretase activity, we have created a variant of mChAPPmGFP with a mutation that inhibits the α -secretase cleavage without perturbing the β -secretase processing. Moreover, we obtained a quantitatively robust estimate of the changes in the red/green ratio for the above conditions by using a flow cytometer able to simultaneously excite and measure the red and green fluorescence. Our novel approach lay the foundation for a bioassay suitable to study the effect of drugs or particular conditions, to investigate in an unbiased way the the proteolytic processing of APP in single living cells in order, and to elucidate the causes of the variability and the factors driving the processing of APP.

Evidence of isotopic fractionation of natural uranium in cultured human cells

NASA Astrophysics Data System (ADS)

Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E.; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

2016-12-01

The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235U isotope with regard to 238U. Efforts were made to develop and then validate a procedure for highly accurate n(238U)/n(235U) determinations in microsamples of cells. We found that intracellular U is enriched in 235U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO22+) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes.

The role of cannabinoids in adult neurogenesis

PubMed Central

Prenderville, Jack A; Kelly, Áine M; Downer, Eric J

2015-01-01

The processes underpinning post-developmental neurogenesis in the mammalian brain continue to be defined. Such processes involve the proliferation of neural stem cells and neural progenitor cells (NPCs), neuronal migration, differentiation and integration into a network of functional synapses within the brain. Both intrinsic (cell signalling cascades) and extrinsic (neurotrophins, neurotransmitters, cytokines, hormones) signalling molecules are intimately associated with adult neurogenesis and largely dictate the proliferative activity and differentiation capacity of neural cells. Cannabinoids are a unique class of chemical compounds incorporating plant-derived cannabinoids (the active components of Cannabis sativa), the endogenous cannabinoids and synthetic cannabinoid ligands, and these compounds are becoming increasingly recognized for their roles in neural developmental processes. Indeed, cannabinoids have clear modulatory roles in adult neurogenesis, probably through activation of both CB1 and CB2 receptors. In recent years, a large body of literature has deciphered the signalling networks involved in cannabinoid-mediated regulation of neurogenesis. This timely review summarizes the evidence that the cannabinoid system is intricately associated with neuronal differentiation and maturation of NPCs and highlights intrinsic/extrinsic signalling mechanisms that are cannabinoid targets. Overall, these findings identify the central role of the cannabinoid system in adult neurogenesis in the hippocampus and the lateral ventricles and hence provide insight into the processes underlying post-developmental neurogenesis in the mammalian brain. PMID:25951750

Evidence of isotopic fractionation of natural uranium in cultured human cells

PubMed Central

Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E.; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

2016-01-01

The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235U isotope with regard to 238U. Efforts were made to develop and then validate a procedure for highly accurate n(238U)/n(235U) determinations in microsamples of cells. We found that intracellular U is enriched in 235U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO22+) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes. PMID:27872304

Evidence of isotopic fractionation of natural uranium in cultured human cells.

PubMed

Paredes, Eduardo; Avazeri, Emilie; Malard, Véronique; Vidaud, Claude; Reiller, Pascal E; Ortega, Richard; Nonell, Anthony; Isnard, Hélène; Chartier, Frédéric; Bresson, Carole

2016-12-06

The study of the isotopic fractionation of endogen elements and toxic heavy metals in living organisms for biomedical applications, and for metabolic and toxicological studies, is a cutting-edge research topic. This paper shows that human neuroblastoma cells incorporated small amounts of uranium (U) after exposure to 10 µM natural U, with preferential uptake of the 235 U isotope with regard to 238 U. Efforts were made to develop and then validate a procedure for highly accurate n( 238 U)/n( 235 U) determinations in microsamples of cells. We found that intracellular U is enriched in 235 U by 0.38 ± 0.13‰ (2σ, n = 7) relative to the exposure solutions. These in vitro experiments provide clues for the identification of biological processes responsible for uranium isotopic fractionation and link them to potential U incorporation pathways into neuronal cells. Suggested incorporation processes are a kinetically controlled process, such as facilitated transmembrane diffusion, and the uptake through a high-affinity uranium transport protein involving the modification of the uranyl (UO 2 2+ ) coordination sphere. These findings open perspectives on the use of isotopic fractionation of metals in cellular models, offering a probe to track uptake/transport pathways and to help decipher associated cellular metabolic processes.

Investigation of Low Cost Sensor-Based Leak Detection System for Fence Line Applications

EPA Science Inventory

With recent technological advances, low-cost time-resolved sensors may become effective tools to support time-integrated passive sampling strategies by helping to decipher origin of emissions in real-time. As part of the Petroleum Refinery Risk and Technology Review, New Source ...

Development: facial makeup enhancing our looks.

PubMed

Rohner, Nicolas; Tschopp, Patrick; Tabin, Cliff

2014-01-06

A recent study in mice deciphers the complex genetic regulatory network underlying the morphogenesis of the face. The enhancer landscape underlying craniofacial development provides multiple entry points to understand what makes up the face, in natural variation or pathological conditions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Deciphering drought-induced metabolic responses and regulation in developing maize kernels

USDA-ARS?s Scientific Manuscript database

Aspergillus flavus is a facultative pathogen of crops such as maize and peanut which produces carcinogenic aflatoxins during infection, particularly in drought stressed host plants. Reactive oxygen species (ROS) have been shown to both accumulate in host plant tissues during drought and to stimulate...

Necrotizing Enterocolitis (NEC)

MedlinePlus

... Snapshot of Pregnancy & Infant Development Advances Snapshot of Child Development Advances Snapshot of Adult & Family Health Advances NICHD ... decipher how group of proteins regulate immune cell development in mice Getting to Know the New NICHD Director Addressing Infants’ ... Safe to Sleep® National Child & Maternal Health Education Program RELATED WEBSITES NIH.gov ...

Inquiring Minds

Science.gov Websites

-performance Computing Grid Computing Networking Mass Storage Plan for the Future State of the Laboratory to help decipher the language of high-energy physics. Virtual Ask-a-Scientist Read transcripts from past online chat sessions. last modified 1/04/2005 email Fermilab Fermi National Accelerator Laboratory

Visual Thinking Strategies = Creative and Critical Thinking

ERIC Educational Resources Information Center

Moeller, Mary; Cutler, Kay; Fiedler, Dave; Weier, Lisa

2013-01-01

Implementation of Visual Thinking Strategies (VTS) into the Camelot Intermediate School curriculum in Brookings, South Dakota, has fostered the development of creative and critical thinking skills in 4th- and 5th-grade students. Making meaning together by observing carefully, deciphering patterns, speculating, clarifying, supporting opinions, and…

Deciphering Maya Hieroglyphic Writing: The State of the Art.

ERIC Educational Resources Information Center

Fields, Virginia M.

1990-01-01

Describes the historical approaches to the decipherment of ancient Maya writing. Asserts that Mayan hieroglyphics are recognized as true writing because they represent the sounds and structure of spoken language. Discusses the history of Maya hieroglyphic writing and how it was used in that civilization. (PRA)

Deciphering the bacterial microbiome in huanglongbing-affected citrus treated with thermotherapy and sulfonamide antibiotics

USDA-ARS?s Scientific Manuscript database

Huanglongbing (HLB) is a serious citrus disease that threatens the citrus industry. In previous studies, sulfonamide antibiotics and heat treatment suppressed ‘Candidatus Liberibacter asiaticus’ (Las), but did not completely eliminate the Las. Furthermore, there are few reports studying the bacteria...

Deciphering the roles of acyl-CoA-binding proteins in plant cells.

PubMed

Lung, Shiu-Cheung; Chye, Mee-Len

2016-09-01

Lipid trafficking is vital for metabolite exchange and signal communications between organelles and endomembranes. Acyl-CoA-binding proteins (ACBPs) are involved in the intracellular transport, protection, and pool formation of acyl-CoA esters, which are important intermediates and regulators in lipid metabolism and cellular signaling. In this review, we highlight recent advances in our understanding of plant ACBP families from a cellular and developmental perspective. Plant ACBPs have been extensively studied in Arabidopsis thaliana (a dicot) and to a lesser extent in Oryza sativa (a monocot). Thus far, they have been detected in the plasma membrane, vesicles, endoplasmic reticulum, Golgi apparatus, apoplast, cytosol, nuclear periphery, and peroxisomes. In combination with biochemical and molecular genetic tools, the widespread subcellular distribution of respective ACBP members has been explicitly linked to their functions in lipid metabolism during development and in response to stresses. At the cellular level, strong expression of specific ACBP homologs in specialized cells, such as embryos, stem epidermis, guard cells, male gametophytes, and phloem sap, is of relevance to their corresponding distinct roles in organ development and stress responses. Other interesting patterns in their subcellular localization and spatial expression that prompt new directions in future investigations are discussed.

Broad AOX expression in a genetically tractable mouse model does not disturb normal physiology

PubMed Central

Szibor, Marten; Dhandapani, Praveen K.; Dufour, Eric; Holmström, Kira M.; Zhuang, Yuan; Salwig, Isabelle; Wittig, Ilka; Heidler, Juliana; Gizatullina, Zemfira; Fuchs, Helmut; Gailus-Durner, Valérie; de Angelis, Martin Hrabě; Nandania, Jatin; Velagapudi, Vidya; Wietelmann, Astrid; Rustin, Pierre; Gellerich, Frank N.; Braun, Thomas

2017-01-01

ABSTRACT Plants and many lower organisms, but not mammals, express alternative oxidases (AOXs) that branch the mitochondrial respiratory chain, transferring electrons directly from ubiquinol to oxygen without proton pumping. Thus, they maintain electron flow under conditions when the classical respiratory chain is impaired, limiting excess production of oxygen radicals and supporting redox and metabolic homeostasis. AOX from Ciona intestinalis has been used to study and mitigate mitochondrial impairments in mammalian cell lines, Drosophila disease models and, most recently, in the mouse, where multiple lentivector-AOX transgenes conferred substantial expression in specific tissues. Here, we describe a genetically tractable mouse model in which Ciona AOX has been targeted to the Rosa26 locus for ubiquitous expression. The AOXRosa26 mouse exhibited only subtle phenotypic effects on respiratory complex formation, oxygen consumption or the global metabolome, and showed an essentially normal physiology. AOX conferred robust resistance to inhibitors of the respiratory chain in organello; moreover, animals exposed to a systemically applied LD50 dose of cyanide did not succumb. The AOXRosa26 mouse is a useful tool to investigate respiratory control mechanisms and to decipher mitochondrial disease aetiology in vivo. PMID:28067626

Diagnostic examination of thermally abused high-power lithium-ion cells

NASA Astrophysics Data System (ADS)

Abraham, D. P.; Roth, E. P.; Kostecki, R.; McCarthy, K.; MacLaren, S.; Doughty, D. H.

The inherent thermal instability of lithium-ion cells is a significant impediment to their widespread commercialization for hybrid-electric vehicle applications. Cells containing conventional organic electrolyte-based chemistries are prone to thermal runaway at temperatures around 180 °C. We conducted accelerating rate calorimetry measurements on high-power 18650-type lithium-ion cells in an effort to decipher the sequence of events leading to thermal runaway. In addition, electrode and separator samples harvested from a cell that was heated to 150 °C then air-quenched to room temperature were examined by microscopy, spectroscopy, and diffraction techniques. Self-heating of the cell began at 84 °C. The gases generated in the cell included CO 2 and CO, and smaller quantities of H 2, C 2H 4, CH 4, and C 2H 6. The main changes on cell heating to 150 °C were observed on the anode surface, which was covered by a thick layer of surface deposits that included LiF and inorganic and organo-phosphate compounds. The sources of gas generation and the mechanisms leading to the formation of compounds observed on the electrode surfaces are discussed.

Enhancing gene regulatory network inference through data integration with markov random fields

DOE PAGES

Banf, Michael; Rhee, Seung Y.

2017-02-01

Here, a gene regulatory network links transcription factors to their target genes and represents a map of transcriptional regulation. Much progress has been made in deciphering gene regulatory networks computationally. However, gene regulatory network inference for most eukaryotic organisms remain challenging. To improve the accuracy of gene regulatory network inference and facilitate candidate selection for experimentation, we developed an algorithm called GRACE (Gene Regulatory network inference ACcuracy Enhancement). GRACE exploits biological a priori and heterogeneous data integration to generate high- confidence network predictions for eukaryotic organisms using Markov Random Fields in a semi-supervised fashion. GRACE uses a novel optimization schememore » to integrate regulatory evidence and biological relevance. It is particularly suited for model learning with sparse regulatory gold standard data. We show GRACE’s potential to produce high confidence regulatory networks compared to state of the art approaches using Drosophila melanogaster and Arabidopsis thaliana data. In an A. thaliana developmental gene regulatory network, GRACE recovers cell cycle related regulatory mechanisms and further hypothesizes several novel regulatory links, including a putative control mechanism of vascular structure formation due to modifications in cell proliferation.« less

Enhancing gene regulatory network inference through data integration with markov random fields

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

Banf, Michael; Rhee, Seung Y.

Here, a gene regulatory network links transcription factors to their target genes and represents a map of transcriptional regulation. Much progress has been made in deciphering gene regulatory networks computationally. However, gene regulatory network inference for most eukaryotic organisms remain challenging. To improve the accuracy of gene regulatory network inference and facilitate candidate selection for experimentation, we developed an algorithm called GRACE (Gene Regulatory network inference ACcuracy Enhancement). GRACE exploits biological a priori and heterogeneous data integration to generate high- confidence network predictions for eukaryotic organisms using Markov Random Fields in a semi-supervised fashion. GRACE uses a novel optimization schememore » to integrate regulatory evidence and biological relevance. It is particularly suited for model learning with sparse regulatory gold standard data. We show GRACE’s potential to produce high confidence regulatory networks compared to state of the art approaches using Drosophila melanogaster and Arabidopsis thaliana data. In an A. thaliana developmental gene regulatory network, GRACE recovers cell cycle related regulatory mechanisms and further hypothesizes several novel regulatory links, including a putative control mechanism of vascular structure formation due to modifications in cell proliferation.« less

Mg2+-induced DNA compaction, condensation, and phase separation in gene delivery vehicles based on zwitterionic phospholipids: a dynamic light scattering and surface-enhanced Raman spectroscopic study.

PubMed

Süleymanoğlu, Erhan

2017-12-01

Despite the significant efforts towards applying improved non-destructive and label-free measurements of biomolecular structures of lipid-based gene delivery vectors, little is achieved in terms of their structural relevance in gene transfections. Better understanding of structure-activity relationships of lipid-DNA complexes and their gene expression efficiencies thus becomes an essential issue. Raman scattering offers a complimentary measurement technique for following the structural transitions of both DNA and lipid vesicles employed for their transfer. This work describes the use of SERS coupled with light scattering approaches for deciphering the bioelectrochemical phase formations between nucleic acids and lipid vesicles within lipoplexes and their surface parameters that could influence both the uptake of non-viral gene carriers and the endocytic routes of interacting cells. As promising non-viral alternatives of currently employed risky viral systems or highly cytotoxic cationic liposomes, complexations of both nucleic acids and zwitterionic lipids in the presence of Mg 2+ were studied applying colloidal Ag nanoparticles. It is shown that the results could be employed in further conformational characterizations of similar polyelectrolyte gene delivery systems.

Insights into crustal structure of the Eastern North American Margin from community multichannel seismic and potential field data

NASA Astrophysics Data System (ADS)

Davis, J. K.; Becel, A.; Shillington, D. J.; Buck, W. R.

2017-12-01

In the fall of 2014, the R/V Marcus Langseth collected gravity, magnetic, and reflection seismic data as part of the Eastern North American Margin Community Seismic Experiment. The dataset covers a 500 km wide section of the Mid-Atlantic passive margin offshore North Carolina, which formed after the Mesozoic breakup of the supercontinent Pangaea. Using these seismic and potential field data, we present observations and interpretations along two cross margin and one along-margin profiles. Analyses and interpretations are conducted using pre-stack depth migrated reflection seismic profiles in conjunction with forward modeling of shipboard gravity and magnetic anomalies. Preliminary interpretations of the data reveal variations in basement character and structure across the entire transition between continental and oceanic domains. These interpretations help provide insight into the origin and nature of the prominent East Coast and Blake Spur magnetic anomalies, as well as the Inner Magnetic Quiet Zone which occupies the domain between the anomalies. Collectively, these observations can aid in deciphering the rift-to-drift transition during the breakup of North America and West Africa and formation of the Central Atlantic.

Deciphering visible light photoreductive conversion of CO2 to formic acid and methanol using waste prepared material.

PubMed

Zhang, Qian; Lin, Cheng-Fang; Chen, Bor-Yann; Ouyang, Tong; Chang, Chang-Tang

2015-02-17

As gradual increases in atmospheric CO2 and depletion of fossil fuels have raised considerable public concern in recent decades, utilizing the unlimited solar energy to convert CO2 to fuels (e.g., formic acid and methanol) apparently could simultaneously resolve these issues for sustainable development. However, due to the complicated characteristics of CO2 reduction, the mechanism has yet to be disclosed. To clarify the postulated pathway as mentioned in the literature, the technique of electron paramagnetic resonance (ESR) was implemented herein to confirm the mechanism and related pathways of CO2 reduction under visible light using graphene-TiO2 as catalyst. The findings indicated that CO(-•) radicals, as the main intermediates, were first detected herein to react with several hydrogen ions and electrons for the formation of CH3OH. For example, the generation of CO(-•) radicals is possibly the vital rate-controlling step for conversion of CO2 to methanol as hypothesized elsewhere. The kinetics behind the proposed mechanism was also determined in this study. The mechanism and kinetics could provide the in-depth understanding to the pathway of CO2 reduction and disclose system optimization of maximal conversion for further application.

Bathymetrically controlled velocity-shear front at a tidal river confluence

NASA Astrophysics Data System (ADS)

Blain, Cheryl Ann; Mied, Richard P.; McKay, Paul; Chen, Wei; Rhea, W. Joseph

2015-08-01

Nonbuoyant front formation at the confluence of Nanjemoy Creek and the main Potomac River (MD) channel is examined. Terra satellite ASTER imagery reveals a sediment color front emerging from Nanjemoy Creek when the Potomac is near maximum ebb. Nearly contemporaneous ASTER and Landsat ETM+ imagery are used to extract surface velocities, which suggest a velocity shear front is collocated with the color front. In situ velocities (measured by RiverRay traverses near the Nanjemoy Creek mouth) confirm the shear front's presence. A finite-element simulation (using ADCIRC) replicates the observed velocity-shear front and is applied to decipher its physics. Three results emerge: (1) the velocity-shear front forms, confined to a shoal downstream of the creek-river confluence for most of the tidal cycle, (2) a simulation with a flat bottom in Nanjemoy Creek and Potomac River (i.e., no bathymetry variation) indicates the velocity-shear front never forms, hence the front cannot exist without the bathymetry, and (3) an additional simulation with a blocked-off Creek entrance demonstrates that while the magnitude of the velocity shear is largely unchanged without the creek, shear front formation is delayed in time. Without the Creek, there is no advection of the M6 tidal constituent (generated by nonlinear interaction of the flow with bottom friction) onto the shoals, only a locally generated contribution. A tidal phase difference between Nanjemoy and Potomac causes the ebbing Nanjemoy Creek waters to intrude into the Potomac as far south as its deep channel, and draw from a similar location in the Potomac during Nanjemoy flood.

Chapter 6: cubic membranes the missing dimension of cell membrane organization.

PubMed

Almsherqi, Zakaria A; Landh, Tomas; Kohlwein, Sepp D; Deng, Yuru

2009-01-01

Biological membranes are among the most fascinating assemblies of biomolecules: a bilayer less than 10 nm thick, composed of rather small lipid molecules that are held together simply by noncovalent forces, defines the cell and discriminates between "inside" and "outside", survival, and death. Intracellular compartmentalization-governed by biomembranes as well-is a characteristic feature of eukaryotic cells, which allows them to fulfill multiple and highly specialized anabolic and catabolic functions in strictly controlled environments. Although cellular membranes are generally visualized as flat sheets or closely folded isolated objects, multiple observations also demonstrate that membranes may fold into "unusual", highly organized structures with 2D or 3D periodicity. The obvious correlation of highly convoluted membrane organizations with pathological cellular states, for example, as a consequence of viral infection, deserves close consideration. However, knowledge about formation and function of these highly organized 3D periodic membrane structures is scarce, primarily due to the lack of appropriate techniques for their analysis in vivo. Currently, the only direct way to characterize cellular membrane architecture is by transmission electron microscopy (TEM). However, deciphering the spatial architecture solely based on two-dimensionally projected TEM images is a challenging task and prone to artifacts. In this review, we will provide an update on the current progress in identifying and analyzing 3D membrane architectures in biological systems, with a special focus on membranes with cubic symmetry, and their potential role in physiological and pathophysiological conditions. Proteomics and lipidomics approaches in defined experimental cell systems may prove instrumental to understand formation and function of 3D membrane morphologies.

Bacillus subtilis δ Factor Functions as a Transcriptional Regulator by Facilitating the Open Complex Formation.

PubMed

Prajapati, Ranjit Kumar; Sengupta, Shreya; Rudra, Paulami; Mukhopadhyay, Jayanta

2016-01-15

Most bacterial RNA polymerases (RNAP) contain five conserved subunits, viz. 2α, β, β', and ω. However, in many Gram-positive bacteria, especially in fermicutes, RNAP is associated with an additional factor, called δ. For over three decades since its identification, it had been thought that δ functioned as a subunit of RNAP to enhance the level of transcripts by recycling RNAP. In support of the previous observations, we also find that δ is involved in recycling of RNAP by releasing the RNA from the ternary complex. We further show that δ binds to RNA and is able to recycle RNAP when the length of the nascent RNA reaches a critical length. However, in this work we decipher a new function of δ. Performing biochemical and mutational analysis, we show that Bacillus subtilis δ binds to DNA immediately upstream of the promoter element at A-rich sequences on the abrB and rrnB1 promoters and facilitates open complex formation. As a result, δ facilitates RNAP to initiate transcription in the second scale, compared with minute scale in the absence of δ. Using transcription assay, we show that δ-mediated recycling of RNAP cannot be the sole reason for the enhancement of transcript yield. Our observation that δ does not bind to RNAP holo enzyme but is required to bind to DNA upstream of the -35 promoter element for transcription activation suggests that δ functions as a transcriptional regulator. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Deciphering and Imaging Pathogenesis and Cording of Mycobacterium abscessus in Zebrafish Embryos

PubMed Central

Bernut, Audrey; Dupont, Christian; Sahuquet, Alain; Herrmann, Jean-Louis; Lutfalla, Georges; Kremer, Laurent

2015-01-01

Zebrafish (Danio rerio) embryos are increasingly used as an infection model to study the function of the vertebrate innate immune system in host-pathogen interactions. The ease of obtaining large numbers of embryos, their accessibility due to external development, their optical transparency as well as the availability of a wide panoply of genetic/immunological tools and transgenic reporter line collections, contribute to the versatility of this model. In this respect, the present manuscript describes the use of zebrafish as an in vivo model system to investigate the chronology of Mycobacterium abscessus infection. This human pathogen can exist either as smooth (S) or rough (R) variants, depending on cell wall composition, and their respective virulence can be imaged and compared in zebrafish embryos and larvae. Micro-injection of either S or R fluorescent variants directly in the blood circulation via the caudal vein, leads to chronic or acute/lethal infections, respectively. This biological system allows high resolution visualization and analysis of the role of mycobacterial cording in promoting abscess formation. In addition, the use of fluorescent bacteria along with transgenic zebrafish lines harbouring fluorescent macrophages produces a unique opportunity for multi-color imaging of the host-pathogen interactions. This article describes detailed protocols for the preparation of homogenous M. abscessus inoculum and for intravenous injection of zebrafish embryos for subsequent fluorescence imaging of the interaction with macrophages. These techniques open the avenue to future investigations involving mutants defective in cord formation and are dedicated to understand how this impacts on M. abscessus pathogenicity in a whole vertebrate. PMID:26382225

Time scale bias in erosion rates of glaciated landscapes

PubMed Central

Ganti, Vamsi; von Hagke, Christoph; Scherler, Dirk; Lamb, Michael P.; Fischer, Woodward W.; Avouac, Jean-Philippe

2016-01-01

Deciphering erosion rates over geologic time is fundamental for understanding the interplay between climate, tectonic, and erosional processes. Existing techniques integrate erosion over different time scales, and direct comparison of such rates is routinely done in earth science. On the basis of a global compilation, we show that erosion rate estimates in glaciated landscapes may be affected by a systematic averaging bias that produces higher estimated erosion rates toward the present, which do not reflect straightforward changes in erosion rates through time. This trend can result from a heavy-tailed distribution of erosional hiatuses (that is, time periods where no or relatively slow erosion occurs). We argue that such a distribution can result from the intermittency of erosional processes in glaciated landscapes that are tightly coupled to climate variability from decadal to millennial time scales. In contrast, we find no evidence for a time scale bias in spatially averaged erosion rates of landscapes dominated by river incision. We discuss the implications of our findings in the context of the proposed coupling between climate and tectonics, and interpreting erosion rate estimates with different averaging time scales through geologic time. PMID:27713925

Shared Sulfur Mobilization Routes for tRNA Thiolation and Molybdenum Cofactor Biosynthesis in Prokaryotes and Eukaryotes

PubMed Central

Leimkühler, Silke; Bühning, Martin; Beilschmidt, Lena

2017-01-01

Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm5s2U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure. The trafficking and delivery of sulfur nucleosides is a complex process carried out by sulfur relay systems involving numerous proteins, which not only deliver sulfur to the specific tRNAs but also to other sulfur-containing molecules including iron–sulfur clusters, thiamin, biotin, lipoic acid and molybdopterin (MPT). Among the biosynthesis of these sulfur-containing molecules, the biosynthesis of the molybdenum cofactor (Moco) and the synthesis of thio-modified tRNAs in particular show a surprising link by sharing protein components for sulfur mobilization in pro- and eukaryotes. PMID:28098827

Xenopus egg extract: A powerful tool to study genome maintenance mechanisms.

PubMed

Hoogenboom, Wouter S; Klein Douwel, Daisy; Knipscheer, Puck

2017-08-15

DNA repair pathways are crucial to maintain the integrity of our genome and prevent genetic diseases such as cancer. There are many different types of DNA damage and specific DNA repair mechanisms have evolved to deal with these lesions. In addition to these repair pathways there is an extensive signaling network that regulates processes important for repair, such as cell cycle control and transcription. Despite extensive research, DNA damage repair and signaling are not fully understood. In vitro systems such as the Xenopus egg extract system, have played, and still play, an important role in deciphering the molecular details of these processes. Xenopus laevis egg extracts contain all factors required to efficiently perform DNA repair outside a cell, using mechanisms conserved in humans. These extracts have been used to study several genome maintenance pathways, including mismatch repair, non-homologous end joining, ICL repair, DNA damage checkpoint activation, and replication fork stability. Here we describe how the Xenopus egg extract system, in combination with specifically designed DNA templates, contributed to our detailed understanding of these pathways. Copyright © 2017. Published by Elsevier Inc.

Time scale bias in erosion rates of glaciated landscapes.

PubMed

Ganti, Vamsi; von Hagke, Christoph; Scherler, Dirk; Lamb, Michael P; Fischer, Woodward W; Avouac, Jean-Philippe

2016-10-01

Deciphering erosion rates over geologic time is fundamental for understanding the interplay between climate, tectonic, and erosional processes. Existing techniques integrate erosion over different time scales, and direct comparison of such rates is routinely done in earth science. On the basis of a global compilation, we show that erosion rate estimates in glaciated landscapes may be affected by a systematic averaging bias that produces higher estimated erosion rates toward the present, which do not reflect straightforward changes in erosion rates through time. This trend can result from a heavy-tailed distribution of erosional hiatuses (that is, time periods where no or relatively slow erosion occurs). We argue that such a distribution can result from the intermittency of erosional processes in glaciated landscapes that are tightly coupled to climate variability from decadal to millennial time scales. In contrast, we find no evidence for a time scale bias in spatially averaged erosion rates of landscapes dominated by river incision. We discuss the implications of our findings in the context of the proposed coupling between climate and tectonics, and interpreting erosion rate estimates with different averaging time scales through geologic time.

Enhanced post wash retention of combed DNA molecules by varying multiple combing parameters.

PubMed

Yadav, Hemendra; Sharma, Pulkit

2017-11-01

Recent advances in genomics have created a need for efficient techniques for deciphering information hidden in various genomes. Single molecule analysis is one such technique to understand molecular processes at single molecule level. Fiber- FISH performed with the help of DNA combing can help us in understanding genetic rearrangements and changes in genome at single DNA molecule level. For performing Fiber-FISH we need high retention of combed DNA molecules post wash as Fiber-FISH requires profuse washing. We optimized combing process involving combing solution, method of DNA mounting on glass slides and coating of glass slides to enhance post-wash retention of DNA molecules. It was found that average number of DNA molecules observed post-wash per field of view was maximum with our optimized combing solution. APTES coated glass slides showed lesser retention than PEI surface but fluorescent intensity was higher in case of APTES coated surface. Capillary method used to mount DNA on glass slides also showed lesser retention but straight DNA molecules were observed as compared to force flow method. Copyright © 2017 Elsevier Inc. All rights reserved.

Listeria monocytogenes, a down-to-earth pathogen

PubMed Central

Vivant, Anne-Laure; Garmyn, Dominique; Piveteau, Pascal

2013-01-01

Listeria monocytogenes is the causative agent of the food-borne life threatening disease listeriosis. This pathogenic bacterium received much attention in the endeavor of deciphering the cellular mechanisms that underlie the onset of infection and its ability to adapt to the food processing environment. Although information is available on the presence of L. monocytogenes in many environmental niches including soil, water, plants, foodstuff and animals, understanding the ecology of L. monocytogenes in outdoor environments has received less attention. Soil is an environmental niche of pivotal importance in the transmission of this bacterium to plants and animals. Soil composition, microbial communities and macrofauna are extrinsic edaphic factors that direct the fate of L. monocytogenes in the soil environment. Moreover, farming practices may further affect its incidence. The genome of L. monocytogenes presents an extensive repertoire of genes encoding transport proteins and regulators, a characteristic of the genome of ubiquitous bacteria. Postgenomic analyses bring new insights in the process of soil adaptation. In the present paper focussing on soil, we review these extrinsic and intrinsic factors that drive environmental adaptation of L. monocytogenes. PMID:24350062

Listeria monocytogenes, a down-to-earth pathogen.

PubMed

Vivant, Anne-Laure; Garmyn, Dominique; Piveteau, Pascal

2013-01-01

Listeria monocytogenes is the causative agent of the food-borne life threatening disease listeriosis. This pathogenic bacterium received much attention in the endeavor of deciphering the cellular mechanisms that underlie the onset of infection and its ability to adapt to the food processing environment. Although information is available on the presence of L. monocytogenes in many environmental niches including soil, water, plants, foodstuff and animals, understanding the ecology of L. monocytogenes in outdoor environments has received less attention. Soil is an environmental niche of pivotal importance in the transmission of this bacterium to plants and animals. Soil composition, microbial communities and macrofauna are extrinsic edaphic factors that direct the fate of L. monocytogenes in the soil environment. Moreover, farming practices may further affect its incidence. The genome of L. monocytogenes presents an extensive repertoire of genes encoding transport proteins and regulators, a characteristic of the genome of ubiquitous bacteria. Postgenomic analyses bring new insights in the process of soil adaptation. In the present paper focussing on soil, we review these extrinsic and intrinsic factors that drive environmental adaptation of L. monocytogenes.

Managing the innovation supply chain to maximize personalized medicine.

PubMed

Waldman, S A; Terzic, A

2014-02-01

Personalized medicine epitomizes an evolving model of care tailored to the individual patient. This emerging paradigm harnesses radical technological advances to define each patient's molecular characteristics and decipher his or her unique pathophysiological processes. Translated into individualized algorithms, personalized medicine aims to predict, prevent, and cure disease without producing therapeutic adverse events. Although the transformative power of personalized medicine is generally recognized by physicians, patients, and payers, the complexity of translating discoveries into new modalities that transform health care is less appreciated. We often consider the flow of innovation and technology along a continuum of discovery, development, regulation, and application bridging the bench with the bedside. However, this process also can be viewed through a complementary prism, as a necessary supply chain of services and providers, each making essential contributions to the development of the final product to maximize value to consumers. Considering personalized medicine in this context of supply chain management highlights essential points of vulnerability and/or scalability that can ultimately constrain translation of the biological revolution or potentiate it into individualized diagnostics and therapeutics for optimized value creation and delivery.

Multiple calmodulin-like proteins in Arabidopsis are induced by insect-derived (Spodoptera littoralis) oral secretion

PubMed Central

Vadassery, Jyothilakshmi; Scholz, Sandra S.; Mithöfer, Axel

2012-01-01

In plant cells, diverse environmental changes often induce transient elevation in the intracellular calcium concentrations, which are involved in signaling pathways leading to the respective cellular reactions. Therefore, these calcium elevations need to be deciphered into specific downstream responses. Calmodulin-like-proteins (CMLs) are calcium-sensing proteins present only in higher plants. They are involved in signaling processes induced by both abiotic as well as biotic stress factors. However, the role of CMLs in the interaction of plants with herbivorous insects is almost unknown. Here we show that in Arabidopsis thaliana a number of CMLs genes (CML9, 11,12,16,17 and 23) are upregulated due to treatments with oral secretion of larvae of the herbivorous insect Spodoptera littoralis. We identified that these genes belong to two groups that respond with different kinetics to the treatment with oral secretion. Our data indicate that signaling networks involving multiple CMLs very likely have important functions in plant defense against insect herbivores, in addition to their involvement in many other stress-induced processes in plants. PMID:22902684

Investigation of a Low Cost Sensor-Based Leak Detection System for Fence Line Applications

EPA Science Inventory

With recent technological advances, low-cost time-resolved sensors may become effective tools to support time-integrated passive sampling strategies by helping to decipher origin of emissions in real-time. As part of the Petroleum Refinery Risk and Technology Review, New Source P...

Deciphering potential mechanisms of anaerobic soil disinfestation (ASD)-mediated control of Pratylenchus penetrans

USDA-ARS?s Scientific Manuscript database

Pratylenchus penetrans is a component of the apple replant disease (ARD) causal pathogen complex. The potential role for biological mechanisms contributing to ASD-mediated suppression of P. penetrans was examined in greenhouse study using orchard soil with a history of ARD. Populations of P. penetra...

Multi-omics approaches to deciphering a hypervirulent strain of Campylobacter jejuni

USDA-ARS?s Scientific Manuscript database

Background: Campylobacter jejuni clone SA recently emerged as the predominant cause of sheep abortion in the U.S. and is also associated with foodborne gastroenteritis in humans. A distinct phenotype of this clone is its ability to induce bacteremia and abortion. To facilitate understanding the path...

Deciphering landscape complexity to predict (non)linear responses to extreme climatic events

USDA-ARS?s Scientific Manuscript database

Extreme events are increasing in frequency and magnitude for many landscapes globally. Ecologically, most of the focus on extreme climatic events has been on effects of either short-term pulses (floods, freezes) or long-term drought. Multi-year increases in precipitation are also occurring with litt...

Deciphering the Genome Sequences of the Hydrophobic Cyanobacterium Scytonema tolypothrichoides VB-61278

PubMed Central

Das, Abhishek; Panda, Arijit; Singh, Deeksha; Chandrababunaidu, Mathu Malar; Mishra, Gyan Prakash; Bhan, Sushma

2015-01-01

Scytonema tolypothrichoides VB-61278, a terrestrial cyanobacterium, can be exploited to produce commercially important products. Here, we report for the first time a 10-Mb draft genome assembly of S. tolypothrichoides VB-61278, with 214 scaffolds and 7,148 putative protein-coding genes. PMID:25838486

Cryptology

ERIC Educational Resources Information Center

Tech Directions, 2011

2011-01-01

Cryptology, or cryptography, is the study of writing and deciphering hidden messages in codes, ciphers, and writings. It is almost as old as writing itself. Ciphers are messages in which letters are rearranged or substituted for other letters or numbers. Codes are messages in which letters are replaced by letter groups, syllables, or sentences.…

Harry Potter and the Cryptography with Matrices

ERIC Educational Resources Information Center

Chua, Boon Liang

2006-01-01

This article describes Cryptography, defined as the science of encrypting and deciphering messages written in secret codes, it has played a vital role in securing information since ancient times. There are several cryptographic techniques and many make extensive use of mathematics to secure information. The author discusses an activity built…

Normalizing Social Networking in a Beginners' Japanese Course

ERIC Educational Resources Information Center

Morofushi, Mari; Pasfield-Neofitou, Sarah Ellen

2014-01-01

With the spread of the Internet, students now have greater opportunities to use Japanese outside of the classroom. For example, they can interact with other Japanese speakers through instant messaging or social networking, or utilize online dictionaries and translation tools to decipher websites in ways that would be impossible with traditional…